Related papers: Microcanonical rates, gap times, and phase space d…
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…
We investigate the phase space structure and dynamics of a Hamiltonian isokinetic thermostat, for which ergodic thermostat trajectories at fixed (zero) energy generate a canonical distribution in configuration space. Model potentials…
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…
The aim of this paper is to provide a new set of branching ratios for interstellar and planetary chemical networks based on a semi empirical model. We applied, instead of zero order theory (i.e. only the most exoergic decaying channel is…
The accuracy of rate constants calculated using transition state theory depends crucially on the correct identification of a recrossing--free dividing surface. We show here that it is possible to define such optimal dividing surface in…
HNC and HCN, typically used as dense gas tracers in molecular clouds, are a pair of isomers that have great potential as a temperature probe because of temperature dependent, isomer-specific formation and destruction pathways. Previous…
Particles confined to a single file, in a narrow quasi-one dimensional channel, exhibit a dynamic crossover from single file diffusion to Fickian diffusion as the channel radius increases and the particles can begin to pass each other. The…
The behavior of a particle in a solvent has been framed using stochastic dynamics since the early theory of Kramers. A particle in a chemical reaction reacts slower in a diluted solvent because of the lack of energy transfer via collisions.…
Chemical master equation plays an important role to describe the time evolution of homogeneous chemical system. In addition to the reaction process, it is also accompanied by physical diffusion of the reactants in complex system that is…
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…
Simple bimolecular reactions $A_1+A_2\rightleftharpoons A_3+A_4$ are analyzed within the framework of the Boltzmann equation in the initial stage of a chemical reaction with the system far from chemical equilibrium. The Chapman-Enskog…
Semiclassical instanton theory is a form of quantum transition-state theory which can be applied to computing thermal reaction rates for complex molecular systems including quantum tunneling effects. There have been a number of attempts to…
We take into consideration the evolution of particle size in a monodisperse aerosol population during activation and deactivation of cloud condensation nuclei (CCN). The phase portrait of the system derived through a weakly-nonlinear…
The framework of transition state theory relies on the determination of a geometric structure identifying reactivity. It replaces the laborious exercise of following many trajectories for a long time to provide chemical reaction rates and…
We review the reactions involving HCN and HNC in dark molecular clouds to elucidate new chemical sources and sinks of these isomers. We find that the most important reactions for the HCN-HNC system are Dissociative Recombination (DR)…
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We…
Making sense of complex inhomogeneous systems composed of many interacting species is a grand challenge that pervades basically all natural sciences. Phase separation and pattern formation in reaction-diffusion systems have been largely…
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…
The large-time asymptotics of weak solutions to Maxwell--Stefan diffusion systems for chemically reacting fluids with different molar masses and reversible reactions are investigated. The diffusion matrix of the system is generally neither…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…