mjohn218

NERDSS

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

StoichiometricBalance

Given 1) a protein interaction network, with interfaces resolved and 2) Copy numbers for some of the proteins, Quantify degree of stoichiometric balance in protein copy numbers

FPR_rot

Rotational rigid-body reaction-diffusion code

KineticAssembly_AD

Python code for numerical simulations of self-assemly with optimization by automatic differentiation

multi_assembly

network_sampling_MC

Given a protein-protein interaction network (PPIN) sample possible structures of interface interaction networks (IINs). Performs random sampling of network, and biased sampling based on the fitness function defined in Holland, D. et al., Sci. Reports, 7, 5631 (2017):https://www.nature.com/articles/s41598-017-05686-2

oned_rd

code to test 1D reaction diffusion

dynamin_model

code and inputs for models of dynamin clustering

fpr_implicit

RD code using the FPR algorithm, with an implicit lipid model for membrane binding

FPR_simulator

c++ code for running single-particle reaction-diffusion simulations using the Free-Propagator Reweighting algorithm

mjohn218/io_nerdss

Primarily python code for developing user-friendly analysis for model set-up (input) and analysis of output

mjohn218/KineticAssembly_AD

Python code for numerical simulations of self-assemly with optimization by automatic differentiation

mjohn218/multi_assembly

mjohn218/NERDSS

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

mjohn218/dynamin_model

code and inputs for models of dynamin clustering

mjohn218/tip4pew

parallelized c++ MD code for the tip4p-ew water model

mjohn218/oned_rd

code to test 1D reaction diffusion

mjohn218/StoichiometricBalance

Given 1) a protein interaction network, with interfaces resolved and 2) Copy numbers for some of the proteins, Quantify degree of stoichiometric balance in protein copy numbers

mjohn218/testcases

mjohn218/NIMBioS-Data

Data files from simulations of benchmark model problems

mjohn218/fpr_implicit

RD code using the FPR algorithm, with an implicit lipid model for membrane binding

mjohn218/FPR_rot

Rotational rigid-body reaction-diffusion code

mjohn218/network_sampling_MC

Given a protein-protein interaction network (PPIN) sample possible structures of interface interaction networks (IINs). Performs random sampling of network, and biased sampling based on the fitness function defined in Holland, D. et al., Sci. Reports, 7, 5631 (2017):https://www.nature.com/articles/s41598-017-05686-2

mjohn218/FPR_simulator

c++ code for running single-particle reaction-diffusion simulations using the Free-Propagator Reweighting algorithm