Related papers: Coupling a reactive potential with a harmonic appr…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
We discuss various approaches to modeling the interatomic interactions for molecular dynamics with special focus on the geometrical structural properties. The type of interactions considered are so called reactive force fields, i.e.…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
We consider the N-body problem in a layered geometry containing cold polar molecules with dipole moments that are polarized perpendicular to the layers. A harmonic approximation is used to simplify the hamiltonian and bound state properties…
We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
In this paper, phase combinations among martensitic variants in shape memory alloys patches and bars are simulated by a hybrid optimization methodology. The mathematical model is based on the Landau theory of phase transformations. Each…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
Materials used in commercial D-T fusion reactors will be exposed to irradiation and a mixture of helium and hydrogen plasma. Modeling the microstructural evolution of such materials requires the use of large-scale molecular dynamics…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…