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CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological inte...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

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...

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related are...

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC,...

A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and block...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

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...

Summary Recent work by Reiss and Ogden provides a theoretical basis for sometimes preferring restricted maximum likelihood (REML) to generalized cross-validation (GCV) for smoothing parameter selection in semiparametric ...

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...

The promise of quantum computers is that certain computational tasks might be executed exponentially faster on a quantum processor than on a classical processor1. A fundamental challenge is to build a high-fidelity proce...

Materie / parole chiave: numerical methods, computational mathematics, computer networks, computational modeling, computational methodology, computational simulation; Science: Mathematics

Materie / parole chiave: computational engineering, physical modeling, civil engineering, mechanical engineering, materials science, simulation; Technology: Electrical engineering. Electronics. Nuclear engineering: Electronics: Computer engineer...

Materie / parole chiave: materials modeling and theory, novel materials, computational methods, theoretical simulation; Technology: Electrical engineering. Electronics. Nuclear engineering: Materials of engineering and construction. Mechanics of...

Materie / parole chiave: partial differential equations, monte carlo and quasi-monte carlo simulation, soft computing, computational chemistry and physic, energy conversion and transfer in systems, optimization of civil structures and structural...

Materie / parole chiave: mathematical biophysics, computational biophysics, mathematical molecular bioscience, biomolecular simulations, biomolecular data deep leaning, rational drug discovery; Technology: Chemical technology: Biotechnology; Sci...

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

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...

First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a...

MOTIVATION: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation...

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simu...

Materie / parole chiave: Electron paramagnetic resonance; MATLAB; Computation; Software; Software package; Computational science; Toolbox; Spins; Computer science; Scope (computer science); Spin (aerodynamics); Computational physics

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 ...

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assist...