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Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
Molecular dynamics simulations have been performed to understand true atomic resolution, which has been observed on the Si(111)-7$\times$7 surface by dynamic force microscopy in ultra high vacuum(UHV). Stable atomic-scale contrast is…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale…
Two roads are presently being followed in order to establish the existence of a liquid-gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
The application of molecular dynamics (MD) simulations to quasistatic loading is severely limited by the large separation between atomic vibration timescales and experimentally relevant deformation rates. In this work we employ the…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
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…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
A procedure is introduced for deriving a coarse-grained dissipative particle dynamics from molecular dynamics. The rules of the dissipative particle dynamics are derived from the underlying molecular interactions, and a Langevin equation is…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
Ab initio wavefunction methods provide accurate molecular simulations but their computational scaling restricts applications to small systems. We develop a workflow combining quantum embedding to decompose a molecule into fragments with a…
The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This…
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,…
We extend the Bell forced dissociation rate model to take account into dynamic disorder. The motivation of the present work is from the recent forced dissociation experiments of the adhesive receptor-ligand complexes, in which some…