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Coarse-graining biochemical reactions
From Q-bio
Nikolai Sinitsyn and Ilya Nemenman
- Abstract
- Elementary biochemical reactions in living cells are organized in networks to perform more complicated tasks. Theoretical and numerical study of these networks is complicated by mesoscopic character of many processes. Typically, the number of available molecules is so small that reactions must be considered as chains of discrete stochastic events. Numerical simulations of such stochastic processes are usually very challenging already for a relatively small number of chemical species.
- Fortunately, variables in biochemical networks can be partitioned into slow and fast once. I will present the new technique that employs such a time-scale separation in stochastic networks and strongly reduces the number of degrees of freedom in numerical simulations without a loss of information about mesoscopic fluctuations. Moreover, I will show that the analysis of time-scale separation uncovers an unusual phenomenon, which can be theoretically considered as the Berry phase effect in purely classical stochastic dynamics.
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