Related papers: Molecular Dynamics in a Grand Ensemble: Bergmann-L…
In gas dynamics, the connection between the continuum physics model offered by the Navier-Stokes equations and the heat equation and the molecular model offered by the kinetic theory of gases has been understood for some time, especially…
In this paper we present an exact Grassmann stochastic Schr\"{o}dinger equation for the dynamics of an open fermionic quantum system coupled to a reservoir consisting of a finite or infinite number of fermions. We use this stochastic…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Classical simulation of quantum systems plays an important role in the study of many-body phenomena and in the benchmarking and verification of quantum technologies. Exact simulation is often limited to small systems because the dimension…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Molecular fluids show rich and complicated dynamics close to the glass transition. Some of these observations are related to the fact that translational and orientational degrees of freedom couple in nontrivial ways. A model system which…
Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while…
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…
Wave--current interaction (WCI) dynamics energizes and mixes the ocean thermocline by producing a combination of Langmuir circulation, internal waves and turbulent shear flows, which interact over a wide range of time scales. Two…
Precise physical descriptions of molecules can be obtained by solving the Schrodinger equation; however, these calculations are intractable and even approximations can be cumbersome. Force fields, which estimate interatomic potentials based…
For a gas-solid interfacial system where chemical species undergo reversible adsorption, we develop a mesoscopic stochastic modeling method that simulates both gas-phase hydrodynamics and surface coverage dynamics by coupling the Langmuir…
Large-scale cosmological simulations of galaxy formation currently do not resolve the densities at which molecular hydrogen forms, implying that the atomic-to-molecular transition must be modeled either on the fly or in postprocessing. We…
A previously proposed [X. Shan and H. Chen, Phys. Rev. E {\bf 47}, 1815, (1993)] lattice Boltzmann model for simulating fluids with multiple components and interparticle forces is described in detail. Macroscopic equations governing the…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
We present a hybrid Boltzmann-BGK model for inert mixtures, where each kind of binary interaction may be described by a classical Boltzmann integral or by a suitable relaxation-type operator. We allow also the possibility of changing the…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…