Related papers: A simple time coarse graining method for molecular…
Molecular dynamics simulations frequently employ periodic boundary conditions where the positions of the periodic images are manipulated in order to apply deformation to the material sample. For example, Lees-Edwards conditions use moving…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
By exact projection in phase space we derive the generalized Langevin equation (GLE) for time-filtered observables. We employ a general convolution filter that directly acts on arbitrary phase-space observables and can involve low-pass,…
The notion of mutual unbiasedness for coarse-grained measurements of quantum continuous variable systems is considered. It is shown that while the procedure of "standard" coarse graining breaks the mutual unbiasedness between conjugate…
We perform molecular dynamics simulation on a glass-forming liquid binary mixture with the soft-core potential in three dimensions. We investigate crossover of the configuration changes caused by stringlike jump motions. With lowering the…
Simulating the dynamics of complex quantum systems is a central application of quantum devices. Here, we propose leveraging the power of measurements to simulate short-time quantum dynamics of physically prepared quantum states in classical…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
A novel scheme to simulate the evolution of a restricted set of observables of a quantum system is proposed. The set comprises the spectrum-generating algebra of the Hamiltonian. The idea is to consider a certain open-system evolution,…
An expression for the stress tensor near an external boundary of a discrete mechanical system is derived explicitly in terms of the constituents' degrees of freedom and interaction forces. Starting point is the exact and general coarse…
We present here the preliminary results obtained for two experiments on randomly agitated granular assemblies using a novel way of shaking. First we discuss the transport properties of a 2D model system undergoing classical shaking that…
We describe a fast implementation of the quasi-centroid molecular dynamics (QCMD) method in which the quasi-centroid potential of mean force is approximated as a separable correction to the classical interaction potential. This correction…
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…
We consider stochastic inflation coarse-grained using a general class of exponential filters. Such a coarse-graining prescription gives rise to inflaton-Langevin equations sourced by colored noise that is correlated in $e$-fold time. The…
Coarse-graining is central to reducing dimensionality in molecular dynamics, and is typically characterized by a mapping which projects the full state of the system to a smaller class of variables. While extensive literature has been…
In the current work we propose a theory for an additional mass diffusion effect in the conventional gas dynamics equations. We find that this effect appears as a homogenization time limit correction, when the deterministic interaction…
We investigate modifications of a stochastic polymer picture through a shift in the boundary between the system and an external environment. A conventional bead-and-spring model serving as the coarse-graining model is given by the Langevin…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…
The interaction between a fluid and a wall is described with a certain boundary condition for the fluid velocity at the wall. To understand how fluids behave near a rough wall, the fluid velocity at every point of the rough surface may be…
We study the classical motion of a particle subject to a stochastic force. We then present a perturbative schema for the associated Fokker-Planck equation where, in the limit of a vanishingly small noise source, a consistent dynamical model…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…