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Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
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…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
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…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
In order to reduce the computational cost of the simulation of electromagnetic responses in geophysical settings that involve highly heterogeneous media, we develop a multiscale finite volume method with oversampling for the quasi-static…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
We present an optimized implementation of the recently proposed symmetric gradient domain machine learning (sGDML) model. The sGDML model is able to faithfully reproduce global potential energy surfaces (PES) for molecules with a few dozen…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…