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From the Publisher: This second edition of Modeling and Analysis includes a chapter on Simulation in Manufacturing Systems and examples. The text is designed for a one-term or two-quarter course in simulation offered in ...

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...

This paper is an attempt to define how a specific data structure might be used to store, in a persistent manner, temporal information during a computer simulation. In particular, it considers the sort of temporal informa...

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...

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...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

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...

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...

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...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExact stochastic simulation of coupled chemical reactionsDaniel T. GillespieCite this: J. Phys. Chem. 1977, 81, 25, 2340–2361Publication Date (Print):December 1, 1977Publicat...

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...

The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give mislea...

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...

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 ...

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...

The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations func...

In 21st century, convergences of technologies and services in heterogeneous environment have contributed multi-traffic. This scenario will affect computer network on learning system in higher educational Institutes. Impl...

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the o...

The parallel computing model used in this paper, the Collective Computing Model (CCM), is a variant of the well-known Bulk Synchronous Parallel (BSP) model. The synchronicity imposed by the BSP model restricts the set of...

Nosotros presentamos una herramienta CASE para la construcción de hiperme- dias basada en OOHDM (Object-Oriented Hypermedia Design Model). Esta herramienta permite realizar los pasos: 2 (diseño navegacional), 3 (diseñ...

Preface to the Fourth Edition. 1 Biomechanics as an Interdiscipline. 1.0 Introduction. 1.1 Measurement, Description, Analysis, and Assessment. 1.2 Biomechanics and its Relationship with Physiology and Anatomy. 1.3 Scope ...

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...

We propose a flexible technique to easily calibrate a camera. It only requires the camera to observe a planar pattern shown at a few (at least two) different orientations. Either the camera or the planar pattern can be f...

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...