Anne Jeannin-Girardon, Pascal Ballet and Vincent Rodin.
An Efficient Biomechanical Cell Model to Simulate Large Multi-cellular
Tissue Morphogenesis: Application to Cell Sorting Simulation on GPU.
TPNC 2013, 2nd International Conference on the Theory and Practice of
Natural Computing, Cáceres (Spain), 3-5 December 2013.
Published in Lecture Notes in Computer Science (LNCS), Springer,
volume 8273, pages 96-107, December 2013.
Abstract:
Abstract. In the context of tissue morphogenesis study, in silico simulations
can be seen as experiments in a virtual lab bench. Such simulations can
facilitate the comprehension of a system, the test of hypotheses or the
incremental refining of a model and its parameters. In silico simulations
must be efficient and provide the possibility to simulate large tissues,
containing thousands of cells. We propose to study tissue morphogenesis
at the cellular level using our virtual biomechanical cell model. This
model is based on a mass/spring system and coupled to a multi-agent
system. We validated the relevance of our model through a case study:
a cell sorting. Moreover, we took advantage of the large parallelism offered
by graphics processing units (GPU), which contain up to thousands of
cores: we implemented our model with the OpenCL framework. We ran
large scale simulations, with up to 106 of our virtual cells. We studied the
performance of our system on a CPU Intel Core i7 860, and two GPUs:
a NVidia GeForce GT440 and a Nvidia GeForce GTX 690. The absence
of synchronization in our implementation allowed the full benefits of the
parallelism of these hardwares.
Keywords:
Virtual cell, Multi-Agent Systems, Virtual biology, Tissue morphogenesis,
OpenCL, High-performance simulation.
[doi:10.1007/978-3-642-45008-2_8]
[Jeannin13c.pdf]