Supplementary materials for: Coupling Mechanical and Metabolic Behavior in Huxley-type Muscle Models

Coupling Mechanical and Metabolic Behavior in Huxley-type Muscle Models This repository contains the MATLAB source code and accompanying data associated with the scientific article "Coupling Mechanical and Metabolic Behavior in Huxley-type Muscle Models". The repository is organized into two directories: Code/: MATLAB scripts and helper functions for parameter optimization, simulation, and analysis. Data/: MATLAB (.mat) files containing optimization results and simulation outputs. The code was developed in MATLAB R2024a and requires the Optimization Toolbox. The Parallel Computing Toolbox is optional for parallel optimization. Users should extract the downloaded archive while preserving the directory structure, as the scripts access the data files using relative paths. The repository includes scripts to: reproduce the analyses and figures presented in the manuscript; optimize the parameters of the Huxley-type muscle model; optimize the muscle stimulation input; perform dynamic and isometric muscle simulations. The data directory contains optimized Huxley model parameters, optimized Fourier coefficients for muscle stimulation, dynamic and isometric simulation results, and summary files identifying the best optimization trials. Simulation result files include variables such as muscle force, joint angle, contraction velocity, calcium concentration, cross-bridge distributions, and simulation time. The software in the Code/ directory is distributed under the GNU General Public License v3.0 (GPL-3.0), while the data in the Data/ directory are distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Please refer to the included README.md for detailed documentation, software requirements, file descriptions, and instructions for reproducing the analyses.