cellGPU: massively parallel simulations of dynamic vertex models
Department of Physics, Syracuse University, Syracuse, New York 13244, USA
arXiv:1702.02939 [physics.bio-ph], (9 Feb 2017)
@article{sussman2017cellgpu,
title={cellGPU: massively parallel simulations of dynamic vertex models},
author={Sussman, Daniel M.},
year={2017},
month={feb},
archivePrefix={"arXiv"},
primaryClass={physics.bio-ph}
}
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations.
February 14, 2017 by hgpu
