Simulating bistable biochemical systems by means of reactive multiparticle collision dynamics |
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Institution: | 1. Department of Physics, Hangzhou Dianzi University, Hangzhou 310018, China;2. Department of Mathematics, Hangzhou Dianzi University, Hangzhou 310018, China;3. Department of Physics, Zhejiang University, Hangzhou 310027, China;1. School of Mathematical Sciences and Physics, North China Electric Power University, Beijing 102206, China;2. School of Economics and Management, North China Electric Power University, Beijing 102206, China;1. Université d’Avignon et des Pays de Vaucluse, UMR 1114 EMMAH, F-84018 Avignon Cedex, France;2. UMR 1114 EMMAH, Centre INRA d’Avignon, F-84914 Avignon Cedex 9, France;1. Department of Automatization, Wuhan University, Wuhan 430072, PR China;2. School of Mathematics and Statistics, Wuhan University, Wuhan 430072, PR China;3. College of Electrical and Information Engineering, Hunan University, Changsha 410082, PR China;1. P.N. Lebedev Physical Institute, Moscow 119991, Russia;2. Institute of Theoretical and Experimental Physics, Moscow, Russia |
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Abstract: | Based on a reactive multiple particle collision method, we construct a mesoscopic dynamics model to simulate chemical system. The validity of the reactive multiple particle collision method under various conditions in a double-feedback bi-stable chemical system is studied. Then, we extend it to simulate diffusion-limited reactions with fast reaction rate in cellular environment. Using the improved method, we observe bi-stable behavior with randomly distributed reactants and spatial domain separation of opposite phases. The particle-based mesoscopic method is computationally efficient, although hydrodynamic interactions and fluctuation are both properly accounted for. Stochastic effects shown to play dominant roles in biochemical dynamics are also considered. The improved method could be used to explore a variety of reactions with disparate scale of reaction rates. |
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Keywords: | Bi-stable system Reactive multiple particle collision method Fast reaction Domain separation |
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