Related papers: Symplectic algorithm for constant-pressure molecul…
In this paper, we consider mathematical modeling and numerical simulation of non-isothermal compressible multi-component diffuse-interface two-phase flows with realistic equations of state. A general model with general reference velocity is…
We present a quantum algorithm based on repeated measurement to solve initial-value problems for nonlinear ordinary differential equations (ODEs), which may be generated from partial differential equations in plasma physics. We map a…
We study the dynamics of an ensemble of non-interacting harmonic oscillators in a nonlinear dissipative environment described by the Nos\'e - Hoover model. Using numerical simulation we find the histogram for total energy, which agrees with…
The thermodynamics of mesoscopic systems driven by time-varying temperatures is crucial for understanding biological systems, designing nanoscale engines, and performing micro-particle cooling. In this work, we analyze an underdamped…
We develop a semi-classical method to simulate the motion of atoms in a dissipative optical lattice. Our method treats the internal states of the atom quantum mechanically, including all nonadiabatic couplings, while position and momentum…
Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nose-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in…
Nonequilibrium molecular dynamics simulations often use mechanisms called thermostats to regulate the temperature. A Hamiltonian is presented for the case of the isoenergetic (constant internal energy) thermostat corresponding to a tunable…
Predicting the behaviors of Hamiltonian systems has been drawing increasing attention in scientific machine learning. However, the vast majority of the literature was focused on predicting separable Hamiltonian systems with their kinematic…
We introduce a new mesoscopic model for nematic liquid crystals (LCs). We extend the particle-based stochastic rotation dynamics method, which reproduces the Navier-Stokes equation, to anisotropic fluids by including a simplified…
We extend the nested sampling algorithm to simulate materials under periodic boundary and constant pressure conditions, and show how it can be used to determine the complete equilibrium phase diagram, for a given potential energy function,…
We propose a new generalized-ensemble algorithm, which we refer to as the multibaric-multithermal Monte Carlo method. The multibaric-multithermal Monte Carlo simulations perform random walks widely both in volume space and in potential…
Compositional simulation is challenging, because of highly nonlinear couplings between multi-component flow in porous media with thermodynamic phase behavior. The coupled nonlinear system is commonly solved by the fully-implicit scheme.…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
We study numerical methods for sampling probability measures in high dimension where the underlying model is only approximately identified with a gradient system. Extended stochastic dynamical methods are discussed which have application to…
The adoption of the Kolmogorov-Sinai (KS) entropy is becoming a popular research tool among physicists, especially when applied to a dynamical system fitting the conditions of validity of the Pesin theorem. The study of time series that are…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
Many PDEs (Burgers' equation, KdV, Camassa-Holm, Euler's fluid equations,...) can be formulated as infinite-dimensional Lie-Poisson systems. These are Hamiltonian systems on manifolds equipped with Poisson brackets. The Poisson structure is…
In this work, a kernel-based surrogate for integrating Hamiltonian dynamics that is symplectic by construction and tailored to large prediction horizons is proposed. The method learns a scalar potential whose gradient enters a…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…