Related papers: Discretization errors in molecular dynamics simula…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
This paper presents a geometric variational discretization of compressible fluid dynamics. The numerical scheme is obtained by discretizing, in a structure preserving way, the Lie group formulation of fluid dynamics on diffeomorphism groups…
The performance of several popular water models (TIP3P, TIP4P, TIP5P and TIP4P/2005) is analysed. For that purpose the predictions for ten different properties of water are investigated, namely: 1. vapour-liquid equilibria (VLE) and…
We introduce a novel approach to sample the canonical ensemble at constant temperature and applied electric potential. Our approach can be straightforwardly implemented into any density-functional theory code. Using thermopotentiostat…
We have studied the composition dependence of density of liquid water-DMSO mixtures at different temperatures by using the isobaric-isothermal (NPT) molecular dynamics computer simulations. The non-polarizable semi-flexible, P1 and P2…
We have developed x-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 C) under normal pressure. Using a spherically curved Ge crystal an energy…
A systematic comparison was carried out to assess the influence of representative thermostat methods in constant-temperature molecular dynamics simulations. The thermostat schemes considered include the Nos\'e--Hoover thermostat and its…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration (SQE)…
Ice Ih has been studied by path-integral molecular dynamics simulations, using the effective q-TIP4P/F potential model for flexible water. This has allowed us to analyze finite-temperature quantum effects in this solid phase from 25 to 300…
We study the phase equilibrium between liquid water and ice Ih modeled by the TIP4P/Ice interatomic potential using enhanced sampling molecular dynamics simulations. Our approach is based on the calculation of ice Ih-liquid free energy…
We have computed the two and three-particle contribution to the entropy of a Weeks-Chandler-Andersen fluid via molecular dynamics simulations. The three-particle correlation function and entropy were computed with a new method which…
Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…
Statistical solutions have recently been introduced as a an alternative solution framework for hyperbolic systems of conservation laws. In this work we derive a novel a posteriori error estimate in the Wasserstein distance between…
Calibration is one area in measurement where our country is still in the process of improvement. The absence of confirmed approaches and actions for identifying the features of calibration baths by numerous laboratories disallowed them to…
Dynamics of adsorption and desorption of (4S)-N on amorphous solid water are analyzed using molecular dynamics simulations. The underlying potential energy surface was provided by machine-learned interatomic potentials. Binding energies…
In this work, we investigate a numerical procedure for recovering a space-dependent diffusion coefficient in a (sub)diffusion model from the given terminal data, and provide a rigorous numerical analysis of the procedure. By exploiting…
We develop quantitative error estimates connecting microscopic fluctuation of interacting particle systems with the mobilities of their hydrodynamic limits. Focusing on the Symmetric Simple Exclusion Process and systems of independent…
The Stoermer-Verlet-leapfrog group of integrators commonly used in molecular dynamics simulations has long become a textbook subject and seems to have been studied exhaustively. There are, however, a few striking effects in performance of…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…