相关论文: Discretization errors in molecular dynamics simula…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
The temperature equilibration rate in dense hydrogen (for both T_{i}>T_{e} and T_i<T_e) has been calculated with molecular dynamics simulations for temperatures between 10 and 600 eV and densities between 10^{20}/cc to 10^{24}/cc. Careful…
Stochastic reaction networks governed by Chemical Langevin Equations (CLE) exhibit pronounced multiscale dynamics spanning fast molecular reactions, intermediate transport, and slow cellular regulation, posing significant challenges for…
We analyze the nature of the structural order established in liquid TIP4P water in the framework provided by the multi-particle correlation expansion of the statistical entropy. Different regimes are mapped onto the phase diagram of the…
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar…
The prediction of stochastic dynamical systems and the capture of dynamical behaviors are profound problems. In this article, we propose a data-driven framework combining Reservoir Computing and Normalizing Flow to study this issue, which…
With an ever-increasing interest in water properties, many intermolecular force fields have been proposed to describe the behavior of water. Unfortunately, good models for liquid water usually cannot provide simultaneously an accurate…
We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid-structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation-dissipation…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of…
Entropy stable schemes can be constructed with a specific choice of the numerical flux function. First, an entropy conserving flux is constructed. Secondly, an entropy stable dissipation term is added to this flux to guarantee dissipation…
Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME) mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the…
Quantum transport simulations often use explicit, yet finite, electronic reservoirs. These should converge to the correct continuum limit, albeit with a trade-off between discretization and computational cost. Here, we study this interplay…
The developments over the last five decades concerning numerical discretisations of the incompressible Navier--Stokes equations have lead to reliable tools for their approximation: those include stable methods to properly address the…
We consider systematic numerical approximation of a viscoelastic phase separation model that describes the demixing of a polymer solvent mixture. An unconditionally stable discretisation method is proposed based on a finite element…
The liquid-vapor critical behavior of water is strongly influenced by both ionic solutes and confinement. Molecular dynamics simulations of aqueous NaCl solutions using the TIP4P/2005 water model and the Madrid-2019 ion parameters reveal a…
The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of…
We propose a general methodology for calculating the self-diffusion tensor from molecular dynamics for a liquid with a liquid-gas or liquid-solid interface. The standard method used in bulk fluids, based on computing the mean square…
Moist thermodynamics is a fundamental driver of atmospheric dynamics across all scales, making accurate modeling of these processes essential for reliable weather forecasts and climate change projections. However, atmospheric models often…
We study the evolution of dynamic fluctuations averaged over different space lengths and time scales to characterize spatially and temporally heterogeneous behavior of TIP4P/2005 water in liquid and supercooled states. Analysing a million…