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A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make possible molecular simulations with the accuracy of quantum mechanical density functional theory, at a cost only…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions…
Light-matter interaction models invariably rely on the multipole expansion of the electromagnetic potentials generated by complex charge distributions. These multipoles are typically taken to be traceless, however, for a correct evaluation…
We propose to use a new platform - ultracold polar molecules - for quantum computing with switchable interactions. The on/off switch is accomplished by selective excitation of one of the "0" or "1" qubits - long-lived molecular states - to…
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…
We study the realization of lattice models, where cold atoms and molecules move as extra particles in a dipolar crystal of trapped polar molecules. The crystal is a self-assembled floating mesoscopic lattice structure with quantum dynamics…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We present classical and quantum mechanical descriptions of lattice dynamics, from the atomic to the continuum scale, using atomic scale symmetry modes and their constraint equations. This approach is demonstrated for a one-dimensional…
This paper presents a consistent approach to prescribe traction boundary conditions in atomistic models. Due to the typical multiple-neighbor interactions, finding an appropriate boundary condition that models a desired traction is a…
Mesoscale phenomena -- involving a level of description between the finest atomistic scale and the macroscopic continuum -- can be studied by a variation on the usual atomistic-level molecular dynamics (MD) simulation technique. In…
We introduce two approaches to modeling the quantum dynamics of optical $\chi^{(3)}$ solitons. Taking an open-system viewpoint, we project the underlying quantum field into system (soliton) and residual reservoir components. The reservoir…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
Time-discrete dynamical systems on a finite state space have been used with great success to model natural and engineered systems such as biological networks, social networks, and engineered control systems. They have the advantage of being…
Aggregates immersed in a plasma or radiative environment will have charge distributed over their extended surface. Previous studies have modeled the aggregate charge using the monopole and dipole terms of a multipole expansion, with results…
We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Rydberg atoms are remarkable tools for the quantum simulation of spin arrays. Circular Rydberg atoms open the way to simulations over very long time scales, using a combination of laser trapping of the atoms and spontaneous-emission…