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A computer is generally considered to be a universal computational device; i.e., it is believed able to simulate any physical computational device with a cost in computation time of at most a polynomial factor: It is not...

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and wide...

In the Python world, NumPy arrays are the standard representation for numerical data and enable efficient implementation of numerical computations in a high-level language. As this effort shows, NumPy performance can be ...

Materias / palabras clave: Solubility; Drug discovery; Chemistry; Thermodynamics; Permeability (electromagnetism); Hildebrand solubility parameter; Permeation; Work (physics); Computational chemistry; Organic chemistry; Physics; Membrane

Materias / palabras clave: Exposition (narrative); Computer science; Automaton; Computation; Theory of computation; Theoretical computer science; Automata theory; Formal language; Model of computation; Programming language; Art; Literature

Materias / palabras clave: Turbulence; Turbulence kinetic energy; Computation; K-epsilon turbulence model; K-omega turbulence model; Dissipation; Mechanics; Flow (mathematics); Statistical physics; Turbulence modeling; Range (aeronautics); Physics

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...

Abstract In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing co...

CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-g...

Abstract We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb pot...

Abstract A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up t...

Evolutionary algorithms (EAs) are often well-suited for optimization problems involving several, often conflicting objectives. Since 1985, various evolutionary approaches to multiobjective optimization have been develope...

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...

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, an...

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platfor...

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 optimization of nonlinear functions using particle swarm methodology is described. Implementations of two paradigms are discussed and compared, including a recently developed locally oriented paradigm. Benchmark test...

A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented. For each element only one auxiliary basis set is needed to approximate Coulomb energies in conjunctio...

Papers from the 2006 flagship meeting on neural computation, with contributions from physicists, neuroscientists, mathematicians, statisticians, and computer scientists. The annual Neural Information Processing Systems (...

An analogy with the way ant colonies function has suggested the definition of a new computational paradigm, which we call ant system (AS). We propose it as a viable new approach to stochastic combinatorial optimization. ...

We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute sum...

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...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

The hallmarks of cancer conceptualization is a heuristic tool for distilling the vast complexity of cancer phenotypes and genotypes into a provisional set of underlying principles. As knowledge of cancer mechanisms has p...