Related papers: Multiple Time Step Integrators in Ab Initio Molecu…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
We change a previous time-stepping algorithm for solving a multi-scale Vlasov-Poisson system within a Particle-In-Cell method, in order to do accurate long time simulations. As an exponential integrator, the new scheme allows to use large…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Validity of fluid models breaks down for non-thermal or weakly collisional plasmas which often occur e.g. in the solar wind. In these regimes one has to resort to modelling through the first-principle Vlasov-Maxwell system, but its…
We investigate time complexities of finite difference methods for solving the high-dimensional linear heat equation, the high-dimensional linear hyperbolic equation and the multiscale hyperbolic heat system with quantum algorithms (hence…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Ultrafast chemical reactions are difficult to simulate because they involve entangled, many-body wavefunctions whose computational complexity grows rapidly with molecular size. In photochemistry, the breakdown of the Born-Oppenheimer…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
We address the formulation and analysis of energy and momentum conserving time integration schemes in the context of particle dynamics, and in particular atomic systems. The article identifies three critical aspects of these models that…
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…
The spatio-temporally periodic (STP) potential is interesting in Physics due to the intimate coupling between its time and spatial components. In this paper we begin with a brief discussion of the dynamical behaviors of a single particle in…
This paper introduces coordinate-independent methods for analysing multiscale dynamical systems using numerical techniques based on the transfer operator and its adjoint. In particular, we present a method for testing whether an arbitrary…
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…
An efficient numerical algorithm is presented for massively parallel simulations of dispersion-managed wavelength-division-multiplexed optical fiber systems. The algorithm is based on a weak nonlinearity approximation and independent…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
In energy management, it is common that strategic investment decisions (storage capacity, production units) are made at a slow time scale, whereas operational decisions (storage, production) are made at a fast time scale: for such problems,…
For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with…
For many decades, quantum chemical method development has been dominated by algorithms which involve increasingly complex series of tensor contractions over one-electron orbital spaces. Procedures for their derivation and implementation…