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This paper presents a novel methodology for the direct numerical modeling and simulation of turbulent flows. The kinetic model equation is firstly extended to turbulent flow with the account of coupled evolution of kinetic, thermal, and…
We develop the kinetic theory of collisionless relaxation for systems with long-range interactions in relation to the statistical theory of Lynden-Bell. We treat the multi-level case. We make the connection between the kinetic equation…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
The protein-ligand residence time, tau, influences molecular function in biological networks and has been recognized as an important determinant of drug efficacy. To predict tau, computational methods must overcome the problem that tau…
We introduce a class of exponential Runge-Kutta integration methods for kinetic equations. The methods are based on a decomposition of the collision operator into an equilibrium and a non equilibrium part and are exact for relaxation…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
Rayleigh-Taylor (RT) instability commonly arises in compressible systems with time-dependent acceleration in practical applications. To capture the complex dynamics of such systems, a two-component discrete Boltzmann method is developed to…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
We study computationally and statistically efficient Reinforcement Learning algorithms for the linear Bellman Complete setting. This setting uses linear function approximation to capture value functions and unifies existing models like…
In plasma edge simulations, kinetic Monte Carlo (MC) is often used to simulate neutral particles and estimate source terms. For large-sized reactors, like ITER and DEMO, high particle collision rates lead to a substantial computational cost…
We investigate the kinetic theory of two-temperature plasmas for reactive polyatomic gas mixtures. The Knudsen number is taken proportional to the square root of the mass ratio between electrons and heavy-species, and thermal…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
A reduced kinetic method (RKM) with a first-principle collision operator is introduced in a 1D2V planar geometry and implemented in a computationally inexpensive code to investigate non-local ion heat transport in multi-species plasmas. The…
Nonadiabatic ring-polymer molecular dynamics employs the mapping approach to describe nonadiabatic effects within the ring-polymer ansatz. In this paper, it is generalized to allow for the nuclear and electronic degrees of freedom to be…
Dynamic treatment regimes are sequential decision rules that adapt treatment according to individual time-varying characteristics and outcomes to achieve optimal effects, with applications in precision medicine, personalized…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…