bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma Protein Adsorption and Platelet Adhesion on Poly[Bis(Trifluoroethoxy)Phosphazene]
Authors: Welle Alexander , Grunze Michael , Tur Dsidra 
Published: April 2011

AbstractPoly[bis(trifluoroethoxy)phosphazene] (PTFEP) with a high purity and high molar mass is a biocompatible material [1] used as bulk material in medical implants. We developed a process to coat surfaces with PTFEP films and performed ELISA experiments designed to understand their blood compatibility. We observed that PTFEP adsorbs preferentially albumin from plasma, and only small amounts of coagulation or inflammation stimulating proteins. In general, there is a good correlation between increasing content of albumin in the adsorbed protein film and reduced platelet adhesion. Another important prerequisite of blood compatibility is the stabilization of the native state of adsorbed proteins, since denaturated proteins stimulate platelet adhesion. The elutability of adsorbed proteins by sodiumdodecylsulfate solution was used to quantify the amount of irreversible attached and presumably denaturated proteins. PTFEP showed a low amount of irreversibly adsorbed proteins of the coagulation cascade. Circular dichroism measurements of adsorbed fibrinogen and albumin showed only weak distortions of the secondary structure of these proteins on the surface of PTFEP.We conclude that PTFEP has a unique blood compatibility because of the favorable composition and the stabilization of the protein layer against denaturation.
The Influence of Intracellular Transport Developmenttransport on Axonal Development
Authors: Hentschel H.G.E. , Fine A. 
Published: April 2011

AbstractWe describe how axonal differentiation during neuronal growth is dependent on intracellular transport. The interaction of diffusion and active transport of a morphogen whose concentration at the neurite tips influences the growth rate can lead to an instability involving winner-take-all growth, forming a single, quickly growing neurite (the axon) and inhibiting the growth of the other neurites. We discuss the dynamics of this process and its dependence on cell parameters.
Movement of Vesicles in Eucariotic Cells. Role of Intravesicle Protons as a Fuel and Modulation of Their Concentration by Drugs or Metabolic Changes.
Authors: Pescarmona G. P. , Morra E. , Aldieri E. , Ghigo D. , Bosia A. 
Published: April 2011

AbstractImport (endocytosis) and export (secretion) of molecules from the cells is mediated by vesicles (lysosomes, endosomes) sliding along microtubules or actin filaments. These vesicles share a common feature: an internal pH of about 5, with an inner protons concentration 1000 fold higher than in the surrounding cytoplasm. As the proton gradient in mitochondria is able to drive ATP synthesis we can expect a similar role (energy supplier) for protons in all acidic vesicles. To experimentally test the vesicles' transport we have loaded them with a fluorescent dye (chloroquine) and then measured its efflux over 5 hours. This efflux was reduced by all treatments lowering the actual concentration of protons in the vesicles, independently of the properties. Treatments included lowering intracellular NADH, inhibitors of ATP-dependent proton translocase and/or the Na+/H+antiport, drugs that accumulate into lysosomes, buffering its acidity (chloroquine, doxorubicin). These results support the idea of a role of a proton gradient as a fuel for protein motors.
Viscoelasticity and its Microscopic Characterization in Semiflexible Biopolymer Solutions
Authors: Mackintosh F. C. , Gittes F. , Schnurr B. , Olmsted P. D. , Schmidt C. F. 
Published: April 2011

AbstractPlant and animal cells contain a complex polymeric network known as the cytoskeleton. A principal component of this is the actin cortex, a gel-like network of F-actin protein filaments. Recently, solutions of reconstituted F-actin have provided in vitro models of the actin cortex, as well as excellent model systems in which to study semiflexible polymers. We describe models of viscoelasticity in semifexible polymers, and report theoretical and experimental results for thermal fluctuations of embedded particles, which act as local viscoelastic probes of soft materials such as biopolymer solutions. Specifically, we report high-frequency scaling behavior of the shear modulus, as the 3/4 power of frequency, in contrast with the behavior of flexible polymer systems.
Electrostatically Induced Bundle Formation of Rodlike Polyelectrolytes: Comparison of Predictions from Monte Carlo Simulations with Experiments on Fd And M13 Virus Particles.
Authors: Nordenskiöld Lars , Lyubartsev Alexander , Tang Jay X. , Janmey Paul A. 
Published: April 2011

AbstractThis work compares the electrostatic bundling of two Inovirus particles: fd and M13, that are structurally identical except that the effective axial charge density of M 13 is approximately 30% lower than that of fd. The electrostatic force (or osmotic pressure) between these ordered biopolyelectrolytes, as a function of inter-rod separation, has been calculated with Monte Carlo simulations. Comparison is made with experiments on the bundling of fd and M 13 caused by divalent ions, as detected by light scattering. In the theoretical calculations, the bundling results from electrostatic attraction between the neighbouring polyelectrolytes, caused by the correlated interactions between the ion clouds. The importance of this effect (i. e. capacity to induce bundling) is governed by surface charge density of the polyelectrolyte, amount of multivalent ion present, charge and size of the hydrated multivalent ion. These predictions are in very good agreement with the presented experimental results on bundling of fd and M 13 caused by Ca2+ and Mg2+
Comparison of Experimental with Theoretical Melting of the Yeast Genome and Individual Yeast Chromosome Denaturation Mapping Using the Program Meltsim
Authors: Bizzaro J. W. , Marx Kenneth A. , Blake R. D. 
Published: April 2011

AbstractThe yeast S. cereviseae represents the first eukaryotic organism whose genome has been entirely sequenced as a result of the Human Genome Project(1). In this report we demonstrate the good agreement between an experimental high resolution melting curve of total nuclear S. cereviseae DNA and the theoretical melting calculated for the complete yeast DNA genome (12,067,277 bp: Saccharomyces Genome Database) by the statistical thermodynamics program MELTSIM, parameterized for long DNA sequences(2,3). The experimental and theoretical melting curves are both fairly symmetrical and possess nearly identical Tmvalues. Calculated melting of coding and flanking DNA regions indicates that flanking DNAs are more (A+T)-rich than coding sequences and account for the earliest melting DNA. Calculated melting curves of the 16 individual yeast chromosomes are very similar and with few exceptions exhibit symmetric melting curves. MELTSIM was also used to calculate a theoretical denaturation map of Chromosome III DNA. The agreement between MELTSIM calculated and experimental melting data demonstrates our ability to accurately simulate long DNA sequence melting in complex eukaryotic genomes, whose sequences are becoming increasingly available for study in public databases. This has important consequences for the understanding of sequence dependent energetic properties of DNA in their biological sequence context and also for their potential use in biomaterials applications.
Influence of RTP on Vacancy Concentrations
Authors: JACOB M. , Pichler P. , Wohs M. , Ryssel H. , Falster R. 
Published: April 2011

ABSTRACTThe increase and reduction of the vacancy concentration by rapid thermal processing (RTP) was investigated by platinum diffusion. Direct experimental evidence is presented for the consumption of vacancies during oxidation and for the introduction of vacancies during processing in ammonia and nitrogen. These results confirm the indirect conclusions from dopant diffusion and from the growth and shrinkage of extended defects. In addition, it was possible to establish an upper limit for the equilibrium concentration of vacancies at 1180 °C which is lower than previously reported values.
A New Practical Approach to Implement a Transient Enhanced Diffusion Model into an Fem-Based 2-D Process Simulator
Authors: Sugiyasu Noriyuki , Suzuki Kaina , Kojima Syuichi , Ohyama Yasushi 
Published: April 2011

ABSTRACTWe have proposed a coupled and de-coupled combined method to solve partial differential equations for a transient enhanced diffusion model. In the case of a boron diffusion process, the sum of concentrations of interstitial Si and of impurity-interstitial pair, the sum of concentrations of vacancy and of impurity-vacancy pair and each chemical impurity concentration are kept constant. The charge neutrality law is also applied. This procedure has realized a robust solution system which is implemented into our in-house FEM-based 2-D process simulator, and transient enhanced diffusion simulations for a sub-quarter micron nMOSFET have been demonstrated.
Use of Rigorous Three-Dimensional Electromagnetic Simulation to Evaluate the Effectiveness of Optical Proximity Correction for Nonplanar Lithography
Authors: Yeung M. S. , Barouch E. 
Published: April 2011

ABSTRACTA rigorous three-dimensional lithography simulator based on a recently developed single integral equation formulation for electromagnetic scattering is used in a simulation study of the effectiveness of using pre-distortions of mask patterns to compensate for linewidth variations in the resist patterns on nonplanar substrate topography. An efficient simulation methodology is used to reduce the number of required scattering calculations. Simulation results for different mask shapes and defocus conditions are presented.
Finite Element Analysis of a MOCVD Reactor Having a Close-Spaced Injector
Authors: Sun Yang Ren , Weyburne David W. , Paduano Qing S. 
Published: April 2011

ABSTRACTA 2-D axisymmetric finite element analysis has been performed on a vertical MOCVD reactor having a close-spaced water-cooled injector for which the gas is injected only 1.6 cm above the rotating disk. The analysis showed that the system has a much higher flow stability, in terms of suppression of unwanted thermally driven convection, than conventional reactors. In addition, the flow study has identified two kinds of flow recirculation, a purely thermally driven convection and a geometry assisted one. The former is initiated with gas flowing upward near the center of the disk circulating clockwise, the latter one is located near the chamber wall circulating counterclockwise. This result is important in interpreting experiments.
The Effect of a Thin Sample on the Extended Defect Evolution in Si+ Implanted Si
Authors: Li Jing-Hong , Jones Kevin S. 
Published: April 2011

ABSTRACTThe annealing kinetics of implant damage in Si+ implanted Si has been investigated using in-situ and ex-situ annealing of transmission electron microscopy (TEM) samples prepared prior to annealing. The defect evolution at 800°C was studied for a Si wafer implanted with Si+ at 100keV to a dose of 2×1014 cm-2. This implant was above the sub-threshold loop formation threshold allowing one to study simultaneously the {311} defect dissolution and dislocation loop nucleation and growth. In order to study the effect on the defect evolution of using a thin sample for an in-situ annealing experiment, a pair of samples, one thick and one thinned into a TEM sample, were annealed in a furnace simultaneously. It was found that the presence of a second surface 2000Å below the implant damage did not affect the extended defect evolution. For the in-situ annealing study it was found that the {311} dissolution process and sub-threshold dislocation loop formation process was not affected by the TEM electron beam at 160kV as long as an 800°C furnace pre-anneal was done prior to in-situ annealing. The dissolution rate of the {311} defects was used to confirm the TEM holder furnace temperature. The results of both the in-situ the {311} defects is released during the 311 dissolution process and 30% comes to reside in dislocation loops. Thus, the loops appear to contain a significant fraction of the total interstitial concentration introduced by the implant.
Physical Model and Numerical Results of Dissociation Kinetics of Hydrogen-Passivated Si/SiO2 Interface Defects
Authors: Gadiyak G. V. 
Published: April 2011

ABSTRACTA simple model of thermal dissociation and recovery of hydrogen-passivated silicon defects at the Si/SiO2 interface, such as Pb - centers, during vacuum thermal annealing has been suggested. This model considers reactions of hydrogen with defect states at the Si/SiO2 interface and diffusion of liberated atomic and molecular hydrogen in a silicon dioxide film. An excellent agreement was obtained between the experimental and numerical simulation results for oxides with different thickness (200–1024 Å), grown both (111) and (100) samples and annealed in the temperature range (480–700° C).
Nucleation and Growth of Voids in Silicon
Authors: Plekhanov P. S. , Gösele U. M. , Tan T. Y. 
Published: April 2011

ABSTRACTNucleation of voids and vacancy-type dislocation loops in Si under vacancy supersaturation conditions has been considered. Based upon nucleation barrier calculations, it has been found that voids can be nucleated, but not dislocation loops. The homogeneous nucleation rate of voids has been calculated for different temperatures by assuming different enthalpy values of Si vacancy formation. The process of void growth due to precipitation of vacancies has been numerically simulated. Comparing results of the nucleation and the growth modeling and taking into account the competition between the two processes, the limited time available, and the crystal cooling rate after growth, it has been shown that homogeneous nucleation of voids to experimentally observed densities and void growth to observed sizes is possible if enthalpy of Si vacancy formation is within the range of 2.9 to 3.6 eV with the nucleation temperature in the range of 980–1080 °C.
Modeling of Atom Diffusion and Segregation in Semiconductor Heterostructures
Authors: Bracht Hartmut , Walukiewicz Wladek , Haller Eugene E. 
Published: April 2011

ABSTRACTWe propose a new approach for modeling of impurity diffusion at semiconductor heterointerfaces. The approach is based on the notion of a common energy reference for highly localized defects. It is shown that in the kick-out process, the segregation of group II acceptors is controlled by the valence band offsets among different constituent layers of the heterostructure. Extensive numerical modeling of the diffusion provides an explanation for the experimentally observed strong segregation of Zn and Be acceptors in the lattice matched InP/InGaAs, InP/InGaAsP and GaAs/AlGaAs heterostructures.
Simulation of Under- and Supersaturation of Gallium Vacancies in Gallium Arsenide During Silicon in- and Outdiffusion
Authors: Chen C.-H. , Gösele U. , Tan T. Y. 
Published: April 2011

ABSTRACTThe diffusivity of Si in GaAs shows a dependence on the cubic power of its concentration or the concentration of electrons n under both in- and outdiffusion conditions. Hence, the diffusion of Si in GaAs is consistent with the Fermi-level effect model invoking the triply-negatively-charged Ga vacancies, , as the point defect species responsible for diffusion to occur on the Ga sublattice under n-doping condition. However, the Si diffusivity values of the indiffusion cases is several orders of magnitude smaller than those of the outdiffusion cases at the same Si concentrations. This means that the two apparent Si diffusivity values under intrinsic conditions will contain also the same discrepancy, which has been previously assessed to be due to a undersaturation in indiffusion cases and a supersaturation in outdiffusion cases. In this study we have calculated the under- and supersaturation values using the known Si diffusivities. We found that the GaAs surface states play a key role in the development of the under- and supersaturations.
Interactions of Point and Extended Defects in Structural Intermetallics: Real-Space Lmto-Recursion Calculations
Authors: Kontsevoi O. Yu. , Mryasov O. N. , Gornostyrev Yu. N. , Freeman A. J. 
Published: April 2011

ABSTRACTA real-space TB-LMTO-recursion method for electronic structure calculations is applied to the study of interacting extended and point defects in NiAl. Results of calculations for the pure intermetallic and with ternary additions (within a supercell model) show good agreement with band structure results. Further, electronic structure and total energy calculations of point (single impurity, M=Ti, V, Cr, Mn, Fe and Co) and planar defects such as anti-phase boundaries (APB) were carried out and the interaction between them was determined. We found that for the ½〈111〉{110} APB in NiAl, ternary additions occupy exclusively the 3d-metal sublattice and decrease the APB energy (except for Co). Finally, we employ TB-LMTO-REC to study the electronic structure of the most complex extended defect, a dislocation. We demonstrate for the 〈100〉{010} edge dislocation in NiAl that: (i) quasi-localized states may exist as a result of specific lattice distortions in the dislocation core with a type of “broken” bonds; (ii) the electronic structure changes appreciably in the process of dislocation motion; (iii) van-Hove singularities present in the ideal crystal may be shifted to E;r as a result of the dipolar character of the deformations in the dislocation core.
Let there be Light in Tight Binding
Authors: Vogl P. , Graf M. , Görling A. 
Published: April 2011

ABSTRACTEmpirical tight-binding theory is generalized to incorporate time-dependent electromagnetic fields in a systematic and gauge-invariant manner that does not introduce any extra adjustable parameters. It is shown that this approach successfully predicts a wide range of solid state properties that have not been accessible within the tight binding method so far. We present applications such as optical constants, luminescence in heterostructures, properties in ultra-high magnetic fields and lattice dynamics in polar materials.
Ordering effects in Disordered Metallic Alloys
Authors: Pasturel A. 
Published: April 2011

ABSTRACTThis paper reviews recent progress in the theory of the atomic and electronic structure of disordered metallic alloys containing transition metals (TM). Realistic structural models are obtained using molecular dynamics simulations based on pair interatomic forces derived from a tight-binding-bond method. This approach describes quantitatively compositional trends in chemical and topological short-range order in agreement with diffraction experiments.
How Far to Use Tight-Binding Potentials for Bimetallic Surface Modelling?
Authors: Tréglia G. , Legrand B. 
Published: April 2011

ABSTRACTModelling in a realistic way both equilibrium and dynamical processes on bimetallic surfaces requires the availability of interatomic potentials sufficiently simple (i.e. analytical) although derived from the electronic structure. This is possible in the framework of Tight-Binding formalism. We present here a review of the applications of such potentials, together with some reflexions about their limitations.
Semi-Empirical Tight-Binding Parameters for Total Energy Calculation in Zinc
Authors: Bere A. , Hairie A. , Nouet G. , Paumier E. 
Published: April 2011

ABSTRACTThe semi-empirical tight-binding method is used to build up an interatomic potential in zinc. Using relaxed structures, the parameters are fitted to the lattice parameters, the elastic constants and the vacancy formation energy. The total energy calculation predicts the stability of the h.c.p. structure. The potential is used to calculate the energy of some extended defects: the basal stacking fault and two twin boundaries.
Effects of Grain-Boundaries in Superconducting Materials
Authors: Hogan-O'Neill J. J. , Martin A. M. , Annett James F. 
Published: April 2011

ABSTRACTWe examine the effects of grain-boundaries on the order-parameter and critical-currents in superconductors. We use a geometrical model of the lattice structure of grain-boundaries. We solve the Bogoliubov-de Gennes equation using the Recursion Method to obtain the self-consistent BCS gap function Δ and the local density of states N(E) near the boundary. Imposing a phase difference across the boundary we calculate the supercurrent and hence obtain the critical-current, Ic, of the junction.
A Comparison of Linear Scaling Tight Binding Methods
Authors: Horsfield A. P. , Bowler D. R. , Goringe C. M. , Pettifor D. G. , Aoki M. 
Published: April 2011

ABSTRACTFour linear scaling tight binding methods (the density matrix method, bond order potentials, the global density of states method, and the Fermi operator expansion) are described and compared to show relative computational efficiency for a given accuracy. The density matrix method proves to be most efficient for systems with narrow features in their energy gaps, while recursion based moments methods prove to be most efficient for metallic systems.
Total Energy Differences Between Silicon Carbide Polytypes and their Implications for Crystal Growth
Authors: Llmpijumnong Sukit , Lambrecht Walter R. L. 
Published: April 2011

ABSTRACTThe energy differences between various SiC polytypes are calculated using the full-potential linear muffin-tin orbital method and analyzed in terms of the anisotropie next nearest neighbor interaction (ANNNI) model. The fact that J1 + 2J2 < 0 with J1 > 0 implies that twin boundaries in otherwise cubic material are favorable unless twins occur as nearest neighbor layers. Contrary to some other recent calculations we find J1 > |J2|. We discuss the consequences of this for stabilization of cubic SiC in epitaxial growth, including considerations of the island size effects.
Copper Corrosion Mechanisms of Polysulfides
Authors: Chaka Anne M. , Harris John , Li X. P. 
Published: April 2011

ABSTRACTCorrosive behavior of commercial organopolysulfides of the type R-(S)n-R is known to increase dramatically towards copper-based alloys when n ≥ 4, whereas di- and trisulfides are essentially inert. Three possible reasons for this behavior are examined using local and nonlocal density-functional theory as well as post-Hartree-Fock theory at the MP2 level. The hypotheses are: the shorter chains are protected from the surface by steric hindrance of the terminal organic groups, longer polysulfides can chelate copper atoms and remove them from the surface, and S-S bonds become weaker and more reactive as the polysulfide chains become longer. We find the predominant reason for the increase in corrosive behavior to be a dramatic decrease in S-S bond dissociation energy when n ≥ 4 due to stabilization of the unpaired electron via delocalization in RSS• thiyl radicals. The thiyl radicals are thus the species which is capable of attacking and corroding the copper surface. Chelation is eliminated as a possible mechanism, and steric protection and oil solubility afforded by the organic terminal groups are found to play a minor role.