Search results for "Computer simulation"
showing 10 items of 1054 documents
Transport properties of 2F = F2 in a temperature gradient as studied by molecular dynamics simulations
2007
International audience; We calculate transport properties of a reacting mixture of F and F2 from results of nonequilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, whic…
Inhibition of Eimeria tenella CDK-related kinase 2: From target identification to lead compounds.
2010
Apicomplexan parasites encompass several human- and animal-pathogenic protozoans such as Plasmodium falciparum, Toxoplasma gondii, and Eimeria tenella. E. tenella causes coccidiosis, a disease that afflicts chickens, leading to tremendous economic losses to the global poultry industry. The considerable increase in drug resistance makes it necessary to develop new therapeutic strategies against this parasite. Cyclin-dependent kinases (CDKs) are key molecules in cell-cycle regulation and are therefore prominent target proteins in parasitic diseases. Bioinformatics analysis revealed four potential CDK-like proteins, of which one—E. tenella CDK-related kinase 2 (EtCRK2)—has already been charact…
Diatropicity of tetraazanaphthalenes
2006
Tetraazanaphthalenes are diatropic molecules, whose magnetic response to a magnetic field perpendicular to the molecular plane closely resembles that of naphthalene. The out-of-plane component of the magnetic susceptibility tensor and its strong anisotropy can be used as quantifiers of magnetic aromaticity. Maps showing streamlines and modulus of the current density field provide clear evidence for diatropicity of these systems. They also explain the strong anisotropy of carbon and nitrogen magnetic shielding, which is determined by the big out-of-plane component of the nuclear shielding tensor. The electronic ring currents observed in the map deshield the nuclei of ring hydrogens by enforc…
Computational design of biological catalysts
2008
The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze related reactions. The second possibility is the use of immune systems that recognize stable molecules resembling the transition structure of the target reaction. We finally show how computational techniques are able to provide an enormous quantity of information, providing clues to guide the development of new biological catalysts
Experimental and DFT Studies on Competitive Heterocyclic Rearrangements. 3. A Cascade Isoxazole−1,2,4-Oxadiazole−Oxazole Rearrangement
2008
The thermal rearrangements of 3-acylamino-5-methylisoxazoles 1 have been investigated under basic and neutral conditions and interpreted with the support of computational data. The density functional theory (DFT) study on the competitive routes available for the base-catalyzed thermal rearrangement of isoxazoles 1 showed that the Boulton-Katritzky (BK) rearrangement, producing the less stable 3-acetonyl-1,2,4-oxadiazoles 5, is a much more favored process than either the migration-nucleophilic attack-cyclization (MNAC) or the ring contraction-ring expansion (RCRE). In turn, an increase in reaction temperature will promote the MNAC of oxadiazoles 5, producing the more stable 2-acylaminooxazol…
Natural micro-scale heterogeneity induced solute and nanoparticle retardation in fractured crystalline rock.
2011
Abstract We studied tracer (Tritiated Water (HTO); Tritium replaces one of the stable hydrogen atoms in the H 2 O molecule) and nanoparticle (quantum dots (QD)) transport by means of column migration experiments and comparison to 3D CFD modeling. Concerning the modeling approach, a natural single fracture was scanned using micro computed tomography (μCT) serving as direct input for the model generation. The 3D simulation does not incorporate any chemical processes besides the molecular diffusion coefficient solely reflecting the impact of fracture heterogeneity on mass (solute and nanoparticles) transport. Complex fluid velocity distributions (flow channeling and flowpath heterogeneity) evo…
Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies
2019
The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experim…
Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches
2017
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on the ability of surfactants to self-assemble and constitute supramolecular struc…
Computer simulations of SiO2 and GeO2
2004
Classical Molecular Dynamics (MD) simulations are used to study structural and dynamic properties of amorphous germania (GeO2) in comparison to those of silica (SiO2). The total structure factor, as obtained from these simulations, is in very good agreement with that of neutron scattering experiments, both for germania and silica. The tetrahedral network structure in silica and germania leads to a prepeak in the structure factor that appears at slightly smaller wavenumbers in GeO2 than in SiO2. At high temperatures the diffusion constants are very similar in both systems whereas at low temperatures diffusion is significantly faster in germania than in silica. We also outline the strategy fo…
Selective Change Driven Imaging: A Biomimetic Visual Sensing Strategy
2011
Selective Change Driven (SCD) Vision is a biologically inspired strategy for acquiring, transmitting and processing images that significantly speeds up image sensing. SCD vision is based on a new CMOS image sensor which delivers, ordered by the absolute magnitude of its change, the pixels that have changed after the last time they were read out. Moreover, the traditional full frame processing hardware and programming methodology has to be changed, as a part of this biomimetic approach, to a new processing paradigm based on pixel processing in a data flow manner, instead of full frame image processing.