Three-dimensional random Voronoi tessellations: From cubic crystal lattices to Poisson point processes

We perturb the SC, BCC, and FCC crystal structures with a spatial Gaussian noise whose adimensional strength is controlled by the parameter a, and analyze the topological and metrical properties of the resulting Voronoi Tessellations (VT). The topological properties of the VT of the SC and FCC crystals are unstable with respect to the introduction of noise, because the corresponding polyhedra are geometrically degenerate, whereas the tessellation of the BCC crystal is topologically stable even against noise of small but finite intensity. For weak noise, the mean area of the perturbed BCC and FCC crystals VT increases quadratically with a. In the case of perturbed SCC crystals, there is an optimal amount of noise that minimizes the mean area of the cells. Already for a moderate noise (a>0.5), the properties of the three perturbed VT are indistinguishable, and for intense noise (a>2), results converge to the Poisson-VT limit. Notably, 2-parameter gamma distributions are an excellent model for the empirical of of all considered properties. The VT of the perturbed BCC and FCC structures are local maxima for the isoperimetric quotient, which measures the degre of sphericity of the cells, among space filling VT. In the BCC case, this suggests a weaker form of the recentluy disproved Kelvin conjecture. Due to the fluctuations of the shape of the cells, anomalous scalings with exponents >3/2 is observed between the area and the volumes of the cells, and, except for the FCC case, also for a->0. In the Poisson-VT limit, the exponent is about 1.67. As the number of faces is positively correlated with the sphericity of the cells, the anomalous scaling is heavily reduced when we perform powerlaw fits separately on cells with a specific number of faces.

Crystal structures of the copper and nickel complexes of RNase A: Metal-induced interprotein interactions and identification of a novel copper binding motif

We report the crystal structures of the copper and nickel complexes of RNase A. The overall topology of these two complexes is similar to that of other RNase A structures. However, there are significant differences in the mode of binding of copper and nickel. There are two copper ions per molecule of the protein, but there is only one nickel ion per molecule of the protein. Significant changes occur in the interprotein interactions as a result of differences in the coordinating groups at the common binding site around His-105. Consequently, the copper- and nickel-ion-bound dimers of RNase A act as nucleation sites for generating different crystal lattices for the two complexes. A second copper ion is present at an active site residue His-119 for which all the ligands are from one molecule of the protein. At this second site, His-119 adopts an inactive conformation (B) induced by the copper. We have identified a novel copper binding motif involving the α-amino group and the N-terminal residues.

Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly.

The human immunodeficiency virus type 1 (HIV-1) matrix protein forms a structural shell associated with the inner viral membrane and performs other essential functions throughout the viral life cycle. The crystal structure of the HIV-1 matrix protein, determined at 2.3 angstrom resolution, reveals that individual matrix molecules are composed of five major helices capped by a three-stranded mixed beta-sheet. Unexpectedly, the protein assembles into a trimer in three different crystal lattices, burying 1880 angstrom2 of accessible surface area at the trimer interfaces. Trimerization appears to create a large, bipartite membrane binding surface in which exposed basic residues could cooperate with the N-terminal myristoyl groups to anchor the protein on the acidic inner membrane of the virus.

Microstructure of an artificial grain boundary weak link in an YBa2Cu3O(7-δ) thin film grown on a (100)(110), [001]-tilt Y-ZrO2 bicrystal

The microstructure of an artificial grain boundary in an YBa2Cu3O7-δ (YBCO) thin film grown on a (100)(110), [001]-tilt yttria-stabilized-zirconia (YSZ) bicrystal substrate has been studied using transmission electron microscopy (TEM). The orientation relationship between the YBCO film and the YSZ substrate was [001]YBCO∥[001]YSZ and [110]YBCO∥[100]YSZ for each half of the bicrystal film. However, the exact boundary geometry of the bicrystal substrate was not transferred to the film. The substrate boundary was straight while the film boundary was wavy. In several cases there was bending of the lattice confined within a distance of a few basal-plane lattice spacings from the boundary plane and microfaceting. No intergranular secondary phase was observed but about 25% of the boundary was covered by c-axis-tilted YBCO grains and a-axis-oriented grains, both of which were typically adjacent to CuO grains or surrounded by a thin Cu-rich amorphous layer.

Microstructure and properties of artificial grain boundaries in epitaxial YBA2Cu3O7-δ thin films grown on [001] tilt YZrO2 bicrystals

The microstructure of artificial grain boundaries in YBa2Cu3O7-δ (YBCO) thin films grown on [001] tilt YZrO2 (YSZ) bicrystal substrates has been characterized using transmission electron microscopy and atomic force microscopy. Despite a relatively straight morphology of the substrate boundaries, the film boundaries were wavy. The waviness was a result of the combined effects of grooving at the substrate boundaries prior to the film deposition and an island-growth mechanism for YBCO on YSZ substrates. The dihedral angle of the groove walls varied with the misorientation angle and depended on the symmetry of the substrate boundary. The amplitudes of the film boundary waviness compared well with the widths of the grooves. In addition, the grooves induced local bending of the YBCO lattice planes and additional tilt components perpendicular to the c-axis close to the film boundaries. © 1995.

Continuous synthesis of high quality CdSe quantum dots in supercritical fluids

We demonstrate in here a powerful scalable technology to synthesize continuously high quality CdSe quantum dots (QDs) in supercritical hexane. Using a low cost, highly thermally stable Cd-precursor, cadmium deoxycholate, the continuous synthesis is performed in 400 mu m ID stainless steel capillaries resulting in CdSe QDs having sharp full-width-at-half-maxima (23 nm) and high photoluminescence quantum yields (45-55%). Transmission electron microscopy images show narrow particles sizes distribution (sigma <= 5%) with well-defined crystal lattices. Using two different synthesis temperatures (250 degrees C and 310 degrees C), it was possible to obtain zinc blende and wurtzite crystal structures of CdSe QDs, respectively. This synthetic approach allows achieving substantial production rates up to 200 mg of QDs per hour depending on the targeted size, and could be easily scaled to gram per hour.

Quantum information processing in the wall of cytoskeletal microtubules

Microtubules (MT) are composed of 13 protofilaments, each of which is a series of two-state tubulin dimers. In the MT wall, these dimers can be pictured as "lattice" sites similar to crystal lattices. Based on the pseudo-spin model, two different location states of the mobile electron in each dimer are proposed. Accordingly, the MT wall is described as an anisotropic two-dimensional (2D) pseudo-spin system considering a periodic triangular "lattice". Because three different "spin-spin" interactions in each cell exist periodically in the whole MT wall, the system may be shown to be an array of three types of two-pseudo-spin-state dimers. For the above-mentioned condition, the processing of quantum information is presented by using the scheme developed by Lloyd.

Caracterização de um sistema digital de aquisição de imagens radiográficas utilizando nêutrons térmicos e raios gama para a inspeção de componentes mecânicos.

Ensaio não destrutivo é uma ferramenta essencial quando um equipamento, dispositivo ou componente não pode ser submetido a procedimentos destrutivos ou invasivos devido a razões de segurança, alto custo ou outras restrições físicas ou logísticas. Dentro deste quadro radiografias por transmissão com raios gama e nêutrons térmicos são técnicas singulares para inspecionar um objeto e desvendar sua estrutura interna devido à capacidade de atravessar uma vasta gama de materiais utilizados na indústria. Grosso modo, raios gama são mais atenuados por materiais pesados enquanto nêutrons térmicos são mais atenuados por materiais mais leves, tornando-as ferramentas complementares. Este trabalho apresenta os resultados obtidos na inspeção de vários componentes mecânicos, através da radiografia por transmissão com nêutrons térmicos e raios gama. O fluxo de nêutrons térmicos de 4,46x105 n.cm-2.s-1 disponível no canal principal do reator de pesquisa Argonauta do Instituto de Engenharia Nuclear foi usado como fonte para as imagens radiográficas com nêutrons. Raios dekeV emitidos pelo 198Au, também produzido no reator, foram usados como fonte de radiação para radiografias . Imaging Plates, especificamente produzidos para operar com nêutrons térmicos ou com raios X, foram empregados como detectores e dispositivos de armazenamento e captação de imagens para cada uma dessas radiações. Esses dispositivos exibem varias vantagens quando comparados ao filme radiográfico convencional. Com efeito, além de maior sensibilidade e serem reutilizáveis não são necessários câmaras escuras e processamento químico para a revelação. Em vez disso, ele é lido por um feixe de laser que libera elétrons armadilhados na rede cristalina durante a exposição à radiação, fornecendo uma imagem final digital. O desempenho de ambos os sistemas de aquisição de imagens, assim constituído, foi avaliado com respeito à sensibilidade, resolução espacial, linearidade e range dinâmico, incluído uma comparação com sistemas radiográficos com nêutrons empregando filmes e folhas de gadolínio como conversor de nêutrons em partículas carregadas. Além desta caracterização, diversos equipamentos e componentes foram radiografados com ambos os sistemas visando-se avaliar suas capacidades de desvendar a estrutura interna desses objetos e detectar estruturas e estados anormais. Dentro desta abordagem, uma neutrongrafia detectou a presença de material cerâmico remanescente empregado como molde no processo de fabricação nos canais de refrigeração de uma aleta do estator de uma turbina tipo turbo-fan, que deveria estar livre desse material. O reostato danificado de um sensor de pressão automotivo, foi identificado por neutrongrafia, embora nesse caso a radiografia também conseguiu realizar essa tarefa com melhor resolução, corroborando assim as curvas de resolução espacial obtidas na caracterização dos dois sistemas. A homogeneidade da distribuição do material encapsulado em uma gaxeta explosiva de chumbo utilizada na indústria aeroespacial foi igualmente verificada por neutrongrafia porque esse metal é relativamente transparente para nêutrons, mas suficientemente opaco para o explosivo rico em hidrogênio. Diversos outros instrumentos e componentes tais como variômetro, altímetro, bússola aeronáutica, injetor automotivo de combustível, foto-camera, disco rígido de computador, motor de passo, conectores eletrônicos e projéteis foram radiografados com ambos os sistemas visando avaliar suas habilidades em desvendar diferentes peculiaridades em função do agente interrogador.

Effect of the technology of implanting nitrogen into buried oxide on the radiation hardness of the top gate oxide for partially depleted SOIPMOSFET

The effect of implanting nitrogen into buried oxide on the top gate oxide hardness against total irradiation does has been investigated with three nitrogen implantation doses (8 x 10(15), 2 x 10(16) and 1 x 10(17) cm(-2)) for partially depleted SOI PMOSFET. The experimental results reveal the trend of negative shift of the threshold voltages of the studied transistors with the increase of nitrogen implantation dose before irradiation. After the irradiation with a total dose of 5 x 10(5) rad(Si) under a positive gate voltage of 2V, the threshold voltage shift of the transistors corresponding to the nitrogen implantation dose 8 x 10(15) cm(-2) is smaller than that of the transistors without implantation. However, when the implantation dose reaches 2 x 10(16) and 1 x 10(17) cm(-2), for the majority of the tested transistors, their top gate oxide was badly damaged due to irradiation. In addition, the radiation also causes damage to the body-drain junctions of the transistors with the gate oxide damaged. All the results can be interpreted by tracing back to the nitrogen implantation damage to the crystal lattices in the top silicon.

Interaction of scopolamine and cholesterol with sphingomyelin bilayers by FT-Raman spectroscopy

The interaction of scopolamine and cholesterol with sphingomyelin bilayers has been investigated by FT-Raman spectroscopy in head-group region (600-1000 cm(-1)), the C-C stretching (1000-1200 cm(-1)), CH2 deformation (1400-1500 cm(-1)) and the C-H stretching (2800-3000 cm(-1)) mode regions. The results indicate that scopolamine and cholesterol do not change the conformation of O-C-C-N+ backbone in the choline group of sphingomyelin bilayers, the polar headgroup is still extending parallel to the bilayer surface and O-C-C-N+ group is still in its gauche conformer. Scopolamine and cholesterol lower the order of the interface, the interchain, CH2 crystal lattices and the lateral chain-chain packing, and increase their fluidity.

Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. They are endowed with important physiological functions but until now only few of them have been studied. Here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. Sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxification, in sulfide-dependent respiration and photosynthesis, and in heavy metal tolerance. It may also play a crucial role in mammals, including humans, because sulfide acts as a neurotransmitter in these organisms. We isolated and purified sulfide:quinone oxidoreductase from the native membranes of the hyperthermophilic bacterium Aquifex aeolicus. We studied the pure and solubilized enzyme by denaturing and non-denaturing polyacrylamide electrophoresis, size-exclusion chromatography, cross-linking, analytical ultracentrifugation, visible and ultraviolet spectroscopy, mass spectrometry and electron microscopy. Additionally, we report the characterization of its enzymatic activity before and after crystallization. Finally, we discuss the crystallization of sulfide:quinone oxidoreductase in respect to its membrane topology and we propose a classification of monotopic membrane protein crystal lattices. Our data support and complement an earlier description of the three-dimensional structure of A. aeolicus sulfide:quinone oxidoreductase (M. Marcia, U. Ermler, G. Peng, H. Michel, Proc Natl Acad Sci USA, 106 (2009) 9625-9630) and may serve as a reference for further studies on monotopic membrane proteins. (C) 2010 Elsevier B.V. All rights reserved.

Anharmonic Helmholtz free energy to O(lambdaâ ´) in the non- leading term approximation /|nby Leslie Wilk. -- 260 St. Catharines, Ont. : [s. n.],

Expressions for the anharmonic Helmholtz free energy contributions up to o( f ) ,valid for all temperatures, have been obtained using perturbation theory for a c r ystal in which every atom is on a site of inversion symmetry. Numerical calculations have been carried out in the high temperature limit and in the non-leading term approximation for a monatomic facecentred cubic crystal with nearest neighbour c entralforce interactions. The numbers obtained were seen to vary by a s much as 47% from thos e obtai.ned in the leading term approximati.on,indicating that the latter approximati on is not in general very good. The convergence to oct) of the perturbation series in the high temperature limit appears satisfactory.

A treatment of atomic mean square displacement in higher order perturbation theory

A general derivation of the anharmonic coefficients for a periodic lattice invoking the special case of the central force interaction is presented. All of the contributions to mean square displacement (MSD) to order 14 perturbation theory are enumerated. A direct correspondance is found between the high temperature limit MSD and high temperature limit free energy contributions up to and including 0(14). This correspondance follows from the detailed derivation of some of the contributions to MSD. Numerical results are obtained for all the MSD contributions to 0(14) using the Lennard-Jones potential for the lattice constants and temperatures for which the Monte Carlo results were calculated by Heiser, Shukla and Cowley. The Peierls approximation is also employed in order to simplify the numerical evaluation of the MSD contributions. The numerical results indicate the convergence of the perturbation expansion up to 75% of the melting temperature of the solid (TM) for the exact calculation; however, a better agreement with the Monte Carlo results is not obtained when the total of all 14 contributions is added to the 12 perturbation theory results. Using Peierls approximation the expansion converges up to 45% of TM• The MSD contributions arising in the Green's function method of Shukla and Hubschle are derived and enumerated up to and including 0(18). The total MSD from these selected contributions is in excellent agreement with their results at all temperatures. Theoretical values of the recoilless fraction for krypton are calculated from the MSD contributions for both the Lennard-Jones and Aziz potentials. The agreement with experimental values is quite good.

On the equation of state and atomic mean square displacement of crystals

We have presented a Green's function method for the calculation of the atomic mean square displacement (MSD) for an anharmonic Hamil toni an . This method effectively sums a whole class of anharmonic contributions to MSD in the perturbation expansion in the high temperature limit. Using this formalism we have calculated the MSD for a nearest neighbour fcc Lennard Jones solid. The results show an improvement over the lowest order perturbation theory results, the difference with Monte Carlo calculations at temperatures close to melting is reduced from 11% to 3%. We also calculated the MSD for the Alkali metals Nat K/ Cs where a sixth neighbour interaction potential derived from the pseudopotential theory was employed in the calculations. The MSD by this method increases by 2.5% to 3.5% over the respective perturbation theory results. The MSD was calculated for Aluminum where different pseudopotential functions and a phenomenological Morse potential were used. The results show that the pseudopotentials provide better agreement with experimental data than the Morse potential. An excellent agreement with experiment over the whole temperature range is achieved with the Harrison modified point-ion pseudopotential with Hubbard-Sham screening function. We have calculated the thermodynamic properties of solid Kr by minimizing the total energy consisting of static and vibrational components, employing different schemes: The quasiharmonic theory (QH), ).2 and).4 perturbation theory, all terms up to 0 ().4) of the improved self consistent phonon theory (ISC), the ring diagrams up to o ().4) (RING), the iteration scheme (ITER) derived from the Greens's function method and a scheme consisting of ITER plus the remaining contributions of 0 ().4) which are not included in ITER which we call E(FULL). We have calculated the lattice constant, the volume expansion, the isothermal and adiabatic bulk modulus, the specific heat at constant volume and at constant pressure, and the Gruneisen parameter from two different potential functions: Lennard-Jones and Aziz. The Aziz potential gives generally a better agreement with experimental data than the LJ potential for the QH, ).2, ).4 and E(FULL) schemes. When only a partial sum of the).4 diagrams is used in the calculations (e.g. RING and ISC) the LJ results are in better agreement with experiment. The iteration scheme brings a definitive improvement over the).2 PT for both potentials.

Thermodynamic properties and Debye-Waller factor of fee materials

We have calculated the equation of state and the various thermodynamic properties of monatomic fcc crystals by minimizing the Helmholtz free energy derived in the high temperature limit for the quasiharmonic theory, QH, and the lowest-order (cubic and quartic), 'A2, anharmonic terms of the perturbation theory, PT. The total energy in each case is obtained by adding the static energy. The calculation of the thermal properties was carried out for a nearest-neighbour central-force model of the fcc lattice by means of the appropriate thermodynamic relations. We have calculated the lattice constant, the thermal expansion, the coefficient of volume expansion, the specific heat at constant volume and at constant pressure, the isothermal and adiabatic bulk moduli, and the Griineisen parameter, for the rare-gas solids Kr and Xe, and gold. Morse potential and modified Morse potential were each used to represent the atomic interaction for the three fcc materials. For most of the calculated thermodynamic properties from the QH theory, the results for Kr and Xe with the modified Morse potential show an improvement over the results for the Morse potential when compared with the experimental data. However, the results of the 'A 2 equation of state with the modified Morse potential are in good agreement with experiment only in the case of the specific heat at constant volume and at constant pressure. For Au we have calculated the lattice contribution from the QH and 'A 2 PT and the electronic contribution to the thermal properties. The electronic contribution was taken into account by using the free electron model. The results of the thermodynamic properties calculated with the modified Morse potential were similar to those obtained with the Morse potential. U sing the minimized equation of state we also calculated the Mossbauer recoilless fraction for Kr and Xe and the Debye-Waller factor (DWF) for Pb, AI, eu, Ag, and Au. The Mossbauer recoilless fraction was obtained for the above two potentials and Lennard-Jones potential. The L-J potential gives the best agreement with experiment for Kr. No experimental data exists for Xe. At low temperature the calculated DWF results for Pb, AI, and eu show a good agreement with experimental values, but at high temperature the experimental DWF results increase very rapidly. For Ag the computed values were below the expected results at all temperatures. The DWF results of the modified Morse potential for Pb, AI, eu and Ag were slightly better than those of the Morse potential. In the case of Au the calculated values were in poor agreement with experimental results. We have calculated the quasiharmonic phonon dispersion curves for Kr, Xe, eu, Ag, and Au. The calculated and experimental results of the frequencies agree quite well for all the materials except for Au where the longitudinal modes show serious discrepancies with the experimental results. In addition, the two lowest-order anharmonic contributions to the phonon frequency were derived using the Green's function method. The A 2 phonon dispersion curves have been calculated only for eu, and the results were similar to those of the QH dispersion curves. Finally, an expression for the Griineisen parameter "( has been derived from the anharmonic frequencies, and calculated for these materials. The "( results are comparable with those obtained from the thermodynamic definition.