Related papers: A Reverse Non-Equilibrium Molecular Dynamics (RNEM…
We discuss three related subjects well suited to graduate research. The first, Nonequilibrium molecular dynamics or "NEMD", makes possible the simulation of atomistic systems driven by external fields, subject to dynamic constraints, and…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
A cylindrical and inclined jet in crossflow is studied under two distinct velocity ratios, $r=1$ and $r=2$, using highly resolved large eddy simulations (LES). First, an investigation of turbulent scalar mixing sheds light onto the…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
We present a new phase-field formulation for the non-equilibrium interface kinetics. The diffuse interface is considered an integral of numerous representative volume elements (RVEs), in which there is a two-phase mixture with two conserved…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
We propose a new algorithm for non-equilibrium molecular dynamics simulations of thermal gradients. The algorithm is an extension of the heat exchange algorithm developed by Hafskjold and co-workers [Mol. Phys. 80, 1389 (1993); Mol. Phys.…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
Conventional approaches for simulating steady-state distributions of particles under diffusive and advective transport at high P\'eclet numbers involve solving the diffusion and advection equations in at least two dimensions. Here, we…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
Recent in-situ and remote observations suggest that the transport regime associated with shock accelerated particles may be anomalous {i.e., the Mean Square Displacement (MSD) of such particles scales non-linearly with time}. We use…
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…
A filtered density function (FDF) model based on deep neural network (DNN), termed DNN-FDF, is introduced for large eddy simulation (LES) of turbulent flows involving conserved scalar transport. The primary objectives of this study are to…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
A new computational methodology, termed "PeleLM-FDF" is developed and utilized for high fidelity large eddy simulation (LES) of complex turbulent combustion systems. This methodology is constructed via a hybrid scheme combining the Eulerian…
Bulk thermal conductivity estimates based on predictions from non-equilibrium molecular dynamics (NEMD) using the so-called direct method are known to be severely under-predicted since finite simulation length-scales are unable to mimic…
A procedure is presented to estimate the diffusion coefficient of a uniform patch of argon gas in a uniform background of helium gas. Molecular Dynamics (MD) simulations of the two gases interacting through the Lennard-Jones potential are…