Related papers: Polarisable force fields: What do they add in biom…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019…
Molecular dynamics simulations, with full Coulomb interaction and self-consistent field emission, are used to examine mutual space-charge interactions between beams originating from several emitter areas, in a planar infinite diode. The…
Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
In this contribution, we report on recent progress in coupled-cluster simulations of open-shell atomic nuclei using interactions consistently derived from chiral effective field theory. In particular, we compare different coupled-cluster…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
We briefly review recent theoretical and simulation studies of charged colloidal dispersions in alternating electric fields (AC fields). The response of single colloid to an external field can be characterized by a complex polarizability,…
We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the…
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields use harmonic expressions to treat bonding stretches, which is a…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
Applying electric fields is an attractive way to control and manipulate single particles or molecules, e.g., in lab-on-a-chip devices. However, the response of nanosize objects in electrolyte solution to external fields is far from trivial.…
Force field have for decades proven to be an indispensable tool for molecular simulations which are out of reach for ab-initio methods. Recent efforts to improve the accuracy of these simulations have focused on the inclusion of many-body…
Particle acceleration in collisionless plasma systems is a central question in astroplasma and astroparticle physics. The structure of the acceleration regions, electron-ion energy equilibration, preacceleration of particles at shocks to…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…