Asynchronous adaptive time step in quantitative cellular automata modeling

BMC Bioinformatics
Hao ZhuPawan Dhar

Abstract

The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4-5 is achieved in the given example. Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 x 100 x 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment.

References

Jul 1, 1978·IEEE Transactions on Bio-medical Engineering·S Rush, H Larsen
Sep 1, 1975·The Journal of Physiology·R E McAllisterR W Tsien
Jan 1, 1980·The Japanese Journal of Physiology·K YanagiharaH Irisawa
Jan 7, 1993·Journal of Theoretical Biology·G B Ermentrout, L Edelstein-Keshet
Mar 24, 1998·IEEE Transactions on Bio-medical Engineering·W QuanH M Hastings
Oct 15, 1998·IEEE Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society·N V ThakorJ M Ferrero
Oct 29, 1998·Computers and Biomedical Research, an International Journal·P SiregarP Le Beux
Sep 24, 1999·IEEE Transactions on Bio-medical Engineering·Z Qu, A Garfinkel
Jan 19, 2000·Molecular Biology of the Cell·K C ChenJ J Tyson
Oct 4, 2000·Physical Review Letters·E M CherryC S Henriquez
Dec 12, 2001·Journal of Theoretical Biology·A A PatelR A Gatenby
Jun 4, 2002·Nature Reviews. Molecular Cell Biology·Denis Noble
Nov 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Daniel SegrèGeorge M Church

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Software Mentioned

MatLab
Cellang
Celluar

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