Computational methods for diffusion-influenced biochemical reactions
نویسندگان
چکیده
منابع مشابه
Computational methods for diffusion-influenced biochemical reactions
MOTIVATION We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. RESULTS In the regime where the number of molecules is small an...
متن کاملThe intrinsic rate constants in diffusion-influenced reactions.
Intrinsic rate constants play a dominant role in the theory of diffusion-influenced reactions, but usually as abstract quantities that are implicitly assumed to be known. However, recently it has become clear that modeling complex processes requires explicit knowledge of these intrinsic rates. In this paper we provide microscopic expressions for the intrinsic rate constants for association and ...
متن کاملNon-Markovian reversible diffusion-influenced reactions in two dimensions
We investigate the reversible diffusion-influenced reaction of an isolated pair in the presence of a non-Markovian generalization of the backreaction boundary condition in two space dimensions. Following earlier work by Agmon and Weiss, we consider residence time probability densities that decay slower than an exponential and that are characterized by a parameter 0 < σ ≤ 1. We calculate an exac...
متن کاملUnified path integral approach to theories of diffusion-influenced reactions.
Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path deco...
متن کاملFinite Element Methods for Convection Diffusion Equation
This paper deals with the finite element solution of the convection diffusion equation in one and two dimensions. Two main techniques are adopted and compared. The first one includes Petrov-Galerkin based on Lagrangian tensor product elements in conjunction with streamlined upwinding. The second approach represents Bubnov/Petrov-Galerkin schemes based on a new group of exponential elements. It ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2007
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btm278