Stochastic Transient Analysis of Biochemical Systems and Its Application to the Design of Biochemical Logic Gates

In order to better characterize the behavior of biochemical systems, it is sometimes helpful and necessary to introduce time-dependent input signals. If the state of a biochemical system with such signals is assumed to evolve deterministically and continuously, then it can be readily analyzed by solving ordinary differential equations. However, if it assumed to evolve discretely and stochastically, then existing simulation methods cannot be applied. In this paper, we incorporate conditions for transient analysis into stochastic simulation and we develop the corresponding simulation algorithm. Applying our method to examples, we demonstrate that it can yield new insights into the dynamics of biochemical systems; specifically, it can be used to verify the design of biochemical logic gates.

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