Related papers: An efficient time-stepping scheme for ab initio mo…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Combustion stabilization and enhancement of the flammability limits are mandatory objectives to improve nowadays combustion chambers. At this purpose, the use of an electric field in the flame region provides a solution which is, at the…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
In this work, we develop an accelerated sharp-interface method based on (Hu et al., JCP, 2006) and (Luo et al., JCP, 2015) for multiphase flows simulations. Traditional multiphase simulation methods use the minimum time step of all fluids…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
We present two types of meta-algorithm that can greatly improve the accuracy of existing algorithms for integrating the equations of motion of dynamical systems. The first meta-algorithm takes an integrator that is time-symmetric only for…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Neural networks have been applied to tackle many-body electron correlations for small molecules and physical models in recent years. Here we propose a new architecture that extends molecular neural networks with the inclusion of periodic…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
A new approach for simulating flows over complex geometries is developed by introducing an accurate virtual interpolation point scheme as well as a virtual local stencil approach. The present method is based on the concept of point…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…