Related papers: Coupling methods for efficient simulation of spati…
Finding conditions that support synchronization is a fertile and active area of research with applications across multiple disciplines. Here we present and analyze a scheme for synchronizing chaotic dynamical systems by transiently…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Complex applications such as big data analytics involve different forms of coupling relationships that reflect interactions between factors related to technical, business (domain-specific) and environmental (including socio-cultural and…
We examine the use of synchronization as a mechanism for extracting parameter and state information from experimental systems. We focus on important aspects of this problem that have received little attention previously, and we explore them…
Machine learning methods have shown promise in learning chaotic dynamical systems, enabling model-free short-term prediction and attractor reconstruction. However, when applied to large-scale, spatiotemporally chaotic systems, purely…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
We analyze the collective behavior of a lattice model of pulse-coupled oscillators. By means of computer simulations we find the relation between the intrinsic dynamics of each member of the population and their mutual interaction that…
Collaborative training can improve the accuracy of a model for a user by trading off the model's bias (introduced by using data from other users who are potentially different) against its variance (due to the limited amount of data on any…
Cosimulation methods allow combination of simulation tools of physical systems running in parallel to act as a single simulation environment for a big system. As data is passed across subsystem boundaries instead of solving the system as…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
A new scheme that tightly couples kinetic turbulence codes across a spatial interface is introduced. This scheme evolves from considerations of competing strategies and down-selection. It is found that the use of a composite kinetic…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
We study analytically the performance of a recently proposed algorithm for learning the couplings of a random asymmetric kinetic Ising model from finite length trajectories of the spin dynamics. Our analysis shows the importance of the…
We study the dynamics of an ensemble of globally coupled chaotic logistic maps under the action of a learning algorithm aimed at driving the system from incoherent collective evolution to a state of spontaneous full synchronization.…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
This paper is concerned with elucidating a relationship between two common coupling methods for the continuous time Markov chain models utilized in the cell biology literature. The couplings considered here are primarily used in a…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
We analyse the stochastic comparison of interacting particle systems allowing for multiple arrivals, departures and non-conservative jumps of individuals between sites. That is, if $k$ individuals leave site $x$ for site $y$, a possibly…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
We propose a dynamic allocation procedure that increases power and efficiency when measuring an average treatment effect in sequential randomized trials. Subjects arrive iteratively and are either randomized or paired via a matching…