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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_rot

Rotational rigid-body reaction-diffusion code

fpr_simulator

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

io_nerdss

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

kineticassembly_ad

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

multi_assembly

nerdss

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

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

nimbios-data

Data files from simulations of benchmark model problems

oned_rd

code to test 1D reaction diffusion

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

testcases

tip4pew

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