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The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
Contemporary materials science research is heavily conducted in silico, involving massive simulations of the atomic-scale evolution of materials. Cataloging basic patterns in the atomic displacements is key to understanding and predicting…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Self-assembly of sub-micron particles suspended in a water film is investigated numerically. The liquid medium is allowed to evaporate leaving only the sub-micron particles. A coupled CFD-DEM approach is used for the simulation of…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development,…
The microstructure of materials evolves through chemical reactions and mechanical stress, often strongly coupled in phenomena such as pressure solution or crystallization pressure. This article presents MASKE: a simulator to address the…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
Understanding the dynamics of naturally fractured systems and fractured reservoirs in terms of flow, heat transport and fracture stability (e.g. induced seismicity) is important for a range of applications associated with waste water…
Simulating the dynamics of molecular excitons in complex nanophotonic environments requires integrating rigorous electromagnetic simulations with accurate treatments of open quantum system dynamics. In this work, we develop MQED-QD…