ya||a: GPU-Powered spheroid models for mesenchyme and epithelium

Abstract

Simulating morphogenesis of both mesenchyme and epithelium has typically required complex and computationally expensive models. To meet this challenge, we developed ya||a-yet another parallel agent-based model. Our model extends the spheroid model by the addition of spin-like polarities to simulate epithelial sheets and tissue polarity using pairwise interactions only. This design is simple and lends itself to parallelization, and we implemented it together with recent models for protrusions and migration for GPUs for high performance. ya||a is written in concise, plain CUDA/C++ and available at github.com/germannp/yalla under the MIT license.

This work was supported by the Spanish Ministry of Economy and Competitiveness through Centro de Excelencia Severo Ochoa 2013-2017, SEV-2012-0208, the Swiss National Science Foundation through Sinergia grants CR23I3_156234 and CRSII3_141918, and the European Research Council through SIMBIONT (project no. 670555).