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In these notes, we present an alternative version of discrete Dirac mechanics using Dirac structures. We first establish a notion of 'continuous Dirac system' and then propose a definition of discrete Dirac system, proving that it is…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Spin-dynamics techniques can now be used to study the deterministic time-dependent behavior of magnetic systems containing over 10^5 spins with quite good accuracy. This approach will be introduced, including the theoretical foundations of…
The Glauber model on a one-dimensional lattice with boundaries (for the ferromagnetic- and anti-ferromagnetic case) is considered. The large-time behaviour of the one-point function is studied. It is shown that, for any positive…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
In this paper we introduce 1-$D$ and 2-$D$ discrete models for the dynamic granular matter formation process in the form of a system of difference equations. This approach allows us to differentiate between the influx of the rolling layer…
Recently proposed non-adiabatic ring polymer molecular dynamics (NRPMD) approach has shown to provide accurate quantum dynamics by incorporating explicit electronic state descriptions and nuclear quantizations. Here, we present a rigorous…
We consider the asymmetric simple exclusion process with Langmuir kinetics in the closed boundary condition. We analytically obtain the exact stationary state and a series of excited states of the system in the limit where Langmuir kinetics…
We introduce an efficient scheme for the molecular dynamics of electronic systems by means of quantum Monte Carlo. The evaluation of the (Born-Oppenheimer) forces acting on the ionic positions is achieved by two main ingredients: i) the…
Broadband dielectric spectroscopy was used to study the molecular orientational dynamics of the glass-forming, thioether-linked cyanobiphenyl liquid crystal dimers. As was expected theoretically, two different relaxation processes that…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Using a new result on the integral involving the product of Bessel functions and associated Laguerre polynomials, published in the mathematical literature some time ago, we present an alternative method for calculating discrete-discrete…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Magneto-hydrodynamics is one of the foremost models in plasma physics with applications in inertial confinement fusion, astrophysics and elsewhere. Advanced numerical methods are needed to get an insight into the complex physical phenomena.…
We have recently presented an extension of the standard variational calculus to include the presence of deformed derivatives in the Lagrangian of a system of particles and in the Lagrangian density of field-theoretic models. Classical…
We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of…
An arbitrary Lagrangian--Eulerian finite element method and numerical implementation for curved and deforming lipid membranes is presented here. The membrane surface is endowed with a mesh whose in-plane motion need not depend on the…
Taking advantage of the flexibility of the variational method with coordinate transformations, we derive a self-consistent set of equations of motion from a discretized Lagrangian to study kinetic plasmas using a Fourier decomposed…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
In this paper we apply the method of Lagrangian descriptors to explore the geometrical structures in phase space that govern the dynamics of dissipative systems. We demonstrate through many classical examples taken from the nonlinear…