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Materias / palabras clave: Partial differential equation; Nonlinear system; Artificial neural network; Context (archaeology); Inverse problem; Partial derivative; Computer science; Automatic differentiation; Applied mathematics; Physical law; Math...

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...

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...

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Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build struct...

Materias / palabras clave: Charge density; Charge (physics); Cluster (spacecraft); Atom (system on chip); Grid; Crystal (programming language); Point particle; Atoms in molecules; Algorithm; Chemistry; Molecule; Topology (electrical circuits)

The authors describe a general-purpose, representation-independent method for the accurate and computationally efficient registration of 3-D shapes including free-form curves and surfaces. The method handles the full six...

Materias / palabras clave: Hybrid functional; Range (aeronautics); Chemistry; Density functional theory; Computational chemistry; Function (biology); Coulomb; Thermodynamics; Physics; Materials science; Quantum mechanics; Composite material

A structure refinement method is described which does not use integrated neutron powder intensities, single or overlapping, but employs directly the profile intensities obtained from step-scanning measurements of the pow...

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-...

Anomaly detection is an important problem that has been researched within diverse research areas and application domains. Many anomaly detection techniques have been specifically developed for certain application domains...

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 We investigate the use of multiple transmitting and/or receiving antennas for single user communications over the additive Gaussian channel with and without fading. We derive formulas for the capacities and erro...

The dispersion and absorption of a considerable number of liquid and dielectrics are represented by the empirical formula ε*−ε∞=(ε0−ε∞)/[1+(iωτ0)1−α]. In this equation, ε* is the complex dielectric cons...

Materias / palabras clave: Ab initio; Hamiltonian (control theory); Basis set; Plane wave; Statistical physics; Ab initio quantum chemistry methods; Density functional theory; Electronic structure; Phonon; Degrees of freedom (physics and chemistry...

We present a simple procedure to generate first-principles norm-conserving pseudopotentials, which are designed to be smooth and therefore save computational resources when used with a plane-wave basis. We found that the...

Materias / palabras clave: Parallel computing; Computer science; Benchmark (surveying); Parallel algorithm; Intel iPSC; Algorithm; Range (aeronautics); Molecular dynamics; Supercomputer; Node (physics); Computational science; Physics

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete...

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...

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...

Materias / palabras clave: Message passing; Computer science; Parallel computing; Message Passing Interface; Dynamics (music); Computational science; Molecular dynamics; Physics; Acoustics; Quantum mechanics

Materias / palabras clave: Range (aeronautics); Software; Set (abstract data type); Tracking (education); Computer science; Physics; Systems engineering; Computational science; Aerospace engineering; Programming language; Engineering; Pedagogy

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...

Learning to store information over extended time intervals by recurrent backpropagation takes a very long time, mostly because of insufficient, decaying error backflow. We briefly review Hochreiter's (1991) analysis of t...