Hash-life algorithm on 3D excitable medium application to integrative biology

Authors:
Jonathan Caux;Pridi Siregar;David Hill
Affiliations:
Université Blaise Pascal, LIMOS, BP and CNRS, LIMOS, ISIMA, BP, Aubiere;Integrative Biocomputing, Nouvelles Structures -- Place du Granier, Chantepie;Université Blaise Pascal, LIMOS, BP and CNRS, LIMOS, ISIMA, BP, Aubiere
Venue:
Proceedings of the 2010 Summer Computer Simulation Conference
Year:
2010

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Abstract

In this paper, we explore the possibility of using the Hash-Life algorithm for the simulation of 3D excitable media. Such media are commonly used to create model of biological behaviors like cardiac myocytes stimulation and are easily modeled with cellular automata. To speed up these automata, hardware or software acceleration can be used. The Hash-Life algorithm, which used memoisation to allow significant speed up, is the most efficient on 2D determinist cellular automata [Gosper 1984]. When used in 3D, the combinatorial explosion of the number of configurations of cells can severely impact its performance and restricts its use. We have implemented a 3D Hash-Life and tested its execution on excitable medium to determine in which conditions this algorithm could be useful. Results show that Hash-Life capacity to compute numerous iterations in advance still enables very good performance when simulating the functioning of an excitable medium.