bluuebunny/crossref_metadata_2025 huggingface dataset:
Topology of the substrate-binding site of a Lys49-phospholipase A2 influences Ca2+-independent membrane-damaging activity
Authors: SÁ Juliana Martha , CHIOATO Lucimara , FERREIRA Tatiana Lopes , de OLIVEIRA Arthur H. C. , RULLER Roberto , ROSA José César , GREENE Lewis J. , WARD Richard J.
Published: August 2004

BthTx-I (bothropstoxin-I) is a myotoxic Lys49-PLA2 (phospholipase A2 with Lys49) isolated from Bothrops jararacussu venom, which damages liposome membranes by a Ca2+-independent mechanism. The highly conserved Phe5/Ala102/Phe106 motif in the hydrophobic substrate-binding site of the Asp49-PLA2s is substituted by Leu5/Val102/Leu106 in the Lys49-PLA2s. The Leu5/Val102/Leu106 triad in BthTx-I was sequentially mutated via all single- and double-mutant combinations to the Phe5/Ala102/Phe106 mutant. All mutants were expressed as inclusion bodies in Escherichia coli, and the thermal stability (Tm), together with the myotoxic and Ca2+-independent membrane-damaging activities of the recombinant proteins, were evaluated. The far-UV CD profiles of the native, wild-type recombinant and the L106F (Leu106→Phe) and L5F/F102A/L106F mutant proteins were identical. The L5F, V102A, L5F/V102A and V102A/L106F mutants showed distorted far-UV CD profiles; however, only the L5F and L5F/V102A mutants showed significant decreases in Tm. Alterations in the far-UV CD spectra correlated with decreased myotoxicity and protein-induced release of a liposome-entrapped marker. However, the V102A/L106F and L5F/V102A/L106F mutants, which presented high myotoxic activities, showed significantly reduced membrane-damaging activity. This demonstrates that the topology of the substrate-binding region of BthTx-I has a direct effect on the Ca2+-independent membrane damage, and implies that substrate binding retains an important role in this process.
Cell detachment and apoptosis induction of immortalized human prostate epithelial cells are associated with early accumulation of a 45 kDa nuclear isoform of clusterin
Authors: CACCAMO Alessandro E. , SCALTRITI Maurizio , CAPORALI Andrea , D'ARCA Domenico , SCORCIONI Francesca , ASTANCOLLE Serenella , MANGIOLA Massimo , BETTUZZI Saverio
Published: August 2004

Clusterin, ubiquitously distributed in mammalians, was cloned and identified as the most potently induced gene during rat prostate involution following androgen deprivation. Also found to be involved in many other patho-physiological processes, its biological significance is still controversial, particularly with regard to apoptosis. We previously showed that transient over-expression of clusterin blocked cell cycle progression of simian-virus-40-immortalized human prostate epithelial cell lines PNT1A and PNT2. We show in the present study that the accumulation of an intracellular 45 kDa clusterin isoform was an early event closely associated with death of PNT1A cells caused by cell detachment followed by apoptosis induction (anoikis). Cell morphological changes, decreased proliferation rate and cell cycle arrest at G0/G1–S-phase checkpoint were all strictly associated with the production and early translocation to the nucleus of a 45 kDa clusterin isoform. Later, nuclear clusterin was found accumulated in detached cells and apoptotic bodies. These results suggest that a 45 kDa isoform of clusterin, when targeted to the nucleus, can decrease cell proliferation and promotes cell-detachment-induced apoptosis, suggesting a possible major role for clusterin as an anti-proliferative gene in human prostate epithelial cells.
Analysis of two CBP (cAMP-response-element-binding protein-binding protein) interacting sites in GRIP1 (glucocorticoid-receptor-interacting protein), and their importance for the function of GRIP1
Authors: HUANG Shih-Ming , CHENG Yi-Shan
Published: August 2004

The p160 co-activators, SRC1 (steroid receptor co-activator 1), GRIP1 (glucocorticoid-receptor-interacting protein 1) and ACTR (activator for thyroid hormone and retinoid receptors), have two ADs (activation domains), AD1 and AD2. AD1 is a binding site for the related co-activators, CBP (cAMP-response-element-binding protein-binding protein) and p300, whereas AD2 binds to another co-activator, co-activator-associated arginine methyltransferase 1 (CARM1). Here, we identified two CBP-interacting sites [amino acids 1075–1083 (site I) and 1095–1106 (site II)] in a so-called CBP-dependent transactivation domain (AD1; amino acids 1057–1109) of GRIP1. Site I was the major site for CBP-dependent AD1 transactivation activity of GRIP1 whereas, following the deletion of site II, full or partial transactivation activity was retained without the recruitment of CBP in yeast, HeLa, human embryonic kidney 293 and CV-1 cells. GRIP1 (with a deletion of site II) expressed stronger co-activator activity than that of wild-type GRIP1 in the TR (thyroid receptor) and the AR (androgen receptor), but not the ER (oestrogen receptor), systems in HeLa cells. We also demonstrated that these CBP-binding sites of GRIP1 are not the only functional domains for its AD1 function in TR, AR and ER systems in HeLa cells by the exogenous overexpression of one E1A mutant, which led to a lack of CBP-binding ability. Our results suggest that these two CBP-interacting sites in the GRIP AD1 domain not only determine its AD1 activity, but are also involved in its co-activator functions in some nuclear receptors.
The tyrosine kinase FRK/RAK participates in cytokine-induced islet cell cytotoxicity
Authors: WELSH Michael , WELSH Charlotte , EKMAN Maria , DIXELIUS Johan , HÄGERKVIST Robert , ANNERÉN Cecilia , ÅKERBLOM Björn , MAHBOOBI Siavosh , CHANDRASEKHARAN Subhashini , LIU Edison T.
Published: August 2004

Hallmarks of the inflammatory process in Type I diabetes are macrophage activation, local release of β-cell-toxic cytokines and infiltration of cytotoxic T lymphocytes. We have observed recently that mice overexpressing active FRK (fyn-related kinase)/RAK (previously named GTK/Bsk/IYK, where GTK stands for gut tyrosine kinase, Bsk for β-cell Src-homology kinase and IYK for intestinal tyrosine kinase) in β-cells exhibit increased susceptibility to β-cell-toxic events, and therefore, we now attempt to find a more precise role for FRK/RAK in these processes. Phosphopeptide mapping of baculovirus-produced mouse FRK/RAK revealed an autophosphorylation pattern compatible with Tyr-394 being the main site. No evidence for in vitro phosphorylation of the C-terminal regulatory sites Tyr-497 and Tyr-504 was obtained, nor was there any indication of in vitro regulation of FRK/RAK kinase activity. Screening a panel of known tyrosine kinase inhibitors for their ability to inhibit FRK/RAK revealed several compounds that inhibited FRK/RAK, with a potency similar to that reported for their ability to inhibit other tyrosine kinases. Cytokine-induced islet toxicity was reduced in islets isolated from FRK/RAK knockout mice and this occurred without effects on the production of nitric oxide. Addition of the nitric oxide inhibitor nitroarginine to FRK/RAK knockout islets exposed to cytokines decreased cell death to a basal level. In normal islets, cytokine-induced cell death was inhibited by the addition of two FRK/RAK inhibitors, SU4984 and D-65495, or by transfection with short interfering RNA against FRK/RAK. It is concluded that FRK/RAK contributes to cytokine-induced β-cell death, and inhibition of this kinase could provide means to suppress β-cell destruction in Type I diabetes.
Mycobacterium tuberculosis DnaA initiator protein: purification and DNA-binding requirements
Authors: ZAWILAK Anna , KOIS Agnieszka , KONOPA Grażyna , SMULCZYK-KRAWCZYSZYN Aleksandra , ZAKRZEWSKA-CZERWIŃSKA Jolanta
Published: August 2004

The Mycobacterium tuberculosis oriC (the origin of chromosomal replication) region contains 13 non-perfect DnaA boxes. The M. tuberculosis initiator protein, DnaA, was overexpressed in Escherichia coli as a soluble His-tagged fusion protein. The purified protein His6MtDnaA was investigated for its binding properties to DnaA boxes from the oriC region. Gel retardation demonstrated that the DnaA from M. tuberculosis requires two DnaA boxes for efficient binding. Electron microscopy as well as DNase I footprinting showed that the His6MtDnaA protein binds to four specific regions, which correspond to the location of 11 out of 13 previously identified DnaA boxes within the M. tuberculosis oriC. Probably, in M. tuberculosis, DnaA molecules by co-operative binding of numerous ‘non-perfect’ DnaA boxes assemble along the oriC region and subsequently form a massive nucleoprotein complex.
The role of the LRPPRC (leucine-rich pentatricopeptide repeat cassette) gene in cytochrome oxidase assembly: mutation causes lowered levels of COX (cytochrome c oxidase) I and COX III mRNA
Authors: XU Fenghao , MORIN Charles , MITCHELL Grant , ACKERLEY Cameron , ROBINSON Brian H.
Published: August 2004

Leigh syndrome French Canadian (LSFC) is a variant of cytochrome oxidase deficiency found in Québec and caused by mutations in the LRPPRC (leucine-rich pentatricopeptide repeat cassette) gene. Northern blots showed that the LRPPRC mRNA levels seen in skeletal muscle>heart>placenta>kidney>liver>lung=brain were proportionally almost opposite in strength to the severity of the enzymic cytochrome oxidase defect. The levels of COX (cytochrome c oxidase) I and COX III mRNA visible on Northern blots were reduced in LSFC patients due to the common (A354V, Ala354→Val) founder mutation. The amount of LRPPRC protein found in both fibroblast and liver mitochondria from LSFC patients was consistently reduced to <30% of control levels. Import of [35S]methionine LRPPRC into rat liver mitochondria was slower for the mutant (A354V) protein. A titre of LRPPRC protein was also found in nuclear fractions that could not be easily accounted for by mitochondrial contamination. [35S]Methionine labelling of mitochondrial translation products showed that the translation of COX I, and perhaps COX III, was specifically reduced in the presence of the mutation. These results suggest that the gene product of LRPPRC, like PET 309p, has a role in the translation or stability of the mRNA for mitochondrially encoded COX subunits. A more diffuse distribution of LRPPRC in LSFC cells compared with controls was evident when viewed by immunofluorescence microscopy, with less LRPPRC present in peripheral mitochondria.
Free aminothiols, glutathione redox state and protein mixed disulphides in aging Drosophila melanogaster
Authors: REBRIN Igor , BAYNE Anne-Cécile V. , MOCKETT Robin J. , ORR William C. , SOHAL Rajindar S.
Published: August 2004

The main purpose of the present study was to test the hypothesis that the aging process is associated with a pro-oxidizing shift in the cellular redox state. The amounts of the redox-sensitive free aminothiols (glutathione, cysteine, Cys-Gly and methionine) and protein mixed disulphides were measured at different ages and ambient temperatures in Drosophila melanogaster. GSH/GSSG ratios decreased significantly with increasing age of the flies, due to an increase in GSSG content. Concentrations of Cys-Gly increased and methionine decreased with age. The amounts of protein mixed disulphides, measured as protein-cysteinyl, protein-Cys-Gly and protein-glutathionyl mixed disulphides, increased as a function of age. The pattern of changes in free aminothiol content, glutathione-redox state and protein mixed disulphides varied in proportion to the ambient temperature, which is inversely related to the life expectancy of the flies. Collectively, these results support the idea that the pro-oxidizing shift in the glutathione-redox state, the decrease in methionine content and increase in abundance of protein mixed disulphides are associated with the life expectancy of flies, and are indicative of enhanced oxidative stress during aging.
The pre-mRNA-splicing factor SF3a66 functions as a microtubule-binding and -bundling protein
Authors: TAKENAKA Kei , NAKAGAWA Hiroyuki , MIYAMOTO Shigeaki , MIKI Hiroaki
Published: August 2004

SF3a (splicing factor 3a) complex is an essential component of U2 snRNPs (small nuclear ribonucleoprotein particles), which are involved in pre-mRNA splicing. This complex consists of three subunits: SF3a60, SF3a66 and SF3a120. Here, we report a possible non-canonical function of a well-characterized RNA-splicing factor, SF3a66. Ectopic expression experiments using each SF3a subunit in N1E 115 neuroblastoma cells reveals that SF3a66 alone can induce neurite extension, suggesting that SF3a66 functions in the regulation of cell morphology. A screen for proteins that bind to SF3a66 clarifies that SF3a66 binds to β-tubulin, and also to microtubules, with high affinity, indicating that SF3a66 is a novel MAP (microtubule-associated protein). Electron microscopy experiments show that SF3a66 can bundle microtubules, and that bundling of microtubules is due to cross-bridging of microtubules by high-molecular-mass complexes of oligomerized SF3a66. These results indicate that SF3a66 is likely to be a novel MAP, and can function as a microtubule-bundling protein independently of RNA splicing.
Identification of a novel receptor for an invertebrate oxytocin/vasopressin superfamily peptide: molecular and functional evolution of the oxytocin/vasopressin superfamily
Authors: KAWADA Tsuyoshi , KANDA Atsuhiro , MINAKATA Hiroyuki , MATSUSHIMA Osamu , SATAKE Honoo
Published: August 2004

Annetocin is structurally related to an OT (oxytocin)/VP (vasopressin) family peptide, which has been isolated from the earthworm Eisenia foetida and has been shown to induce OT-like egg-laying behaviour. We now report the identification of an endogenous AnR (annetocin receptor). The deduced AnR precursor displays high sequence similarity with OT/VP receptors. Genomic analysis of the AnR gene revealed that the intron-inserted position is conserved between the AnR gene and the mammalian OT/VP receptor genes. These results indicate that AnR and mammalian OT/VP receptors share a common ancestor gene. Administration of annetocin to the AnR expressed in Xenopus oocytes induced a calcium-dependent signal transduction. Reverse transcriptase–PCR analysis and in situ hybridization showed that the AnR gene is expressed specifically in the nephridia located in the clitellum region, although the nephridia are distributed throughout the worm body. This result suggests that annetocin induces egg-laying behaviour through its action on the nephridia. This is the first description concerning the functional correlation between an invertebrate OT/VP-related peptide and egg-laying behaviour.
PTEN function: how normal cells control it and tumour cells lose it
Authors: LESLIE Nick R. , DOWNES C. Peter
Published: August 2004

The PTEN (phosphatase and tensin homologue deleted on chromosome 10) tumour suppressor is a PI (phosphoinositide) 3-phosphatase that can inhibit cellular proliferation, survival and growth by inactivating PI 3-kinase-dependent signalling. It also suppresses cellular motility through mechanisms that may be partially independent of phosphatase activity. PTEN is one of the most commonly lost tumour suppressors in human cancer, and its deregulation is also implicated in several other diseases. Here we discuss recent developments in our understanding of how the cellular activity of PTEN is regulated, and the closely related question of how this activity is lost in tumours. Cellular PTEN function appears to be regulated by controlling both the expression of the enzyme and also its activity through mechanisms including oxidation and phosphorylation-based control of non-substrate membrane binding. Therefore mutation of PTEN in tumours disrupts not only the catalytic function of PTEN, but also its regulatory aspects. However, although mutation of PTEN is uncommon in many human tumour types, loss of PTEN expression seems to be more frequent. It is currently unclear how these tumours lose PTEN expression in the absence of mutation, and while some data implicate other potential tumour suppressors and oncogenes in this process, this area seems likely to be a key focus of future research.
Polarization consistent basis sets. V. The elements Si–Cl
Authors: Jensen Frank , Helgaker Trygve
Published: August 2004

Polarization consistent basis sets, optimized for density functional calculations, are proposed for the elements Si–Cl. Their performance for atomization energies, equilibrium geometries, harmonic vibrational frequencies, and associated infrared intensities is compared with other commonly used basis sets. Atomization energies can be predicted to within 0.01 kJ/mol per atom of the basis set limit by extrapolation of the pc-2, -3, and -4 results. Equilibrium bond distances and harmonic vibrational frequencies can be calculated to within 10−5 Å and 0.5 cm−1, respectively, of the basis set limit. The pc-n basis sets are shown to give comparable or better accuracy than other alternatives, while containing fewer or equal number of primitive basis functions.
Internuclear distance and effects of Born–Oppenheimer breakdown for PtS, determined from its pure rotational spectrum
Authors: Cooke Stephen A. , Gerry Michael C. L.
Published: August 2004

Platinum monosulfide PtS has been prepared in its X0+ ground electronic state by laser ablation of Pt in the presence of H2S. The rotational spectra of eight isotopic species have been measured with a cavity pulsed jet Fourier-transform microwave spectrometer. Spectral analysis using a multi-isotopomer Dunham-type expression produced values for Y01, Y02, Y11, and Y21, along with large values for Born–Oppenheimer breakdown (BOB) parameters for both atoms of the molecule. The BOB parameters are rationalized in terms of the molecular electronic structure and nuclear field shift effects. A large negative Pt195 nuclear spin-rotation constant has been rationalized in terms of the electron-nucleus dipole-dipole hyperfine constant. The equilibrium bond length in the Born–Oppenheimer approximation has been evaluated.
Is molecular rotation really influenced by subtle changes in molecular shape?
Authors: Dutt G. B. , Ghanty T. K.
Published: August 2004

In an attempt to seek out whether the reorientation time of a solute molecule is influenced by marginal changes to its shape, rotational relaxation of four coumarin solutes that are almost identical in size but subtly distinct in shape has been investigated in a viscous nonpolar solvent as a function of temperature. It has been observed that the reorientation times of the four coumarins differ significantly from one another. The four solutes have been treated as asymmetric ellipsoids and Stokes-Einstein-Debye hydrodynamic theory has been employed to calculate the shape factors and boundary condition parameters. The measured reorientation times when normalized by respective shape factors and boundary condition parameters can be scaled on a common curve, which is an indication that ellipsoid based hydrodynamic theory is adequate to model the reorientation times even when the differences in the shapes of the solute molecules are minimal.
Surface phase separation in complex mixed adsorbing systems: An interface-bulk coupling effect
Authors: Pugnaloni Luis A. , Ettelaie Rammile , Dickinson Eric
Published: August 2004

The interfacial thermodynamics and structure of ternary mixtures of the type A+B+solvent are investigated. According to the Gibbs phase rule, the coupling between the bulk phase and the interfacial region—which is related to the reversibility of the adsorption of the corresponding species—is a determinant as to whether phase separation can be observed at the interface. For an n-component adsorbing solution, at least one of the species has to adsorb irreversibly over the experimental time scales in order not to fix more intensive variables than those required to observe surface phase separation. We present results for a lattice model planar interface consisting of the ternary mixture A+B+solvent. The solvent molecules and the type A molecules have fixed chemical potentials at the interface since they are equilibrated with a bulk solution. In contrast, the type B molecules are irreversibly adsorbed at the interface and do not equilibrate with the bulk. Mean-field theory is compared with Monte Carlo simulation. Interestingly, the spinodal line in the interaction-composition plane shows a reentrant on the B-rich phase side. We discuss the implications of these results for surface phase separation of adsorbing mixtures of proteins and low-molecular-weight surfactants.
Instantaneous normal mode analysis of orientational motions in liquid water: Local structural effects
Authors: Chang S. L. , Wu Ten-Ming , Mou Chung-Yuan
Published: August 2004

We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.
Momentum and stress relaxation in fluids illustrating caging
Authors: Evans Glenn T.
Published: August 2004

The self diffusion coefficient, shear viscosity, and velocity time correlation function are calculated for a hard sphere fluid under a severe assumption, namely, the friction arises from uncorrelated binary collisions and from correlated backscattering (caging) collisions as represented in the memory function. Relaxation of the memory function from its zerotime caging value is described as a diffusion process. Derived diffusion coefficients and the shear viscosities, relative to their Enskog values decrease and increase with density, respectively, in a monotonic and gradual fashion in contrast with simulation values that show a precipitous change near the fluid-solid transition. In the present pair diffusion model, the velocity time correlation function vanishes at the proper time but its tail is overly damped relative to the simulation data. A weak breakdown of the Stokes-Einstein relation is also predicted.
Diagrammatic kinetic theory for a lattice model of a liquid. II. Comparison of theory and simulation results
Authors: Feng Edward H. , Andersen Hans C.
Published: August 2004

We compare the predictions of the mean field, the two site multiple scattering, and the simple mode coupling approximation developed in the previous paper for the dynamics of a tagged particle in an excluded volume lattice gas with the results of computer simulations. The tagged particle has a transition rate of γ while the background particles have transition rates of αγ. We consider the tracer diffusion coefficient and the incoherent intermediate scattering function (IISF) for low, intermediate, and high concentrations of particles and for simple square and cubic lattices. In general, the approximate kinetic theories are more accurate in predicting simulations results at low concentrations, high dimensions, and large α. For the tracer diffusion coefficient, the mean field approximation is the least accurate, the two site multiple scattering approximation is more accurate, and the simple mode coupling approximation is the most accurate; all three approximate theories overestimate the simulation results. For the IISF, the mean field approximation is quantitatively accurate in the limit of small concentration and large α but in general decays too quickly. The two site multiple scattering approximation is quantitatively accurate at low and intermediate concentrations for large wave vectors; it is always more accurate than the mean field approximation and always decays more quickly than the simulation results. The simple mode coupling approximation is the most accurate of the three approximations in most cases and especially so for small wave vectors, high concentration, and small α; unfortunately, its predictions are not quantitatively accurate in these highly nonmean field regimes. We discuss the implications of these results for developing diagrammatic kinetic theories.
A general diagrammatic algorithm for contraction and subsequent simplification of second-quantized expressions
Authors: Bochevarov Arteum D. , Sherrill C. David
Published: August 2004

We present a general computer algorithm to contract an arbitrary number of second-quantized expressions and simplify the obtained analytical result. The functions that perform these operations are a part of the program Nostromo which facilitates the handling and analysis of the complicated mathematical formulas which are often encountered in modern quantum-chemical models. In contrast to existing codes of this kind, Nostromo is based solely on the Goldstone-diagrammatic representation of algebraic expressions in Fock space and has capabilities to work with operators as well as scalars. Each Goldstone diagram is internally represented by a line of text which is easy to interpret and transform. The calculation of matrix elements does not exploit Wick’s theorem in a direct way, but uses diagrammatic techniques to produce only nonzero terms. The identification of equivalent expressions and their subsequent factorization in the final result is performed easily by analyzing the topological structure of the diagrammatic expressions.
Multiconfigurational time-dependent Hartree calculations for dissociative adsorption of H2 on Cu(100)
Authors: van Harrevelt Rob , Manthe Uwe
Published: August 2004

The efficiency of the multiconfigurational time-dependent Hartree (MCTDH) method for calculating the initial-state selected dissociation probability of H2(v=0,j=0) on Cu(100) is investigated. The MCTDH method is shown to be significantly more efficient than standard wave packet methods. A large number of single-particle functions is required to converge the initial-state selected reaction probability for dissociative adsorption. Employing multidimensional coordinates in the MCTDH ansatz (mode combination) is found to be crucial for the efficiency of these MCTDH calculations. Perspectives towards the application of the MCTDH approach to study dissociative adsorption of polyatomic molecules on surfaces are discussed.
Time-dependent amorphization of ice at 0.8–0.9 GPa
Authors: Andersson Ove , Johari G. P.
Published: August 2004

Thermal conductivity measurements show that ice continues to amorphize for several days when kept at a fixed pressure p in the 0.79–0.88 GPa range, and fixed temperature T in the 127–130 K range. Thermal conductivity κ decreases according to a stretched exponential in time, and its limiting long time value κ(∞) varies with p and T. At 0.8 GPa and 128 K, κ(∞) remains 2.5 times the value observed for high-density amorph. Consequences of these findings for our understanding of amorphization are discussed.
Computation of the equation of state of the quantum hard-sphere fluid utilizing several path-integral strategies
Authors: Sesé Luis M.
Published: August 2004

The compressibility factor of the quantum hard-sphere fluid within the region (ρN*⩽0.8,λB*⩽0.9) is computed by following four distinct routes involving the three pair radial correlation functions that are significant in the path-integral context, namely, instantaneous, pair linear response, and centroids. These functions are calculated with path-integral Monte Carlo simulations involving the Cao-Berne propagator. The first route to the equation of state is the instantaneous standard one, i.e., the usual volume derivative of the partition function expressed in terms of the instantaneous pair radial correlations. The other three routes stem from the extended compressibility theorem, which associates the isothermal compressibility with the three pair radial structures mentioned above and involves the solving of appropriate Ornstein-Zernike equations. An analysis of the error bars in the quantities computed is reported, and it is proven the usefulness of the centroid pair correlations to fix quantum equations of state. Also, the regions where the fluid-solid changes of phase should take place are identified with the use of indicators sensitive to order in the sample. The consistency of the current results is assessed and comparison with data available in the literature is made wherever possible.
Stability of thin polymer films: Influence of solvents
Authors: Lin Yu-Cheng , Müller Marcus , Binder Kurt
Published: August 2004

The interface and surface properties and the wetting behavior of polymer-solvent mixtures are investigated using Monte Carlo simulations and self-consistent field calculations. We carry out Monte Carlo simulations in the framework of a coarse-grained bead-spring model using short chains (oligomers) of NP=5 beads and a monomeric solvent, NS=1. The self-consistent field calculations are based on a simple phenomenological equation of state for compressible binary mixtures and we employ Gaussian chain model. The bulk behavior of the polymer-solvent mixture belongs to type III in the classification of van Konynenburg and Scott [Phil. Trans. R. Soc. London, Ser. A 298, 495 (1980)]. It is characterized by a triple line on which the polymer-liquid coexists with solvent-vapor and a solvent-rich liquid. The solvent is not homogeneously distributed across the dense polymer film but tends to accumulate at the surface and the polymer-vapor interface. This solvent enrichment at the interface and surface becomes more pronounced upon increasing the vapor pressure and alters the surface and interface tensions. This effect gives rise to a nonmonotonic dependence of the contact angle on the vapor pressure and one might observe reentrant wetting. The results of the Monte Carlo simulations and the self-consistent field calculations qualitatively agree. The profiles of drops are investigated by Monte Carlo simulations and a pronounced solvent enrichment is observed at the wedge formed by the substrate and the liquid-vapor interface at the three-phase contact line.
Theory of femtosecond stimulated Raman spectroscopy
Authors: Lee Soo-Y. , Zhang Donghui , McCamant David W. , Kukura Philipp , Mathies Richard A.
Published: August 2004

Femtosecond broadband stimulated Raman spectroscopy (FSRS) is a new technique that produces high-resolution (time-resolved) vibrational spectra from either the ground or excited electronic states of molecules, free from background fluorescence. FSRS uses simultaneously a narrow bandwidth ∼1–3 ps Raman pump pulse with a continuum ∼30–50 fs Stokes probe pulse to produce sharp Raman gains, at positions corresponding to vibrational transitions in the sample, riding on top of the continuum Stokes probe spectrum. When FSRS is preceded by a femtosecond actinic pump pulse that initiates the photochemistry of interest, time-resolved Raman spectroscopy can be carried out. We present two theoretical approaches to FSRS: one is based on a coupling of Raman pump and probe light waves with the vibrations in the medium, and another is a quantum-mechanical description. The latter approach is used to discuss the conditions of applicability and limitations of the coupled-wave description. Extension of the quantum-mechanical description to the case where the Raman pump beam is on resonance with an excited electronic state, as well as when FSRS is used to probe a nonstationary vibrational wave packet prepared by an actinic pump pulse, is also discussed.
Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics
Authors: Craig Ian R. , Manolopoulos David E.
Published: August 2004

We propose an approximate method for calculating Kubo-transformed real-time correlation functions involving position-dependent operators, based on path integral (Parrinello-Rahman) molecular dynamics. The method gives the exact quantum mechanical correlation function at time zero, exactly satisfies the quantum mechanical detailed balance condition, and for correlation functions of the form C̃Ax(t) and C̃xB(t) it gives the exact result for a harmonic potential. It also works reasonably well at short times for more general potentials and correlation functions, as we illustrate with some example calculations. The method provides a consistent improvement over purely classical molecular dynamics that is most apparent in the low-temperature regime.
Comparative study of magnetization reversal in isolated and strayfield coupled microcontacts
Authors: Meier Guido , Eiselt René , Bolte Markus , Barthelmeß Miriam , Eimüller Thomas , Fischer Peter
Published: August 2004

Ferromagnetic microcontacts are key components for future spintronic devices in full metal as well as in hybrid ferromagnet/semiconductor systems. Control of the micromagnetic behavior and especially the reversal process is crucial for the functionality of such devices. We have prepared isolated and strayfield coupled micron sized rectangular Ni∕Fe double layer contacts on silicon nitride membranes. High-resolution magnetic microscopy studies in external fields are performed on identical samples comparing full field magnetic transmission x-ray microscopy and magnetic-force microscopy. The results of both techniques are in good agreement. We find evidence for a strayfield-induced coupling of the domain structure in adjacent contacts in accordance with micromagnetic simulations.
Interface structures in MgB2 thin films on (0001) SiC
Authors: Wu J. S. , Jiang N. , Jiang B. , Spence J. C. H. , Pogrebnyakov A. V. , Redwing J. M. , Xi X. X.
Published: August 2004

The structure of the MgB2∕SiC interface has been studied by high-resolution electron microscopy. Most of the defects at the interface are dislocations with Burgers vector [0001]. In addition, a minority of dislocations with Burgers vector [112¯0]∕3 are also generated to relax the mismatch stress between film and substrate. Energy loss spectra obtained from nanometer regions show that the interface is not affected by oxygen.
Morphological healing evolution of penny-shaped fatigue microcracks in pure iron at elevated temperatures
Authors: Zhang H. L. , Huang P. Z. , Sun J. , Gao H.
Published: August 2004

This letter reports a joint experimental and numerical investigation of high temperature morphological healing of micron-sized intragranular microcracks in pure iron. Irregular penny-shaped microcracks were first created by low-cycle fatigue and then subjected to annealing in vaccum at 1173K. It is shown theoretically that, depending on its initial aspect ratio, a penny-shaped microcrack may evolve via surface diffusion into an isolated spherical void, or a doughnut-shaped channel pore with or without a central spherical void. Subsequent evolution causes the doughnut-shaped channel pore to break up into a ring of spherical voids via Rayleigh’s instabilities. These results were confirmed with experimental observations of typical configurations of voids that result from the crack healing process. The experimentally observed evolution time is also in good agreement with the predictions of finite element simulations of the evolution process.
Dark spatial solitons in bulk azo-dye-doped polymer using photoinduced molecular reorientation
Authors: Bian Shaoping , Kuzyk Mark G.
Published: August 2004

We report the generation of dark spatial solitons in bulk Disperse Red 1 doped poly(methyl methacrylate) using photoinduced reorientation of azo-dye molecules. Planar solitions are formed when illuminated with a continuous-wave laser at intensities of the order of hundreds of miliwatts per square centimeter. The width of the soliton saturates to a minimum value at high intensity; and when the width of the initial dark notch is reduced, the equilibrium minimum width is unchanged.
Measurements of low-frequency noise spectral densities for a small-sized stack of intrinsic Josephson junctions of Bi2Sr2CaCu2Oy single crystal
Authors: Saito A. , Ishida H. , Hamasaki K. , Irie A. , Oya G.
Published: August 2004

We measured the low-frequency-voltage noise properties of a small-sized stack of intrinsic Josephson junctions formed on the surface of a cleaved Bi2Sr2CaCu2Oy (Bi-2212) single crystal, containing a few intrinsic Josephson junctions. A stack with an area of 2×2μm was fabricated by electron-beam lithography and argon-ion-milling. The current–voltage (I–V) characteristics along the c-axis direction of the stack were measured by a three-terminal method. The stack showed (I–V) and dV∕dI-V curves without backbending due to heating effects. Five discrete resistive branches with hysteresis were observed in the low-voltage region of these curves. The measured noise-voltage spectral density SV(f) had a 1∕f dependence on frequency. We estimated the magnitude of the 1∕f noise parameter η from SV(f) in a Bi-2212 stack and found that above the sum-gap voltage in a small-sized stack η was almost the same as that for low-Tc Nb∕Al+AlOx∕Nb high-quality tunnel junctions.
Stress-induced magnetization for epitaxial spinel ferrite filmsthrough interface engineering
Authors: Wakiya Naoki , Shinozaki Kazuo , Mizutani Nobuyasu
Published: August 2004

This study found “stress-induced magnetization” for epitaxial ferrite films with spinel structure. We grew (111)- and (001)-epitaxial Ni0.17Zn0.23Fe2.60O4(NZF) films on CeO2∕Y0.15Zr0.85O1.93(YSZ)∕Si(001) and oxide single-crystal substrates, respectively. There is a window of lattice mismatch (between 0 and 6.5%) to achieve bulk saturation magnetization (Ms). An NZF film grown on CeO2∕YSZ∕∕Si(001) showed tensile stress, but that stress was relaxed by introducing a ZnCo2O4(ZC) buffer layer. NZF films grown on SrTiO3(ST)(001) and (La,Sr)(Al,Ta)O3(LSAT)(001) had compressive stress, which was enhanced by introducing a ZC buffer layer. In both cases, bulk Ms was achieved by introducing the ZC buffer layer. This similarity suggests that magnetization can be controlled by the stress.
Strained layer instabilities on vicinal surfaces: Ge0.8Si0.2 epitaxy on laser textured Si(001)
Authors: Watanabe Fumiya , Cahill David G. , Hong Sukwon , Greene Joseph E.
Published: August 2004

Laser textured substrates enable a combinatorial study of strained layer growth morphology as a function of substrate miscut. Si(001) substrates with miscut θ<15° off (001) are produced by texturing with nanosecond laser pulses. Ge0.8Si0.2 growth rates are varied over a wide range, 1.7–90 monolayers per minute, at a fixed substrate temperature of 600°C. Film morphologies at all growth rates show strong dependence on the local miscut θ within the dimpled regions of the substrate: the results demonstrate the importance of anisotropy in surface stiffness for the formation of epitaxial nanostructures. The length scales of all structures display a similar trend of decreasing size with increasing growth rate due to the suppression of coarsening at high growth rates.
Chirp effects in femtosecond laser-induced surface second-harmonic generation from metals
Authors: Teng H. , Guo Chunlei
Published: August 2004

Chirp effects are studied in femtosecond laser-induced surface second-harmonic generation (SHG) from gold. We observe a higher SHG yield when the incident laser pulses are negatively chirped, compared to using the transform-limited or positively chirped pulses. This study indicates that SHG is critically dependent on the exciting wavelength sequence within the femtosecond pulse bandwidth when electrons contributing to SHG are heated to a sufficiently high temperature and are in thermal nonequilibrium distribution with the lattice.
Oxygen precipitate denuded zone in polycrystalline sheet silicon
Authors: Lu Jinggang , Rozgonyi George , Rand James , Jonczyk Ralf
Published: August 2004

The spatial variation of oxygen precipitation across the thickness of polycrystalline sheet silicon has been investigated by Fourier transform infrared (FTIR) microspectroscopy and preferential etching/optical microscopy. FTIR shows that interstitial oxygen is depleted near the top surface of the as-grown sample, thereby suppressing oxygen precipitation during subsequent annealing. Preferential etching and electron-beam-induced current imaging of polished cross sections revealed a 250-μm-wide precipitate denuded zone near the top surface. Evidently, growth-induced near-surface reduction of the oxygen profile keeps the oxygen supersaturation below a critical level for precipitate nucleation. Considering that the minority carrier diffusion length of current finished sheet silicon solar cells ranges from 50to100μm, it is anticipated that optimization of the 250-μm-wide precipitate denuded zone will improve solar cell performance.
Intelligent integration of optical power splitter with optically switchable cross-connect based on multimode interference principle in SiGe∕Si
Authors: Li Baojun , Chua Soo-Jin , Fitzgerald Eugene A. , Chaudhari Bharat S. , Jiang Shaoji , Cai Zhigang
Published: August 2004

An intelligent and monolithic integration of optical power splitter with optically switchable cross-connect has been proposed. It is fabricated on the multimode interference principle in Si-based SiGe material system and configured for a 3×2 symmetrical structure of the three input waveguides and the two output waveguides. The central waveguide section is based on a multimode interference and incorporated with an activated carrier injection element. The operating wavelengths of the device are specially designed for 1545, 1550, and 1555nm conventional-band wavelengths. The measured crosstalk is at around −17dB and the average insertion loss is about 5.25dB. At switch-ON state, the measured injection current is 370mA corresponding to an injection current density of 950A∕cm2.
Midgap state-based π-junctions for digital applications
Authors: Testa G. , Monaco A. , Esposito E. , Sarnelli E. , Kang D.-J. , Mennema S. H. , Tarte E. J. , Blamire M. G.
Published: August 2004

Midgap state-based YBa2Cu3O7−x π-junctions have been fabricated by a focused ion-beam system using 45° symmetric [001] tilt SrTiO3 bicrystal substrates. Measurements, performed by inserting the junctions in a superconducting loop (as a double-phase sensitive test), show both an unconventional nonmonotonic temperature dependence of the Josephson current, with a local minimum at a crossover temperature T* and, around T*, a half flux quantum shift in the critical current versus magnetic field modulations, clear signs of a 0–π crossover with temperature. Such results demonstrate that conventional 45° symmetric grain boundary junctions may have potential for applications, from digital circuits to quantum computing.
X-ray fluoresced high-Z (up to Z=82) K x rays produced by LiNbO3 and LiTaO3 pyroelectric crystal electron accelerators
Authors: Brownridge James D. , Shafroth Stephen M.
Published: August 2004

High-energy bremsstrahlung and K x rays were used to produce nearly background-free K x-ray spectra of up to 87keV (Pb) via x-ray fluorescence. The fluorescing radiation was produced by electron accelerators, consisting of heated and cooled cylindrical LiTaO3 and LiNbO3 crystals at mTorr pressures. The process of gas amplification whereby the ambient gas pressure is optimized to maximize the electron energy was used to produce energetic electrons which when incident on a W∕Bi target, gave rise to a radiation field consisting of high-energy bremsstrahlung as well as W and Bi K x rays. These photons were used to fluoresce Ta and Pb K x rays.
Quartz micromachining using laser plasma soft x raysand ultraviolet laser light
Authors: Makimura Tetsuya , Mitani Shinjo , Kenmotsu Youichi , Murakami Kouichi , Mori Michiaki , Kondo Kiminori
Published: August 2004

We have investigated a technique for micromachining inorganic transparent materials. In the technique, patterning and coloration are performed by the direct irradiation of materials with pulsed laser soft x rays and the patterned areas are ablated using ultraviolet laser light. The technique utilizes the high precision of the soft x rays and the high energy density of conventional laser light. For demonstration, we irradiated quartz plates with Ta laser plasma soft x rays. This results in generation of transient surface opaque layers that absorb more than 40% of the 266nm Nd:YAG laser light. Applying the technique, quartz plates are found to be ablated smoothly at 85nm∕shots.
Electric-pulse-induced reflectance change in the thin film of perovskite manganite
Authors: Aoyama K. , Waku K. , Asanuma A. , Uesu Y. , Katsufuji T.
Published: August 2004

We demonstrate a nonvolatile, reversible change of infrared reflectance from the thin film of perovskite manganite (Pr1−xCaxMnO3) by applying electric pulse. The result provides a possibility to use the electric-pulse-induced phenomena of this compound in optical devices.
Crystallization and phase transformations in amorphous NiTi thin films for microelectromechanical systems
Authors: Lee Hoo-Jeong , Ramirez Ainissa G.
Published: August 2004

Amorphous sputtered nickel–titanium thin films were deposited onto micromachined silicon-nitride membranes and subjected to heating and cooling conditions. Their associated microstructure was monitored directly and simultaneously with in situ transmission electron microscopy. These electron-transparent membranes constrained the NiTi films and rendered it possible for observation of the complete transformation cycle, which includes: the crystallization of the amorphous phase to austenite phase (cubic B2 structure) with heating; and the conversion of austenite (B2) to martensite (monoclinic B19′ structure) with cooling. Electron micrographs show the nucleation and growth of grains occurs at a temperature of 470°C and at a rate that indicates a polymorphic transformation. The onset of martensitic transformation occurs between 25 and 35°C. Calorimetric measurements are consistent with the observed crystallization.
Band offset design with quantum-well gate insulating structures
Authors: Schimizu Tatsuo , Yamaguchi Takeshi
Published: August 2004

The authors propose a concept, a nanoscaled quantum-well gate insulating structure. The effective conduction band offset (ΔEc) can be controlled with an appropriate combination of high-K and high-ΔEc materials. The electronic structures of SrTiO3 and Sr2TiO4 were studied by means of first-principles calculations to investigate the change in the band structures induced by SrO-layer intercalation. The ΔEc of Sr2TiO4 is raised by about +0.8eV. A quantum-well gate insulating structure with off-resonance condition is also proposed. The ΔEc becomes as high as the barrier height of the barrier material.
Hetero-epitaxy of perovskite oxides on GaAs(001) by molecular beam epitaxy
Authors: Liang Y. , Kulik J. , Eschrich T. C. , Droopad R. , Yu Z. , Maniar P.
Published: August 2004

Hetero-epitaxy of single-crystal perovskite SrTiO3 on GaAs(001) was achieved using molecular beam epitaxy. The growth was accomplished by deposition of a submonolayer of titanium on GaAs(001), followed by the co-deposition of strontium and titanium initiated at a low-temperature, low-oxygen-pressure condition. X-ray photoelectron spectroscopy showed that the Ti prelayer reacted with As and formed TiAs-like species on the As terminated GaAs(001) surface. Reflection-high-energy-electron diffraction showed that SrTiO3 grew coherently on the GaAs(001) at early stage of growth. This coherent behavior began to degrade when SrTiO3 thickness exceeded 20Å. Cross-sectional transmission electron microscopy revealed an abrupt interface between SrTiO3 and GaAs and good crystallinity of the SrTiO3 film. An epitaxial relationship between SrTiO3 and GaAs was further confirmed by x-ray diffraction. The success of growth of SrTiO3 on GaAs paves the way for integration of various functional perovskite oxides with GaAs.