Related papers: Extending ring polymer molecular dynamics rate the…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
Complex systems can be advantageously modeled by formal reaction systems (RS), a.k.a. chemical reaction networks in chemistry. Reaction-based models can indeed be interpreted in a hierarchy of semantics, depending on the question at hand,…
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional…
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…
Temperature dependence of the thermal rate constants and kinetic isotope effects (KIE) of the CN + C2H6 gas-phase hydrogen abstraction reaction was theoretically determined within the 25-1000 K temperature range, i.e., from ultra-low to…
Classical rate theories often fail in cases where the observable(s) or order parameter(s) used are poor reaction coordinates or the observed signal is deteriorated by noise, such that no clear separation between reactants and products is…
Metallic nanoparticles embedded in stimuli-responsive polymers can be regarded as nanoreactors since their catalytic activity can be changed within wide limits: the physicochemical properties of the polymer network can be tuned and switched…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
This paper proposes to apply the Ultra-Relativistic Quantum Molecular Dynamic (UrQMD) approach to implement the PANDA project (GSI). Modeling of $\bar{p}$A-interactions has been performed at antiproton energies from 1 GeV to 200 GeV by…
A novel quantum dynamical method to simulate vibronic reaction dynamics in molecules at metal surfaces is proposed. The method is based on the hierarchical quantum master equation approach and uses a discrete variable representation of the…
Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in…
In a dynamical system, the transition between reactants and products is typically mediated by an energy barrier whose properties determine the corresponding pathways and rates. The latter is the flux through a dividing surface (DS) between…
Unlike gas-phase reactions, chemical reactions taking place on interstellar dust grain surfaces cannot always be modeled by rate equations. Due to the small grain sizes and low flux,these reactions may exhibit large fluctuations and thus…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic…
Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…
We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space.…
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…
We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer…