Related papers: Implementing Reactivity in Molecular Dynamics Simu…
The construction of accurate interatomic potentials, and related fields of forces, from equilibrium conformational distributions of molecules is a crucial step in coarse-grained modeling. In this work we show that in order to develop…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
An important challenge in design of modulation schemes for molecular communication is positivity of the transmission signal (only a positive concentration of molecules can be released in the environment). This restriction makes handling of…
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…
Phase field crystals (PFC) are a tool for simulating materials at the atomic level. They combine the small length-scale resolution of molecular dynamics (MD) with the ability to simulate dynamics on mesoscopic time scales. We show how PFC…
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…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD…
We perform two-dimensional (2D) implosion simulations using a Monte Carlo kinetic particle code. The paper is motivated by the importance of non-equilibrium effects in inertial confinement fusion (ICF) capsule implosions. These cannot be…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient…
Intermodulation atomic force microscopy (ImAFM) is a mode of dynamic atomic force microscopy that probes the nonlinear tip-surface force by measurement of the mixing of multiple tones in a frequency comb. A high $Q$ cantilever resonance and…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Quantum computing is viewed as a promising technology because of its potential for polynomial growth in complexity, in contrast to the exponential growth observed in its classical counterparts. In the current Noisy Intermediate-Scale…
In this work, the Immersed Boundary Method (IBM) with feedback forcing introduced by Goldstein et al. (1993) and often referred in the literature as the Virtual Boundary Method (VBM), is addressed. The VBM has been extensively applied both…
Synthesizing new metal-organic frameworks (MOFs) is a challenging task, as the size, morphology, polymorph and type and number of defects present on the synthesis product may depend on many variables, including temperature, solvent,…
The interfacial free energy between a crystal and a fluid, {\gamma} cf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring {\gamma} cf experimentally, computer…
An analytical framework is proposed to describe the elasticity, viscosity and fragility of metallic glasses in relation to their atomic-level structure and the effective interatomic interaction. The bottom-up approach starts with forming an…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…