Related papers: Surface molecular dynamics simulation with two ort…
Molecular dynamics simulations are typically constrained to have a fixed number of particles, which limits our capability to simulate chemical and physical processes where the composition of the system changes during the simulation time.…
Investigation of dynamic processes in cell biology very often relies on the observation in two dimensions of 3D biological processes. Consequently, the data are partial and statistical methods and models are required to recover the…
Due to the improvement of computer power and the development of efficient algorithms it is now possible to combine high-dimensional quantum dynamical calculations of the dissociative adsorption of molecular beams with reliable ab-initio…
In this manuscript, we undertake an examination of a classical plasma deployed on two finite co-planar surfaces: a circular region $\Omega_{in}$ into an annular region $\Omega_{out}$ with a gap in between. It is studied both from the point…
Atoms at liquid metal surfaces are known to form layers parallel to the surface. We analyze the two-dimensional arrangement of atoms within such layers at the surface of liquid sodium, using ab initio molecular dynamics (MD) simulations…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
This work aims at generating a model of the ocean surface and its dynamics from one or more video cameras. The idea is to model wave patterns from video as a first step towards a larger system of photogrammetric monitoring of marine…
We propose a novel approach to continuum modelling of dynamics of crystal surfaces. Our model follows the evolution of an ensemble of step configurations, which are consistent with the macroscopic surface profile. Contrary to the usual…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
We propose a novel approach to continuum modeling of the dynamics of crystal surfaces. Our model follows the evolution of an ensemble of step configurations, which are consistent with the macroscopic surface profile. Contrary to the usual…
A simple solid-on-solid model, proposed earlier to describe overlayer-induced faceting of bcc(111) surface, is applied to faceting of spherical surfaces covered by adsorbate monolayer. Monte Carlo simulation results show that morphology of…
We experimentally examine the dynamics of two-particle collisions occuring on a surface. We find that in two-particle collisions a standard coefficient of restitution model may not capture crucial dynamics of this system. Instead, for a…
A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Dissipative particle dynamics (DPD) is an effective mesoscopic particle model with a lower computational cost than molecular dynamics because of the soft potentials that it employs. However, the soft potential is not strong enough to…
Molecular dynamics (MD) simulations are employed to investigate the capillary fluctuations of steps on the surface of a model metal system. The fluctuation spectrum, characterized by the wave number ($k$) dependence of the mean squared…
A continuum theory is used to predict scaling laws for the morphological relaxation of crystal surfaces in two independent space dimensions. The goal is to unify previously disconnected experimental observations of decaying surface…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to…