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Nonadiabatic molecular dynamics simulations aim to describe the coupled electron-nuclear dynamics of molecules in excited electronic states. These simulations have been applied to understand a plethora of photochemical and photophysical…
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…
Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can…
Formation of the nonequilibrium subsystem in dynamical processes during defect generation is simulated by means of molecular dynamics. A particular process of dissipation of the low-frequency acoustic emission into high-frequency…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
We investigate the effect of pressure, temperature and acidity on the composition of water-rich carbon-bearing fluids at thermodynamic conditions that correspond to the Earth's deep Crust and Upper Mantle. Our first-principles molecular…
In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a million particles were conducted with a massively parallel MD…
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…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Aqueous solutions provide a medium for many important reactions in chemical synthesis, industrial processes, environmental chemistry, and biological functions. It is an accepted fact that aqueous solvents can be direct participants to the…
In conventional fluid mechanics, the chemical composition and thermodynamic state of a fluid-solid interface are not considered when establishing velocity-field boundary conditions. As a consequence, fluid simulations are usually not able…
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…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…