Repositories list

• smart

  Public
  Spatial Modeling Algorithms for Reactions and Transport

  Python

  •

  GNU Lesser General Public License v3.0

  •3•9•17•4•Updated Jul 21, 2025Jul 21, 2025

• multimodel-inference

  Public
  Code for multimodel inference project

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• SkelMuscleCa

  Public
  MATLAB code for ODE-based model of calcium in skeletal muscle

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Jun 9, 2025Jun 9, 2025

• CIUKF-MCMC

  Public
  Comprehensive uncertainty quantification framework for system biology

  Jupyter Notebook

  •2•5•0•0•Updated May 26, 2025May 26, 2025

• 2022-mitochondria-lipidomics-md

  Public
  Jupyter Notebook

  •0•1•0•0•Updated May 19, 2025May 19, 2025

• smart-nanopillars

  Public
  Model of mechanotransduction for cells on nanopillars, using SMART.

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •1•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• smart-tutorial

  Public
  A simple SMART tutorial to get started!

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated Mar 9, 2025Mar 9, 2025

• SpineApparatus

  Public
  Python

  •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• Mem3DG

  Public
  3D computational model for lipid membranes

  simulationmembranediscrete-differential-geometry

  C++

  •

  Mozilla Public License 2.0

  •10•25•6•1•Updated Feb 17, 2025Feb 17, 2025

• Tension-Propagation

  Public
  MATLAB

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• Dynamic_multimerization

  Public
  This repository has all the source code, input files, analysis scripts, and sample data used to simulate dynamic dimerization of proteins within condensates.

  C++

  •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

• membrane-spectrin-skeleton

  Public
  Theoretical model of spectrin membrane skeleton

  MATLAB

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• ActuAtorForceEstimation

  Public
  Estimating forces on the membrane by ActuAtor

  automatic-differentiationdiscrete-differential-geometrymembrane-mechanics+ 1mem3dg

  Jupyter Notebook

  •

  Mozilla Public License 2.0

  •1•0•0•1•Updated Sep 20, 2024Sep 20, 2024

• Collagen_matrix_degradation

  Public
  collagen degradation by mmps; single fibril; matrix microarchitecture

  MATLAB

  •1•0•0•0•Updated Aug 9, 2024Aug 9, 2024

• MechanoCircadian

  Public
  MATLAB-based implementation of the coupling between the cell Circadian clock and mechanotransduction.

  MATLAB

  •

  MIT License

  •0•0•0•0•Updated Jul 5, 2024Jul 5, 2024

• smart-comp-sci

  Public
  Examples and numerical tests for SMART scientific computing paper.

  Python

  •

  Creative Commons Attribution Share Alike 4.0 International

  •1•1•0•0•Updated Jun 7, 2024Jun 7, 2024

• Lpd_droplets

  Public
  Files used to simulate LPD droplet dynamics

  0•0•0•0•Updated Apr 28, 2024Apr 28, 2024

• FBP_NWASP_Nanopillar

  Public
  0•0•0•0•Updated Apr 10, 2024Apr 10, 2024

• Spectrin-topological-transition

  Public
  MATLAB

  •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• 2020-Mem3DG-Applications

  Public
  Jupyter Notebook

  •1•3•0•0•Updated Mar 7, 2024Mar 7, 2024

• VASP_droplet_CytoSim

  Public
  This repository carries the inputfiles, analyzed *.csv files of the simulations used in https://doi.org/10.1101/2023.05.26.542517.

  Jupyter Notebook

  •0•0•0•0•Updated Feb 27, 2024Feb 27, 2024

• Qiao_et_al_cAMP-Calcium-on-AKAP-AC-nanodomains

  Public
  0•0•0•0•Updated Jan 29, 2024Jan 29, 2024

• 2023-IDP-bending

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 7, 2023Dec 7, 2023

• Biophysical-3D-modeling-of-actin-mediated-structural-plasticity

  Public
  MATLAB

  •0•0•0•0•Updated Nov 11, 2023Nov 11, 2023

• spatial_mito_model

  Public
  This repository contains all the material generated for the publication "Mitochondrial morphology governs ATP production rate"

  Python

  •

  Other

  •1•0•0•0•Updated Aug 21, 2023Aug 21, 2023

• 2023-axon-pearling

  Public
  Python

  •

  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

• Qiao_et_al_Dose-response-alignment

  Public
  MATLAB

  •0•1•0•0•Updated Jan 31, 2023Jan 31, 2023

• AMPKmTOR2022

  Public
  MATLAB

  •2•0•0•0•Updated Jan 5, 2023Jan 5, 2023

• Coupled-switches-secretion

  Public
  MATLAB

  •0•0•0•0•Updated Dec 19, 2022Dec 19, 2022

• cableEquation

  Public
  MATLAB

  •0•0•0•0•Updated Nov 14, 2022Nov 14, 2022