RangamaniLabUCSD

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52 repositories

Mem3DG
Public
3D computational model for lipid membranes
simulation membrane discrete-differential-geometry
C++
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Mozilla Public License 2.0
•11•19•4•2•Updated Dec 20, 2024Dec 20, 2024
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
smart
Public
Spatial Modeling Algorithms for Reactions and Transport
Python
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GNU Lesser General Public License v3.0
•3•7•17•1•Updated Nov 13, 2024Nov 13, 2024
smart-nanopillars
Public
Model of mechanotransduction for cells on nanopillars, using SMART.
Jupyter Notebook
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Creative Commons Attribution Share Alike 4.0 International
•1•0•0•0•Updated Oct 29, 2024Oct 29, 2024
ActuAtorForceEstimation
Public
Estimating forces on the membrane by ActuAtor
automatic-differentiation discrete-differential-geometry membrane-mechanics mem3dg
Jupyter Notebook
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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
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MIT License
•0•0•0•0•Updated Jul 5, 2024Jul 5, 2024
multimodel-inference
Public
Code for multimodel inference project
Jupyter Notebook
•0•0•0•0•Updated Jun 17, 2024Jun 17, 2024
2022-mitochondria-lipidomics-md
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 12, 2024Jun 12, 2024
smart-comp-sci
Public
Examples and numerical tests for SMART scientific computing paper.
Python
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Creative Commons Attribution Share Alike 4.0 International
•1•0•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
SpineApparatus
Public
Python
•0•0•0•0•Updated Sep 29, 2023Sep 29, 2023
spatial_mito_model
Public
This repository contains all the material generated for the publication "Mitochondrial morphology governs ATP production rate"
Python
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Other
•1•0•0•0•Updated Aug 21, 2023Aug 21, 2023
2023-axon-pearling
Public
Python
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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
CIUKF-MCMC
Public
Comprehensive uncertainty quantification framework for system biology
Jupyter Notebook
•2•3•0•0•Updated Aug 19, 2022Aug 19, 2022
AMPAR-PDE-Bell
Public
COMSOL files for AMPAR PDE work
MATLAB
•0•0•0•0•Updated Jun 13, 2022Jun 13, 2022
AMPAR-ODE-Bell
Public
Files for Bell et al, ODE AMPAR paper
MATLAB
•0•0•0•0•Updated Jun 13, 2022Jun 13, 2022
Modeling_membrane_curvature_generation_using_mechanics_and_machine_learning
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Jun 4, 2022Jun 4, 2022