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
Jun 1, 1991·Circulation Research·C H Luo, Y Rudy
Jan 1, 1980·The Japanese Journal of Physiology·K YanagiharaH Irisawa
Oct 1, 1993·Circulation·Y LiuJ Jalife
Jan 7, 1993·Journal of Theoretical Biology·G B Ermentrout, L Edelstein-Keshet
Jan 24, 1998·Circulation Research·A NygrenW R Giles
Mar 24, 1998·IEEE Transactions on Bio-medical Engineering·W QuanH M Hastings
Jun 17, 1998·The Journal of Physiology·R Vogel, R Weingart
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
Mar 30, 2002·Nature Biotechnology·Birgit SchoeberlGertraud Müller
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