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Atomistic Simulations (atomistic + simulation)
Selected AbstractsAtomistic Simulation of the Surface Energy of Spinel MgAl2O4JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 8 2000Chang Ming Fang Atomistic simulations with atomic potentials including anion polarizibility have been performed for the low-index surfaces of spinel MgAl2O4 with various terminations. The calculations show that for the most stable surface the surface energy is 2.27 J/m2 for the {100}, about 2.85 J/m2 for the {110}, and 3.07 J/m2 for the {111} orientation. The ratio between the experimental values to the calculated relaxed surface energies is about 1.5. Strong surface relaxation was found for the {110} and {111} orientation but only moderate surface relaxation for the {100} surface. [source] Atomistic Simulation of the Lattice Constants and Lattice Vibrations in LnM4Al8 (Ln: Nd, Sm; M: Cr, Mn, Cu, Fe).CHEMINFORM, Issue 39 2003Yan-mei Kang No abstract is available for this article. [source] Nanocomposite Synthesis: Embryonic States of Fluorapatite,Gelatine Nanocomposites and Their Intrinsic Electric-Field-Driven Morphogenesis: The Missing Link on the Way from Atomistic Simulations to Pattern Formation on the Mesoscale (Adv. Funct.ADVANCED FUNCTIONAL MATERIALS, Issue 22 2009Mater. Fractal aggregates of fluorapatite,gelatine nanocomposites (SEM image taken by Yigit Öztan, MPI CPfS),which bears a strong resemblance to the biosystem hydroxyapatite,collagen, a key material in human bones and teeth,are formed from bundles of calcified protein molecules representing the first (embryonic) states of shape development and leading to extended processes of self-organisation. This process has been studied in detail by P. Simon et al., and is reported on page 3596. [source] Embryonic States of Fluorapatite,Gelatine Nanocomposites and Their Intrinsic Electric-Field-Driven Morphogenesis: The Missing Link on the Way from Atomistic Simulations to Pattern Formation on the MesoscaleADVANCED FUNCTIONAL MATERIALS, Issue 22 2009Paul Simon Abstract The shape development of fluorapatite (FAP),gelatine nanocomposites is revealed by means of HRTEM investigations starting from molecular dimensions up to the formation of mesoscaled (elongated) hexagonal prisms. The composite nature of the aggregates is proved by IR spectroscopy and by chemical analyses on all states of shape development. The initial states are characterized by triple-helical fiber protein bundles, which are mineralized step-by-step forming and fixing nanoplatelets of FAP in a mosaic arrangement. After being fully mineralized the bundles form elongated composite nanoboards. In the next step of the growth process the boards aggregate to bundles of boards which are in a more or less parallel alignment with respect to each other. By adding up more and more composite nanoboards a critical size is reached and an electric field is developed, which takes over control and directs the further development of the aggregates. This kind of electric-field-directed growth of the elongated polar nanoboards additionally leads to the formation and inclusion of protein nanofibrils into the growing composite aggregate. By this method, cone-like nanofibril structures develop along the long axis of the aggregates accompanied by more perfect parallel alignment of the composite boards within the aggregates. Further shape development is characterized by adding up composite nanoboards, in particular to increase the third dimension in volume. This thickening process preferably takes place in the middle part of the elongated aggregates and finally proceeds to their basal ends until a perfect hexagonal prismatic seed is formed, which then is ready for further shape development on the micrometer scale. [source] Understanding Macroscopic Diffusion of Adsorbed Molecules in Crystalline Nanoporous Materials via Atomistic SimulationsCHEMINFORM, Issue 37 2006David S. Sholl Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Prediction of the Three-Dimensional Structure for the Rat Urotensin,II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic SimulationsCHEMMEDCHEM, Issue 9 2010Soo-Kyung Kim Dr. Abstract Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known. Thus, a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders. However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in preclinical animal disease models. ACT058362 is a selective antagonist for the human U-II receptor (hUT2R) with a reported Kd value of ,4,nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with a Kd value of ,1,500,nM. In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (Kd=,9,nM) and rUT2R (Kd=,21,nM). To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 in both hUT2R and rUT2R to explain the dramatically lower (,400-fold) affinity of ACT058362 for rUT2R and the similar affinity (,10,nM) of SB706375 for both UT2Rs. These studies used MembStruk and MSCDock to predict the UT2R structure and the binding site of ACT058362 and SB706375. Based on binding energies, we found two binding modes each with D1303.32 as the crucial anchoring point (Ballesteros,Weinstein numbering given in superscript). We predict that ACT058362 (an aryl,amine,aryl or ANA ligand) binds in the transmembrane (TM) 3456 region, while SB706375 (an aryl,aryl,amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding of the ANA ligand to rat and human receptors, while explaining the similar binding of the AAN compound to rat and human receptors. Moreover the predictions explain currently available structure,activity relationship (SAR) data. To further validate the predicted binding sites of these ligands in hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses between UT2R of different species, potentially indicating novel UT2R antagonists with cross-species high affinity. [source] Atomistic simulation of the self-diffusion in Mg (001) surfaceCRYSTAL RESEARCH AND TECHNOLOGY, Issue 9 2008Jian-Min Zhang Abstract Both the formation energies and the intra- and inter-layer diffuse activation energies of a vacancy in the first six lattice planes of Mg (001) surface have been calculated by combining the modified analytical embedded-atom method (MAEAM) with molecular dynamics (MD). The results show that the effect of the surface on the formation and migration of the vacancy is only down to the third-layer. It is easer for a single vacancy to form and to migrate in the first layer. Furthermore, the vacancy in the second layer is favorable to migrate to the first layer. This is in agreement with the experimental results that the first layer has the highest concentration of the vacancy. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Coarse-grained model of nucleic acid basesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Maciej Maciejczyk Abstract Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3,5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12,6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson,Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Atomistic Simulation of the Surface Energy of Spinel MgAl2O4JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 8 2000Chang Ming Fang Atomistic simulations with atomic potentials including anion polarizibility have been performed for the low-index surfaces of spinel MgAl2O4 with various terminations. The calculations show that for the most stable surface the surface energy is 2.27 J/m2 for the {100}, about 2.85 J/m2 for the {110}, and 3.07 J/m2 for the {111} orientation. The ratio between the experimental values to the calculated relaxed surface energies is about 1.5. Strong surface relaxation was found for the {110} and {111} orientation but only moderate surface relaxation for the {100} surface. [source] Diffusion in Nanocrystalline Metals and Alloys,A Status Report,ADVANCED ENGINEERING MATERIALS, Issue 5 2003R. Würschum Abstract Diffusion is a key property determining the suitability of nanocrystalline materials for use in numerous applications, and it is crucial to the assessment of the extent to which the interfaces in nanocrystalline samples differ from conventional grain boundaries. The present article offers an overview of diffusion in nanocrystalline metals and alloys. Emphasis is placed on the interfacial characteristics that affect diffusion in nanocrystalline materials, such as structural relaxation, grain growth, porosity, and the specific type of interface. In addition, the influence of intergranular amorphous phases and intergranular melting on diffusion is addressed, and the atomistic simulation of GB structures and diffusion is briefly summarized. On the basis of the available diffusion data, the diffusion-mediated processes of deformation and induced magnetic anisotropy are discussed. [source] Atomistic analysis of B clustering and mobility degradation in highly B-doped junctionsINTERNATIONAL JOURNAL OF NUMERICAL MODELLING: ELECTRONIC NETWORKS, DEVICES AND FIELDS, Issue 4-5 2010Maria Aboy Abstract In this paper we discuss from an atomistic point of view some of the issues involved in the modeling of electrical characteristics evolution in silicon devices as a result of ion implantation and annealing processes in silicon. In particular, evolution of electrically active dose, sheet resistance and hole mobility has been investigated for high B concentration profiles in pre-amorphized Si. For this purpose, Hall measurements combined with atomistic kinetic Monte Carlo atomistic simulations have been performed. An apparent anomalous behavior has been observed for the evolution of the active dose and the sheet resistance, in contrast to opposite trend evolutions reported previously. Our results indicate that this anomalous behavior is due to large variations in hole mobility with active dopant concentration, much larger than that associated to the classical dependence of hole mobility with carrier concentration. Simulations suggest that hole mobility is significantly degraded by the presence of a large concentration of boron-interstitial clusters, indicating the existence of an additional scattering mechanism. Copyright © 2009 John Wiley & Sons, Ltd. [source] Atom,atom partitioning of total (super)molecular energy: The hidden terms of classical force fieldsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007M. Rafat Abstract Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom,atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange). © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Charged soc metal-organic framework for high-efficacy H2 adsorption and syngas purification: Atomistic simulation studyAICHE JOURNAL, Issue 9 2009Jianwen Jiang Abstract H2 adsorption and syngas purification in charged soc metal-organic framework are investigated using atomistic simulations. As experimentally observed, the extraframework NO3, ions are entrapped in carcerand-like capsule with negligible mobility. At low pressure, H2 adsorption occurs concurrently at multiple sites near the exposed indium atoms and organic components. The capsule is accessible at high pressure through the surrounding channels by restricted windows. Adsorption sites identified are remarkably consistent with inelastic neutron scattering measurements. The isotherm and isosteric heat of H2 adsorption predicted match well with experimental data. As loading rises, the isosteric heat remains nearly constant, revealing the homogeneity of adsorption sites. CO2/H2 selectivity in syngas adsorption is up to 600 and substantially higher than other nanoporous materials. With a trace of H2O, the selectivity increases slightly at low pressure due to promoted adsorption of CO2 by H2O bound proximally to the exposed indium atoms, but decreases at high pressure as a consequence of competitive adsorption of H2O over CO2. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source] First principles simulations of F centers in cubic SrTiO3PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 1 2005J. Carrasco Abstract Atomic and electronic structure of regular and O-deficient SrTiO3 have been studied. Several types of first principles atomistic simulations: Hartree-Fock method, Density Functional Theory, and hybrid HF-DFT functionals, have been applied to periodic models that consider supercells of different sizes (ranging between 40 and 240 atoms). We confirm the ionic character of the Sr-O bonds and the high covalency of the Ti-O2 substructure. For the stoichiometric cubic crystal; the lattice constant and bulk modulus correctly reproduce the experimental data whereas the band gap is only properly obtained by the B3PW functional. The relaxed geometry around the F center shows a large expansion of the two nearest Ti ions. Moreover, the vacancy formation energy is extremely sensitive to the size and the shape of the supercell as well as the calculation method. The electronic density map indicates the redistribution of two electrons of the missing O atom between the vacancy and 3d atomic orbitals of the two nearest Ti ions, in contrast to the F centers in ionic oxides where the charge centroid does not change. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Allostery and cooperativity revisitedPROTEIN SCIENCE, Issue 8 2008Qiang Cui Abstract Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/Pauling-KNF descriptions, and point out that the "new view" of allostery, emphasizing "population shifts," is, in fact, an "old view." The presentation offers not only an up-to-date description of allostery from a theoretical/computational perspective, but also helps to resolve several outstanding issues concerning allostery. [source] Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine DehydrogenaseCHEMPHYSCHEM, Issue 12 2007Kara E. Ranaghan Abstract The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions,an area of great current interest,for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified,to either of the carboxylate oxygen atoms of the catalytic base (Asp428,),and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5±0.9 kcal,mol,1 for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal,mol,1. In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474,(MADH)/Thr172,(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471,(MADH)/Phe169,(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions. [source] | ||||||||||||||||