Related papers: Improved Adaptive Resolution Molecular Dynamics Si…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
The numerical simulation of granular systems of even moderate size is a challenging computational problem. In most investigations, either Molecular Dynamics or Event-driven Molecular Dynamics is applied. Here we show that in certain cases,…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
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…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Linear reduced-order modeling (ROM) is widely used for efficient simulation of deformation dynamics, but its accuracy is often limited by the fixed linearization of the reduced mapping. We propose a new adaptive strategy for linear ROM that…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
This article describes a new, fully adaptive Particle-Multiple-Mesh numerical simulation code developed primarily for simulations of small regions (such as a group of galaxies) in a cosmological context. It integrates the equations of…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
Granular systems present surprisingly complicated dynamics. In particular, nonlinear interactions and energy dissipation play important roles in these dynamics. Usually, constant coefficients of restitution are introduced phenomenologically…
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…