My GitLab page hosts software packages I have released in conjunction with some of my computational research. Below are some brief descriptions:
A GPU-accelerated package for simulating models of dense biological tissue. These “vertex” and “Voronoi” models of confluent cells are much slower to simulate than particulate systems, since the topology of the cellular network needs to be maintained. Accelerating these simulations has allowed for orders of magnitude improvements in the time- and length-scales accessible to computational analysis. See the section on biological and active matter for more details.
For some of my work on entangled polymer dynamics in spatially inhomogeneous environments I extended the HOOMD-blue molecular dynamics simulation package to allow for Monte Carlo moves that change polymer chain connectivity. This feature is a staple of using LAMMPS to rapidly equilibrate polymer systems; with my contribution this can now be used in a GPU-accelerated environment.
As part of the Syracuse soft matter group’s “Introduction to Computational Research” seminar series, I have publicly posted some lecture slides:
Introduction to git