Related papers: Simulating structural transitions by direct transi…
Energy-based modeling is a promising approach to unsupervised learning, which yields many downstream applications from a single model. The main difficulty in learning energy-based models with the "contrastive approaches" is the generation…
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…
A Monte Carlo method is presented to evaluate quantum states with many particles moving in the continuum. The scattering state is generated at each time by a Monte Carlo random sampling algorithm. The same calculation are repeated until the…
We use molecular dynamics simulation to study the relationship between structure and dynamics in supercooled binary Lennard--Jones nanoparticles over a range of particle sizes. The glass transition temperature of the nanoparticles is found…
We propose an efficient method for Monte Carlo simulation of quantum lattice models. Unlike most other quantum Monte Carlo methods, a single run of the proposed method yields the free energy and the entropy with high precision for the whole…
Recently, the intrinsic sampling method has been developed in order to obtain, from molecular simulations, the intrinsic structure of the liquid-vapor interface that is presupposed in the classical capillary wave theory. Our purpose here is…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
We study the dynamics of particles in a multi-component 2d Lennard-Jones (LJ) fluid in the limiting case where {\it all the particles are different} (APD). The equilibrium properties of this APD system were studied in our earlier work…
We present a novel way of performing kinetic Monte Carlo simulations which does not require an {\it a priori} list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation,…
We present a model for the dynamics in energy space of multicanonical simulation methods that lends itself to a rather complete analytic characterization. The dynamics is completely determined by the density of states. In the \pm J 2D spin…
The separation of substances into different phases is ubiquitous in nature and important scientifically and technologically. This phenomenon may become drastically different if the species involved, whether molecules or supramolecular…
Process monitoring and control requires detection of structural changes in a data stream in real time. This article introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The…
The optimal conversion of a continuous inter-particle potential to a discrete equivalent is considered here. Existing and novel algorithms are evaluated to determine the best technique for creating accurate discrete forms using the minimum…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It…
We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illustrated on various kinds of crystals and the advantages with respect to previous…
For the description of thermally activated dynamics in systems of classical magnetic moments numerical methods are desirable. We consider a simple model for isolated magnetic particles in a uniform field with an oblique angle to the easy…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…