A GPU Algorithm for Agent-Based Models to Simulate the Integration of Cell Membrane Signals

Simulation of complex biological systems with agent-based models is becoming more relevant with the increase in Graphics Processing Unit (GPU) power. In those simulations, up to millions of virtual cells are individually computed, involving daunting processing times. An important part of computational models is the algorithm that manages how agents perceive their surroundings. This can be particularly problematic in three-dimensional environments where agents have deformable virtual membranes. This article presents a GPU algorithm that gives the possibility for agents to integrate the signals scattered on their virtual membrane. It is detailed to be coded in languages like OpenCL or Cuda. Its performances are tested to show its speed with current GPU devices. Finally, it was implemented inside an existing software to test and illustrate the possibilities it offers.