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Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement

Thomas C. Terwilliger2003-06-27Acta Crystallographica Section D Biological Crystallography

An iterative process for improving the completeness and quality of atomic models automatically built at moderate resolution (up to about 2.8 A) is described. The process consists of cycles of model building interspersed with cycles of refinement and combining phase information from the model with experimental phase in…

Protein Structure and DynamicsRNA and protein synthesis mechanismsEnzyme Structure and Function

Crystallization kinetics of polydisperse colloidal hard spheres: Experimental evidence for local fractionation

S. Garcı́a Martı́n、Gary Bryant、W. van Megen2003-06-27Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics

We present the crystallization kinetics for two polydisperse hard-sphere particle stocks with differing particle size distributions. One of the latexes had a relatively symmetrical distribution, the other had a more polydisperse distribution, which was highly skewed to smaller sizes. The emerging Bragg reflections fro…

Phase Equilibria and ThermodynamicsMaterial Dynamics and PropertiesPickering emulsions and particle stabilization

Low-wave-number Raman scattering fromCdSxSe1−xquantum dots embedded in a glass matrix

M. Ivanda、K. Babocsi、C. Dem 等 6 位作者2003-06-27Physical review. B, Condensed matter

The Raman scattering on acoustical phonons from ${\mathrm{CdS}}_{x}{\mathrm{Se}}_{1\ensuremath{-}x}$ quantum dots in a glass matrix were investigated for in- and off-resonance conditions. By a comparison with a model calculation, the off-resonance scattering showed that the homogeneous broadening mainly contributes to…

Quantum Dots Synthesis And PropertiesChalcogenide Semiconductor Thin FilmsSilicon Nanostructures and Photoluminescence

On the Hydrothermal Stability of Mesoporous Aluminosilicate MCM-48 Materials

Yongde Xia、Robert Mokaya2003-06-27The Journal of Physical Chemistry B

Aluminosilicate MCM-48 materials with Si/Al ratio between 4 and 50 were prepared via direct mixed-gel synthesis, and their hydrothermal stability in boiling water and steam was investigated using a variety of techniques including powder XRD, N 2 sorption studies, and elemental analysis. The stability of Al-containing…

Zeolite Catalysis and SynthesisMesoporous Materials and CatalysisLayered Double Hydroxides Synthesis and Applications

Effect of Solvent Exchange on the Solid Structure and Dissolution Behavior of Cellulose

Daisuke Ishii、Daisuke Tatsumi、Takayoshi Matsumoto2003-06-27Biomacromolecules

Effects of solvent exchange and milling on the solid structure of cellulose were investigated, using small- and wide-angle X-ray scattering and solid-state NMR. The solvent exchange facilitated the dissolution of cellulose in LiCl/DMAc with no change of the crystalline structure of cellulose. In contrast, the milling…

Advanced Cellulose Research StudiesLignin and Wood ChemistryNMR spectroscopy and applications

Using natural seeding material to generate nucleation in protein crystallization experiments

A. D’Arcy、A. Mac Sweeney、Alexander Haber2003-06-27Acta Crystallographica Section D Biological Crystallography

The nucleation event in protein crystallization is a part of the process that is poorly controlled. It is generally accepted that the protein should be in the metastable phase for crystal growth, but for nucleation higher levels of saturation are needed. Formation of nuclei in bulk solvent requires interaction of prot…

Enzyme Structure and FunctionCalcium Carbonate Crystallization and InhibitionCrystallization and Solubility Studies

Variations of the Geometries and Band Gaps of Single-Walled Carbon Nanotubes and the Effect of Charge Injection

Guangyu Sun、J. Kürti、Miklós Kertész 等 4 位作者2003-06-27The Journal of Physical Chemistry B

The geometries of neutral and charged carbon single-walled nanotubes (SWNTs) have been calculated using density functional theory. Periodic boundary conditions, a plane wave basis, and ultrasoft pseudopotentials are used in the generalized gradient approximation for isolated SWNTs with diameters of up to 20 and 12.5 Å…

Carbon Nanotubes in CompositesGraphene research and applicationsFullerene Chemistry and Applications

Microstructure of dense colloid–polymer suspensions and gels

S. A. Shah、Y-L Chen、Subramanian Ramakrishnan 等 5 位作者2003-06-27Journal of Physics Condensed Matter

A systematic experimental study of polymer-induced changes of the collective structure of model hard-sphere nanocolloids in the fluid and gel states has been carried out using ultra-small-angle x-ray scattering. The focus is on small, non-adsorbing polymer depletants where a direct transition from the homogeneous flui…

Phase Equilibria and ThermodynamicsMaterial Dynamics and PropertiesSurfactants and Colloidal Systems

Influence of sulfur on the adhesion of the nickel/alumina interface

Weihua Zhang、John R. Smith、X.-G. Wang 等 4 位作者2003-06-27Physical review. B, Condensed matter

The effects of sulfur on the adhesion of ${\mathrm{N}\mathrm{i}/\mathrm{A}\mathrm{l}}_{2}{\mathrm{O}}_{3}$ interfaces are determined from first principles. The interfacial bonding is analyzed in terms of its ionic, covalent, and metallic components as well as its local electron orbital symmetries. The results reveal t…

Advanced ceramic materials synthesisCorrosion Behavior and InhibitionMetal and Thin Film Mechanics

Synthesis, Electronic Structure, and Electron Transfer Dynamics of (Aryl)ethynyl-Bridged Donor−Acceptor Systems

Naomi P. Redmore、Igor V. Rubtsov、Michael J. Therien2003-06-27Journal of the American Chemical Society

The ET dynamics of a series of donor-spacer-acceptor (D-Sp-A) systems featuring (porphinato)zinc(II), (aryl)ethynyl bridge, and arene diimide units were investigated by pump-probe transient absorption spectroscopy. Analysis of these data within the context of the Marcus-Levich-Jortner equation suggests that the pi-con…

Radical Photochemical ReactionsPorphyrin and Phthalocyanine ChemistryPhotochemistry and Electron Transfer Studies

Determination of the antiferromagnetic spin axis in epitaxialLaFeO3films by x-ray magnetic linear dichroism spectroscopy

J. Lüning、F. Nolting、A. Schöll 等 8 位作者2003-06-27Physical review. B, Condensed matter

We report x-ray magnetic linear dichroism (XMLD) measurements at the Fe ${L}_{2,3}$ absorption edges of thin antiferromagnetic (AFM) ${\mathrm{LaFeO}}_{3}$ films grown epitaxially on ${\mathrm{SrTiO}}_{3}$ (100) and (110) substrates and a stepped (100) substrate with a 2\ifmmode^\circ\else\textdegree\fi{} miscut. The…

Magnetic properties of thin filmsMagnetic and transport properties of perovskites and related materialsMultiferroics and related materials

High-Frequency and -Field EPR Spectroscopy of Tris(2,4-pentanedionato)manganese(III): Investigation of Solid-State versus Solution Jahn−Teller Effects

J. Krzystek、Gregory J. Yeagle、Ju‐Hyun Park 等 7 位作者2003-06-27Inorganic Chemistry

High-frequency and -field electron paramagnetic resonance (HFEPR) spectroscopy of a classical coordination complex, Mn(acac)(3) (Hacac = 2,4-pentanedione), has been performed on both solid powder and frozen solution (in CH(2)Cl(2)/toluene, 3:2 v/v) samples. Parallel mode detection X-band EPR spectra exhibiting resolve…

Metal complexes synthesis and propertiesMagnetism in coordination complexesLanthanide and Transition Metal Complexes

Choice of data-collection parameters based on statistic modelling

А. Н. Попов、Gleb Bourenkov2003-06-27Acta Crystallographica Section D Biological Crystallography

A new method and the software program BEST for optimal planning of X-ray data collection from protein crystals using the rotation method are presented. From one or a few initial diffraction images, BEST estimates the statistical characteristics of the data set for different combinations of data-collection parameters a…

Protein Structure and DynamicsEnzyme Structure and FunctionX-ray Spectroscopy and Fluorescence Analysis

Nature of the First-Order Phase Transition in Fluid Phosphorus at High Temperature and Pressure

G. Monaco、S. Falconi、Wilson A. Crichton 等 4 位作者2003-06-27Physical Review Letters

An in situ x-ray diffraction experiment has been performed on phosphorus to characterize the liquid-liquid transition which occurs at high temperature and pressure. The transition line has been measured over an extended temperature range up to 2200 degrees C at 0.3 GPa. From the shape of this line, a thermodynamic cha…

Phase Equilibria and ThermodynamicsHigh-pressure geophysics and materialsMaterial Dynamics and Properties

Atomic oxygen species on silver: Photoelectron spectroscopy and x-ray absorption studies

V. I. Bukhtiyarov、Michael Hävecker、В. В. Каичев 等 6 位作者2003-06-27Physical review. B, Condensed matter

Two oxygen species, which are constituents of the active centers for ethylene epoxidation over silver, have been characterized by a number of physical methods sensitive to adsorbate electronic structure such as x-ray photoelectron, ultraviolet photoelectron, Auger, and x-ray-absorption near-edge structure spectroscopy…

Catalytic Processes in Materials ScienceCatalysis and Oxidation ReactionsElectron and X-Ray Spectroscopy Techniques

Effect of dye doping on the charge carrier balance in PPV light emitting diodes as measured by admittance spectroscopy

I. N. Hulea、R. F. J. van der Scheer、H. B. Brom 等 6 位作者2003-06-27arXiv

Dye doping is a promising way to increase the spectral purity of polymer light-emitting diodes (LEDs). Here we analyze the frequency and field dependence of the complex admittance of Al-Ba-PPV-PEDOT-ITO LEDs with and without dye. We compare the charge carrier mobilities of pristine and dye-doped double-carrier and hol…

Materials ScienceSoft Condensed Matter

Radiation pattern of a classical dipole in a photonic crystal: photon focusing

Dmitry N. Chigrin2003-06-27arXiv

The asymptotic analysis of the radiation pattern of a classical dipole in a photonic crystal possessing an incomplete photonic bandgap is presented. The far-field radiation pattern demonstrates a strong modification with respect to the dipole radiation pattern in vacuum. Radiated power is suppressed in the direction o…

Materials ScienceSoft Condensed Matter

Schrodinger Equation for Nanoscience

J. Marciak-Kozlowska、M. Kozlowski2003-06-27arXiv

The second order (in time) Schrodinger equation is proposed. The additional term (in comparison to Schrodinger equation) describes the interaction of particles with vacuum filled with virtual particle-antiparticle pairs (zitterbewegung). Key words: Schrodinger equation; Nanoscience; Zitterbewegung.

Materials Science

The One-Dimensional Boltzmann Equation for the Heat Transport Induced by Ultra-Short Laser Pulses

J. Marciak-Kozlowska、M. Kozlowski2003-06-27arXiv

In this paper the Boltzmann transport equation for thermal processes induced by ultra-short laser pulses is formulated and solved. For thermal process where the duration of the laser pulse (femtoseconds - attoseconds) is shorter than the relaxation time, the solution of Boltzmann equation differs from the solution of…

Materials Science

Experimental Demonstration for the Morphological Evolution of Crystals Grown in Gel Media

Yuya Oaki、Hiroaki Imai2003-06-27Crystal Growth & Design

The morphological evolution of the inorganic crystals (Ba(NO 3 ) 2, NH 4 Cl, H 3 BO 3, and K 2 Cr 2 O 7 ) was demonstrated in various kinds of organic gel media (agar, gelatin, pectin, and poly (vinyl alcohol)). As the gel density increased, the morphology grown in the gel matrix remarkably changed from polyhedral sin…

Bone Tissue Engineering MaterialsCalcium Carbonate Crystallization and InhibitionCrystallization and Solubility Studies