Related papers: NVU dynamics. III. Simulating molecules at constan…
We study an approach to simulating the stochastic relativistic advection-diffusion equation based on the Metropolis algorithm. We show that the dissipative dynamics of the boosted fluctuating fluid can be simulated by making random…
Recently we proposed a new constant-pressure molecular dynamics method for finite systems. In this paper, we discuss the current understanding of this method and its technique details. We also review the recent theoretical advances of…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
We study a novel alternative approach for the computation of transport coefficients at mesoscales. While standard nonequilibrium molecular dynamics (NEMD) approaches fix the forcing and measure the average induced flux in the system driven…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
We present a detailed description of semi-quantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian…
Material characterization in nano-mechanical tests requires precise interatomic potentials for the computation of atomic energies and forces with near-quantum accuracy. For such purposes, we develop a robust neural-network interatomic…
Confined granular fluids, placed in a shallow box that is vibrated vertically, can achieve homogeneous stationary states thanks to energy injection mechanisms that take place throughout the system. These states can be stable even at high…
We present a novel method for guaranteeing linear momentum in learned physics simulations. Unlike existing methods, we enforce conservation of momentum with a hard constraint, which we realize via antisymmetrical continuous convolutional…
A port-Hamiltonian model for compressible Newtonian fluid dynamics is presented in entirely coordinate-independent geometric fashion. This is achieved by use of tensor-valued differential forms that allow to describe describe the…
The steady-state homogeneous vapor-to-liquid nucleation and the succeeding liquid droplet growth process are studied for water system by means of the coarse-grained molecular dynamics simulations with the mW-model suggested originally in…
Simulations of nano- to micro-meter scale fluidic systems under thermal gradients require consistent mesoscopic methods accounting for both hydrodynamic interactions and proper transport of energy. One such method is dissipative particle…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
Accurate models of robot dynamics are critical for safe and stable control and generalization to novel operational conditions. Hand-designed models, however, may be insufficiently accurate, even after careful parameter tuning. This…
We develop randomized quantum algorithms to simulate quantum collision models, also known as repeated interaction schemes, which provide a rich framework to model various open-system dynamics. The underlying technique involves composing…
We analyze the transport properties of a low density ensemble of identical macroscopic particles immersed in an active fluid. The particles are modeled as inelastic hard spheres (granular gas). The non-homogeneous active fluid is modeled by…
We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…