Plato: A localised orbital based density functional theory code

Fortran programs for the time-dependent Gross–Pitaevskii equation in a fully anisotropic trap

ROOT — A C++ framework for petabyte data storage, statistical analysis and visualization

ExHuME 1.3: A Monte Carlo event generator for exclusive diffraction

aCLIMAX 4.0.1, The new version of the software for analyzing and interpreting INS spectra

Linear response approach to collective electronic excitations of solids and surfaces

PLNoise: a package for exact numerical simulation of power-law noises

wannier90: A tool for obtaining maximally-localised Wannier functions

We have investigated the importance of polarization by the enzyme dihydrofolate reductase (DHFR) on its substrates, folate and dihydrofolate, using a series of quantum mechanical (QM) techniques (Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2), local density approximation (LDA) and generalized gradient approximation (GGA) density functional theory (DFT) calculations) in which the bulk enzyme is included in the calculations as point charges. Polarization, in terms of both charges on components (residues) of the folate and dihydrofolate molecules and changes in the electron density, particularly of the pterin ring of the substrates, and the implications for the catalytic reduction are discussed. Significant differences in polarization behavior are observed for the different theoretical methods employed. The consequences of this, particularly for choosing an appropriate model for quantum mechanical/molecular mechanical (QM/MM) calculations, are pointed out. The HF and MP2 QM methods show small polarizations (approximately 0.04 electrons) of the pterin ring but quite large polarizations with both LDA and GGA DFT methods (0.3-0.5 electrons). This large difference in polarization for both folate and dihydrofolate arises as a result of substantial differences between the charge distributions for the gasphase DFT and HF calculations, specifically the charges on the dianionic glutamate side chain. Some recent literature reports of incorrect representation of anionic systems by DFT methods are noted. The DFT results are similar to the previously reported LDA DFT results of Bajorath et al. predicting a large polarization of the pterin ring of folate (Proteins 9:217-224, 1991) and dihydrofolate (PNAS 88:6423-6426, 1991) of approximately 0.5-0.6 electrons.

A Monte Carlo C-code for calculating transmission efficiency of recoil separators and viewing residue trajectories

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

FDCSUSYDecay: An MSSM decay package

Accelerating numerical solution of stochastic differential equations with CUDA

Automatic calculation of supersymmetric renormalization group equations and loop corrections

Gmat. A software tool for the computation of the rovibrational G matrix

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach