Related papers: Extrapolating molecular dynamics simulations to ze…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
Realistic simulations in engineering or in the materials sciences can consume enormous computing resources and thus require the use of massively parallel supercomputers. The probability of a failure increases both with the runtime and with…
We report modifications of the ph-AFQMC algorithm that allow the use of large time steps and reliable time step extrapolation. Our modified algorithm eliminates size-consistency errors present in the standard algorithm when large time steps…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Hamiltonian splitting methods are an established technique to derive stable and accurate integration schemes in molecular dynamics, in which additional accuracy can be gained using force gradients. For rigid bodies, a tradition exists in…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
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…
Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
Exa-scale simulations are on the horizon but almost no new design for the output has been proposed in recent years. In simulations using individual time steps, the traditional snapshots are over resolving particles/cells with large time…
In this work, we describe various improved implementations of the mapping approach to surface hopping (MASH) for simulating nonadiabatic dynamics. These include time-reversible and piecewise-continuous integrators, which is only formally…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…
Symplectic numerical schemes for reversible dynamical systems predict the solution reliably over large times as well, and are a good starting point for extension to schemes for simulating irreversible situations like viscoelastic wave…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
The interface between liquid water and the Pt(111) metal surface is characterized structurally and thermodynamically via reactive molecular dynamics (MD) simulations within the ReaxFF framework. The formation of a distinct buckled adsorbate…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…