Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints

Diffusion-Controlled Reaction Kinetics

Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions.

Several stochastic simulation algorithms (SSAs) have recently been proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecu...

Reaction rates for mesoscopic reaction-diffusion kinetics.

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are bette...

Orientation Map: A Reaction-Diffusion Based Model

We show that models for orientation map formation, which invoke convolution in the dynamic equation, are in fact invoking non-local reaction diffusion. In the early stages of development it is unlikely that non-local interactions take place. We present a non-linear reaction diffusion model based on near neighbour interaction for formation of orientation map. Besides capturing all the essential ...

A comparison of bimolecular reaction models for stochastic reaction-diffusion systems.

Stochastic reaction-diffusion models have become an important tool in studying how both noise in the chemical reaction process and the spatial movement of molecules influences the behavior of biological systems. There are two primary spatially-continuous models that have been used in recent studies: the diffusion limited reaction model of Smoluchowski, and a second approach popularized by Doi. ...