Related papers: Direct simulation of electron transfer using ring …

Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…

We propose a way to properly interpret the apparent thermal conductivity obtained for finite systems using equilibrium molecular dynamics simulations (EMD) with fixed or open boundary conditions in the transport direction. In such systems…

We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…

We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…

Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…

A dynamic mode decomposition (DMD) based reduced-order model (ROM) is developed for tracking, detection, and prediction of kinetic plasma behavior. DMD is applied to the high-fidelity kinetic plasma model based on the electromagnetic…

We describe a fast implementation of the quasi-centroid molecular dynamics (QCMD) method in which the quasi-centroid potential of mean force is approximated as a separable correction to the classical interaction potential. This correction…

In a previous paper [Phys.Rev.E 83, 051911] we have shown that the results of a quantum-mechanical calculation of electronic energy transfer (EET) over aggregates of coupled monomers can be described also by a model of interacting classical…

Feynman path integrals (PIs) have found many uses in approximate quantum dynamics methods that are able to efficiently calculate real-time quantum correlation functions. The PIs typically take the form of discrete imaginary time slices over…

Chemical reactions at ultracold temperature provide an ideal platform to study chemical reactivity at the fundamental level, and to understand how chemical reactions are governed by quantum mechanics. Recent years have witnessed the…

The algebraic reformulation of molecular Quantum Electrodynamics (mQED) at finite temperatures is applied to Nuclear Magnetic Resonance (NMR) in order to provide a foundation for the reconstruction of much more detailed molecular…

We describe how the fast quasi-centroid molecular dynamics (f-QCMD) method can be applied to condensed phase systems by approximating the quasi-centroid potential of mean force as a sum of inter- and intra-molecular corrections to the…

Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…

This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is…

Direct photon produced from first proton-neutron ($p$-$n$) collision during the early stage of heavy ion reaction is a sensitive probe to reflect energy and momentum distribution of nucleons. In this work, we embedded the hard photon…

We present a data-driven reduced-order modeling of the space-charge dynamics for electromagnetic particle-in-cell (EMPIC) plasma simulations based on dynamic mode decomposition (DMD). The dynamics of the charged particles in kinetic plasma…

The diffusion process through an ideal polymer network is studied by applying the effective medium theory (EMT) to a lattice-gas model. Polymers are modeled by random walks on the lattice bonds, across which molecules can hop with a certain…

For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is…

In a previous article [J. Chem. Phys. 138, 084108 (2013)], we showed that the $t\to 0_+$ limit of ring-polymer molecular dynamics (RPMD) rate-theory is also the $t\to 0_+$ limit of a new type of quantum flux-side time-correlation function,…