Our group’s GitHub page hosts software packages we have released in conjunction with our 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.
Vertex models in curved space
This GPU-accelerated package combines some of the topological relations used in cellGPU to define neighbors with a general d-Dimensional simulation package (on which open Qmin was built) to allow for the simulation of 2D vertex models in curved space. See the section on cells on spheres for more details.
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.
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