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The newly developed GSAS-II software is a general purpose package for data reduction, structure solution and structure refinement that can be used with both single-crystal and powder diffraction data from both neutron an...

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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...

Subjects / keywords: 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...

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional pe...

Absorption effects usually present the most serious source of systematic error in the determination of structure factors from single-crystal X-ray diffraction measurements if the crystal is not ground to a sphere or cyli...

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-...

Subjects / keywords: Atom (system on chip); Type (biology); Minification; Computer science; Molecule; Molecular dynamics; Bond energy; Algorithm; Chemistry; Computational chemistry; Chemical physics; Topology (electrical circuits)

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is pr...

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...

Subjects / keywords: Workstation; Homogeneous space; Computer science; Point (geometry); Computational science; Group (periodic table); Physics; Mathematics; Operating system; Quantum mechanics; Geometry

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few...

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...

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

Subjects / keywords: 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...

▪ Abstract We present an overview of the lattice Boltzmann method (LBM), a parallel and efficient algorithm for simulating single-phase and multiphase fluid flows and for incorporating additional physical complexities....

Subjects / keywords: Physics; Least-squares function approximation; Spectrum (functional analysis); Distortion (music); Noise (video); Statistics; Gaussian noise; Gaussian; Non-linear least squares; Total least squares; Computational physics...

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop n...

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, i...

Abstract A new method for obtaining optimized parameters for semiempirical methods has been developed and applied to the modified neglect of diatomic overlap (MNDO) method. The method uses derivatives of calculated value...

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 Whereas much of organic chemistry has classically dealt with the preparation and study of the properties of individual molecules, an increasingly significant portion of the activity in chemical research involves...