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Understanding electron energy dynamics in low-temperature plasmas such as capacitively coupled plasmas (CCPs), including energy absorption, conversion, transport, and dissipation, is essential for interpreting discharge physics and process…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion…
Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from…
Reaction-diffusion processes play an important role in a variety of physical, chemical, and biological systems. Conventionally, the kinetics of these processes are described by the law of mass action. However, there are various cases where…
Quite recently I have proposed a nonperturbative dynamical effective field model (DEFM) to quantitatively describe the dynamics of interacting ferrofluids. Its predictions compare very well with the results from simulations. In this paper I…
We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and…
We develop a general method for constructing the many-body Hamiltonian of pairwise interactions describing homonuclear mixtures of atoms occupying states with different total angular momenta or other quantum numbers. The advantage of the…
This article presents a new force model for performing quantitative simulations of dense granular materials. Interactions between multiple contacts (MC) on the same grain are explicitly taken into account. Our readily applicable method…
Insulating systems are characterized by their insensitivity to twisted boundary conditions as quantified by the charge stiffness and charge localization length. The latter quantity was shown to be related to the expectation value of the…
We introduce EMMA, a physics-informed multimodal framework that recovers all identifiable dynamical parameters of a system directly from raw video, audio, and image-based time-series observations. Unlike prior video-only approaches that…
The Many-Body Expansion (MBE) is a useful tool to simulate condensed phase chemical systems, often avoiding the steep computational cost of usual electronic structure methods. However, it often requires higher than 2-body terms to achieve…
The many-body dispersion (MBD) framework is a successful approach for modeling the long-range electronic correlation energy and optical response of systems with thousands of atoms. Inspired by field theory, here we develop a…
Searches for intrinsic electric dipole moments (EDMs) of nucleons, atoms and molecules are precision flavor-diagonal probes of new $CP$-odd physics, as motivated by the need to explain the matter-antimatter asymmetry in the universe. We…
The Cellular Potts Model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or…
A framework is introduced for expressing electromagnetic (EM) potentials and fields of single atomic or molecular emitters modeled as oscillating dipoles, which follows a recently proposed method for solving inhomogeneous wave equations for…
In fluid flow simulation, the multi-continuum model is a useful strategy. When the heterogeneity and contrast of coefficients are high, the system becomes multiscale, and some kinds of reduced-order methods are demanded. Combining these…
This paper presents a thermodynamically consistent model for multicomponent electrolyte solutions. The first part of this paper derives the general governing equations for nonequilibrium systems within the theory of nonequilibrium…
We study integral expressions of electromagnetic multipole moments of arbitrary order in Cartesian coordinates. The volume and surface integrals of charge-induced and current-induced multipole moment tensors are formulated and the…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…