Related papers: Speeding-up Ab Initio Molecular Dynamics with Hybr…
Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
We propose a continuous-time scheme for large-scale optimization that introduces individual, adaptive momentum coefficients regulated by the kinetic energy of each model parameter. This approach automatically adjusts to local landscape…
Time integration of stiff systems is a primary source of computational cost in combustion, hypersonics, and other reactive transport systems. This stiffness can introduce time scales significantly smaller than those associated with other…
In condensed matter physics, particularly in perovskite materials, the rotational motion of molecules and ions is associated with important issues such as ion conduction mechanism. Constrained Molecular Dynamics (MD) simulations offer a…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
The basis generation in reduced order modeling usually requires multiple high-fidelity large-scale simulations that could take a huge computational cost. In order to accelerate these numerical simulations, we introduce a FOM/ROM hybrid…
Constrained molecular dynamics(CoMD) model, previously introduced for nuclear dynamics, has been extended to the atomic structure and collision calculations. Quantum effects corresponding to the Pauli and Heisenberg principle are enforced…
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…
The approximate atomic self-interaction corrections (ASIC) method to density functional theory is put to the test by calculating the exchange interaction for a number of prototypical materials, critical to local exchange and correlation…
Affine Body Dynamics (ABD) within the Incremental Potential Contact (IPC) framework provides accurate simulation of extremely stiff solids exhibiting near-rigid behavior, with strict non-penetration guarantees. However, IPC's globally…
Simulating stiff materials in applications where deformations are either not significant or can safely be ignored is a pivotal task across fields. Rigid body modeling has thus long remained a fundamental tool and is, by far, the most…
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio…
With the rapid development of ultra-fast experimental techniques used for carrier dynamics in solid-state systems, a microscopic understanding of the related phenomena, particularly a first-principle calculation is highly desirable.…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…