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Subjects / keywords: numerical methods, computational mathematics, computer networks, computational modeling, computational methodology, computational simulation; Science: Mathematics

Subjects / keywords: mathematical modeling, computation methods, applied mathematics, computational biology, econophysics, numerical simulation; Technology: Technology (General): Industrial engineering. Management engineering: Applied mathem...

Abstract This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chem...

Abstract We generalize the method proposed by Gelman and Rubin (1992a) for monitoring the convergence of iterative simulations by comparing between and within variances of multiple chains, in order to obtain a family of ...

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of th...

A model for a large network of "neurons" with a graded response (or sigmoid input-output relation) is studied. This deterministic system has collective properties in very close correspondence with the earlier stochastic ...

Multi-objective evolutionary algorithms (MOEAs) that use non-dominated sorting and sharing have been criticized mainly for: (1) their O(MN/sup 3/) computational complexity (where M is the number of objectives and N is th...

Subjects / keywords: Master equation; Statistical physics; Monte Carlo method; Nonlinear system; Stochastic simulation; A priori and a posteriori; Stochastic process; Chemical reaction; Applied mathematics; Chemical equation; Statistical mec...

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is pr...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...

Abstract The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is pres...

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= nei...

Previous article Next article Fractional Brownian Motions, Fractional Noises and ApplicationsBenoit B. Mandelbrot and John W. Van NessBenoit B. Mandelbrot and John W. Van Nesshttps://doi.org/10.1137/1010093PDFBibTexSecti...

Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from a...

Bayesian Data Analysis describes how to conceptualize, perform, and critique statistical analyses from a Bayesian perspective. Using examples largely from the authors' own experiences, the book focuses on modern computat...

A new algorithm called Mersenne Twister (MT) is proposed for generating uniform pseudorandom numbers. For a particular choice of parameters, the algorithm provides a super astronomical period of 2 19937 −1 and 623-dime...

Variable selection is fundamental to high-dimensional statistical modeling, including nonparametric regression. Many approaches in use are stepwise selection procedures, which can be computationally expensive and ignore ...

Abstract An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordina...

Subjects / keywords: mathematics, statistics, data analysis, operational research, actuarial statistics, simulation; Social Sciences: Statistics; Science: Mathematics; Technology: Electrical engineering. Electronics. Nuclear engineering: Ele...

Subjects / keywords: modeling, algorithms, simulations, software; Science: Mathematics: Instruments and machines: Electronic computers. Computer science

Subjects / keywords: modeling and simulation, mathematical physics, computer science; Science: Mathematics: Instruments and machines: Electronic computers. Computer science

Subjects / keywords: computer simulation, computational methods, process control, instrumentation, multiscale experiments; Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software

Subjects / keywords: artificial intelligence, computational simulation, complex systems, intelligent data analytics; Science: Mathematics: Instruments and machines: Electronic computers. Computer science; Technology: Technology (General): In...