B

Biophysics

NAMD is a parallel molecular dynamics code for large biomolecular systems. NAMD is free with source code.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

A optimized simulation framework, originally written in C++ then compiled into a python module using Cython. With MemTropy, one can simulate protein-lipid and protein-protein interaction networks on a cellular membrane to explore aspects of proximity to a thermodynamic critical point. Now with a GUI!

Code produced for the course PHYS 519 - Advanced Biophysics

Quantitative analysis of cryo-electron tomography data in the context of podosomes.