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Computational science (Page 1)
field concerned with constructing mathematical models and quantitative analysis techniques and using computers to analyze and solve scientific problems
Subconcepts:
- Adaptive mesh refinement
- Computational Science and Engineering
- Computational simulation
- Computer software
- Problem solver
- Product model
- R package
- Stencil
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2010
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Meep: A flexible free-software package for electromagnetic simulations by the FDTD method
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2003
Cited 2158 times
The Xplor-NIH NMR molecular structure determination package
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2011
Cited 2139 times
MadGraph 5: going beyond
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2005
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SUNDIALS
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XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density
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1983
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Adaptive Mesh Refinement for Hyperbolic Partial Differential Equations
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2001
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DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution
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1996
Cited 2023 times
DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package
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2011
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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
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2006
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Pvclust: an R package for assessing the uncertainty in hierarchical clustering
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2011
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The university of Florida sparse matrix collection
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2015
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MatConvNet
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2012
Cited 1968 times
CALYPSO: A method for crystal structure prediction
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1987
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EMS - a software package for electron diffraction analysis and HREM image simulation in materials science
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2014
Cited 1888 times
FeynRules 2.0 — A complete toolbox for tree-level phenomenology
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2018
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Real-space refinement in<i>PHENIX</i>for cryo-EM and crystallography
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Numerical Recipes in FORTRAN
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2017
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UpSetR: an R package for the visualization of intersecting sets and their properties
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1965
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Algorithm for computer control of a digital plotter
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2016
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
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2005
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<b>spatstat</b>: An<i>R</i>Package for Analyzing Spatial Point Patterns
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2021
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VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code
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2014
Cited 1834 times
ShengBTE: A solver of the Boltzmann transport equation for phonons
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2008
Cited 1821 times
Automatic Time Series Forecasting: The<b>forecast</b>Package for<i>R</i>
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1989
Cited 1793 times
Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics
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2017
Cited 1793 times
The atomic simulation environment—a Python library for working with atoms
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2013
Cited 1781 times
<scp>cp2k:</scp> atomistic simulations of condensed matter systems
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1996
Cited 1777 times
<i>POWDER CELL</i> – a program for the representation and manipulation of crystal structures and calculation of the resulting X-ray powder patterns
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1978
Cited 1775 times
A graphics model building and refinement system for macromolecules
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2009
Cited 1738 times
BIOMOD – a platform for ensemble forecasting of species distributions
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2007
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Reshaping Data with the<b>reshape</b>Package
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2016
Cited 1726 times
mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models
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2012
Cited 1723 times
ACPYPE - AnteChamber PYthon Parser interfacE
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2017
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Hardware-efficient variational quantum eigensolver for small molecules and quantum magnets
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2010
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Gabedit—A graphical user interface for computational chemistry softwares
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1996
Cited 1656 times
Reduced surface: An efficient way to compute molecular surfaces
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2014
Cited 1655 times
CHARMM-GUI<i>Membrane Builder</i>toward realistic biological membrane simulations
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1989
Cited 1638 times
Parallel and Distributed Computation: Numerical Methods
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2003
Cited 1616 times
Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale
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2007
Cited 1603 times
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
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2012
Cited 1577 times
New developments in the<i>ATSAS</i>program package for small-angle scattering data analysis
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2012
Cited 1569 times
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
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1997
Cited 1554 times
An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
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2012
Cited 1554 times
GAPIT: genome association and prediction integrated tool
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2007
Cited 1552 times
A multiplatform code for the analysis of energy-dispersive X-ray fluorescence spectra
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2012
Cited 1530 times
An overview of the Amber biomolecular simulation package
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2013
Cited 1511 times
PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear <i>d</i>‐ and <i>f</i>‐block complexes
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2008
Cited 1503 times
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
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2017
Cited 1502 times
<b>ranger</b>: A Fast Implementation of Random Forests for High Dimensional Data in <i>C++</i> and <i>R</i>
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2010
Cited 1496 times
k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields
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2011
Cited 1495 times
SIMPSON: A general simulation program for solid-state NMR spectroscopy
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2007
Cited 1494 times
DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method
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2000
Cited 1475 times
Electronic structure, properties, and phase stability of inorganic crystals: A pseudopotential plane-wave study
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2009
Cited 1470 times
<i>DAMMIF</i>, a program for rapid<i>ab-initio</i>shape determination in small-angle scattering
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1984
Cited 1467 times
Adaptive mesh refinement for hyperbolic partial differential equations
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1965
Cited 1455 times
Ab Initio Computations in Atoms and Molecules
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2015
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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1991
Cited 1437 times
The Nas Parallel Benchmarks
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1997
Cited 1430 times
Multilevel fast multipole algorithm for electromagnetic scattering by large complex objects
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2000
Cited 1427 times
Toward a design theory of problem solving
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2017
Cited 1426 times
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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2021
Cited 1418 times
<i>CrystalExplorer</i>: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals
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2000
Cited 1415 times
SIMPSON: A General Simulation Program for Solid-State NMR Spectroscopy
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2020
Cited 1407 times
Risk‐of‐bias VISualization (robvis): An R package and Shiny web app for visualizing risk‐of‐bias assessments
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2013
Cited 1406 times
QuTiP 2: A Python framework for the dynamics of open quantum systems
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2010
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Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method
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2011
Cited 1400 times
SwissParam: A fast force field generation tool for small organic molecules
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2014
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MNE software for processing MEG and EEG data
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1989
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GRASP: A general-purpose relativistic atomic structure program
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2020
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
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2009
Cited 1374 times
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
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2008
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General purpose molecular dynamics simulations fully implemented on graphics processing units
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1981
Cited 1351 times
A new computer program for Rietveld analysis of X-ray powder diffraction patterns
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2012
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<b>mirt</b>: A Multidimensional Item Response Theory Package for the<i>R</i>Environment
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2004
Cited 1326 times
Anharmonic vibrational properties by a fully automated second-order perturbative approach
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1989
Cited 1325 times
The design and application of upwind schemes on unstructured meshes
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2011
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An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
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Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences
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1999
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The GROMOS Biomolecular Simulation Program Package
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2001
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GADGET: a code for collisionless and gasdynamical cosmological simulations
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1996
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Automated docking of flexible ligands: Applications of autodock
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1999
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XCrySDen—a new program for displaying crystalline structures and electron densities
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2018
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<i>TOPAS</i> and <i>TOPAS-Academic</i>: an optimization program integrating computer algebra and crystallographic objects written in C++
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2007
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Version 1.2 of the Crystallography and NMR system
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1993
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SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules
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1978
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Error Estimates for Adaptive Finite Element Computations
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2004
Cited 1252 times
A Simple Mesh Generator in MATLAB
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2012
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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
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2015
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<scp>Molcas</scp> 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table
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2012
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openair — An R package for air quality data analysis
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Improvements to the <scp>APBS</scp> biomolecular solvation software suite
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1998
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WinXAS: a Program for X-ray Absorption Spectroscopy Data Analysis under MS-Windows
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1998
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SBDART: A Research and Teaching Software Tool for Plane-Parallel Radiative Transfer in the Earth's Atmosphere
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2002
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<i>FOX</i>, `free objects for crystallography': a modular approach to<i>ab initio</i>structure determination from powder diffraction
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1990
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Semi-direct algorithms for the MP2 energy and gradient
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pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels
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CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations
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2007
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PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals
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Algorithm 832
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NVIDIA Tesla: A Unified Graphics and Computing Architecture