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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…
Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. While previous implementations have been limited to atomic monopole charge…
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and…
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…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the…
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…
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
The nucleation of gas hydrates is of great interest in flow assurance, global energy demand, and carbon capture and storage. A complex molecular understanding is critical to control hydrate nucleation and growth in the context of potential…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel,…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
We describe a new model for the study of weakly-collisional, magnetized plasmas derived from exploiting the separation of the dynamics parallel and perpendicular to the magnetic field. This unique system of equations retains the particle…
Detonation of a three-dimensional reactive non-isotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave.…
The origin of the dramatic changes in the behavior of liquids as they approach their vitreous state - increases of many orders of magnitude in transport properties and dynamic time scales - is a major unsolved problem in condensed matter.…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…