Search results for "ALGORITHMS"
showing 10 items of 1716 documents
Characterizing cavities in model inclusion molecules: a comparative study
1998
We have selected fullerene-60 and -70 cavities as model systems in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecule taken as a unitary sphere, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and a cubic lattice approach to a molecular space. Accurate measures of the molecular volume and surface area have been performed with the pseudo-random Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the…
Stereoelectronic Requirements for Optimal Hydrogen-Bond-Catalyzed Enolization
2011
Protein crystallographic analysis of the active sites of enolizing enzymes and structural analysis of hydrogen-bonded carbonyl compounds in small molecule crystal structures, complemented by quantum chemical calculations on related model enolization reactions, suggest a new stereoelectronic model that accounts for the observed out-of-plane orientation of hydrogen-bond donors (HBDs) in the oxyanion holes of enolizing enzymes. The computational results reveal that the lone-pair directionality of HBDs characteristic for hydrogen-bonded carbonyls is reduced upon enolization, and the enolate displays almost no directional preference for hydrogen bonding. Positioning the HBDs perpendicular to the…
On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study
2012
The mechanism of the intramolecular Diels#8211;Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition stat…
Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.
2009
Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membra…
Engineering thermal conductance using a two-dimensional phononic crystal
2014
Controlling thermal transport has become relevant in recent years. Traditionally, this control has been achieved by tuning the scattering of phonons by including various types of scattering centres in the material (nanoparticles, impurities, etc). Here we take another approach and demonstrate that one can also use coherent band structure effects to control phonon thermal conductance, with the help of periodically nanostructured phononic crystals. We perform the experiments at low temperatures below 1 K, which not only leads to negligible bulk phonon scattering, but also increases the wavelength of the dominant thermal phonons by more than two orders of magnitude compared to room temperature…
Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance
2004
AbstractInformation on protein internal motions is usually obtained through the analysis of atomic mean-square displacements, which are a measure of variability of the atomic positions distribution functions. We report a statistical approach to analyze molecular dynamics data on these displacements that is based on probability distribution functions. Using a technique inspired by the analysis of variance, we compute unbiased, reliable mean-square displacements of the atoms and analyze them statistically. We applied this procedure to characterize protein thermostability by comparing the results for a thermophilic enzyme and a mesophilic homolog. In agreement with previous experimental observ…
Modification of Nanocrystalline WO3 with a Dicationic Perylene Bisimide: Applications to Molecular Level Solar Water Splitting
2015
[(N,N?-Bis(2-(trimethylammonium)ethylene) perylene 3,4,9,10-tetracarboxylic acid bisimide)(PF6)2] (1) was observed to spontaneously adsorb on nanocrystalline WO3 surfaces via aggregation/hydrophobic forces. Under visible irradiation (? > 435 nm), the excited state of 1 underwent oxidative quenching by electron injection (kinj > 108 s-1) to WO3, leaving a strongly positive hole (Eox ? 1.7 V vs SCE), which allows to drive demanding photo-oxidation reactions in photoelectrochemical cells (PECs). The casting of IrO2 nanoparticles (NPs), acting as water oxidation catalysts (WOCs) on the sensitized electrodes, led to a 4-fold enhancement in photoanodic current, consistent with hole transfer from …
Random walks and random numbers from supercontinuum generation
2012
International audience; We report a numerical study showing how the random intensity and phase fluctuations across the bandwidth of a broadband optical supercontinuum can be interpreted in terms of the random processes of random walks and L´evy flights. We also describe how the intensity fluctuations can be applied to physical random number generation. We conclude that the optical supercontinuum provides a highly versatile means of studying and generating a wide class of random processes at optical wavelengths.
An efficient dissipative particle dynamics-based algorithm for simulating electrolyte solutions
2015
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the concentration of the ionic species is described using Brownian pseudo particles. The method is designed especially for systems with high salt concentrations, as explicit treatment of the salt ions becomes computationally expensive. For illustration, we apply the method to electro-osmotic flow over patterned, superhydrophobic surfaces. The results are in good agreement with recent theoretical predictions.
Protein structure prediction assisted with sparse NMR data in CASP13
2019
CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15 N-1 H residual dipolar coupling data, typical of that obtained for 15 N,13 C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CAS…