Coarse graining of master equations with fast and slow states.
نویسندگان
چکیده
We propose a general method for simplifying master equations by eliminating from the description rapidly evolving states. The physical recipe we impose is the suppression of these states and a renormalization of the rates of all the surviving states. In some cases, this decimation procedure can be analytically carried out and is consistent with other analytical approaches, such as in the problem of the random walk in a double well potential. We discuss the application of our method to nontrivial examples: diffusion in a lattice with defects and a model of an enzymatic reaction outside the steady state regime.
منابع مشابه
Quantitative comparison of alternative methods for coarse-graining biological networks.
Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesi...
متن کاملEliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch.
In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network tha...
متن کاملCoarse graining the dynamics of heterogeneous oscillators in networks with spectral gaps.
We present a computer-assisted approach to coarse graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph Laplacian suggests that the graph dynamics may quickly become low dimensional. Our first choice of coarse variables consists of the components of the oscillator sta...
متن کاملThe Mathematical Procedure of Coarse Graining: From Grad's Ten-Moment Equations to Hydrodynamics
We employ systematic coarse graining techniques to derive hydrodynamic equations from Grad’s ten-moment equations. The coarse graining procedure is designed such that it manifestly preserves the thermodynamic structure of the equations. The relevant thermodynamic structure and the coarse graining recipes suggested by statistical mechanics are described in detail and are illustrated by the examp...
متن کاملAdiabatic coarse-graining and simulations of stochastic biochemical networks.
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born-Oppenheimer approximation in quantum mechanics and follows from the stochastic path integral representation...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- The Journal of chemical physics
دوره 128 15 شماره
صفحات -
تاریخ انتشار 2008