Related papers: Surface molecular dynamics simulation with two ort…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…
Accurate description of nonadiabatic dynamics of molecules at metal surfaces involving electron transfer has been a longstanding challenge for theory. Here, we tackle this problem by first constructing high-dimensional neural network…
We investigate the influence of step edge diffusion (SED) and desorption on Molecular Beam Epitaxy (MBE) using kinetic Monte-Carlo simulations of the solid-on-solid (SOS) model. Based on these investigations we propose two strategies to…
Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material's surface affect its ability to form…
The thermodynamics of strongly anisotropic crystalline surfaces is analogous to that of a binary mixture exhibiting phase separation. On a metastable planar surface, formation of stable orientations requires a nucleation process, in which…
This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
The smoothed particle hydrodynamics (SPH) method has been increasingly used to study fluid problems in recent years; but its computational cost can be high if high resolution is required. In this study, an adaptive resolution method based…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
Vacuum breakdowns in particle accelerators and other devices operating at high electric fields is a common problem in the operation of these devices. It has been proposed that the onset of vacuum breakdowns is associated with appearance of…
In this paper we have explored computationally the solidification process of large nickel clusters. This process has the characteristic features of the first order phase transition occurring in a finite system. The focus of our research is…
Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different…
In this paper we propose a dual-time stepping scheme for the Smoothed Particle Hydrodynamics (SPH) method. Dual-time stepping has been used in the context of other numerical methods for the simulation of incompressible fluid flows. Here we…
Sequential Monte Carlo methods have been a major breakthrough in the field of numerical signal processing for stochastic dynamical state-space systems with partial and noisy observations. However, these methods still present certain…
The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…
Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…