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Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering…
Past research has conclusively shown that confined pockets of water exhibit properties that differ from those of unconfined ("bulk") water. The differences between confined water and bulk, as well as between different types of confined…
Considering the unphysical result obtained in the calculation of the free-energy cost for twisting the boundary conditions in a spin glass, we trace it to the negative multiplicities associated with the Parisi replica-symmetry breaking…
We propose a new method for the determination of the weight factor for the simulated tempering method. In this method a short replica-exchange simulation is performed and the simulated tempering weight factor is obtained by the…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function…
We present an $rp$-adaptation strategy for high-fidelity simulation of compressible inviscid flows with shocks. The mesh resolution in regions of flow discontinuities is increased by using a variational optimiser to $r$-adapt the mesh and…
A new symplectic time-reversible algorithm for numerical integration of the equations of motion in magnetic liquids is proposed. It is tested and applied to molecular dynamics simulations of a Heisenberg spin fluid. We show that the…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…
Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
With the stagnation of processor core performance, further reductions in the time-to-solution for geophysical fluid problems are becoming increasingly difficult with standard time integrators. Parallel-in-time exposes and exploits…
Several competing artificial compressibility methods for the incompressible flow equations are examined using the high-order flux reconstruction method. The established artificial compressibility method (ACM) of \citet{Chorin1967} is…
Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple…
The dynamics of ultrafast energy transfer to water clusters and to bulk water by a highly intense, sub-cycle THz pulse of duration $\approx$~150~fs is investigated in the context of force-field molecular dynamics simulations. We focus our…
A new classical interaction potential for water simulations is presented. Water is modeled as a fully dissociable set of atoms with a point dipole, determined self-consistently, on every oxygen atom. The oxygen polarizability is not fixed…
Anomalous behaviour of the excess entropy ($S_e$) and the associated scaling relationship with diffusivity are compared in liquids with very different underlying interactions but similar water-like anomalies: water (SPC/E and TIP3P models),…
We propose high-order well-balanced finite-volume schemes for a broad class of hydrodynamic systems with attractive-repulsive interaction forces and linear and nonlinear damping. Our schemes are suitable for free energies containing…
We provide exact solutions of the Stokes equations for a squirming sphere close to a no-slip surface, both planar and spherical, and for the interactions between two squirmers, in three dimensions. These allow the hydrodynamic interactions…
In this paper, a new efficient and generalized consistency correction method for weakly-compressible smoothed particle hydrodynamics is proposed and successfully implemented in the simulation of violent free-surface flow exhibiting breaking…