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A new combination of first principle molecular dynamics (MD) simulations with a rate equation model presented in the preceding paper (paper I) is applied to analyze in detail the scattering of argon atoms from a platinum (111) surface. The…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
The random phase approximation (RPA) has received a considerable interest in the field of modeling systems where noncovalent interactions are important. Its advantages over widely used density functional theory (DFT) approximations are the…
The Lagrange-mesh $R$-matrix method is generalized to inhomogeneous equations. This method is numerically stable and efficient. It can be directly used for transfer reactions with the formalism discussed by Ascuitto and Glendenning [Phys.…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…
In this work, we prove rigorous error estimates for a hybrid method introduced in [15] for solving the time-dependent radiation transport equation (RTE). The method relies on a splitting of the kinetic distribution function for the…
Nonparametric estimation for semilinear SPDEs, namely stochastic reaction-diffusion equations in one space dimension, is studied. We consider observations of the solution field on a discrete grid in time and space with infill asymptotics in…
To take into account nuclear quantum effects on the dynamics of atoms, the path integral molecular dynamics (PIMD) method used since 1980s is based on the formalism developed by R. P. Feynman. However, the huge computation time required for…
Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…
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 chemical master equation (CME) is the exact mathematical formulation of chemical reactions occurring in a dilute and well-mixed volume. The reaction-diffusion master equation (RDME) is a stochastic description of reaction-diffusion…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
Our knowledge about the "cold" Universe often relies on molecular spectra. A general property of such spectra is that the energy level populations are rarely at local thermodynamic equilibrium. Solving the radiative transfer thus requires…
Short-range potential has been added into an extended quantum molecular dynamics (EQMD) model. The RMS radius, binding energy and momentum distribution of $^{12}$C with different initial structures and short-range potential parameters have…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
Smoothed Dissipative Particle Dynamics (SDPD) is a mesoscopic method which allows to select the level of resolution at which a fluid is simulated. The aim of this work is to extend SDPD to chemically reactive systems.To this end, an…
The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, precise defining…