相关论文: Discretization errors in molecular dynamics simula…
A methodology is proposed for the calculation of the truncation error of finite volume discretisations of the incompressible Navier-Stokes equations on colocated grids. The truncation error is estimated by restricting the solution obtained…
In this article we derive the effective pairwise interactions in a Langevin type united atoms model of water. The interactions are determined from the trajectories of a detailed molecular dynamics simulation of simple point charge water. A…
Water's unique anomalies are vital in various applications and biological processes, yet the molecular mechanisms behind these anomalies remain debated, particularly in the metastable liquid phase under supercooling and stretching…
Stochastic dynamical systems are fundamental in state estimation, system identification and control. System models are often provided in continuous time, while a major part of the applied theory is developed for discrete-time systems.…
We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of…
A proof of optimal-order error estimates is given for the full discretization of the bulk--surface Cahn--Hilliard system with dynamic boundary conditions in a smooth domain. The numerical method combines a linear bulk--surface finite…
We present a numerical investigation of stochastic transport in ideal fluids. According to Holm (Proc Roy Soc, 2015) and Cotter et al. (2017), the principles of transformation theory and multi-time homogenisation, respectively, imply a…
We report the temperature, pressure and composition dependence of some basic properties of model liquid water-methanol mixtures. For this purpose the isobaric-isothermal molecular dynamics computer simulations are employed. Our principal…
In mixed quantum-classical simulations of molecule-metal surface interactions, the discretization of the metallic electronic continuum typically results in a closed-system representation that fails to capture the open-system nature of the…
We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
Employing physically-consistent numerical methods is an important step towards attaining robust and accurate numerical simulations. When addressing compressible flows, in addition to preserving kinetic energy at a discrete level, as done in…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
We consider the thermal dunking problem, in which a solid body is suddenly immersed in a fluid of different temperature, and study both the temporal evolution of the solid and the associated Biot number -- a non-dimensional heat transfer…
Efficient large-scale computer simulations of aqueous solutions require the use of accurate but simple empirical force fields for water. However, the complexity of these systems evidences the difficulties in describing solution properties…
Sampling from unnormalized target distributions is a fundamental yet challenging task in machine learning and statistics. Existing sampling algorithms typically require many iterative steps to produce high-quality samples, leading to high…
We consider numerical methods for thermodynamic sampling, i.e. computing sequences of points distributed according to the Gibbs-Boltzmann distribution, using Langevin dynamics and overdamped Langevin dynamics (Brownian dynamics). A wide…
By discretising space into compartments and letting system dynamics be governed by the reaction-diffusion master equation, it is possible to derive and simulate a stochastic model of reaction and diffusion on an arbitrary domain. However,…
We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those…
In this article we present an a posteriori error estimator for the spatial-stochastic error of a Galerkin-type discretisation of an initial value problem for a random hyperbolic conservation law. For the stochastic discretisation we use the…