Flexodeal Lite

Check the release notes to learn more about the new features of the latest version!

This is a reduced version of the Flexodeal library which has been structured to follow deal.II tutorial guidelines. It is intended to simulate the deformation of a block of muscle tissue (similar to a biopsy). The stress response has been simplified to include contributions from muscle fibres (Hill-type model) and the base material (hyperelastic, Yeoh).

Check out this cool video of a fully dynamic, fully active, isometric contraction!

This is a library written in C++ meant to be run in Linux and MacOS environments. Windows users can use this library via WSL (Windows Subsystem for Linux). A graphical interface is not yet available.

Brief description of Flexodeal

This code is used to model skeletal muscle in both dynamic and quasi-static experiments, and can include contributions from muscle, aponeurosis, fat, and tendon material. The underlying material properties, numerical algorithms, are described in the following paper:

• Almonacid, J. A., Domínguez-Rivera, S. A., Konno, R. N., Nigam, N., Ross, S. A., Tam, C., & Wakeling, J. M. (2024). A three-dimensional model of skeletal muscle tissues. SIAM Journal on Applied Mathematics, S538-S566. https://doi.org/10.1137/22M1506985

This coding framework has been used in the following studies:

• Ross, S. A., Domínguez, S., Nigam, N., & Wakeling, J. M. (2021). The Energy of Muscle Contraction. III. Kinetic Energy During Cyclic Contractions. Frontiers in Physiology, 12(April), 1–16. https://doi.org/10.3389/fphys.2021.628819

• Konno, R. N., Nigam, N., & Wakeling, J. M. (2021). Modelling extracellular matrix and cellular contributions to whole muscle mechanics. PLoS ONE, 16(4 April 2021), 1–20. https://doi.org/10.1371/journal.pone.0249601

• Ryan, D. S., Domínguez, S., Ross, S. A., Nigam, N., & Wakeling, J. M. (2020). The Energy of Muscle Contraction. II. Transverse Compression and Work. Frontiers in Physiology, 11(November), 1–15. https://doi.org/10.3389/fphys.2020.538522

• Wakeling, J. M., Ross, S. A., Ryan, D. S., Bolsterlee, B., Konno, R., Domínguez, S., & Nigam, N. (2020). The Energy of Muscle Contraction. I. Tissue Force and Deformation During Fixed-End Contractions. Frontiers in Physiology, 11, 1–42. https://doi.org/10.3389/fphys.2020.00813

• Domı́nguez S. From eigenbeauty to large-deformation horror. Ph.D. Thesis, Simon Fraser University. 2020. Available from: http://summit.sfu.ca/item/20968

• Ross, S. A., Ryan, D. S., Dominguez, S., Nigam, N., & Wakeling, J. M. (2018). Size, history-dependent, activation and three-dimensional effects on the work and power produced during cyclic muscle contractions. Integrative and Comparative Biology, 58(2), 232–250. https://doi.org/10.1093/icb/icy021

• Rahemi, H., Nigam, N., & Wakeling, J. M. (2015). The effect of intramuscular fat on skeletal muscle mechanics: implications for the elderly and obese. Journal of The Royal Society Interface, 12(109), 20150365. https://doi.org/10.1098/rsif.2015.0365

• Rahemi, H., Nigam, N., & Wakeling, J. M. (2014). Regionalizing muscle activity causes changes to the magnitude and direction of the force from whole muscles—a modeling study. Frontiers in physiology, 5, 298. https://doi.org/10.3389/fphys.2014.00298

How to use it?

• Make sure you have properly set up deal.II v9.3 (or newer) and its dependencies. For more information, visit their website.
• Get the latest release here. Alternatively, you can clone the repository for bleeding edge updates: git clone https://github.com/sfu-nml/flexodeal-lite.git.
• Navigate to the Flexodeal folder using cd.
• Call CMake:
  • In release mode: cmake . -DCMAKE_BUILD_TYPE=Release -DDEAL_II_DIR=<path/to/deal.II>.
  • In debug mode: cmake . -DCMAKE_BUILD_TYPE=Debug -DDEAL_II_DIR=<path/to/deal.II>.
• Call make. A simple call to make should suffice.
• Run the code. This either achieved by calling make run or ./dynamic-muscle parameters.prm control_points_strain.dat control_points_activation.dat . A folder with the current timestamp will be created. This is where the results of your execution will be stored.

How long does it take to run?

In an Intel i5-9600K (3.70 GHz x 6) machine the code with its default settings (dynamic) takes about 4 minutes to complete 500 ms of simulation. In turn, the quasi-static code (set Type of simulation = quasi-static) takes only 18 seconds! That speaks volumes about the nonlinearity of the dynamic problem.

Latest line count (in main branch)

Sun 01 Dec 2024 01:08:52 PM PST

>> cloc --exclude-dir=.vscode --exclude-lang=JSON,XML,make .
    
    10 text files.
    10 unique files.                              
    8 files ignored.

github.com/AlDanial/cloc v 1.90  T=0.02 s (194.8 files/s, 327488.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              1            693           1110           3129
Markdown                         1             27              0             46
CMake                            1              6             15             18
-------------------------------------------------------------------------------
SUM:                             3            726           1125           3193
-------------------------------------------------------------------------------