Related papers: An efficient time-stepping scheme for ab initio mo…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
We show that accelerated optimization methods can be seen as particular instances of multi-step integration schemes from numerical analysis, applied to the gradient flow equation. In comparison with recent advances in this vein, the…
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…
Ab initio simulations are capable of providing detailed information of material behavior at the nanoscale. Simulating experimentally relevant situations is, however, often computationally intense. Using hybrid approaches between ab initio…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
We propose a novel mesh refinement scheme based on signal processing for boundary integral simulations of inviscid droplet dynamics with axial symmetry. A key idea is to directly access the Fourier coefficients of a principal curvature as a…
The emergence and understanding of new design paradigms that exploit flow induced mechanical instabilities for propulsion or energy harvesting demands robust and accurate flow structure interaction numerical models. In this context, we…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
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…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Fluid dynamical simulations are often performed using cheap macroscopic models like the Euler equations. For rarefied gases under near-equilibrium conditions, however, macroscopic models are not sufficiently accurate and a simulation using…
In this paper we introduce simplified, combinatorially exact formulas that arise in the vortex interaction model found in (Nagem, et al., SIAM J. Appl. Dyn. Syst. 2009). These combinatorial formulas allow for the efficient implementation…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Thermally coupled distillation is a new energy-saving method, but the traditional thermally coupled distillation simulation calculation process is complicated, and the optimization method based on the traditional simulation process is…
Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly…
The accurate, reliable and efficient numerical approximation of multi-physics processes in heterogeneous porous media with varying media coefficients that include fluid flow and structure interactions is of fundamental importance in energy,…