Related papers: Irradiation driven molecular dynamics: A review
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Molecular communication via diffusion (MCvD) is a molecular communication method that utilizes the free diffusion of carrier molecules to transfer information at the nano-scale. Due to the random propagation of carrier molecules,…
Understanding the nature of irradiation damage often requires a multi-scale and multi-physics approach, i.e. it requires a significant amount of information from experiments, simulations and phenomenological models. This paper focuses on…
This work proposes a new framework of model reduction for parametric complex systems. The framework employs a popular model reduction technique dynamic mode decomposition (DMD), which is capable of combining data-driven learning and physics…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
We present a new non-adiabatic ring polymer molecular dynamics (NRPMD) method based on the spin mapping formalism, which we refer to as the spin-mapping NRPMD (SM-NRPMD) approach. We derive the path-integral partition function expression…
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…
Dynamic Mode Decomposition (DMD) describes complex dynamic processes through a hierarchy of simpler coherent features. DMD is regularly used to understand the fundamental characteristics of turbulence and is closely related to Koopman…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…
We present parameter-interpolated dynamic mode decomposition (piDMD), a parametric reduced-order modeling framework that embeds known parameter-affine structure directly into the DMD regression step. Unlike existing parametric DMD methods…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
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…
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at…
Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…
Molecular dynamics (MD) simulations play a crucial role in scientific research. Yet their computational cost often limits the timescales and system sizes that can be explored. Most data-driven efforts have been focused on reducing the…
The application of molecular dynamics (MD) simulations to the interpretation of Raman scattering spectra is hindered by inability of atomistic simulations to account for the dynamic evolution of electronic polarizability, requiring the use…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…