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ICTs

APPLICATIONS

Quantum Mechanics and Dynamics

  • Abinit - compute charge density and electronic structure of molecules with Density Functional Theory
  • ADF - quantum chemistry software package based on Density Functional Theory (DFT)
  • Ampac - fully-featured semiempirical quantum mechanical program
  • ATAT - Alloy Theoretic Automated Toolkit, a collection of alloy theory tools
  • Atomistix ToolKit - software tool for first-principles electronic-structure and transport calculations
  • CPMD (Car–Parrinello Molecular Dynamics) - plane wave and pseudopotential implementation of Density Functional Theory
  • Dalton - molecular electronic structure program
  • DFTB+ - fast and efficient stand-alone implementation of the Density Functional based Tight Binding (DFTB) method
  • FPLO - full-potential local-orbital minimum-basis code to solve the Kohn-Sham equations on a regular lattice
  • GAMESS - program for ab initio molecular quantum chemistry
  • Gaussian - electronic structure program
  • MOLPRO - complete system of ab initio programs for molecular electronic structure calculations
  • MOPAC - semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation
  • NWchem - electronic-structure code that is suitable to perform complex calculations on molecular structure
  • ORCA - ab initio, DFT and semiempirical SCF-MO package
  • PLH - ab initio polymer program
  • Siesta - electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
  • Turbomole - ab initio electronic structure program
  • T-Rex - automatized Romberg procedure for finite field differentiation for a geometrical progression of fields
  • VASP (Vienna Ab-initio Simulation Package) - package for performing ab-initio quantum-mechanical molecular dynamics using pseudopotentials and a plane wave basis set
  • VTST - a VASP package variant for finding saddle points and evaluating transition state theory (TST) rate constants
  • WIEN2k - augmented plane wave plus local orbitals program for calculating crystal properties

Photonics and Material Simulations

  • Meep - FDTD simulation software package to model electromagnetic systems
  • MPB - computes definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors

 Molecular Mechanics and Dynamics

  • Accelrys Discovery Studio - modeling and simulation software for protein modeling and computational chemistry
  • Accelrys Materials Studio - software environment for molecular modeling
  • Adaptive Poisson Boltzmann Solver (APBS) - software package for the numerical solution of the Poisson-Boltzmann equation
  • GOLD Suite - program for calculating the docking modes of small molecules into protein binding sites
  • Gromacs - versatile package to perform molecular dynamics
  • LAMMPS - large scale classical molecular dynamics code
  • MDynaMix - general purpose molecular dynamics code for simulations of mixtures of rigid or flexible molecules
  • NAMD - molecular dynamics code designed for simulation of large biomolecular systems
  • PyRosetta - interactive Python-based interface to Rosetta
  • Rosetta - protein sequence analysis suites
  • Sybyl - molecular modeling and computational informatics platform
  • Tinker - complete and general package for molecular mechanics and dynamics, with some special features for biopolymers

Crystallography

  • Adxv - program to display X-Ray diffraction images
  • CCP4 - collection of disparate programs covering most of the computations required for macromolecular crystallography
  • CNS - program that provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination
  • CSD - the Cambridge Structural Database
  • Coot - program for model building, model completion and validation
  • Mosflm/iMosflm - program for integrating single crystal diffraction data from area detectors
  • Naccess - program that calculates the accessible area of a molecule from a PDB
  • SIR - program for the solution and refinement of crystal structures using single crystal data
  • Phenix - automated macromolecular crystallography software suite
  • XDS - software for processing single-crystal monochromatic diffraction data recorded by the rotation method

Numerical Analysis

  • MATLAB - numerical computing environment
  • Octave - high-level programming language, primarily intended for numerical computations

Physics and Astrophysics

  • DDSCAT - program for calculating scattering and absorption of light by irregular particles
  • e-DDA - program for electron-driven discrete-dipole approximation

Agent-based Modeling

  • RePast - family of advanced agent-based modeling and simulation platforms

Bioscience

  • 13CFLUX - toolkit for Metabolic Flux Analysis
  • MicrobeTracker Suite - software package designed to detect and outline microbial cells in microscopy images and to analyze fluorescence signal inside them

Phylogenetics

Statistics and Data Analysis

Economy and Finance

  • Dynare - software platform to solve, simulate and estimate macroeconomic models

 

Knowledge transfer officer

Laurent Galas
Laurent GALAS                     

Tel +32 (0)81 72 53 39

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