Related papers: Reaction rate calculation with time-dependent inva…
In this work, the rate law for inhomogeneous concentration distributions has been formulated, by applying spatial integration over the products of species concentrations. Reaction rates for typical reactions have been investigated by…
In this work an activator-depleted reaction-diffusion system is investigated on polar coordinates with the aim of exploring the relationship and the corresponding influence of domain size on the types of possible diffusion-driven…
We undertake a detailed analysis of a reaction-advection-diffusion (RAD) equation from the viewpoint of pulse-response studies, with particular attention to effects due to the advection velocity. Our boundary-value problem is a mathematical…
Transition state or minimum energy path finding methods constitute a routine component of the computational chemistry toolkit. Standard analysis involves trajectories conventionally plotted in terms of the relative energy to the initial…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
Heterogenous reactions typically consist of multiple elementary steps and their rate coefficients are of fundamental importance in elucidating the mechanisms and micro-kinetics of these processes. Transition-state theory (TST) for…
The structure of invariant regions and globally attracting regions is fundamental to understanding the dynamical properties of reaction network models. We describe an explicit construction of the minimal invariant regions and minimal…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
Intermolecular hydrogen transfer free radical reactions are common in the combustion process and in a number of organic chemistry reactions. Therefore, evaluating the pressure and temperature-dependent rate constants of them is of great…
Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for…
We propose a numerical technique for parameter inference in Markov models of biological processes. Based on time-series data of a process we estimate the kinetic rate constants by maximizing the likelihood of the data. The computation of…
We review recent results on quantum reactive scattering from a phase space perspective. The approach uses classical and quantum versions of normal form theory and the perspective of dynamical systems theory. Over the past ten years the…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
The concept of an active zone in Laplacian transport is used to obtain an analytical approximation for the reactive effectiveness of a pore with an arbitrary rough geometry. We show that this approximation is in very good agreement with…
Several different methods exist for efficient approximation of paths in multiscale stochastic chemical systems. Another approach is to use bursts of stochastic simulation to estimate the parameters of a stochastic differential equation…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
We consider the existence of invariant manifolds in phase space governing reaction dynamics in situations where there are no saddle points on the potential energy surface in the relevant regions of configuration space. We point out that…
The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the…
A general method for the direct evaluation of the temperature dependence of the quantum-mechanical reaction rate constant in many-dimensional systems is described. The method is based on the quantum instanton approximation for the rate…