Anne Jeannin-Girardon, Pascal Ballet and Vincent Rodin.
Large scale tissue morphogenesis simulation on heterogenous systems based
on a flexible biomechanical cell model.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB),
IEEE, 12(5):1021-1033, September/October 2015.
Abstract:
The complexity of biological tissue morphogenesis makes in silico
simulations of such system very interesting in order to gain a better
understanding of the underliying mechanisms ruling the development of
multicellular tissues. This complexity is mainly due to two elements:
firstly, biological tissues comprise a large amount of cells;
secondly, these cells exhibit complex interactions and behaviors. To
address these two issues, we propose two tools: the first one is a
virtual cell model that comprise two main elements: firstly, a
mechanical structure (membrane, cytoskeleton and cortex) and secondly
the main behaviors exhibited by biological cells i.e., mitosis,
growth, differentiation, molecule consumption and production as well
as the consideration of the physical constraints issued from the
environment. An artificial chemistry is also included in the model.
This virtual cell model is coupled to an agent-based formalism. The
second tool is a simulator that relies on the OpenCL framework. It
allows efficient parallel simulations on heterogenous devices such as
micro-processors or graphics processors. We present two case studies
validating the implementation of our model in our simulator: cellular
proliferation controlled by cell signalling and limb growth in a
virtual organism.
Keywords:
Computational biology, virtual cell, virtual tissue morphogenesis,
multi-agent systems, parallel programing, parallel simulation.
[doi:10.1109/TCBB.2015.2418994]
[Jeannin15a.pdf]