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Parameters of differential equations are essential to characterize intrinsic behaviors of dynamic systems. Numerous methods for estimating parameters in dynamic systems are computationally and/or statistically inadequate, especially for…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
Fermionic Molecular Dynamics (FMD) models a system of fermions by means of many-body states which are composed of antisymmetrized products of single-particle states. These consist of one or several Gaussians localized in coordinate and…
The Green-function technique, termed the irreducible Green functions (IGF) method, that is a certain reformulation of the equation-of motion method for double-time temperature dependent Green functions is presented. This method was…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
Hydrogen fuel cells are a key technology in the transition toward carbon-neutral energy systems, offering clean power with water as the only byproduct. Microfluidic fuel cells, which operate at the microliter scale, are an emerging variant…
We present a molecular extension of our recently proposed Green's function embedding method, interacting-bath dynamical embedding theory (ibDET), for computing charged excitation energies at the $GW$ and EOM-CCSD levels. Starting from…
Classical molecular dynamics (MD) simulations enable modeling of materials and examination of microscopic details that are not accessible experimentally. The predictive capability of MD relies on the force field (FF) used to describe…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
We introduce the first continuous-time score-based generative model that leverages fractional diffusion processes for its underlying dynamics. Although diffusion models have excelled at capturing data distributions, they still suffer from…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Most existing DOA estimation methods assume ideal source incident angles with minimal noise. Moreover, directly using pre-estimated angles to calculate weighted coefficients can lead to performance loss. Thus, a green multi-modal (MM)…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Work presented in this paper describes a general algorithm and its finite element implementation for performing concurrent multiple sub-domain simulations in linear structural dynamics. Using this approach one can solve problems in which…
Simulation of reasonable timescales for any long physical process using molecular dynamics (MD) is a major challenge in computational physics. In this study, we have implemented an approach based on multi-fidelity physics informed neural…
Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…