Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
نویسندگان
چکیده
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ–̺ model for irreversible bimolecular reactions which was introduced in [11]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated.
منابع مشابه
Equilibration in Reversible Bimolecular Reactions
Fast reversible pseudo-unimolecular reactions do not approach equilibrium in the simple exponential fashion predicted by chemical rate equations. Many-body effects in bimolecular reactions have been revealed in an extensive series of Brownian simulations, showing up to three distinct phases in the approach to equilibrium. Recent theoretical developments are compared with the simulation as well ...
متن کاملCoarse-Grained Stochastic Particle-based Reaction-Diffusion Simulation Algorithm
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is to allow for simulations at cell-biologically relevant timescales without neither neglecting important spatial and biochemical properties of the simulated sys...
متن کاملBrownian dynamics simulation of protein-protein diffusional encounter.
Protein association events are ubiquitous in biological systems. Some protein associations and subsequent responses are diffusion controlled in vivo. Hence, it is important to be able to compute bimolecular diffusional association rates for proteins. The Brownian dynamics simulation methodology may be used to simulate protein-protein encounter, compute association rates, and examine their depen...
متن کاملThe Effects of Different SDE Calculus on Dynamics of Nano-Aerosols Motion in Two Phase Flow Systems
Langevin equation for a nano-particle suspended in a laminar fluid flow was analytically studied. The Brownian motion generated from molecular bombardment was taken as a Wiener stochastic process and approximated by a Gaussian white noise. Euler-Maruyama method was used to solve the Langevin equation numerically. The accuracy of Brownian simulation was checked by performing a series of simulati...
متن کاملReaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network.
Brownian Dynamics algorithms have been widely used for simulating systems in soft-condensed matter physics. In recent times, their application has been extended to the simulation of coarse-grained models of biochemical networks. In these models, components move by diffusion and interact with one another upon contact. However, when reactions are incorporated into a Brownian dynamics algorithm, c...
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:
- SIAM Journal of Applied Mathematics
دوره 71 شماره
صفحات -
تاریخ انتشار 2011