Related papers: FEcMD: A multi-physics and multi-scale computation…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
The quantum dynamics of electron-nuclear systems is analyzed from the perspective of the exact factorization of the wavefunction, with the aim of defining gauge invariant equations of motion for both the nuclei and the electrons. For pure…
The Multi-Mode Model (MMM) for turbulent transport was applied to a large set of well-analyzed discharges from the National Spherical Torus Experiment (NSTX) in order to evaluate its sensitivities to a wide range of plasma conditions. MMM…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Cells and tissues are constantly exposed to various chemical and physical signals that intricately regulate various physiological and pathological processes. This study explores the integration of two biophysical methods, Traction Force…
Electrochemical interfaces are of fundamental importance in electrocatalysis, batteries, and metal corrosion. Finite-field methods are one of most reliable approaches for modeling electrochemical interfaces in complete cells under realistic…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
The emergence of new nanoporous materials, based e.g. on 2D materials, offers new avenues for water filtration and energy. There is accordingly a need to investigate the molecular mechanisms at the root of the advanced performances of these…
This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
The extended quantum molecular dynamics (EQMD) model is one of the few quantum molecular dynamics (QMD)-like transport approaches that can be used to study the effective clustering structure as well as heavily deformed nuclei in both ground…
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…
A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential,…
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving…
Recent developments dedicated to the building of multiscale mechanical and chemical constitutive laws for energetic molecular crystals are presented and discussed. In particular, various tools have been specifically incorporated in…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…