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Computer Simulation (Latest Articles)
Latest indexed articles for 'Computer Simulation'
Articles 191 to 200 of 200:
30 Aug 2009 
The acid-base properties of zeolites with group 5 transition metal framework sites are investigated, and a first step into the understanding of their acid/base and redox properties is undertaken using DFT reactivity descriptors. It is evidenced, ...
rec_pub_19130497-exploring-reactivity-framework-vanadium-niobium-tantalum-sites.htm
Rotamer optimization for protein design through MAP estimation and problem-size reduction.
30 Aug 2009 The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization ...
rec_pub_19123203-rotamer-optimization-protein-design-map-estimation-problem-size.htm
In silico prediction of drug solubility: 4. Will simple potentials suffice?
30 Aug 2009 In view of the extreme importance of reliable computational prediction of aqueous drug solubility, we have established a Monte Carlo simulation procedure which appears, in principle, to yield reliable solubilities even for complex drug molecules. A ...
rec_pub_19115279-in-silico-prediction-drug-solubility-4-simple-potentials-suffice.htm
GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics.
30 Aug 2009 GridMAT-MD is a new program developed to aid in the analysis of lipid bilayers from molecular dynamics simulations. It reads a GROMACS coordinate file and generates two types of data: a two-dimensional contour plot depicting membrane thickness, and ...
rec_pub_19090582-gridmat-md-grid-based-membrane-analysis-tool-use-molecular-dynamics.htm
30 Aug 2009 We herein propose the multiple Markov transition matrix method (MMMM), an algorithm by which to estimate the stationary probability distribution from independent multiple molecular dynamics simulations with different Hamiltonians. Applications to ...
rec_pub_19090573-multiple-markov-transition-matrix-method-obtaining-stationary.htm
30 Aug 2009 Ramachandran maps of neutral and ionized HCO-Gly-NH2 and HCO-Ala-NH2 peptide models have been built at the B3LYP/6-31++G(d,p) level of calculation. Direct optimizations using B3LYP and the recently developed MPWB1K functional have also been carried ...
rec_pub_19090571-influence-ionization-conformational-preferences-peptide-models.htm
30 Aug 2009 This article illustrates practical applications to molecular dynamics simulations of the recently developed numerical integrators [Phys Rev E 2006, 73, 026703] for ordinary differential equations. This method consists of extending any set of ...
rec_pub_19090566-numerical-examination-extended-phase-space-volume-preserving.htm
30 Aug 2009 The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole, and purine. Initial parameters for the ...
rec_pub_19090564-polarizable-empirical-force-field-nitrogen-containing-heteroaromatic.htm
30 Aug 2009 Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. ...
rec_pub_19090563-molecular-dynamics-simulations-fluid-methane-properties-using-ab.htm
Comments on "Are the risks from tritium exposures being underestimated?".
30 Aug 2009 
rec_pub_19810288-comments-risks-tritium-exposures-underestimated.htm
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