Related papers: Parallelization of Cellular Automata for Surface R…
We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both…
We discuss an alternative to the traditional gas-phase coupling approach in order to explain synchronized global oscillations in CO oxidation on Pt(110). We use a minimalist microscopic model which includes structural Pt surface…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
A definition for a class of asynchronous cellular arrays is proposed. An example of such asynchrony would be independent Poisson arrivals of cell iterations. The Ising model in the continuous time formulation of Glauber falls into this…
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…
We describe a new algorithm for simulating complex Markoff-processes. We have used a reaction-cell method in order to simulate arbitrary reactions. It can be used for any kind of RDS on arbitrary topologies, including fractal dimensions or…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
Cellular automata represent physical systems where both space and time are discrete, and the associated physical quantities assume a limited set of values. While previous research has applied cellular automata in modeling chemical,…
This paper presents our work on developing parallel computational methods for two-phase flow on modern parallel computers, where techniques for linear solvers and nonlinear methods are studied and the standard and inexact Newton methods are…
We introduce a new class of cellular automata to model reaction-diffusion systems in a quantitatively correct way. The construction of the CA from the reaction-diffusion equation relies on a moving average procedure to implement diffusion,…
Cellular automata are a discrete dynamical system which models massively parallel computation. Much attention is devoted to computations with small time complexity for which the parallelism may provide further possibilities. In this paper,…
In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…
We carried out a Cellular Automata simulation of a model polyelectrolyte solution at infinite dilution, in order to reproduce qualitatively its conformational properties. Our results predict the so called \emph{pearl necklace} structures,…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…
We present a 2-dimensional cellular automaton model for the simulation of pedestrian dynamics. The model is extremely efficient and allows simulations of large crowds faster than real time since it includes only nearest-neighbour…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the…
A simple method for the parallelization of extensive air shower simulations is described. A shower is simulated at fixed steps in altitude. At each step, daughter particles below a specified energy threshold are siphoned off and tabulated…