Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation
نویسندگان
چکیده
منابع مشابه
Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation.
The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when simulating (bio)chemical kinetics. The CLE model is valid in the regime where molecular populations are abundant enough to assume their concentrations...
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The chemical Langevin equation (CLE) is a multivariable Itô stochastic differential equation that describes the time evolution of molecular counts of reacting chemical species (Gillespie, 2000). It lies between the deterministic ordinary differential equation (ODE) model and the discrete probabilistic chemical master equation model in that it is continuous and probabilistic. Suppose n chemical ...
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This chapter presents the foundational theory of the stochastic chemical kinetics for modeling biochemical reaction networks, of which the discreteness in population of species and the randomness of reactions are treated as an intrinsic part. The dynamical behavior of the biochemical reactions, based on the fundamental premise of the stochastic chemical kinetics, is exactly described by the che...
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We address the problem of eliminating fast reaction kinetics in stochastic biochemical systems by employing a quasiequilibrium approximation. We build on two previous methodologies developed by [Haseltine and Rawlings, J. Chem. Phys. 117, 6959 (2002)] and by [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)]. By following Haseltine and Rawlings, we use the numbers of occurrences of the underlying...
متن کاملThe chemical Langevin equation
The stochastic dynamical behavior of a well-stirred mixture of N molecular species that chemically interact through M reaction channels is accurately described by the chemical master equation. It is shown here that, whenever two explicit dynamical conditions are satisfied, the microphysical premise from which the chemical master equation is derived leads directly to an approximate time-evolutio...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2010
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.3380661