Related papers: Mapping Variable Ring Polymer Molecular Dynamics: …

Dynamical electronic- and vibrational-structure theories have received a growing interest in the last years due to their ability to simulate spectra recorded with ultrafast experimental techniques. The exact time evolution of a molecular…

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…

A four-way coupling scheme for the direct numerical simulation of particle-laden flows is developed and analyzed. It employs a novel adaptive multi-relaxation time lattice Boltzmann method to simulate the fluid phase efficiently. The…

The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…

Nonequilibrium dynamics governed by electron-phonon (e-ph) interactions plays a key role in electronic devices and spectroscopies and is central to understanding electronic excitations in materials. The real-time Boltzmann transport…

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…

Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…

This paper presents a novel non-linear model reduction method: Probabilistic Manifold Decomposition (PMD), which provides a powerful framework for constructing non-intrusive reduced-order models (ROMs) by embedding a high-dimensional system…

G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…

An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…

In Part I [J. Chem. Phys. 138, 084108 (2013)] we derived a quantum transition-state theory by taking the t->0+ (short-time) limit of a new form of quantum flux-side time-correlation function containing a ring-polymer dividing surface. This…

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…

Accelerating quantum dynamical simulations with quantum computing has received considerable attention but remains a significant challenge. In variational quantum algorithms for quantum dynamics, designing an expressive and shallow-depth…

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…

Developing new methods for the accurate and efficient calculations of real-time quantum correlation functions is deemed one of the most challenging problems of modern condensed matter theory. Many popular methods, such as centroid molecular…

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to…

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…

This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…

We present a concurrent Monte Carlo (MC) - molecular dynamics (MD) approach to modeling of matter response to excitation of its electronic system. The two methods are combined on-the-fly at each time step in one code, TREKIS-4. The MC model…