Related papers: Mapping continuous potentials to discrete forms
The definition of metastable states is an ubiquitous task in the design and analysis of molecular simulations, and is a crucial input in a variety of acceleration methods for the sampling of long configurational trajectories. Although…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural…
Supercooled liquids are characterized by relaxation times that increase dramatically by cooling or compression. Many liquids have been shown to obey power-law density scaling, according to which the relaxation time is a function of density…
To ensure the discrete maximum principle or solution positivity in finite volume schemes, diffusive flux is sometimes discretized as a conical combination of finite differences. Such a combination may be impossible to construct along…
A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…
By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation…
Compact analytical forms are derived for the interactions involving thin disks in two dimensions using an integration approach. These include interactions between a disk and a material point, between two disks, and between a disk and a…
We use a standard Monte-Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that Monte-Carlo is by far the most efficient way to simulate a stochastic dynamics since…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
Most of the existing classical CO$_2$ models fail to reproduce some or many experimental properties such as surface tension, vapor pressure, density and dielectric constant at difference thermodynamic conditions. Therfore, it is proposed a…
Pseudopotential theory has greatly driven first-principles calculations in materials, replacing the explicit treatment of the chemically inert core electrons with an effective potential acting only on the valence states. This is inherently…
A vast concourse of events and phenomena occur in nature that may be interrelated by a entropy-maximization technique that provides a comprehensible explanation of a range of physical problems, integrating in a new framework the universal…
In a recent article, Wang et al (Phys. Chem. Chem. Phys., 22, 10624 (2020)) introduced a new class of interparticle potential for molecular simulations. The potential is defined by a single range parameter, eliminating the need to decide…
In this contribution we derive and analyze a new numerical method for kinetic equations based on a variable transformation of the moment approximation. Classical minimum-entropy moment closures are a class of reduced models for kinetic…
Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been…
The main objective of this paper is to extend Morse-Forman theory to vector-valued functions. This is mostly motivated by the need to develop new tools and methods to compute multiparameter persistence. To generalize the theory, in addition…
Particle transport through an open, discrete 1-D channel against a mechanical or chemical bias is analyzed within a master equation approach. The channel, externally driven by time dependent site energies, allows multiple occupation due to…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…