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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...

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

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...

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...

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, a...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUFF, a full periodic table force field for molecular mechanics and molecular dynamics simulationsA. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. SkiffCi...

A molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure (T, P, N) ensemble, is proposed. The physical system of...

Watershed models are powerful tools for simulating the effect of watershed processes and management on soil and water resources. However, no comprehensive guidance is available to facilitate model evaluation in terms of ...

Computer simulations using Cellular Automata (CA) have been applied with considerable success in diferent scientific areas, such as chemistry, biochemistry, economy, physics, etc. In this work we use CA in order to speci...

The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on th...

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 multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified...

In this paper a slightly modification is proposed to the original Wong and Gotos ATA method for the computation of elementary functions in IEEE 754 single precision. The identification of a trade-off leads to the proposi...

Thirty years of brain imaging research has converged to define the brain's default network-a novel and only recently appreciated brain system that participates in internal modes of cognition. Here we synthesize past obse...

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecule...

Evolutionary computation techniques, genetic algorithms, evolutionary strategies and genetic programming are motivated by the evolution of nature. A population of individuals, which encode the problem solutions are manip...

The fifth phase of the Coupled Model Intercomparison Project (CMIP5) will produce a state-of-the- art multimodel dataset designed to advance our knowledge of climate variability and climate change. Researchers worldwide ...

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...

If radiocarbon measurements are to be used at all for chronological purposes, we have to use statistical methods for calibration. The most widely used method of calibration can be seen as a simple application of Bayesian...

A fundamental problem that confronts peer-to-peer applications is to efficiently locate the node that stores a particular data item. This paper presents Chord, a distributed lookup protocol that addresses this problem. C...

In this paper, we discuss consensus problems for networks of dynamic agents with fixed and switching topologies. We analyze three cases: 1) directed networks with fixed topology; 2) directed networks with switching topol...

Wireless distributed microsensor systems will enable the reliable monitoring of a variety of environments for both civil and military applications. In this paper, we look at communication protocols, which can have signif...

Time underlies many interesting human behaviors. Thus, the question of how to represent time in connectionist models is very important. One approach is to represent time implicitly by its effects on processing rather tha...

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...