Related papers: Energy-conserving molecular dynamics is not energy…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
Monitoring the dynamics processes in combustors is crucial for safe and efficient operations. However, in practice, only limited data can be obtained due to limitations in the measurable quantities, visualization window, and temporal…
Ferroelectric materials with switchable spontaneous polarization underpin non-volatile memories, transistors, sensors, and emerging neuromorphic chips. Their performance and stability are governed by polarization dynamics and domain…
A molecular gas system in three dimensions is numerically studied by the energy conserving molecular dynamics (MD). The autocorrelation functions for the velocity and the force are computed and the friction coefficient is estimated. From…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular…
At the present paper we have computed non-ergodicity paramater from Molecular Dynamics (MD) Simulation data after the mode-coupling theory (MCT) for a glass transition. MCT of dense liquids marks the dynamic glass-transition through a…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Unlike most static material properties widely studied in the machine learning literature, ionic transport properties are inherently dynamic, making their fast and accurate prediction from static atomic structures challenging. The current…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Ab initio molecular dynamics (AIMD) is a powerful tool to predict properties of molecular and condensed matter systems. The quality of this procedure is based on accurate electronic structure calculations. The development of quantum…
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…