Related papers: A Simple Iterative Approach for Constant Chemical …
The need to use a short time step is a key limit on the speed of molecular dynamics (MD) simulations. Simulations governed by classical potentials are often accelerated by using a multiple-time-step (MTS) integrator that evaluates certain…
The simulation of granular media is usually done either with event-driven codes that treat collisions as instantaneous but have difficulty with very dense packings, or with molecular dynamics methods that approximate rigid grains using a…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
The immersed interface method (IIM) for fluid-structure interaction imposes discontinuities in the fluid stress along immersed boundaries that are generated by forces concentrated along those boundaries. For a viscous incompressible fluid,…
The most interesting step of condensation is the cluster formation up to the critical size. In a closed system, this is an instationary process, as the vapour is depleted by the emerging liquid phase. This imposes a limitation on direct…
Although polymerization and curing reactions govern the performance of advanced materials, their simulation remains challenging owing to the need for accurate, transferable potentials and rarity of chemical events. Conventional reactive…
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…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular…
Fluid-structure systems occur in a range of scientific and engineering applications. The immersed boundary(IB) method is a widely recognized and effective modeling paradigm for simulating fluid-structure interaction(FSI) in such systems,…
Hydrogen fuel cells are a key technology in the transition toward carbon-neutral energy systems, offering clean power with water as the only byproduct. Microfluidic fuel cells, which operate at the microliter scale, are an emerging variant…
We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
We discuss an effective Polyakov loop model for QCD thermodynamics with a chemical potential. Using high temperature expansion techniques the partition sum is mapped exactly onto the partition sum of a flux model. In the flux representation…
Machine-learning interatomic potentials (MLIPs) have greatly extended the reach of atomic-scale simulations, offering the accuracy of first-principles calculations at a fraction of the cost. Leveraging large quantum mechanical databases and…
We propose the Compact Coupling Interface Method (CCIM), a finite difference method capable of obtaining second-order accurate approximations of not only solution values but their gradients, for elliptic complex interface problems with…
Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually…