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Name: Margaret Johnson
Type: User
Bio: theoretical and computational biophysics, protein-protein interactions, protein self-assembly in the cell, membrane-mediated assembly
Location: Johns Hopkins University
Name: Margaret Johnson
Type: User
Bio: theoretical and computational biophysics, protein-protein interactions, protein self-assembly in the cell, membrane-mediated assembly
Location: Johns Hopkins University
code and inputs for models of dynamin clustering
RD code using the FPR algorithm, with an implicit lipid model for membrane binding
Rotational rigid-body reaction-diffusion code
c++ code for running single-particle reaction-diffusion simulations using the Free-Propagator Reweighting algorithm
Primarily python code for developing user-friendly analysis for model set-up (input) and analysis of output
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
NonEquilibrium Reaction-Diffusion Self-assembly Simulator
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
Data files from simulations of benchmark model problems
code to test 1D reaction diffusion
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
parallelized c++ MD code for the tip4p-ew water model
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