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\title{Interesting muscle pathway knockouts, perturbations and potentiations on the C. elegans worm model}
\author{Gábor Funk}
\date{August 2026}

\begin{document}

\maketitle

\tableofcontents

\section{Introduction}

Openworm is the first large scale computational model which aims to mimic the Caenorhabditis elegans (C. elegans), a microscopic roundworm's neural structure. With only an approximately 1000 cells, this creature can solve obstacle detection, predator avoidance, feeding and mating. My goal is to apply knockouts, perturbations and potentiations to the model and look for "mutated" offsprings which are in some form more interesting than the original model.

I will also showcase my facade script system which allows the testing and analyzing of the perturbations, knockouts and potentiations. The system also contains a movement analysis module which can determine the characteristics of the mutated variant based on movement.

I also propose a ranking system for the mutated variants of the C. elegans worm which can also be applied in different species of worms and even insects.

\section{Terminology and Neural Network Interpretation}
\label{sec:terminology_neural_network}

This section defines the terminology used throughout the OpenWorm movement analysis and provides a neural-network interpretation of locomotion phenotypes. In this framework, locomotion is treated as the emergent output of a distributed sensorimotor network in which sensory neurons, interneurons, motor neurons, neuromuscular junctions, muscles, and the mechanical body interact dynamically. Consequently, a behavioral phenotype such as backward crawling or hyperkinetic movement is an observable consequence of changes somewhere within this network rather than necessarily identifying a single defective connection.

\subsection{General Interpretation Framework}

The locomotor nervous system can be represented abstractly as a directed weighted network,

\begin{equation}
\mathbf{x}*{t+1} = F(\mathbf{W}\mathbf{x}*{t} + \mathbf{I}_{t},\boldsymbol{\theta}),
\end{equation}

where $\mathbf{x}*{t}$ represents neuronal activity at time $t$, $\mathbf{W}$ represents effective synaptic connectivity, $\mathbf{I}*{t}$ represents sensory and other external inputs, and $\boldsymbol{\theta}$ represents neuronal parameters such as thresholds, gains, time constants, and adaptation parameters. Motor output is subsequently transformed through neuromuscular coupling and body mechanics into the measured trajectory.

Within this interpretation, three classes of neural manipulation are particularly useful:

\begin{itemize}
\item \textbf{Knockout:} Removal or functional silencing of a neuron, connection, synapse, receptor, or other network component. In a connectivity model, this can be represented by setting an affected connection weight to zero,
\begin{equation}
W_{ij}^{\mathrm{KO}} = 0.
\end{equation}
A neuronal knockout may alternatively be represented by suppressing the neuron's output entirely.

\item \textbf{Perturbation:} A partial or otherwise non-baseline modification of network structure or neuronal dynamics. For a synaptic connection, this may be represented as
\begin{equation}
W_{ij}^{\mathrm{perturbed}} = W_{ij}^{0} + \Delta W_{ij},
\end{equation}
where $W_{ij}^{0}$ is the baseline connection strength and $\Delta W_{ij}$ is the imposed change. Perturbations may also modify thresholds, delays, membrane properties, sensory gain, or neuromuscular coupling.

\item \textbf{Potentiation:} An increase in the effective influence of a neuronal connection or population. For a multiplicative potentiation,
\begin{equation}
W_{ij}^{\mathrm{potentiated}} = \alpha W_{ij}^{0},
\qquad \alpha > 1.
\end{equation}
Potentiation can therefore increase the influence of excitatory drive, inhibitory drive, sensory feedback, or motor commands depending on the identity and sign of the affected connection.

\end{itemize}

These manipulations should not be interpreted as synonymous with behavioral outcomes. The same behavioral phenotype can arise from multiple network mechanisms, while a single neural manipulation can produce multiple behavioral changes through downstream propagation across the network. In the following section, I will propose a ranking system which can help ranking the mutants of the C. elegans into 4 distinct categories.

\subsection{Locomotion State Terminology}

\subsubsection{Forward Crawling}

\textbf{Forward crawling} describes sustained movement in the animal's anatomically defined forward direction (Which by default is the openworm simulation's left facing direction from the camera). At the neural-network level, forward locomotion generally corresponds to coordinated activation of motor pathways that generate a propagating body bend in the appropriate direction. In a simplified network representation, forward command interneurons provide descending or distributed drive to motor neurons, while proprioceptive feedback helps maintain the phase relationship between neighboring body segments.

A reduction in forward-crawling fraction can therefore result from weakened forward command connections, excessive competing backward drive, impaired sensory feedback, or disruption of motor-neuron coordination.

\subsubsection{Backward Crawling}

\textbf{Backward crawling} describes sustained locomotion opposite to the normal forward direction. In a neural-network interpretation, backward crawling indicates that the network is preferentially producing the motor pattern associated with reverse locomotion.

A simplified interpretation is

\begin{equation}
D_{\mathrm{backward}} > D_{\mathrm{forward}},
\end{equation}

where $D$ denotes the effective network drive toward the corresponding locomotor state.

\subsubsection{Stationary State}

\textbf{Stationary} denotes periods in which translational movement falls below the analyzer's movement threshold. Neurally, this can correspond to low motor output, balanced opposing motor commands, insufficient command drive, or a mechanical state in which neural activity does not produce appreciable translation.

A stationary phenotype may therefore arise either from reduced network activation or from excessive cancellation between opposing pathways.

\subsubsection{Reversal}

A \textbf{reversal} is a transition between forward and backward locomotor states. Reversals require coordinated reconfiguration of the locomotor network rather than merely changing the sign of instantaneous velocity.

In network terms, a reversal can be represented as a transition between competing motor-state attractors,

\begin{equation}
\mathcal{A}*{\mathrm{forward}}
\longleftrightarrow
\mathcal{A}*{\mathrm{backward}}.
\end{equation}

The reversal frequency is therefore informative about the stability of these states and the threshold for switching between them. Excessive reversal can indicate unstable command-state competition, altered inhibitory gating, or abnormally strong sensory feedback.

\subsubsection{Omega Turns}

\textbf{Omega turns} are large-amplitude turning events in which the body adopts an approximately $\Omega$-shaped configuration. They require coordinated modulation of body-wall motor neurons and substantial dorsoventral asymmetry.

A reduction in omega turns may indicate impaired turning command pathways, insufficient asymmetric motor drive, or disrupted propagation of the motor pattern along the body.

\subsubsection{Shallow Turns}

\textbf{Shallow turns} are lower-amplitude changes in trajectory that do not constitute a full omega turn. They can arise from smaller imbalances between dorsal and ventral motor activity or from modulation of the undulatory wave.

\subsubsection{Irregular / Abnormal Locomotion}

\textbf{Irregular / abnormal locomotion} describes trajectories that do not satisfy the expected criteria for normal forward, backward, stationary, or turning states. At the network level, this category is particularly relevant to manipulations that disrupt temporal coordination, phase relationships, or sensory-motor feedback.

\subsection{Kinematic and Velocity Terminology}

\subsubsection{Net Displacement}

\textbf{Net displacement} is the magnitude of the overall change in position between the beginning and end of the analyzed trajectory. It measures the resulting translational progress rather than the total amount of movement.

A low net displacement can occur despite substantial internal motor activity if the animal repeatedly changes direction or if opposing movements cancel.

\subsubsection{Gross Distance}

\textbf{Gross distance} is the total distance traveled along the measured trajectory. Unlike net displacement, it captures movement regardless of whether that movement ultimately contributes to progress toward a final position.

The relationship

\begin{equation}
\text{Path Efficiency} = \frac{\text{Net Displacement}}{\text{Gross Distance}}
\end{equation}

provides a measure of how directly movement is translated into net progress.

\subsubsection{Path Efficiency}

\textbf{Path efficiency} ranges from approximately $0$ to $1$. A value near $1$ indicates that most movement contributes directly to net displacement, whereas a low value indicates inefficient movement, such as excessive reversals, turning, or lateral wandering. (Note that a near $1$ value is very unlikely because of the undalatory wave movement.)

From a neural-network perspective, reduced efficiency can reflect poor coordination between command pathways and the distributed motor program. (Compared to the real movement of a C. elegans)

\subsubsection{Mean Speed}

\textbf{Mean speed} is the average magnitude of translational velocity over the analyzed interval. It measures how rapidly the animal moves without inherently specifying the direction of movement.

\subsubsection{Forward and Backward Velocity}

\textbf{Forward velocity} and \textbf{backward velocity} describe the signed translational velocity relative to the animal's anatomical orientation. The sign convention must be preserved when interpreting these values: a negative ``maximum forward velocity'' does not necessarily mean that the animal possesses a negative physical speed but it may indicate that the reported forward-axis velocity was directed backward.

For this reason, signed velocity metrics should always be interpreted together with the analyzer's state classification.

\subsubsection{Median Velocity}

The \textbf{median velocity} is the midpoint of the velocity distribution and is less sensitive to extreme values than the mean. A substantial difference between mean and median velocity can indicate skewed or intermittent movement dynamics.

\subsubsection{Velocity Standard Deviation}

\textbf{Velocity standard deviation} measures temporal variability in velocity. High values indicate that the locomotor output is fluctuating strongly rather than remaining at a stable speed.

In a neural network, such fluctuations can emerge from unstable recurrent dynamics, rapid state transitions, abnormal sensory feedback, or excessive modulation of motor output.

\subsubsection{Velocity RMS}

\textbf{Velocity root-mean-square} measures the overall magnitude of velocity while emphasizing larger deviations. It is useful when comparing locomotor activity even when the signed mean velocity is close to zero.

\subsubsection{Fraction of Time Moving}

The \textbf{fraction of time moving forward}, \textbf{fraction of time moving backward}, and \textbf{fraction of time stationary} describe the proportion of analyzed frames or time intervals assigned to each locomotor direction.

These measurements provide a direct behavioral readout of the relative occupancy of competing network states.

\subsubsection{Acceleration}

\textbf{Mean acceleration} measures the average temporal rate of change in velocity. \textbf{Maximum acceleration} captures the strongest instantaneous acceleration, while \textbf{acceleration RMS} summarizes the overall magnitude of acceleration fluctuations.

Extremely high acceleration values can indicate rapid changes in inferred body position or velocity. They should therefore be interpreted in conjunction with the temporal resolution and numerical filtering of the trajectory data.

\subsubsection{Velocity Autocorrelation}

\textbf{Velocity autocorrelation} measures how strongly velocity at one point in time predicts velocity at later time points. A high value indicates temporally persistent locomotor dynamics.

In network terms, high autocorrelation is consistent with a relatively stable dynamical regime, whereas low autocorrelation can indicate rapid state transitions, noisy motor output, or disrupted recurrent coordination. A high autocorrelation can also occur if the network's locomotor system is immobilized.

\subsubsection{Reversal Frequency}

\textbf{Reversal frequency} measures the rate at which the locomotor direction changes. A high value may indicate unstable competition between forward and backward command states. A slightly high value may appear because the simulations take only approximately $1$ seconds.

\subsubsection{Mean Curvature}

\textbf{Mean curvature} quantifies the degree to which the animal's trajectory or body centerline bends. Higher curvature indicates stronger bending.

At the neural level, curvature is closely related to differential activation of dorsal and ventral motor pathways. If the effective drive to one side of the body exceeds the other,

\begin{equation}
A_{\mathrm{dorsal}} \neq A_{\mathrm{ventral}},
\end{equation}

the resulting torque produces body bending.

\subsubsection{Omega Turn Count}

\textbf{Omega turn count} is the number of detected omega-shaped turning events. A value of zero indicates that no trajectory satisfied the analyzer's omega-turn criteria during the analyzed interval.

\subsection{Undulation Wave Mechanics}

\subsubsection{Crawl Amplitude}

\textbf{Crawl amplitude} describes the magnitude of rhythmic body bending during locomotion. In a neural-network interpretation, amplitude depends on the magnitude of motor-neuron activation, muscle responsiveness, and mechanical coupling between adjacent body segments.

Reduced amplitude can result from weakened motor drive, reduced muscle activation, impaired neuromuscular transmission, or excessive inhibitory influence.

\subsubsection{Dominant Frequency}

The \textbf{dominant frequency} is the strongest periodic component detected in the locomotor signal. It represents the characteristic temporal rhythm of the measured undulatory behavior.

A change in dominant frequency can result from altered oscillatory dynamics within the locomotor network, including changes in synaptic delays, recurrent excitation/inhibition, neuronal time constants, or sensory-feedback gain.

\subsubsection{Wavelength}

\textbf{Wavelength} is the spatial distance associated with one complete cycle of the propagating body-bending wave.

A simplified traveling-wave representation is

\begin{equation}
\theta(s,t) = A \sin\left(\frac{2\pi s}{\lambda} - 2\pi ft + \phi\right)
\end{equation}

where $A$ is amplitude, $\lambda$ is wavelength, $f$ is frequency, and $\phi$ is phase.

\subsubsection{Wave Velocity}

\textbf{Wave velocity} is the propagation speed of the undulatory wave along the body. In an idealized traveling-wave system,

\begin{equation}
v_{\mathrm{wave}} = f\lambda.
\end{equation}

Thus, changes in either dominant frequency or wavelength can alter the propagation velocity of the motor pattern.

\subsubsection{Phase Coherence}

\textbf{Phase coherence} measures how consistently different portions of the body maintain their expected phase relationship during undulation. High coherence indicates an organized propagating motor wave.

Reduced coherence can therefore be interpreted as a breakdown in network synchronization.

\subsubsection{Mean Muscle Activation}

\textbf{Mean muscle activation} represents the average inferred activation of the musculature. It is a downstream quantity and should not automatically be equated with neural activity.

A useful conceptual relationship is

\begin{equation}
M(t) = G_{\mathrm{NMJ}}\left(A_{\mathrm{motor}}(t)\right),
\end{equation}

where $A_{\mathrm{motor}}$ is motor-neuron output and $G_{\mathrm{NMJ}}$ represents neuromuscular transmission and muscle response.

\subsubsection{Mean Hydrodynamic Pressure}

\textbf{Mean hydrodynamic pressure} represents the average fluid-pressure contribution associated with the simulated environment. In a fluid-coupled simulation, pressure and drag provide mechanical feedback to the body and therefore indirectly influence the neural-to-behavioral mapping.

Note that a zero value should not automatically be interpreted as evidence that the animal experiences no mechanical resistance.

\subsection{Phenotype Severity Terminology}

\subsubsection{Phenotype Severity}

\textbf{Phenotype severity} is an aggregate score intended to quantify deviation from a defined baseline phenotype. The score should be understood as the analyzer-specific metric rather than a universal biological scale.

A useful conceptual formulation is

\begin{equation}
S_{\mathrm{overall}} = \sum_{k=1}^{N} w_k S_k
\end{equation}

where $S_k$ is the severity of phenotype domain $k$ and $w_k$ is its weighting factor.

\subsubsection{Locomotion Severity}

\textbf{Locomotion severity} quantifies abnormality in translational movement, including failure to move, incorrect direction, abnormal speed, or inefficient progression.

\subsubsection{Turning Severity}

\textbf{Turning severity} measures abnormalities in the ability to initiate, execute, or terminate turning behaviors.

\subsubsection{Undulation Severity}

\textbf{Undulation severity} represents deviations in wave amplitude, frequency, wavelength, propagation, or phase organization.

\subsubsection{Muscle Output Severity}

\textbf{Muscle output severity} measures abnormalities in the magnitude or temporal organization of inferred muscle activation. High severity may result from altered motor-neuron drive, neuromuscular transmission, or muscle responsiveness.

\subsubsection{Symmetry Severity}

\textbf{Symmetry severity} measures deviation from expected bilateral or dorsoventral symmetry. A high value can indicate strongly unbalanced activation between opposing motor pathways.

For example,

\begin{equation}
S_{\mathrm{symmetry}}
\propto
\left|
A_{\mathrm{dorsal}} -
A_{\mathrm{ventral}}
\right|.
\end{equation}

The exact relationship depends on the implementation of the analyzer.

\subsection{Diagnostic Classification}The labels below describe the full spectrum of phenotypic classifications evaluated by the movement analysis engine:\begin{itemize}\item \textbf{PARALYTIC:} Characterized by near-zero movement speed and minimal muscle activity output ($<$0.001 relative units).
\item \textbf{NEAR-PARALYTIC:} Exhibits extremely suppressed mobility and speed thresholds consistently below the minimal baseline.
\item \textbf{HYPOKINETIC:} Phenotype marked by sluggish, reduced overall movement speed and restricted kinematic range.
\item \textbf{HYPERKINETIC:} Characterized by excessive, abnormally variable, or poorly regulated movement dynamics (distinguished from simply having a high mean speed).
\item \textbf{BACKWARD-BIASED:} Dominated by persistent reverse locomotion patterns where the backward crawl time fraction exceeds 50\%.
\item \textbf{TURNING-BIASED:} Exhibits excessive steering behavior, frequent omega turns ($>5$ counts), or high shallow-turn distribution percentages ($>40\%$).\item \textbf{OSCILLATORY/UNSTABLE:} Marked by low wave phase coherence ($<0.4$) or velocity standard deviation exceeding twice the mean speed.\item \textbf{NORMAL:} Standard wildtype-like locomotion patterns without significant kinematic defects.\end{itemize}


\begin{equation}
\mathrm{Motor\ Output}
\approx
f\left(
E-I+\mathrm{Feedback}
\right),
\end{equation}

where $E$ represents effective excitatory drive and $I$ represents effective inhibitory drive.

Thus, increasing excitation and decreasing inhibition can produce superficially similar behavioral phenotypes even though the underlying neural manipulations are different.

\subsection{Knockouts in a Neural Connectivity Model}

A \textbf{knockout} represents the removal or functional silencing of a network component.

For a connection from neuron $i$ to neuron $j$,

\begin{equation}
W_{ji}^{0}
\rightarrow
W_{ji}^{\mathrm{KO}} = 0.
\end{equation}

For a neuronal knockout, the activity of neuron $i$ can instead be constrained as

\begin{equation}
x_i(t) = 0.
\end{equation}

The behavioral consequence depends on the network position of the removed component.

\begin{itemize}
\item \textbf{Sensory-neuron knockout:} Removes or reduces a source of environmental or proprioceptive information. Expected consequences include impaired feedback, altered state transitions, or reduced behavioral responsiveness.

\item \textbf{Interneuron knockout:} Removes an intermediate computation or command pathway. This can disrupt gating between forward, backward, turning, and other behavioral states.

\item \textbf{Motor-neuron knockout:} Removes part of the motor command distributed to the body. This can produce localized weakness, altered curvature, or asymmetry.

\item \textbf{Synaptic knockout:} Removes a particular directed influence while leaving both neurons otherwise intact. This is especially useful for identifying causal connections within the locomotor circuit.

\item \textbf{Neuromuscular knockout:} Removes the effective transmission from motor neurons to muscle. Neural activity may remain present while mechanical output is strongly reduced.

\end{itemize}

Importantly, knockout effects may be nonlinear. Removing one connection can cause a small phenotype if redundant pathways compensate, while removal of a highly central connection can produce a large behavioral change.

\subsection{Perturbations in a Neural Connectivity Model}

A \textbf{perturbation} represents a controlled departure from the baseline network. Unlike a knockout, a perturbation does not necessarily eliminate the affected component.

Examples include

\begin{equation}
W_{ij}
\rightarrow
W_{ij} + \Delta W_{ij},
\end{equation}

or modification of neuronal parameters,

\begin{equation}
\tau_i \rightarrow \tau_i + \Delta\tau_i,
\qquad
\theta_i \rightarrow \theta_i + \Delta\theta_i,
\end{equation}

where $\tau_i$ is a neuronal time constant and $\theta_i$ is an activation threshold.

Perturbations may therefore represent changes in:

\begin{itemize}
\item synaptic strength;
\item synaptic sign or effective balance;
\item neuronal excitability;
\item firing threshold;
\item adaptation;
\item synaptic delay;
\item sensory gain;
\item inhibitory or excitatory feedback;
\item neuromuscular transmission;
\item muscle responsiveness; or
\item environmental coupling.
\end{itemize}

Perturbation experiments are particularly useful for identifying whether a phenotype is sensitive to the magnitude of a connection rather than simply its presence or absence.

\subsection{Potentiation in a Neural Connectivity Model}

\textbf{Potentiation} is a directional increase in the effective influence of a network component. For a connection $i\rightarrow j$,

\begin{equation}
W_{ji}^{\mathrm{pot}} = \alpha W_{ji}^{0}, \qquad \alpha > 1
\end{equation}

For an excitatory connection, potentiation generally increases downstream excitation. For an inhibitory connection, potentiation increases inhibition and can therefore decrease the activity of the target neuron.

This distinction is critical:

\begin{equation}
\text{Potentiated excitatory connection leads to }
\text{increased target drive},
\end{equation}

whereas

\begin{equation}
\text{Potentiated inhibitory connection leads to }
\text{decreased target drive}.
\end{equation}

Therefore, `potentiation'' should never be interpreted universally as `more movement.'' Its effect depends on the identity, sign, timing, and network context of the connection being potentiated.

\subsection{Recommended Interpretation of Analyzer Outputs}

The analyzer's measurements can be organized into a causal hierarchy:

\begin{equation}
\boxed{
\begin{aligned}
&\text{Neural Connectivity} \\
&\downarrow \\
&\text{Neuronal Activity} \\
&\downarrow \\
&\text{Motor-Neuron Output} \\
&\downarrow \\
&\text{Muscle Activation} \\
&\downarrow \\
&\text{Body Mechanics} \\
&\downarrow \\
&\text{Trajectory} \\
&\downarrow \\
&\text{Phenotype Classification}
\end{aligned}
}
\end{equation}


Accordingly, a behavioral metric should not automatically be interpreted as a direct measurement of a neural connection. For example, a high backward-crawling fraction is an observable behavioral consequence; it is not itself a measurement of the strength of a backward-command synapse.

The strongest causal interpretation is obtained by comparing a manipulated run with a matched baseline and examining how the manipulation changes multiple levels of the hierarchy. A useful experimental comparison is therefore:

\begin{equation}
\Delta M = \frac{M_{\mathrm{KO/perturbed/potentiated}}}{M_{\mathrm{baseline}}}
\end{equation}

where $M$ represents any analyzer metric.

Large, coherent changes across locomotion state, velocity, curvature, undulation, muscle output, and symmetry provide stronger evidence for a systematic network effect than a change in a single metric alone.

\subsection{Summary of Terminology}

\begin{table}[H]
\centering
\caption{Summary of Behavioral Metrics and Their Neural-Network Interpretation}
\label{tab:terminology_summary}
\begin{tabular}{|p{0.25\textwidth}|p{0.65\textwidth}|}
\hline
\textbf{Term} & \textbf{Interpretation} \\
\hline
Forward Crawling & Occupancy of the forward locomotor network state. \\
\hline
Backward Crawling & Occupancy of the reverse locomotor network state. \\
\hline
Stationary & Low translational motor output or balanced opposing drives. \\
\hline
Reversal & Transition between competing locomotor states. \\
\hline
Omega Turn & Large-amplitude coordinated turning motor program. \\
\hline
Shallow Turn & Lower-amplitude asymmetric motor output producing trajectory curvature. \\
\hline
Net Displacement & Overall translational consequence of the motor program. \\
\hline
Gross Distance & Total trajectory length generated by movement. \\
\hline
Path Efficiency & Fraction of movement contributing to net progress. \\
\hline
Velocity & Instantaneous translational output of the locomotor system. \\
\hline
Acceleration & Rate of change of translational motor output. \\
\hline
Velocity Autocorrelation & Temporal persistence of locomotor dynamics. \\
\hline
Curvature & Degree of body/trajectory bending resulting from asymmetric motor activity. \\
\hline
Amplitude & Magnitude of the body-bending motor pattern. \\
\hline
Frequency & Temporal rate of the repeating locomotor rhythm. \\
\hline
Wavelength & Spatial scale of one undulatory cycle. \\
\hline
Wave Velocity & Propagation rate of the locomotor wave. \\
\hline
Phase Coherence & Consistency of timing between distributed body segments. \\
\hline
Muscle Activation & Downstream mechanical output of motor-neuron activity. \\
\hline
Phenotype Severity & Aggregate deviation from the defined baseline phenotype. \\
\hline
Knockout & Functional removal of a neuron, connection, or network component. \\
\hline
Perturbation & Partial modification of connectivity or neuronal parameters. \\
\hline
Potentiation & Increase in effective influence of a network component. \\
\hline
\end{tabular}
\end{table}

\section{Proposal for classifying mutations}

I propose a system which ranks the mutated offsprings in 4 quartiles of the final ranking between 0 to 10, where $X$ is the final ranking number:

\begin{enumerate}
    \item ($0.0 <= X < 2.5$) \textbf{Infantile mutant}: The mutations classified here perform way worse than the baseline model. Most commonly they are immobilized by the mutation or have very low net displacement value.
    \item ($2.5 <= X < 5.0$) \textbf{Slightly degenerate}: The mutations classified here perform only a little worse than the baseline model. Mutations which reach slightly smaller score in the defined categories will be assigned in this ranking category.
    \item ($5.0 <= X < 7.5$) \textbf{Suitable offspring}: The mutations classified here perform a little better than the baseline model. Mutations which reach slightly higher score in the defined categories will be assigned in this ranking category.
    \item ($7.5 <= X <= 10.0$) \textbf{Suitable, but infeasible offspring}: The mutations classified here perform a lot better than the baseline model but in order for them to occur in nature, they would first need to have degenerate traits which nature generally does not allow. Mutations which reach the highest scores in the defined categories and overall scores will be assigned in this ranking category.
\end{enumerate}

This ranking is weighted around the fact, that the baseline model achieves a near $X = 5.0$ value.

You may notice that the higher the value in the code, the more it means an anomaly yet the distribution of the offspring lurk near $5.0$. This is due to the fact that some anomalies are cancelling out. For example the Body Mechanics and Motor-Neuron Output cancel out. But furthermore this is based on empirical measurement and there is no way of me proving it as this is trivial.

\section{Simulation environment}

I have set up a custom simulation environment which allows the ease of trying multiple combinations of knockoffs, perturbations or potentiations. Note, that this framework is merely a facade which communicates with the Openworm instance preset docker container. It can be used to extract and override the sibernetic file. The framework will also generate a movement analysis and based on the analysis script configuration, it will spit out the rating from 0 to 10 in the prespecified standard. It uses modified master and running batch scripts from the Openworm installation 0.9.8 version. \url{https://github.com/openworm/OpenWorm/releases/tag/0.9.8}

\begin{figure}[H]
    \centering
    \includegraphics[width=1\linewidth]{../resources/openworm_facade.png}
    \caption{A basic connection and purpose can be seen for each module here.}
    \label{fig:openworm_uml}
\end{figure}

\section{Simulation Parameters and Experimental Setup}
\label{sec:simulation_parameters}

\begin{figure}
    \centering
    \includegraphics[width=1\linewidth]{../resources/worm.png}
    \caption{An example media generated by the simulation and display program about the C. elegans worm.}
    \label{fig:worm}
\end{figure}

To investigate the effects of neural knockout and perturbation experiments on \textit{Caenorhabditis elegans} using the OpenWorm framework, specific numerical and simulation parameters were established. The core configuration parameters utilized in the simulation runs are summarized in Table~\ref{tab:sim_params}.

\begin{table}[H]
\centering
\caption{Simulation parameters used for the OpenWorm knockout/perturbation experiments.}
\label{tab:sim_params}
\begin{tabular}{lp{6cm}p{5cm}}
\hline
\textbf{Parameter} & \textbf{Value / Setting} & \textbf{Description} \\ \hline
\texttt{duration} & \texttt{sim\_duration} (1.0\,s) & Total simulation duration per run \\
\texttt{dt} & 0.015\,s (Range: 0.01--0.015\,s) & Integration time step \\
\texttt{dtNrn} & 0.08\,s & Neuron simulation time step \\
\texttt{logstep} & 400 & Data logging interval \\
\texttt{reference} & \texttt{"FW"} & Muscle/movement reference \\
\texttt{c302params} & \texttt{"C2"} & Network parameter set \\
\texttt{verbose} & \texttt{False} & Verbose output flag \\
\texttt{device} & \texttt{"GPU"} & Computational execution device \\
\texttt{configuration} & \texttt{configuration} & System configuration profile \\
\texttt{noc302} & \texttt{noc302} & Custom network flag \\
\texttt{datareader} & \texttt{UpdatedSpreadsheetDataReader2} & Data reader backend \\
\texttt{outDir} & \texttt{OW\_OUT\_DIR} & Output directory for simulation logs \\ \hline
\end{tabular}
\end{table}

\begin{longtable}{|l|l|p{3cm}|p{3cm}|}
\caption{c302 network reference configurations} \label{tab:c302-references} \\
\hline
\textbf{Reference string} & \textbf{File} & \textbf{What it contains (summary)} & \textbf{Notes} \\
\hline
\endfirsthead

\multicolumn{4}{c}{{\tablename\ \thetable\ -- continued from previous page}} \\
\hline
\textbf{Reference string} & \textbf{File} & \textbf{What it contains (summary)} & \textbf{Notes} \\
\hline
\endhead

\hline \multicolumn{4}{r}{{Continued on next page}} \\
\endfoot

\hline
\endlastfoot

FW & \texttt{c302\_FW.py} & Forward locomotion circuit (AVB, DB, VB, DD, VD + muscles) & Small, focused on crawling. Does \textbf{not} contain AVA or RME. \\
\hline
Muscles & \texttt{c302\_Muscles.py} & Large set of motor/interneurons that connect to body-wall muscles + AVAL / AVAR / AVBL / AVBR / AVDL / AVDR / PVCL / PVCR + muscles & Contains AVAL, AVAR, RMEL, RMER (and many others). This is what the simulation will use. \\
\hline
Full & \texttt{c302\_Full.py} & Essentially the whole hermaphrodite nervous system ($\approx$302 neurons) + muscles & Largest / most complete. \\
\hline
Pharyngeal & \texttt{c302\_Pharyngeal.py} & Pharyngeal nervous system only (M1--M5, I1--I6, etc.) & Feeding circuit. \\
\hline
Social & \texttt{c302\_Social.py} & Social behaviour related neurons & Smaller specialised circuit. \\
\hline
Oscillator & \texttt{c302\_Oscillator.py} & Oscillator / rhythmic circuit & Used for testing rhythmic activity. \\
\hline
OscillatorM & \texttt{c302\_OscillatorM.py} & Oscillator + muscles variant & --- \\
\hline
Syns & \texttt{c302\_Syns.py} & Focused on synaptic connections (test/example) & --- \\
\hline
IClamp & \texttt{c302\_IClamp.py} & Simple current-clamp examples (few cells) & Not a behavioural circuit. \\
\hline
IClampMuscle & \texttt{c302\_IClampMuscle.py} & Current-clamp + muscle & --- \\
\hline
TargetMuscle & \texttt{c302\_TargetMuscle.py} & Targets specific muscles & --- \\
\hline
TapWithdrawal & \texttt{c302\_TapWithdrawal.py} & Tap-withdrawal circuit & --- \\
\hline
RIA & \texttt{c302\_RIA.py} & RIA-related circuit & --- \\
\hline
MultiSyns & \texttt{c302\_MultiSyns.py} & Multi-synapse examples & --- \\
\hline
MuscleTest & \texttt{c302\_MuscleTest.py} & Muscle testing & --- \\
\hline
MusclesSine & \texttt{c302\_MusclesSine.py} & Muscles network driven by sine-wave current (example) & Variant of Muscles. \\
\hline
\end{longtable}

\subsection{Duration and Time-Step Justification}
Each simulation was configured to run for a duration of $1.0\text{ s}$. This duration was selected because a complete undulation cycle (body wave loop) of the worm is reliably visible across almost all experimental instances within this timeframe, capturing the full dynamic range of locomotion without unnecessary computational overhead. 

The integration time step (\texttt{dt}) was set within the range of $0.01\text{ s}$ to $0.015\text{ s}$ (with a default specific setting of $0.015\text{ s}$), balancing numerical stability and precision for the biomechanical and neural update cycles. Similarly, the neural network time step (\texttt{dtNrn}) was set to $0.08\text{ s}$, ensuring accurate propagation of electrical activity across the c302 network architecture.

\section{Simulated scenarios}

I've split the scenarios to these main groups:

\begin{itemize}
    \item important reciprocal command connections
    \item A-type motor neurons (core reversal pathway)
    \item B-type motor neurons
    \item Cross-talk between command interneurons
    \item AS motor neurons (also part of reversal output)
    \item Strength perturbations
    \item command system lesions
\end{itemize}

There are more groups which I will also denote.

I denote these groups in my run\_knockouts.py file. The facade project can be downloaded here: \url{https://afghangoat.hu/imports/src/mutator_facade/mutator_facade.zip}

% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/analysis_AVAL-DA1.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-10\_16-33-32-AVAL-DA1
% Scenario Tag: AVAL-DA1

\subsection{Movement Analysis: \texttt{AVAL-DA1}}
\label{sec:movement_analysis_AVAL-DA1}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-10\_16-33-32-AVAL-DA1}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-DA1}}
\label{tab:loco_states_AVAL-DA1}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 17.6\% \\
Backward Crawling & 26.1\% \\
Stationary & 0.0\% \\
Reversal & 12.1\% \\
Omega Turns & 26.7\% \\
Shallow Turns & 17.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-DA1}}
\label{tab:kinematics_AVAL-DA1}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.033 & mm \\
Gross Distance & 0.1598 & mm \\
Path Efficiency (Net/Gross) & 0.2062 & [0.0 -- 1.0] \\
Mean Speed & 0.1605 & mm/s \\
Maximum Forward Velocity & 0.741 & mm/s \\
Maximum Backward Velocity & 0.7642 & mm/s \\
Median Velocity & 0.0878 & mm/s \\
Velocity Std Deviation & 0.206 & mm/s \\
Velocity RMS & 0.2611 & mm/s \\
Fraction Time Moving Forward & 50.0\% & ratio \\
Fraction Time Moving Backward & 50.0\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4553 & mm/s$^2$ \\
Maximum Acceleration & 168.7895 & mm/s$^2$ \\
Acceleration RMS & 24.2722 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8273 & correlation \\
Reversal Frequency & 20.0803 & s$^{-1}$ \\
Mean Curvature & 3774.8456 & rad/mm \\
Omega Turn Count & 44 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-DA1}}
\label{tab:undulation_AVAL-DA1}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0071 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.81 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789854 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-DA1}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-DA1}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-DA1}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-DA1}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-DA1}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-DA1}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_16-33-32-AVAL-DA1/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-DA1}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.4 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-DA1}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 1.9 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.0 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.4 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/analysis_AVAR-DA1.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-10\_18-12-16-AVAR-DA1
% Scenario Tag: AVAR-DA1

\subsection{Movement Analysis: \texttt{AVAR-DA1}}
\label{sec:movement_analysis_AVAR-DA1}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-10\_18-12-16-AVAR-DA1}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-DA1}}
\label{tab:loco_states_AVAR-DA1}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 9.1\% \\
Backward Crawling & 30.3\% \\
Stationary & 0.0\% \\
Reversal & 12.1\% \\
Omega Turns & 24.2\% \\
Shallow Turns & 24.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-DA1}}
\label{tab:kinematics_AVAR-DA1}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0446 & mm \\
Gross Distance & 0.149 & mm \\
Path Efficiency (Net/Gross) & 0.2994 & [0.0 -- 1.0] \\
Mean Speed & 0.1496 & mm/s \\
Maximum Forward Velocity & 0.6 & mm/s \\
Maximum Backward Velocity & 0.8391 & mm/s \\
Median Velocity & 0.0901 & mm/s \\
Velocity Std Deviation & 0.1876 & mm/s \\
Velocity RMS & 0.24 & mm/s \\
Fraction Time Moving Forward & 46.4\% & ratio \\
Fraction Time Moving Backward & 53.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.326 & mm/s$^2$ \\
Maximum Acceleration & 168.7897 & mm/s$^2$ \\
Acceleration RMS & 22.11 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8317 & correlation \\
Reversal Frequency & 20.0803 & s$^{-1}$ \\
Mean Curvature & 3739.8273 & rad/mm \\
Omega Turn Count & 40 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-DA1}}
\label{tab:undulation_AVAR-DA1}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.77 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789911 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-DA1}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-DA1}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-DA1}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-DA1}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-DA1}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-DA1}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-DA1}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-10_18-12-16-AVAR-DA1/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-DA1}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-DA1}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.3 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.7 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/analysis_AVAL-DA3.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-11\_10-04-56-AVAL-DA3
% Scenario Tag: AVAL-DA3

\subsection{Movement Analysis: \texttt{AVAL-DA3}}
\label{sec:movement_analysis_AVAL-DA3}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-11\_10-04-56-AVAL-DA3}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-DA3}}
\label{tab:loco_states_AVAL-DA3}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 14.6\% \\
Backward Crawling & 34.5\% \\
Stationary & 0.0\% \\
Reversal & 8.5\% \\
Omega Turns & 20.0\% \\
Shallow Turns & 22.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-DA3}}
\label{tab:kinematics_AVAL-DA3}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0365 & mm \\
Gross Distance & 0.151 & mm \\
Path Efficiency (Net/Gross) & 0.2417 & [0.0 -- 1.0] \\
Mean Speed & 0.1516 & mm/s \\
Maximum Forward Velocity & 0.8695 & mm/s \\
Maximum Backward Velocity & 0.8126 & mm/s \\
Median Velocity & 0.0859 & mm/s \\
Velocity Std Deviation & 0.2009 & mm/s \\
Velocity RMS & 0.2517 & mm/s \\
Fraction Time Moving Forward & 47.6\% & ratio \\
Fraction Time Moving Backward & 52.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4728 & mm/s$^2$ \\
Maximum Acceleration & 168.7738 & mm/s$^2$ \\
Acceleration RMS & 23.2192 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8484 & correlation \\
Reversal Frequency & 14.0562 & s$^{-1}$ \\
Mean Curvature & 2648.8306 & rad/mm \\
Omega Turn Count & 33 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-DA3}}
\label{tab:undulation_AVAL-DA3}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789825 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-DA3}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-DA3}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-DA3}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-DA3}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-DA3}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-DA3}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_10-04-56-AVAL-DA3/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-DA3}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-DA3}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.5 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/analysis_AVAR-DA3.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-11\_12-57-13-AVAR-DA3
% Scenario Tag: AVAR-DA3

\subsection{Movement Analysis: \texttt{AVAR-DA3}}
\label{sec:movement_analysis_AVAR-DA3}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-11\_12-57-13-AVAR-DA3}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-DA3}}
\label{tab:loco_states_AVAR-DA3}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 11.5\% \\
Backward Crawling & 34.5\% \\
Stationary & 0.0\% \\
Reversal & 10.3\% \\
Omega Turns & 23.0\% \\
Shallow Turns & 20.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-DA3}}
\label{tab:kinematics_AVAR-DA3}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0366 & mm \\
Gross Distance & 0.1405 & mm \\
Path Efficiency (Net/Gross) & 0.2607 & [0.0 -- 1.0] \\
Mean Speed & 0.141 & mm/s \\
Maximum Forward Velocity & 0.9613 & mm/s \\
Maximum Backward Velocity & 0.8233 & mm/s \\
Median Velocity & 0.0816 & mm/s \\
Velocity Std Deviation & 0.2037 & mm/s \\
Velocity RMS & 0.2478 & mm/s \\
Fraction Time Moving Forward & 42.2\% & ratio \\
Fraction Time Moving Backward & 57.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4727 & mm/s$^2$ \\
Maximum Acceleration & 168.7928 & mm/s$^2$ \\
Acceleration RMS & 24.4651 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8352 & correlation \\
Reversal Frequency & 17.0683 & s$^{-1}$ \\
Mean Curvature & 5305.6943 & rad/mm \\
Omega Turn Count & 38 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-DA3}}
\label{tab:undulation_AVAR-DA3}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.8 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789879 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-DA3}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-DA3}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-DA3}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-DA3}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-DA3}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-DA3}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-DA3}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-11_12-57-13-AVAR-DA3/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-DA3}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-DA3}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.0 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 1.6 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/analysis_AVAL-VA5.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-15\_13-46-57-AVAL-VA5
% Scenario Tag: AVAL-VA5

\subsection{Movement Analysis: \texttt{AVAL-VA5}}
\label{sec:movement_analysis_AVAL-VA5}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-15\_13-46-57-AVAL-VA5}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-VA5}}
\label{tab:loco_states_AVAL-VA5}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 7.9\% \\
Backward Crawling & 30.3\% \\
Stationary & 0.0\% \\
Reversal & 12.7\% \\
Omega Turns & 26.7\% \\
Shallow Turns & 22.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-VA5}}
\label{tab:kinematics_AVAL-VA5}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0458 & mm \\
Gross Distance & 0.1672 & mm \\
Path Efficiency (Net/Gross) & 0.2738 & [0.0 -- 1.0] \\
Mean Speed & 0.1679 & mm/s \\
Maximum Forward Velocity & 0.6965 & mm/s \\
Maximum Backward Velocity & 0.9217 & mm/s \\
Median Velocity & 0.0926 & mm/s \\
Velocity Std Deviation & 0.2084 & mm/s \\
Velocity RMS & 0.2676 & mm/s \\
Fraction Time Moving Forward & 44.6\% & ratio \\
Fraction Time Moving Backward & 54.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3289 & mm/s$^2$ \\
Maximum Acceleration & 168.7925 & mm/s$^2$ \\
Acceleration RMS & 23.8987 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8316 & correlation \\
Reversal Frequency & 21.0843 & s$^{-1}$ \\
Mean Curvature & 3737.1681 & rad/mm \\
Omega Turn Count & 44 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-VA5}}
\label{tab:undulation_AVAL-VA5}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0066 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789866 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-VA5}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-VA5}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-VA5}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-VA5}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-VA5}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-VA5}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_13-46-57-AVAL-VA5/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-VA5}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-VA5}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.0 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/analysis_AVAR-VA5.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-15\_15-44-05-AVAR-VA5
% Scenario Tag: AVAR-VA5

\subsection{Movement Analysis: \texttt{AVAR-VA5}}
\label{sec:movement_analysis_AVAR-VA5}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-15\_15-44-05-AVAR-VA5}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-VA5}}
\label{tab:loco_states_AVAR-VA5}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.3\% \\
Backward Crawling & 35.1\% \\
Stationary & 0.0\% \\
Reversal & 12.7\% \\
Omega Turns & 27.9\% \\
Shallow Turns & 13.9\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-VA5}}
\label{tab:kinematics_AVAR-VA5}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0528 & mm \\
Gross Distance & 0.1375 & mm \\
Path Efficiency (Net/Gross) & 0.3844 & [0.0 -- 1.0] \\
Mean Speed & 0.138 & mm/s \\
Maximum Forward Velocity & 0.8556 & mm/s \\
Maximum Backward Velocity & 0.8404 & mm/s \\
Median Velocity & 0.071 & mm/s \\
Velocity Std Deviation & 0.199 & mm/s \\
Velocity RMS & 0.2422 & mm/s \\
Fraction Time Moving Forward & 37.4\% & ratio \\
Fraction Time Moving Backward & 62.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4603 & mm/s$^2$ \\
Maximum Acceleration & 168.7669 & mm/s$^2$ \\
Acceleration RMS & 23.6072 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8017 & correlation \\
Reversal Frequency & 21.0843 & s$^{-1}$ \\
Mean Curvature & 4043.3923 & rad/mm \\
Omega Turn Count & 46 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-VA5}}
\label{tab:undulation_AVAR-VA5}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789929 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-VA5}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-VA5}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-VA5}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-VA5}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-VA5}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-VA5}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-VA5}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_15-44-05-AVAR-VA5/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-VA5}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.9 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-VA5}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 2.5 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.9 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/analysis_AVAL-VA8.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-15\_17-32-25-AVAL-VA8
% Scenario Tag: AVAL-VA8

\subsection{Movement Analysis: \texttt{AVAL-VA8}}
\label{sec:movement_analysis_AVAL-VA8}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-15\_17-32-25-AVAL-VA8}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-VA8}}
\label{tab:loco_states_AVAL-VA8}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 15.8\% \\
Backward Crawling & 22.4\% \\
Stationary & 0.0\% \\
Reversal & 13.3\% \\
Omega Turns & 32.1\% \\
Shallow Turns & 15.8\% \\
Irregular / Abnormal & 0.6\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-VA8}}
\label{tab:kinematics_AVAL-VA8}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0382 & mm \\
Gross Distance & 0.1482 & mm \\
Path Efficiency (Net/Gross) & 0.2577 & [0.0 -- 1.0] \\
Mean Speed & 0.1488 & mm/s \\
Maximum Forward Velocity & 0.8347 & mm/s \\
Maximum Backward Velocity & 0.801 & mm/s \\
Median Velocity & 0.0846 & mm/s \\
Velocity Std Deviation & 0.1995 & mm/s \\
Velocity RMS & 0.2488 & mm/s \\
Fraction Time Moving Forward & 48.8\% & ratio \\
Fraction Time Moving Backward & 50.0\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4441 & mm/s$^2$ \\
Maximum Acceleration & 168.7912 & mm/s$^2$ \\
Acceleration RMS & 23.4832 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8135 & correlation \\
Reversal Frequency & 22.0884 & s$^{-1}$ \\
Mean Curvature & 4702.9887 & rad/mm \\
Omega Turn Count & 53 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-VA8}}
\label{tab:undulation_AVAL-VA8}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.77 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789766 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-VA8}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-VA8}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-VA8}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-VA8}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-VA8}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-VA8}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_17-32-25-AVAL-VA8/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-VA8}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-VA8}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.3 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.1 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/analysis_AVAR-VA8.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-15\_19-25-10-AVAR-VA8
% Scenario Tag: AVAR-VA8

\subsection{Movement Analysis: \texttt{AVAR-VA8}}
\label{sec:movement_analysis_AVAR-VA8}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-15\_19-25-10-AVAR-VA8}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-VA8}}
\label{tab:loco_states_AVAR-VA8}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 15.8\% \\
Backward Crawling & 23.6\% \\
Stationary & 0.0\% \\
Reversal & 15.2\% \\
Omega Turns & 26.1\% \\
Shallow Turns & 19.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-VA8}}
\label{tab:kinematics_AVAR-VA8}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0221 & mm \\
Gross Distance & 0.1449 & mm \\
Path Efficiency (Net/Gross) & 0.1528 & [0.0 -- 1.0] \\
Mean Speed & 0.1455 & mm/s \\
Maximum Forward Velocity & 0.801 & mm/s \\
Maximum Backward Velocity & 0.7948 & mm/s \\
Median Velocity & 0.08 & mm/s \\
Velocity Std Deviation & 0.1984 & mm/s \\
Velocity RMS & 0.246 & mm/s \\
Fraction Time Moving Forward & 48.8\% & ratio \\
Fraction Time Moving Backward & 51.2\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4414 & mm/s$^2$ \\
Maximum Acceleration & 168.8079 & mm/s$^2$ \\
Acceleration RMS & 23.4686 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7991 & correlation \\
Reversal Frequency & 25.1004 & s$^{-1}$ \\
Mean Curvature & 5050.7093 & rad/mm \\
Omega Turn Count & 43 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-VA8}}
\label{tab:undulation_AVAR-VA8}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789758 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-VA8}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-VA8}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-VA8}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-VA8}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-VA8}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-VA8}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-VA8}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-15_19-25-10-AVAR-VA8/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-VA8}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-VA8}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/analysis_AVA-DA_bilateral.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-16\_10-33-55-AVA-DA\_bilateral
% Scenario Tag: AVA-DA\_bilateral

\subsection{Movement Analysis: \texttt{AVA-DA\_bilateral}}
\label{sec:movement_analysis_AVA-DA-bilateral}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-16\_10-33-55-AVA-DA\_bilateral}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVA-DA\_bilateral}}
\label{tab:loco_states_AVA-DA-bilateral}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 17.0\% \\
Backward Crawling & 21.8\% \\
Stationary & 0.0\% \\
Reversal & 10.3\% \\
Omega Turns & 27.3\% \\
Shallow Turns & 23.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVA-DA\_bilateral}}
\label{tab:kinematics_AVA-DA-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.018 & mm \\
Gross Distance & 0.1617 & mm \\
Path Efficiency (Net/Gross) & 0.1114 & [0.0 -- 1.0] \\
Mean Speed & 0.1623 & mm/s \\
Maximum Forward Velocity & 1.113 & mm/s \\
Maximum Backward Velocity & 0.8744 & mm/s \\
Median Velocity & 0.1011 & mm/s \\
Velocity Std Deviation & 0.2106 & mm/s \\
Velocity RMS & 0.2659 & mm/s \\
Fraction Time Moving Forward & 54.8\% & ratio \\
Fraction Time Moving Backward & 44.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3912 & mm/s$^2$ \\
Maximum Acceleration & 168.7928 & mm/s$^2$ \\
Acceleration RMS & 25.3843 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8359 & correlation \\
Reversal Frequency & 17.0683 & s$^{-1}$ \\
Mean Curvature & 3802.4853 & rad/mm \\
Omega Turn Count & 45 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVA-DA\_bilateral}}
\label{tab:undulation_AVA-DA-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0071 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789778 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVA-DA-bilateral}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVA-DA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVA-DA-bilateral}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVA-DA-bilateral}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVA-DA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVA-DA-bilateral}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVA-DA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVA-DA-bilateral}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVA-DA-bilateral}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_10-33-55-AVA-DA_bilateral/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVA-DA-bilateral}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVA-DA-bilateral}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.0 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/analysis_AVA-VA_bilateral.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-16\_14-41-41-AVA-VA\_bilateral
% Scenario Tag: AVA-VA\_bilateral

\subsection{Movement Analysis: \texttt{AVA-VA\_bilateral}}
\label{sec:movement_analysis_AVA-VA-bilateral}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-16\_14-41-41-AVA-VA\_bilateral}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVA-VA\_bilateral}}
\label{tab:loco_states_AVA-VA-bilateral}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.7\% \\
Backward Crawling & 24.9\% \\
Stationary & 0.0\% \\
Reversal & 13.3\% \\
Omega Turns & 26.1\% \\
Shallow Turns & 23.0\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVA-VA\_bilateral}}
\label{tab:kinematics_AVA-VA-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0392 & mm \\
Gross Distance & 0.1418 & mm \\
Path Efficiency (Net/Gross) & 0.2766 & [0.0 -- 1.0] \\
Mean Speed & 0.1424 & mm/s \\
Maximum Forward Velocity & 0.628 & mm/s \\
Maximum Backward Velocity & 0.8177 & mm/s \\
Median Velocity & 0.0787 & mm/s \\
Velocity Std Deviation & 0.1902 & mm/s \\
Velocity RMS & 0.2376 & mm/s \\
Fraction Time Moving Forward & 49.4\% & ratio \\
Fraction Time Moving Backward & 50.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3288 & mm/s$^2$ \\
Maximum Acceleration & 168.7979 & mm/s$^2$ \\
Acceleration RMS & 24.1378 & mm/s$^2$ \\
Velocity Autocorrelation & 0.794 & correlation \\
Reversal Frequency & 22.0884 & s$^{-1}$ \\
Mean Curvature & 4492.0114 & rad/mm \\
Omega Turn Count & 43 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVA-VA\_bilateral}}
\label{tab:undulation_AVA-VA-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.81 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789577 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVA-VA-bilateral}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVA-VA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVA-VA-bilateral}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVA-VA-bilateral}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVA-VA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVA-VA-bilateral}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVA-VA-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVA-VA-bilateral}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVA-VA-bilateral}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_14-41-41-AVA-VA_bilateral/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVA-VA-bilateral}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.4 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVA-VA-bilateral}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 1.9 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.1 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.4 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/analysis_AVAR-PVCL_chem.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-16\_19-12-52-AVAR-PVCL\_chem
% Scenario Tag: AVAR-PVCL\_chem

\subsection{Movement Analysis: \texttt{AVAR-PVCL\_chem}}
\label{sec:movement_analysis_AVAR-PVCL-chem}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-16\_19-12-52-AVAR-PVCL\_chem}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-PVCL\_chem}}
\label{tab:loco_states_AVAR-PVCL-chem}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.1\% \\
Backward Crawling & 25.4\% \\
Stationary & 0.0\% \\
Reversal & 10.9\% \\
Omega Turns & 27.3\% \\
Shallow Turns & 24.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-PVCL\_chem}}
\label{tab:kinematics_AVAR-PVCL-chem}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0376 & mm \\
Gross Distance & 0.1436 & mm \\
Path Efficiency (Net/Gross) & 0.2615 & [0.0 -- 1.0] \\
Mean Speed & 0.1442 & mm/s \\
Maximum Forward Velocity & 0.5715 & mm/s \\
Maximum Backward Velocity & 0.8616 & mm/s \\
Median Velocity & 0.0776 & mm/s \\
Velocity Std Deviation & 0.194 & mm/s \\
Velocity RMS & 0.2417 & mm/s \\
Fraction Time Moving Forward & 50.6\% & ratio \\
Fraction Time Moving Backward & 48.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.397 & mm/s$^2$ \\
Maximum Acceleration & 168.5681 & mm/s$^2$ \\
Acceleration RMS & 23.1361 & mm/s$^2$ \\
Velocity Autocorrelation & 0.805 & correlation \\
Reversal Frequency & 18.0723 & s$^{-1}$ \\
Mean Curvature & 3467.7248 & rad/mm \\
Omega Turn Count & 45 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-PVCL\_chem}}
\label{tab:undulation_AVAR-PVCL-chem}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789687 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-PVCL-chem}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-PVCL-chem}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-PVCL-chem}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-PVCL-chem}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-PVCL-chem}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-PVCL-chem}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-PVCL-chem}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-PVCL-chem}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-PVCL-chem}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-16_19-12-52-AVAR-PVCL_chem/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-PVCL-chem}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-PVCL-chem}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/analysis_AVAR-PVCL_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-17\_08-39-22-AVAR-PVCL\_GJ
% Scenario Tag: AVAR-PVCL\_GJ

\subsection{Movement Analysis: \texttt{AVAR-PVCL\_GJ}}
\label{sec:movement_analysis_AVAR-PVCL-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-17\_08-39-22-AVAR-PVCL\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-PVCL\_GJ}}
\label{tab:loco_states_AVAR-PVCL-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 13.3\% \\
Backward Crawling & 29.7\% \\
Stationary & 0.0\% \\
Reversal & 13.3\% \\
Omega Turns & 27.3\% \\
Shallow Turns & 16.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-PVCL\_GJ}}
\label{tab:kinematics_AVAR-PVCL-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0397 & mm \\
Gross Distance & 0.1422 & mm \\
Path Efficiency (Net/Gross) & 0.2791 & [0.0 -- 1.0] \\
Mean Speed & 0.1428 & mm/s \\
Maximum Forward Velocity & 1.0113 & mm/s \\
Maximum Backward Velocity & 0.7735 & mm/s \\
Median Velocity & 0.0786 & mm/s \\
Velocity Std Deviation & 0.2006 & mm/s \\
Velocity RMS & 0.2462 & mm/s \\
Fraction Time Moving Forward & 42.2\% & ratio \\
Fraction Time Moving Backward & 57.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4351 & mm/s$^2$ \\
Maximum Acceleration & 168.7679 & mm/s$^2$ \\
Acceleration RMS & 25.0487 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7836 & correlation \\
Reversal Frequency & 22.0884 & s$^{-1}$ \\
Mean Curvature & 4088.0379 & rad/mm \\
Omega Turn Count & 45 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-PVCL\_GJ}}
\label{tab:undulation_AVAR-PVCL-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789967 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-PVCL-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-PVCL-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-PVCL-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-PVCL-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-PVCL-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-PVCL-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-PVCL-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-PVCL-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-PVCL-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_08-39-22-AVAR-PVCL_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-PVCL-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-PVCL-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 1.6 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/analysis_AVAR-PVCL_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-17\_15-15-20-AVAR-PVCL\_both
% Scenario Tag: AVAR-PVCL\_both

\subsection{Movement Analysis: \texttt{AVAR-PVCL\_both}}
\label{sec:movement_analysis_AVAR-PVCL-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-17\_15-15-20-AVAR-PVCL\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-PVCL\_both}}
\label{tab:loco_states_AVAR-PVCL-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 14.6\% \\
Backward Crawling & 26.1\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 21.2\% \\
Shallow Turns & 26.7\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-PVCL\_both}}
\label{tab:kinematics_AVAR-PVCL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0274 & mm \\
Gross Distance & 0.1657 & mm \\
Path Efficiency (Net/Gross) & 0.1656 & [0.0 -- 1.0] \\
Mean Speed & 0.1664 & mm/s \\
Maximum Forward Velocity & 0.6941 & mm/s \\
Maximum Backward Velocity & 0.8846 & mm/s \\
Median Velocity & 0.1062 & mm/s \\
Velocity Std Deviation & 0.1949 & mm/s \\
Velocity RMS & 0.2563 & mm/s \\
Fraction Time Moving Forward & 51.8\% & ratio \\
Fraction Time Moving Backward & 48.2\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4719 & mm/s$^2$ \\
Maximum Acceleration & 168.5698 & mm/s$^2$ \\
Acceleration RMS & 22.8415 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8591 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 2922.1599 & rad/mm \\
Omega Turn Count & 35 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-PVCL\_both}}
\label{tab:undulation_AVAR-PVCL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.76 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789747 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-PVCL-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-PVCL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-PVCL-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-PVCL-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-PVCL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-PVCL-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-PVCL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-PVCL-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-PVCL-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_15-15-20-AVAR-PVCL_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-PVCL-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-PVCL-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.4 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.4 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/analysis_AVA-PVC_bilateral.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-17\_16-49-54-AVA-PVC\_bilateral
% Scenario Tag: AVA-PVC\_bilateral

\subsection{Movement Analysis: \texttt{AVA-PVC\_bilateral}}
\label{sec:movement_analysis_AVA-PVC-bilateral}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-17\_16-49-54-AVA-PVC\_bilateral}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVA-PVC\_bilateral}}
\label{tab:loco_states_AVA-PVC-bilateral}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 14.6\% \\
Backward Crawling & 27.9\% \\
Stationary & 0.0\% \\
Reversal & 10.9\% \\
Omega Turns & 27.9\% \\
Shallow Turns & 18.8\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVA-PVC\_bilateral}}
\label{tab:kinematics_AVA-PVC-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0236 & mm \\
Gross Distance & 0.1465 & mm \\
Path Efficiency (Net/Gross) & 0.1614 & [0.0 -- 1.0] \\
Mean Speed & 0.1471 & mm/s \\
Maximum Forward Velocity & 0.733 & mm/s \\
Maximum Backward Velocity & 0.7593 & mm/s \\
Median Velocity & 0.0847 & mm/s \\
Velocity Std Deviation & 0.1883 & mm/s \\
Velocity RMS & 0.239 & mm/s \\
Fraction Time Moving Forward & 47.0\% & ratio \\
Fraction Time Moving Backward & 53.0\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4934 & mm/s$^2$ \\
Maximum Acceleration & 168.7694 & mm/s$^2$ \\
Acceleration RMS & 22.6017 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8105 & correlation \\
Reversal Frequency & 18.0723 & s$^{-1}$ \\
Mean Curvature & 3966.7257 & rad/mm \\
Omega Turn Count & 46 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVA-PVC\_bilateral}}
\label{tab:undulation_AVA-PVC-bilateral}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 1.0 & Hz \\
Wavelength & 1.66 & mm \\
Wave Velocity & 1.67 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789408 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVA-PVC-bilateral}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVA-PVC-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVA-PVC-bilateral}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVA-PVC-bilateral}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVA-PVC-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVA-PVC-bilateral}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVA-PVC-bilateral}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVA-PVC-bilateral}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVA-PVC-bilateral}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-17_16-49-54-AVA-PVC_bilateral/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVA-PVC-bilateral}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVA-PVC-bilateral}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.6 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/analysis_AVAL-PVCR_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_08-04-13-AVAL-PVCR\_both
% Scenario Tag: AVAL-PVCR\_both

\subsection{Movement Analysis: \texttt{AVAL-PVCR\_both}}
\label{sec:movement_analysis_AVAL-PVCR-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_08-04-13-AVAL-PVCR\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-PVCR\_both}}
\label{tab:loco_states_AVAL-PVCR-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.7\% \\
Backward Crawling & 38.2\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 24.2\% \\
Shallow Turns & 13.3\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-PVCR\_both}}
\label{tab:kinematics_AVAL-PVCR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0406 & mm \\
Gross Distance & 0.1524 & mm \\
Path Efficiency (Net/Gross) & 0.2663 & [0.0 -- 1.0] \\
Mean Speed & 0.153 & mm/s \\
Maximum Forward Velocity & 0.7893 & mm/s \\
Maximum Backward Velocity & 0.7932 & mm/s \\
Median Velocity & 0.0961 & mm/s \\
Velocity Std Deviation & 0.1938 & mm/s \\
Velocity RMS & 0.247 & mm/s \\
Fraction Time Moving Forward & 38.0\% & ratio \\
Fraction Time Moving Backward & 61.5\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4843 & mm/s$^2$ \\
Maximum Acceleration & 168.6062 & mm/s$^2$ \\
Acceleration RMS & 23.852 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8343 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 4423.3797 & rad/mm \\
Omega Turn Count & 40 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-PVCR\_both}}
\label{tab:undulation_AVAL-PVCR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0066 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789819 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-PVCR-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-PVCR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-PVCR-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-PVCR-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-PVCR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-PVCR-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-PVCR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-PVCR-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-PVCR-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_08-04-13-AVAL-PVCR_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-PVCR-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.9 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-PVCR-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 2.3 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.9 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/analysis_AVAL-AVAR_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_09-47-25-AVAL-AVAR\_both
% Scenario Tag: AVAL-AVAR\_both

\subsection{Movement Analysis: \texttt{AVAL-AVAR\_both}}
\label{sec:movement_analysis_AVAL-AVAR-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_09-47-25-AVAL-AVAR\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-AVAR\_both}}
\label{tab:loco_states_AVAL-AVAR-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 17.0\% \\
Backward Crawling & 19.4\% \\
Stationary & 0.0\% \\
Reversal & 10.9\% \\
Omega Turns & 30.9\% \\
Shallow Turns & 21.8\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-AVAR\_both}}
\label{tab:kinematics_AVAL-AVAR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0165 & mm \\
Gross Distance & 0.1392 & mm \\
Path Efficiency (Net/Gross) & 0.1182 & [0.0 -- 1.0] \\
Mean Speed & 0.1397 & mm/s \\
Maximum Forward Velocity & 0.6542 & mm/s \\
Maximum Backward Velocity & 0.895 & mm/s \\
Median Velocity & 0.0787 & mm/s \\
Velocity Std Deviation & 0.1958 & mm/s \\
Velocity RMS & 0.2405 & mm/s \\
Fraction Time Moving Forward & 50.6\% & ratio \\
Fraction Time Moving Backward & 48.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4685 & mm/s$^2$ \\
Maximum Acceleration & 168.8009 & mm/s$^2$ \\
Acceleration RMS & 21.7904 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8642 & correlation \\
Reversal Frequency & 18.0723 & s$^{-1}$ \\
Mean Curvature & 4688.8245 & rad/mm \\
Omega Turn Count & 51 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-AVAR\_both}}
\label{tab:undulation_AVAL-AVAR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789792 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-AVAR-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-AVAR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-AVAR-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-AVAR-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-AVAR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-AVAR-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-AVAR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-AVAR-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-AVAR-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_09-47-25-AVAL-AVAR_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-AVAR-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-AVAR-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/analysis_AVBL-VB1_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_12-51-52-AVBL-VB1\_GJ
% Scenario Tag: AVBL-VB1\_GJ

\subsection{Movement Analysis: \texttt{AVBL-VB1\_GJ}}
\label{sec:movement_analysis_AVBL-VB1-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_12-51-52-AVBL-VB1\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVBL-VB1\_GJ}}
\label{tab:loco_states_AVBL-VB1-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.9\% \\
Backward Crawling & 33.3\% \\
Stationary & 0.0\% \\
Reversal & 10.9\% \\
Omega Turns & 26.7\% \\
Shallow Turns & 18.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVBL-VB1\_GJ}}
\label{tab:kinematics_AVBL-VB1-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0494 & mm \\
Gross Distance & 0.1508 & mm \\
Path Efficiency (Net/Gross) & 0.3278 & [0.0 -- 1.0] \\
Mean Speed & 0.1514 & mm/s \\
Maximum Forward Velocity & 0.7547 & mm/s \\
Maximum Backward Velocity & 0.9115 & mm/s \\
Median Velocity & 0.0887 & mm/s \\
Velocity Std Deviation & 0.2025 & mm/s \\
Velocity RMS & 0.2528 & mm/s \\
Fraction Time Moving Forward & 43.4\% & ratio \\
Fraction Time Moving Backward & 56.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.2126 & mm/s$^2$ \\
Maximum Acceleration & 168.7816 & mm/s$^2$ \\
Acceleration RMS & 23.5169 & mm/s$^2$ \\
Velocity Autocorrelation & 0.821 & correlation \\
Reversal Frequency & 18.0723 & s$^{-1}$ \\
Mean Curvature & 3901.8403 & rad/mm \\
Omega Turn Count & 44 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVBL-VB1\_GJ}}
\label{tab:undulation_AVBL-VB1-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.79001 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVBL-VB1-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVBL-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVBL-VB1-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVBL-VB1-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVBL-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVBL-VB1-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVBL-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVBL-VB1-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVBL-VB1-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_12-51-52-AVBL-VB1_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVBL-VB1-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVBL-VB1-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.3 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/analysis_AVBR-VB1_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_14-46-16-AVBR-VB1\_GJ
% Scenario Tag: AVBR-VB1\_GJ

\subsection{Movement Analysis: \texttt{AVBR-VB1\_GJ}}
\label{sec:movement_analysis_AVBR-VB1-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_14-46-16-AVBR-VB1\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVBR-VB1\_GJ}}
\label{tab:loco_states_AVBR-VB1-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 17.6\% \\
Backward Crawling & 27.9\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 23.0\% \\
Shallow Turns & 20.0\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVBR-VB1\_GJ}}
\label{tab:kinematics_AVBR-VB1-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.02 & mm \\
Gross Distance & 0.1482 & mm \\
Path Efficiency (Net/Gross) & 0.1352 & [0.0 -- 1.0] \\
Mean Speed & 0.1488 & mm/s \\
Maximum Forward Velocity & 0.7835 & mm/s \\
Maximum Backward Velocity & 0.7273 & mm/s \\
Median Velocity & 0.0988 & mm/s \\
Velocity Std Deviation & 0.183 & mm/s \\
Velocity RMS & 0.2359 & mm/s \\
Fraction Time Moving Forward & 49.4\% & ratio \\
Fraction Time Moving Backward & 50.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3988 & mm/s$^2$ \\
Maximum Acceleration & 168.7648 & mm/s$^2$ \\
Acceleration RMS & 22.8884 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8198 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 4170.9753 & rad/mm \\
Omega Turn Count & 38 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVBR-VB1\_GJ}}
\label{tab:undulation_AVBR-VB1-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 1.0 & Hz \\
Wavelength & 1.66 & mm \\
Wave Velocity & 1.67 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789907 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVBR-VB1-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVBR-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVBR-VB1-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVBR-VB1-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVBR-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVBR-VB1-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVBR-VB1-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVBR-VB1-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVBR-VB1-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_14-46-16-AVBR-VB1_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVBR-VB1-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVBR-VB1-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.1 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/analysis_AVBL-VB2_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_16-28-02-AVBL-VB2\_GJ
% Scenario Tag: AVBL-VB2\_GJ

\subsection{Movement Analysis: \texttt{AVBL-VB2\_GJ}}
\label{sec:movement_analysis_AVBL-VB2-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_16-28-02-AVBL-VB2\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVBL-VB2\_GJ}}
\label{tab:loco_states_AVBL-VB2-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 13.9\% \\
Backward Crawling & 29.1\% \\
Stationary & 0.0\% \\
Reversal & 12.1\% \\
Omega Turns & 24.9\% \\
Shallow Turns & 20.0\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVBL-VB2\_GJ}}
\label{tab:kinematics_AVBL-VB2-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0208 & mm \\
Gross Distance & 0.1507 & mm \\
Path Efficiency (Net/Gross) & 0.1377 & [0.0 -- 1.0] \\
Mean Speed & 0.1513 & mm/s \\
Maximum Forward Velocity & 0.9235 & mm/s \\
Maximum Backward Velocity & 0.7152 & mm/s \\
Median Velocity & 0.0852 & mm/s \\
Velocity Std Deviation & 0.1969 & mm/s \\
Velocity RMS & 0.2483 & mm/s \\
Fraction Time Moving Forward & 46.4\% & ratio \\
Fraction Time Moving Backward & 53.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4619 & mm/s$^2$ \\
Maximum Acceleration & 168.7748 & mm/s$^2$ \\
Acceleration RMS & 23.1613 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8169 & correlation \\
Reversal Frequency & 20.0803 & s$^{-1}$ \\
Mean Curvature & 3480.7488 & rad/mm \\
Omega Turn Count & 41 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVBL-VB2\_GJ}}
\label{tab:undulation_AVBL-VB2-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.78998 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVBL-VB2-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVBL-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVBL-VB2-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVBL-VB2-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVBL-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVBL-VB2-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVBL-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVBL-VB2-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVBL-VB2-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_16-28-02-AVBL-VB2_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVBL-VB2-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVBL-VB2-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.7 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/analysis_AVBR-VB2_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-18\_19-24-29-AVBR-VB2\_GJ
% Scenario Tag: AVBR-VB2\_GJ

\subsection{Movement Analysis: \texttt{AVBR-VB2\_GJ}}
\label{sec:movement_analysis_AVBR-VB2-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-18\_19-24-29-AVBR-VB2\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVBR-VB2\_GJ}}
\label{tab:loco_states_AVBR-VB2-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 17.6\% \\
Backward Crawling & 24.9\% \\
Stationary & 0.0\% \\
Reversal & 10.3\% \\
Omega Turns & 23.0\% \\
Shallow Turns & 24.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVBR-VB2\_GJ}}
\label{tab:kinematics_AVBR-VB2-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0176 & mm \\
Gross Distance & 0.152 & mm \\
Path Efficiency (Net/Gross) & 0.1155 & [0.0 -- 1.0] \\
Mean Speed & 0.1526 & mm/s \\
Maximum Forward Velocity & 0.8491 & mm/s \\
Maximum Backward Velocity & 0.779 & mm/s \\
Median Velocity & 0.1023 & mm/s \\
Velocity Std Deviation & 0.1942 & mm/s \\
Velocity RMS & 0.247 & mm/s \\
Fraction Time Moving Forward & 53.0\% & ratio \\
Fraction Time Moving Backward & 47.0\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4889 & mm/s$^2$ \\
Maximum Acceleration & 168.7875 & mm/s$^2$ \\
Acceleration RMS & 23.2082 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8242 & correlation \\
Reversal Frequency & 17.0683 & s$^{-1}$ \\
Mean Curvature & 3345.2634 & rad/mm \\
Omega Turn Count & 38 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVBR-VB2\_GJ}}
\label{tab:undulation_AVBR-VB2-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.77 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789929 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVBR-VB2-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVBR-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVBR-VB2-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVBR-VB2-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVBR-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVBR-VB2-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVBR-VB2-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVBR-VB2-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVBR-VB2-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-18_19-24-29-AVBR-VB2_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVBR-VB2-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVBR-VB2-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.3 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.6 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/analysis_AVB-VB_bilateral_GJ.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-19\_08-50-02-AVB-VB\_bilateral\_GJ
% Scenario Tag: AVB-VB\_bilateral\_GJ

\subsection{Movement Analysis: \texttt{AVB-VB\_bilateral\_GJ}}
\label{sec:movement_analysis_AVB-VB-bilateral-GJ}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-19\_08-50-02-AVB-VB\_bilateral\_GJ}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVB-VB\_bilateral\_GJ}}
\label{tab:loco_states_AVB-VB-bilateral-GJ}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.1\% \\
Backward Crawling & 26.7\% \\
Stationary & 0.0\% \\
Reversal & 14.6\% \\
Omega Turns & 29.1\% \\
Shallow Turns & 17.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVB-VB\_bilateral\_GJ}}
\label{tab:kinematics_AVB-VB-bilateral-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0403 & mm \\
Gross Distance & 0.1426 & mm \\
Path Efficiency (Net/Gross) & 0.2824 & [0.0 -- 1.0] \\
Mean Speed & 0.1431 & mm/s \\
Maximum Forward Velocity & 0.7181 & mm/s \\
Maximum Backward Velocity & 0.6649 & mm/s \\
Median Velocity & 0.0869 & mm/s \\
Velocity Std Deviation & 0.1852 & mm/s \\
Velocity RMS & 0.2341 & mm/s \\
Fraction Time Moving Forward & 43.4\% & ratio \\
Fraction Time Moving Backward & 55.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4871 & mm/s$^2$ \\
Maximum Acceleration & 168.7893 & mm/s$^2$ \\
Acceleration RMS & 22.4432 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7753 & correlation \\
Reversal Frequency & 24.0964 & s$^{-1}$ \\
Mean Curvature & 3901.942 & rad/mm \\
Omega Turn Count & 48 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVB-VB\_bilateral\_GJ}}
\label{tab:undulation_AVB-VB-bilateral-GJ}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.790137 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVB-VB-bilateral-GJ}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVB-VB-bilateral-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVB-VB-bilateral-GJ}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVB-VB-bilateral-GJ}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVB-VB-bilateral-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVB-VB-bilateral-GJ}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVB-VB-bilateral-GJ}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVB-VB-bilateral-GJ}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVB-VB-bilateral-GJ}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_08-50-02-AVB-VB_bilateral_GJ/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVB-VB-bilateral-GJ}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVB-VB-bilateral-GJ}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/analysis_AVAL-AVBL.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-19\_10-23-22-AVAL-AVBL
% Scenario Tag: AVAL-AVBL

\subsection{Movement Analysis: \texttt{AVAL-AVBL}}
\label{sec:movement_analysis_AVAL-AVBL}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-19\_10-23-22-AVAL-AVBL}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-AVBL}}
\label{tab:loco_states_AVAL-AVBL}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 14.6\% \\
Backward Crawling & 24.9\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 27.3\% \\
Shallow Turns & 21.8\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-AVBL}}
\label{tab:kinematics_AVAL-AVBL}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0271 & mm \\
Gross Distance & 0.1418 & mm \\
Path Efficiency (Net/Gross) & 0.1913 & [0.0 -- 1.0] \\
Mean Speed & 0.1423 & mm/s \\
Maximum Forward Velocity & 0.9191 & mm/s \\
Maximum Backward Velocity & 0.8249 & mm/s \\
Median Velocity & 0.09 & mm/s \\
Velocity Std Deviation & 0.1964 & mm/s \\
Velocity RMS & 0.2426 & mm/s \\
Fraction Time Moving Forward & 50.0\% & ratio \\
Fraction Time Moving Backward & 49.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3169 & mm/s$^2$ \\
Maximum Acceleration & 168.7871 & mm/s$^2$ \\
Acceleration RMS & 23.6106 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8096 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 3767.1856 & rad/mm \\
Omega Turn Count & 45 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-AVBL}}
\label{tab:undulation_AVAL-AVBL}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0071 & rad (bending) \\
Dominant Frequency & 2.01 & Hz \\
Wavelength & 0.91 & mm \\
Wave Velocity & 1.83 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789889 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-AVBL}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-AVBL}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-AVBL}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-AVBL}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-AVBL}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-AVBL}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-AVBL}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-AVBL}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-AVBL}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_10-23-22-AVAL-AVBL/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-AVBL}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.4 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-AVBL}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.1 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.4 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/analysis_AVAR-AVBL_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-19\_14-05-37-AVAR-AVBL\_both
% Scenario Tag: AVAR-AVBL\_both

\subsection{Movement Analysis: \texttt{AVAR-AVBL\_both}}
\label{sec:movement_analysis_AVAR-AVBL-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-19\_14-05-37-AVAR-AVBL\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-AVBL\_both}}
\label{tab:loco_states_AVAR-AVBL-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 11.5\% \\
Backward Crawling & 25.4\% \\
Stationary & 0.6\% \\
Reversal & 13.3\% \\
Omega Turns & 28.5\% \\
Shallow Turns & 20.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-AVBL\_both}}
\label{tab:kinematics_AVAR-AVBL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0387 & mm \\
Gross Distance & 0.1416 & mm \\
Path Efficiency (Net/Gross) & 0.2734 & [0.0 -- 1.0] \\
Mean Speed & 0.1421 & mm/s \\
Maximum Forward Velocity & 0.7519 & mm/s \\
Maximum Backward Velocity & 0.8256 & mm/s \\
Median Velocity & 0.0789 & mm/s \\
Velocity Std Deviation & 0.1913 & mm/s \\
Velocity RMS & 0.2383 & mm/s \\
Fraction Time Moving Forward & 45.8\% & ratio \\
Fraction Time Moving Backward & 53.0\% & ratio \\
Fraction Time Stationary & 0.6\% & ratio \\
Acceleration (Mean) & -0.4885 & mm/s$^2$ \\
Maximum Acceleration & 168.7795 & mm/s$^2$ \\
Acceleration RMS & 24.3684 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7825 & correlation \\
Reversal Frequency & 22.0884 & s$^{-1}$ \\
Mean Curvature & 10811.9682 & rad/mm \\
Omega Turn Count & 47 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-AVBL\_both}}
\label{tab:undulation_AVAR-AVBL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.790241 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-AVBL-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-AVBL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-AVBL-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-AVBL-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-AVBL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-AVBL-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-AVBL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-AVBL-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-AVBL-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_14-05-37-AVAR-AVBL_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-AVBL-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-AVBL-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.7 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/analysis_AVAL-AVDL_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-19\_17-32-25-AVAL-AVDL\_both
% Scenario Tag: AVAL-AVDL\_both

\subsection{Movement Analysis: \texttt{AVAL-AVDL\_both}}
\label{sec:movement_analysis_AVAL-AVDL-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-19\_17-32-25-AVAL-AVDL\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-AVDL\_both}}
\label{tab:loco_states_AVAL-AVDL-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.3\% \\
Backward Crawling & 31.5\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 26.7\% \\
Shallow Turns & 20.0\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-AVDL\_both}}
\label{tab:kinematics_AVAL-AVDL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0386 & mm \\
Gross Distance & 0.1446 & mm \\
Path Efficiency (Net/Gross) & 0.2671 & [0.0 -- 1.0] \\
Mean Speed & 0.1452 & mm/s \\
Maximum Forward Velocity & 0.8641 & mm/s \\
Maximum Backward Velocity & 0.7662 & mm/s \\
Median Velocity & 0.0851 & mm/s \\
Velocity Std Deviation & 0.1996 & mm/s \\
Velocity RMS & 0.2468 & mm/s \\
Fraction Time Moving Forward & 43.4\% & ratio \\
Fraction Time Moving Backward & 56.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4186 & mm/s$^2$ \\
Maximum Acceleration & 168.7895 & mm/s$^2$ \\
Acceleration RMS & 23.329 & mm/s$^2$ \\
Velocity Autocorrelation & 0.803 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 3807.855 & rad/mm \\
Omega Turn Count & 44 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-AVDL\_both}}
\label{tab:undulation_AVAL-AVDL-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789878 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-AVDL-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-AVDL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-AVDL-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-AVDL-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-AVDL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-AVDL-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-AVDL-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-AVDL-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-AVDL-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_17-32-25-AVAL-AVDL_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-AVDL-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-AVDL-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.3 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/analysis_AVAR-AVDR_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-19\_19-12-00-AVAR-AVDR\_both
% Scenario Tag: AVAR-AVDR\_both

\subsection{Movement Analysis: \texttt{AVAR-AVDR\_both}}
\label{sec:movement_analysis_AVAR-AVDR-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-19\_19-12-00-AVAR-AVDR\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-AVDR\_both}}
\label{tab:loco_states_AVAR-AVDR-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.3\% \\
Backward Crawling & 28.5\% \\
Stationary & 0.0\% \\
Reversal & 13.3\% \\
Omega Turns & 31.5\% \\
Shallow Turns & 16.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-AVDR\_both}}
\label{tab:kinematics_AVAR-AVDR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0413 & mm \\
Gross Distance & 0.1363 & mm \\
Path Efficiency (Net/Gross) & 0.3029 & [0.0 -- 1.0] \\
Mean Speed & 0.1369 & mm/s \\
Maximum Forward Velocity & 0.7071 & mm/s \\
Maximum Backward Velocity & 0.7374 & mm/s \\
Median Velocity & 0.0765 & mm/s \\
Velocity Std Deviation & 0.1898 & mm/s \\
Velocity RMS & 0.234 & mm/s \\
Fraction Time Moving Forward & 42.2\% & ratio \\
Fraction Time Moving Backward & 57.2\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3798 & mm/s$^2$ \\
Maximum Acceleration & 168.7867 & mm/s$^2$ \\
Acceleration RMS & 23.3327 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8188 & correlation \\
Reversal Frequency & 22.0884 & s$^{-1}$ \\
Mean Curvature & 5006.643 & rad/mm \\
Omega Turn Count & 52 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-AVDR\_both}}
\label{tab:undulation_AVAR-AVDR-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789847 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-AVDR-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-AVDR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-AVDR-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-AVDR-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-AVDR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-AVDR-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-AVDR-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-AVDR-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-AVDR-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-19_19-12-00-AVAR-AVDR_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-AVDR-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-AVDR-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 1.5 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/analysis_AVAL-AS10_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-20\_09-32-42-AVAL-AS10\_both
% Scenario Tag: AVAL-AS10\_both

\subsection{Movement Analysis: \texttt{AVAL-AS10\_both}}
\label{sec:movement_analysis_AVAL-AS10-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-20\_09-32-42-AVAL-AS10\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-AS10\_both}}
\label{tab:loco_states_AVAL-AS10-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 15.2\% \\
Backward Crawling & 30.3\% \\
Stationary & 0.0\% \\
Reversal & 9.7\% \\
Omega Turns & 26.1\% \\
Shallow Turns & 18.8\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-AS10\_both}}
\label{tab:kinematics_AVAL-AS10-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.034 & mm \\
Gross Distance & 0.1482 & mm \\
Path Efficiency (Net/Gross) & 0.2294 & [0.0 -- 1.0] \\
Mean Speed & 0.1488 & mm/s \\
Maximum Forward Velocity & 0.7495 & mm/s \\
Maximum Backward Velocity & 0.767 & mm/s \\
Median Velocity & 0.0982 & mm/s \\
Velocity Std Deviation & 0.1872 & mm/s \\
Velocity RMS & 0.2391 & mm/s \\
Fraction Time Moving Forward & 47.6\% & ratio \\
Fraction Time Moving Backward & 52.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4536 & mm/s$^2$ \\
Maximum Acceleration & 168.6328 & mm/s$^2$ \\
Acceleration RMS & 22.2858 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8181 & correlation \\
Reversal Frequency & 16.0643 & s$^{-1}$ \\
Mean Curvature & 3817.7009 & rad/mm \\
Omega Turn Count & 43 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-AS10\_both}}
\label{tab:undulation_AVAL-AS10-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0071 & rad (bending) \\
Dominant Frequency & 1.0 & Hz \\
Wavelength & 1.66 & mm \\
Wave Velocity & 1.67 & mm/s \\
Phase Coherence & 0.8 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789884 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-AS10-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-AS10-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-AS10-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-AS10-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-AS10-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-AS10-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-AS10-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-AS10-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-AS10-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_09-32-42-AVAL-AS10_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-AS10-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-AS10-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.0 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.5 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/analysis_AVAR-AS11_both.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-20\_11-19-41-AVAR-AS11\_both
% Scenario Tag: AVAR-AS11\_both

\subsection{Movement Analysis: \texttt{AVAR-AS11\_both}}
\label{sec:movement_analysis_AVAR-AS11-both}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-20\_11-19-41-AVAR-AS11\_both}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-AS11\_both}}
\label{tab:loco_states_AVAR-AS11-both}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.3\% \\
Backward Crawling & 28.5\% \\
Stationary & 0.0\% \\
Reversal & 12.1\% \\
Omega Turns & 28.5\% \\
Shallow Turns & 20.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-AS11\_both}}
\label{tab:kinematics_AVAR-AS11-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0392 & mm \\
Gross Distance & 0.1239 & mm \\
Path Efficiency (Net/Gross) & 0.3162 & [0.0 -- 1.0] \\
Mean Speed & 0.1244 & mm/s \\
Maximum Forward Velocity & 0.7592 & mm/s \\
Maximum Backward Velocity & 0.6951 & mm/s \\
Median Velocity & 0.0627 & mm/s \\
Velocity Std Deviation & 0.1899 & mm/s \\
Velocity RMS & 0.2271 & mm/s \\
Fraction Time Moving Forward & 43.4\% & ratio \\
Fraction Time Moving Backward & 56.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4731 & mm/s$^2$ \\
Maximum Acceleration & 168.7868 & mm/s$^2$ \\
Acceleration RMS & 22.6306 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7977 & correlation \\
Reversal Frequency & 20.0803 & s$^{-1}$ \\
Mean Curvature & 5350.5948 & rad/mm \\
Omega Turn Count & 47 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-AS11\_both}}
\label{tab:undulation_AVAR-AS11-both}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789792 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-AS11-both}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-AS11-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-AS11-both}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-AS11-both}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-AS11-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-AS11-both}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-AS11-both}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-AS11-both}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-AS11-both}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_11-19-41-AVAR-AS11_both/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-AS11-both}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-AS11-both}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.3 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/analysis_AVA-AS_selected.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-20\_16-49-07-AVA-AS\_selected
% Scenario Tag: AVA-AS\_selected

\subsection{Movement Analysis: \texttt{AVA-AS\_selected}}
\label{sec:movement_analysis_AVA-AS-selected}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-20\_16-49-07-AVA-AS\_selected}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVA-AS\_selected}}
\label{tab:loco_states_AVA-AS-selected}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 7.9\% \\
Backward Crawling & 32.7\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 29.7\% \\
Shallow Turns & 18.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVA-AS\_selected}}
\label{tab:kinematics_AVA-AS-selected}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0433 & mm \\
Gross Distance & 0.136 & mm \\
Path Efficiency (Net/Gross) & 0.3182 & [0.0 -- 1.0] \\
Mean Speed & 0.1366 & mm/s \\
Maximum Forward Velocity & 0.6039 & mm/s \\
Maximum Backward Velocity & 0.7218 & mm/s \\
Median Velocity & 0.0835 & mm/s \\
Velocity Std Deviation & 0.1755 & mm/s \\
Velocity RMS & 0.2224 & mm/s \\
Fraction Time Moving Forward & 41.6\% & ratio \\
Fraction Time Moving Backward & 58.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4992 & mm/s$^2$ \\
Maximum Acceleration & 168.5813 & mm/s$^2$ \\
Acceleration RMS & 21.8582 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8007 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 4343.6962 & rad/mm \\
Omega Turn Count & 49 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVA-AS\_selected}}
\label{tab:undulation_AVA-AS-selected}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0069 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.81 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789656 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVA-AS-selected}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVA-AS-selected}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVA-AS-selected}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVA-AS-selected}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVA-AS-selected}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVA-AS-selected}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVA-AS-selected}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVA-AS-selected}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVA-AS-selected}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_16-49-07-AVA-AS_selected/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVA-AS-selected}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVA-AS-selected}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 1.9 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[==--------]} & 1.7 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/analysis_AVAR-PVCL_STRONG.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-20\_18-33-52-AVAR-PVCL\_STRONG
% Scenario Tag: AVAR-PVCL\_STRONG

\subsection{Movement Analysis: \texttt{AVAR-PVCL\_STRONG}}
\label{sec:movement_analysis_AVAR-PVCL-STRONG}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-20\_18-33-52-AVAR-PVCL\_STRONG}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-PVCL\_STRONG}}
\label{tab:loco_states_AVAR-PVCL-STRONG}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 19.4\% \\
Backward Crawling & 28.5\% \\
Stationary & 0.0\% \\
Reversal & 10.3\% \\
Omega Turns & 20.6\% \\
Shallow Turns & 21.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-PVCL\_STRONG}}
\label{tab:kinematics_AVAR-PVCL-STRONG}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0377 & mm \\
Gross Distance & 0.1847 & mm \\
Path Efficiency (Net/Gross) & 0.2039 & [0.0 -- 1.0] \\
Mean Speed & 0.1854 & mm/s \\
Maximum Forward Velocity & 0.9387 & mm/s \\
Maximum Backward Velocity & 0.908 & mm/s \\
Median Velocity & 0.1081 & mm/s \\
Velocity Std Deviation & 0.2145 & mm/s \\
Velocity RMS & 0.2836 & mm/s \\
Fraction Time Moving Forward & 51.2\% & ratio \\
Fraction Time Moving Backward & 48.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4712 & mm/s$^2$ \\
Maximum Acceleration & 168.7864 & mm/s$^2$ \\
Acceleration RMS & 25.6805 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8487 & correlation \\
Reversal Frequency & 17.0683 & s$^{-1}$ \\
Mean Curvature & 3095.7805 & rad/mm \\
Omega Turn Count & 34 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-PVCL\_STRONG}}
\label{tab:undulation_AVAR-PVCL-STRONG}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0067 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789852 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-PVCL-STRONG}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-PVCL-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-PVCL-STRONG}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-PVCL-STRONG}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-PVCL-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-PVCL-STRONG}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-PVCL-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-PVCL-STRONG}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-PVCL-STRONG}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-20_18-33-52-AVAR-PVCL_STRONG/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-PVCL-STRONG}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-PVCL-STRONG}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/analysis_AVAL-DA3_HALF.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-21\_09-00-03-AVAL-DA3\_HALF
% Scenario Tag: AVAL-DA3\_HALF

\subsection{Movement Analysis: \texttt{AVAL-DA3\_HALF}}
\label{sec:movement_analysis_AVAL-DA3-HALF}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-21\_09-00-03-AVAL-DA3\_HALF}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-DA3\_HALF}}
\label{tab:loco_states_AVAL-DA3-HALF}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 10.3\% \\
Backward Crawling & 31.5\% \\
Stationary & 0.0\% \\
Reversal & 10.9\% \\
Omega Turns & 24.9\% \\
Shallow Turns & 22.4\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-DA3\_HALF}}
\label{tab:kinematics_AVAL-DA3-HALF}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0417 & mm \\
Gross Distance & 0.1451 & mm \\
Path Efficiency (Net/Gross) & 0.2877 & [0.0 -- 1.0] \\
Mean Speed & 0.1456 & mm/s \\
Maximum Forward Velocity & 0.4963 & mm/s \\
Maximum Backward Velocity & 0.6958 & mm/s \\
Median Velocity & 0.0932 & mm/s \\
Velocity Std Deviation & 0.1775 & mm/s \\
Velocity RMS & 0.2296 & mm/s \\
Fraction Time Moving Forward & 45.8\% & ratio \\
Fraction Time Moving Backward & 54.2\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4555 & mm/s$^2$ \\
Maximum Acceleration & 168.779 & mm/s$^2$ \\
Acceleration RMS & 22.0002 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8088 & correlation \\
Reversal Frequency & 18.0723 & s$^{-1}$ \\
Mean Curvature & 4494.6012 & rad/mm \\
Omega Turn Count & 41 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-DA3\_HALF}}
\label{tab:undulation_AVAL-DA3-HALF}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.76 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789827 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-DA3-HALF}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-DA3-HALF}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-DA3-HALF}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-DA3-HALF}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-DA3-HALF}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-DA3-HALF}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-DA3-HALF}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-DA3-HALF}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-DA3-HALF}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_09-00-03-AVAL-DA3_HALF/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-DA3-HALF}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-DA3-HALF}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.4 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.8 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/analysis_AVAR-PVCL_GJ_STRONG.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-21\_10-37-01-AVAR-PVCL\_GJ\_STRONG
% Scenario Tag: AVAR-PVCL\_GJ\_STRONG

\subsection{Movement Analysis: \texttt{AVAR-PVCL\_GJ\_STRONG}}
\label{sec:movement_analysis_AVAR-PVCL-GJ-STRONG}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-21\_10-37-01-AVAR-PVCL\_GJ\_STRONG}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAR-PVCL\_GJ\_STRONG}}
\label{tab:loco_states_AVAR-PVCL-GJ-STRONG}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 11.5\% \\
Backward Crawling & 27.9\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 23.0\% \\
Shallow Turns & 26.1\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAR-PVCL\_GJ\_STRONG}}
\label{tab:kinematics_AVAR-PVCL-GJ-STRONG}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0275 & mm \\
Gross Distance & 0.15 & mm \\
Path Efficiency (Net/Gross) & 0.1831 & [0.0 -- 1.0] \\
Mean Speed & 0.1506 & mm/s \\
Maximum Forward Velocity & 0.5856 & mm/s \\
Maximum Backward Velocity & 0.7237 & mm/s \\
Median Velocity & 0.1013 & mm/s \\
Velocity Std Deviation & 0.1812 & mm/s \\
Velocity RMS & 0.2356 & mm/s \\
Fraction Time Moving Forward & 49.4\% & ratio \\
Fraction Time Moving Backward & 50.6\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3642 & mm/s$^2$ \\
Maximum Acceleration & 168.7655 & mm/s$^2$ \\
Acceleration RMS & 23.0163 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8277 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 3989.8244 & rad/mm \\
Omega Turn Count & 38 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAR-PVCL\_GJ\_STRONG}}
\label{tab:undulation_AVAR-PVCL-GJ-STRONG}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.007 & rad (bending) \\
Dominant Frequency & 1.0 & Hz \\
Wavelength & 1.66 & mm \\
Wave Velocity & 1.67 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789881 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAR-PVCL-GJ-STRONG}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAR-PVCL-GJ-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAR-PVCL-GJ-STRONG}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAR-PVCL-GJ-STRONG}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAR-PVCL-GJ-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAR-PVCL-GJ-STRONG}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAR-PVCL-GJ-STRONG}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAR-PVCL-GJ-STRONG}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAR-PVCL-GJ-STRONG}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_10-37-01-AVAR-PVCL_GJ_STRONG/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAR-PVCL-GJ-STRONG}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.5 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAR-PVCL-GJ-STRONG}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[----------]} & 0.1 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[====------]} & \textbf{4.5 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/analysis_AVAL-VA5_HYPER.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-21\_12-48-32-AVAL-VA5\_HYPER
% Scenario Tag: AVAL-VA5\_HYPER

\subsection{Movement Analysis: \texttt{AVAL-VA5\_HYPER}}
\label{sec:movement_analysis_AVAL-VA5-HYPER}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-21\_12-48-32-AVAL-VA5\_HYPER}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVAL-VA5\_HYPER}}
\label{tab:loco_states_AVAL-VA5-HYPER}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.7\% \\
Backward Crawling & 32.1\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 22.4\% \\
Shallow Turns & 21.2\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVAL-VA5\_HYPER}}
\label{tab:kinematics_AVAL-VA5-HYPER}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0344 & mm \\
Gross Distance & 0.1497 & mm \\
Path Efficiency (Net/Gross) & 0.2296 & [0.0 -- 1.0] \\
Mean Speed & 0.1503 & mm/s \\
Maximum Forward Velocity & 0.6905 & mm/s \\
Maximum Backward Velocity & 0.8032 & mm/s \\
Median Velocity & 0.0939 & mm/s \\
Velocity Std Deviation & 0.184 & mm/s \\
Velocity RMS & 0.2376 & mm/s \\
Fraction Time Moving Forward & 45.2\% & ratio \\
Fraction Time Moving Backward & 54.2\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.3495 & mm/s$^2$ \\
Maximum Acceleration & 168.8 & mm/s$^2$ \\
Acceleration RMS & 22.8276 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8174 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 2704.7174 & rad/mm \\
Omega Turn Count & 37 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVAL-VA5\_HYPER}}
\label{tab:undulation_AVAL-VA5-HYPER}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0071 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.78 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.79008 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVAL-VA5-HYPER}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVAL-VA5-HYPER}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVAL-VA5-HYPER}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVAL-VA5-HYPER}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVAL-VA5-HYPER}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVAL-VA5-HYPER}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVAL-VA5-HYPER}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVAL-VA5-HYPER}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVAL-VA5-HYPER}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_12-48-32-AVAL-VA5_HYPER/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVAL-VA5-HYPER}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVAL-VA5-HYPER}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.2 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 0.9 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/analysis_AVA_full_output_light.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-21\_14-19-18-AVA\_full\_output\_light
% Scenario Tag: AVA\_full\_output\_light

\subsection{Movement Analysis: \texttt{AVA\_full\_output\_light}}
\label{sec:movement_analysis_AVA-full-output-light}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-21\_14-19-18-AVA\_full\_output\_light}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVA\_full\_output\_light}}
\label{tab:loco_states_AVA-full-output-light}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 8.5\% \\
Backward Crawling & 27.3\% \\
Stationary & 0.0\% \\
Reversal & 11.5\% \\
Omega Turns & 30.9\% \\
Shallow Turns & 21.8\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVA\_full\_output\_light}}
\label{tab:kinematics_AVA-full-output-light}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0378 & mm \\
Gross Distance & 0.1378 & mm \\
Path Efficiency (Net/Gross) & 0.2746 & [0.0 -- 1.0] \\
Mean Speed & 0.1383 & mm/s \\
Maximum Forward Velocity & 0.6638 & mm/s \\
Maximum Backward Velocity & 0.9951 & mm/s \\
Median Velocity & 0.072 & mm/s \\
Velocity Std Deviation & 0.2009 & mm/s \\
Velocity RMS & 0.2439 & mm/s \\
Fraction Time Moving Forward & 44.6\% & ratio \\
Fraction Time Moving Backward & 54.8\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4784 & mm/s$^2$ \\
Maximum Acceleration & 168.8289 & mm/s$^2$ \\
Acceleration RMS & 22.0923 & mm/s$^2$ \\
Velocity Autocorrelation & 0.8286 & correlation \\
Reversal Frequency & 19.0763 & s$^{-1}$ \\
Mean Curvature & 6442.7362 & rad/mm \\
Omega Turn Count & 51 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVA\_full\_output\_light}}
\label{tab:undulation_AVA-full-output-light}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.81 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.789294 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVA-full-output-light}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVA-full-output-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVA-full-output-light}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVA-full-output-light}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVA-full-output-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVA-full-output-light}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVA-full-output-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVA-full-output-light}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVA-full-output-light}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_14-19-18-AVA_full_output_light/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVA-full-output-light}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.6 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVA-full-output-light}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 1.9 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.0 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.6 / 10} \\
\hline
\end{tabular}
\end{table}



% --- Scenario fragment: completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/analysis_AVB_forward_light.tex ---
% OpenWorm Movement Analysis LaTeX Report Segment
% Generated for Run: C2\_Muscles\_2026-08-21\_15-51-38-AVB\_forward\_light
% Scenario Tag: AVB\_forward\_light

\subsection{Movement Analysis: \texttt{AVB\_forward\_light}}
\label{sec:movement_analysis_AVB-forward-light}

This section provides an in-depth kinematic breakdown, locomotion state classification, undulation mechanics, and phenotype severity assessment for simulation run \texttt{C2\_Muscles\_2026-08-21\_15-51-38-AVB\_forward\_light}.

\subsubsection{Locomotion State Classification}

\begin{table}[H]
\centering
\caption{Behavioral State Breakdown for \texttt{AVB\_forward\_light}}
\label{tab:loco_states_AVB-forward-light}
\begin{tabular}{|l|r|}
\hline
\textbf{Locomotion State} & \textbf{Time Fraction (\%)} \\
\hline
Forward Crawling & 12.1\% \\
Backward Crawling & 26.7\% \\
Stationary & 0.0\% \\
Reversal & 14.6\% \\
Omega Turns & 29.1\% \\
Shallow Turns & 17.6\% \\
Irregular / Abnormal & 0.0\% \\
\hline
\end{tabular}
\end{table}

\subsubsection{Kinematic \& Velocity Dynamics}

\begin{table}[H]
\centering
\caption{Kinematic and Velocity Metrics for \texttt{AVB\_forward\_light}}
\label{tab:kinematics_AVB-forward-light}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Kinematic Metric} & \textbf{Value} & \textbf{Unit / Scale} \\
\hline
Net Displacement & 0.0403 & mm \\
Gross Distance & 0.1426 & mm \\
Path Efficiency (Net/Gross) & 0.2824 & [0.0 -- 1.0] \\
Mean Speed & 0.1431 & mm/s \\
Maximum Forward Velocity & 0.7181 & mm/s \\
Maximum Backward Velocity & 0.6649 & mm/s \\
Median Velocity & 0.0869 & mm/s \\
Velocity Std Deviation & 0.1852 & mm/s \\
Velocity RMS & 0.2341 & mm/s \\
Fraction Time Moving Forward & 43.4\% & ratio \\
Fraction Time Moving Backward & 55.4\% & ratio \\
Fraction Time Stationary & 0.0\% & ratio \\
Acceleration (Mean) & -0.4871 & mm/s$^2$ \\
Maximum Acceleration & 168.7893 & mm/s$^2$ \\
Acceleration RMS & 22.4432 & mm/s$^2$ \\
Velocity Autocorrelation & 0.7753 & correlation \\
Reversal Frequency & 24.0964 & s$^{-1}$ \\
Mean Curvature & 3901.942 & rad/mm \\
Omega Turn Count & 48 & count \\
\hline
\end{tabular}
\end{table}

\subsubsection{Undulation Wave Mechanics}

\begin{table}[H]
\centering
\caption{Undulation Wave Parameters for \texttt{AVB\_forward\_light}}
\label{tab:undulation_AVB-forward-light}
\begin{tabular}{|l|r|l|}
\hline
\textbf{Undulation Parameter} & \textbf{Value} & \textbf{Unit} \\
\hline
Crawl Amplitude & 0.0068 & rad (bending) \\
Dominant Frequency & 0.0 & Hz \\
Wavelength & 0.82 & mm \\
Wave Velocity & 0.0 & mm/s \\
Phase Coherence & 0.79 & [0.0 -- 1.0] \\
Mean Muscle Activation & 0.790137 & relative \\
Mean Hydrodynamic Pressure & 0.0 & Pa \\
\hline
\end{tabular}
\end{table}


\subsubsection{Worm Motion and Activity Figures}

\needspace{0.54\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_1.png}{\includegraphics[width=0.92\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_1.png}}{\fbox{Missing figure: worm\_motion\_1.png}}
\caption{Midline of worm through time.}
\label{fig:worm_midline_AVB-forward-light}
\end{figure}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_2.png}}{\fbox{Missing figure: worm\_motion\_2.png}}
\caption{Speed of worm along body directions.}
\label{fig:worm_speed_AVB-forward-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_3.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/worm_motion_3.png}}{\fbox{Missing figure: worm\_motion\_3.png}}
\caption{Propagation of curvature along body of worm.}
\label{fig:worm_curvature_AVB-forward-light}
\end{figure}


\needspace{0.52\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscles_activity_buffer.txt.png}{\includegraphics[width=0.88\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscles_activity_buffer.txt.png}}{\fbox{Missing figure: muscles\_activity\_buffer.txt.png}}
\caption{Muscle activities per quadrant.}
\label{fig:muscle_quadrants_AVB-forward-light}
\end{figure}


\subsubsection{Trace Figures}

\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_muscles_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_muscles_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_activity\_Muscles\_C2.png}}
\caption{Traces of muscle activity and potentials.}
\label{fig:trace_muscles_activity_fw_c2_AVB-forward-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_muscles_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_muscles_Muscles_C2.png}}{\fbox{Missing figure: traces\_muscles\_Muscles\_C2.png}}
\caption{Traces of muscle activity.}
\label{fig:trace_muscles_fw_c2_AVB-forward-light}
\end{figure}


\needspace{0.80\textheight}
\begin{figure}[H]
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_neuron_activity_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_neuron_activity_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_activity\_Muscles\_C2.png}}
\caption{Traces of neuron activity and potentials.}
\label{fig:trace_neuron_activity_fw_c2_AVB-forward-light}
\vspace{2em}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_neuron_Muscles_C2.png}{\includegraphics[width=0.9\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/traces_neuron_Muscles_C2.png}}{\fbox{Missing figure: traces\_neuron\_Muscles\_C2.png}}
\caption{Traces of neuron activity.}
\label{fig:trace_neuron_fw_c2_AVB-forward-light}
\end{figure}


\subsubsection{Compact Morphology Grid}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscle_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscle_activity_C2_Muscles.png}}{\fbox{Missing figure: muscle\_activity\_C2\_Muscles.png}}
\par\small Muscle activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscles_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/muscles_C2_Muscles.png}}{\fbox{Missing figure: muscles\_C2\_Muscles.png}}
\par\small Muscles C2 FW.
\end{minipage}
\caption{Muscle activity and morphology, shown as a 2x1 grid for compact comparison (row 1 of 2).}
\label{fig:compact_morphology_grid_row1_AVB-forward-light}
\end{figure}

\needspace{0.30\textheight}
\begin{figure}[H]
\centering
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/neuron_activity_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/neuron_activity_C2_Muscles.png}}{\fbox{Missing figure: neuron\_activity\_C2\_Muscles.png}}
\par\small Neuron activity C2 FW.
\end{minipage}\hfill
\begin{minipage}[t]{0.48\textwidth}
\centering
\IfFileExists{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/neurons_C2_Muscles.png}{\includegraphics[width=\linewidth]{/mnt/d/openworm/openworm/completed_saved/C2_Muscles_2026-08-21_15-51-38-AVB_forward_light/neurons_C2_Muscles.png}}{\fbox{Missing figure: neurons\_C2\_Muscles.png}}
\par\small Neurons C2 FW.
\end{minipage}
\caption{Neuron activity and morphology, shown as a 2x1 grid for compact comparison (row 2 of 2).}
\label{fig:compact_morphology_grid_row2_AVB-forward-light}
\end{figure}



\subsubsection{Phenotype Severity \& Diagnostic Classification}

\begin{itemize}
  \item \textbf{Paralysis / Movement Failure Diagnosis:} \texttt{HYPERKINETIC}
  \item \textbf{Overall Phenotype Severity:} 4.7 / 10.0 (\textbf{MODERATE PHENOTYPE})
  \item \textbf{Mutation Classification:} \textbf{Slightly degenerate}
\end{itemize}

\begin{table}[H]
\centering
\caption{Phenotype Severity Ratings (0.0 = Normal, 10.0 = Severe Defect)}
\label{tab:phenotype_AVB-forward-light}
\begin{tabular}{|l|c|r|}
\hline
\textbf{Domain} & \textbf{Scale} & \textbf{Score / 10} \\
\hline
Locomotion & \texttt{[----------]} & 0.0 / 10 \\
Turning & \texttt{[==========]} & 10.0 / 10 \\
Undulation & \texttt{[==--------]} & 2.1 / 10 \\
Muscle Output & \texttt{[==========]} & 10.0 / 10 \\
Symmetry & \texttt{[=---------]} & 1.2 / 10 \\
\hline
\textbf{Overall Severity} & \texttt{[=====-----]} & \textbf{4.7 / 10} \\
\hline
\end{tabular}
\end{table}




\section{Conclusions}

From the simulations, it is clear that there is no easy way to make something artificially which is better than what nature did. Most subjects performed somewhat same or way worse. Not even potentiations produced outlying results.

Almost all simulations have failed to show a correct undulation which the original unmutated C. elegans had. This also shows that knocking out or potentiating motor connections will likely not produce results which are moving more or further. This also shows that if even possible, finding a "better" mutation will be much more computationally expensive that most simulations.


\begin{thebibliography}{9}
\bibitem{b1} The openworm github repository, \\ \textit{\url{https://github.com/openworm/OpenWorm}}
\bibitem{b2} Official c302 repository, \\ \textit{\url{https://github.com/openworm/c302}}


\bibitem{b3} LEMS file examples, \\ \textit{\url{https://github.com/openworm/c302/tree/master/examples}}
\bibitem{b4} Cell list of muscles, \\ \textit{\url{https://raw.githubusercontent.com/openworm/c302/master/c302/c302_Muscles.py}}
\bibitem{b5} c302 configuration scripts, \\ \textit{\url{https://github.com/openworm/c302/tree/master/c302}}


\end{thebibliography}



\end{document}
