Related papers: Modeling time-resolved kinetics in solids induced …
A kinetic Monte Carlo (KMC) method is presented to simulate the electrodeposition of a metal on a single crystal surface of the same metal under galvanostatic conditions. This method utilizes the multi-body embedded-atom method (EAM)…
Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
We present a method to model the interaction and the dynamics of atoms excited to Rydberg states. We show a way to solve the optical Bloch equations for laser excitation of the frozen gas in good agreement with the experiment. A second…
The dynamics and processes involved in particle-molecule scattering, including nuclear dynamics, are described and analyzed using various quantum information quantities throughout the different stages of the scattering. The main process…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…
Over the past decade, experimental microscopy and spectroscopy have made significant progress in the study of the morphological, optical, electronic and transport properties of materials. These developments include higher spatial…
The event-by-event Monte Carlo code, TREKIS, was recently developed to describe excitation of the electron subsystems of solids in the nanometric vicinity of a trajectory of a nonrelativistic swift heavy ion (SHI) decelerated in the…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
The structural evolution of laser-excited systems of gold has previously been measured through ultrafast MeV electron diffraction. However, there has been a long-standing inability of atomistic simulations to provide a consistent picture of…
We introduce a theoretical approach to study the quantum-dissipative dynamics of electronic excitations in macromolecules, which enables to perform calculations in large systems and cover long time intervals. All the parameters of the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
In this work, we present a comprehensive numerical framework that couples numerical solutions of Maxwell's equations using the Finite-Difference Time-Domain (FDTD) approach, Molecular Dynamics (MD), and the Two-Temperature Model (TTM) to…
In this paper we propose an ab initio method to solve quantum many-body problems of molecular dynamics where both the electronic and the nuclear degrees are represented by ensembles of trajectories and guiding waves in physical space. Both…
We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
Magnetite is an important mineral with many interesting applications related to its magnetic, electrical and thermal properties. Typically studied by electronic structure calculations, these methods are unable to capture the complex ion…
Nucleon-ion and ion-ion collisions at non relativistic bombarding energies can be described by means of Monte Carlo approaches, such as those based on the Quantum Molecular Dynamics (QMD) model. We have developed a QMD code, to simulate the…
We study non-equilibrium phases for interacting two-dimensional self-propelled particles with isotropic pair-wise interactions using a persistent kinetic Monte Carlo (MC) approach. We establish the quantitative phase diagram, including the…
Atom-centered electric multipole moments can be extremely useful in chemistry as they enable the systematic mapping of a complex electrostatic problem to a simpler model. However, since they do not correspond to physical observables, there…