Our group’s GitHub page hosts software packages we have released in conjunction with our computational research. Below are some brief descriptions:

cellGPU

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.

open Qmin

A computational platform for simulating and visualizing a Landau-de Gennes Q-tensor approach to modeling liquid crystals. See the section on liquid crystals for more details.

Educational presentations

Slides for a two-part presentation I gave as part of the Syracuse soft matter group’s “Introduction to Computational Research” seminar series: Introduction to git