bluuebunny/crossref_metadata_2025 huggingface dataset:
Wave propagation through elastic porous media containing two immiscible fluids
Authors: Lo Wei‐Cheng , Sposito Garrison , Majer Ernest
Published: February 2005

Acoustic wave phenomena in porous media containing multiphase fluids have received considerable attention in recent years because of an increasing scientific awareness of poroelastic behavior in groundwater aquifers. To improve quantitative understanding of these phenomena, a general set of coupled partial differential equations was derived to describe dilatational wave propagation through an elastic porous medium permeated by two immiscible fluids. These equations, from which previous models of dilatational wave propagation can be recovered as special cases, incorporate both inertial coupling and viscous drag in an Eulerian frame of reference. Two important poroelasticity concepts, the linearized increment of fluid content and the closure relation for porosity change, originally defined for an elastic porous medium containing a single fluid, also are generalized for a two‐fluid system. To examine the impact of relative fluid saturation and wave excitation frequency (50, 100, 150, and 200 Hz) on free dilatational wave behavior in unconsolidated porous media, numerical simulations of the three possible modes of wave motion were conducted for Columbia fine sandy loam containing either an air‐water or oil‐water mixture. The results showed that the propagating (P1) mode, which results from in‐phase motions of the solid framework and the two pore fluids, moves with a speed equal to the square root of the ratio of an effective bulk modulus to an effective density of the fluid‐containing porous medium, regardless of fluid saturation and for both fluid mixtures. The nature of the pore fluids exerts a significant influence on the attenuation of the P1 wave. In the air‐water system, attenuation was controlled by material density differences and the relative mobilities of the pore fluids, whereas in the oil‐water system an effective kinematic shear viscosity of the pore fluids was the controlling parameter. On the other hand, the speed and attenuation of the two diffusive modes (P2, resulting from out‐of‐phase motions of the solid framework and the fluids, and P3, the result of capillary pressure fluctuations) were closely associated with an effective dynamic shear viscosity of the pore fluids. The P2 and P3 waves also had the same constant value of the quality factor, and by comparison of our results with previous research on these two dilatational wave modes in sandstones, both were found to be sensitive to the state of consolidation of the porous medium.
Global change impacts on hydrological processes in Alpine catchments
Authors: Zierl Bärbel , Bugmann Harald
Published: February 2005

This analysis assesses the impacts of global change on hydrological processes in Alpine catchments. We applied the regional hydroecological simulation system RHESSys to five case studies from different climatic zones in the European Alps. Seven scenarios based on the so‐called SRES emission scenarios of the Intergovernmental Panel on Climate Change were used to describe changes in climate and land use. Shifts in runoff regimes and annual and summer runoff were investigated. The focus was on analyzing differences in the hydrological responses of different Alpine climate zones, exploring differences between SRES scenarios (A1FI, A2, B1, and B2), and analyzing the importance of applying several global circulation models (HadCM3, CGCM2, CSIRO2, and PCM). Under all scenarios, rising temperatures were projected to strongly affect runoff regimes via the impact on snow cover. The overall effect is a substantial runoff regime shift across the Alps, with specific differences depending on the climatic zone considered.
Characteristic dimensions of the step‐pool bed configuration: An experimental study
Authors: Curran Joanna C. , Wilcock Peter R.
Published: February 2005

The dominant dimension of the step‐pool bed form is its spacing, which is determined by the locations at which large, step‐forming grains are deposited. We conducted laboratory experiments involving active transport of widely sorted sediment, including large grains whose deposition readily formed steps. Direct observation of step development indicates that deposition of step‐forming grains was predominantly associated with bed roughness impeding transport or with earlier flow and transport conditions not contemporaneous with step development. Neither mechanism is likely to occur at regular locations on the bed. Measured step spacing was found to follow a Poisson distribution, supporting the conclusion that steps do not develop in preferred or regular locations. This contrasts with previous arguments that regular step spacing develops in response to deposition forced at regular locations beneath water surface waves. We observe neither the regular distribution nor the associated depositional mechanism, although the observed step distribution is well defined with a strong mode that could be interpreted as indicating regular spacing.
Analysis of normal and mutant iduronate-2-sulphatase conformation
Authors: PARKINSON-LAWRENCE Emma , TURNER Christopher , HOPWOOD John , BROOKS Doug
Published: February 2005

Mammalian sulphatases (EC 3.1.6) are a family of enzymes that have a high degree of similarity in amino acid sequence, structure and catalytic mechanism. IDS (iduronate-2-sulphatase; EC 3.1.6.13) is a lysosomal exo-sulphatase that belongs to this protein family and is involved in the degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate. An IDS deficiency causes the lysosomal storage disorder MPS II (mucopolysaccharidosis type II). To examine the structural alterations in heat-denatured and mutant IDS, a panel of four monoclonal antibodies was raised to the denatured protein and used as probes of protein conformation. The linear sequence epitope reactivity of a polyclonal antibody raised against the native protein and the monoclonal antibodies were defined and mapped to distinct regions on the IDS protein. The antigenicity of native IDS was higher in regions without glycosylation, but reactivity was not restricted to protein surface epitopes. One monoclonal epitope was relatively surface accessible and in close proximity to an N-linked glycosylation site, while three others required additional thermal energy to expose the epitopes. The monoclonal antibodies demonstrated the capacity to differentiate progressive structural changes in IDS and could be used to characterize the severity of MPS type II in patients based on variable denatured microstates.
Activation of ryanodine receptors induces calcium influx in a neuroblastoma cell line lacking calcium influx factor activity
Authors: BOSE Diptiman D. , RAHIMIAN Roshanak , THOMAS David W.
Published: February 2005

We have further characterized the Ca2+ signalling properties of the NG115-401L (or 401L) neuroblastoma cell line, which has served as an important cell line for investigating SOC (store-operated channel) influx pathways. These cells possess an unusual Ca2+ signalling phenotype characterized by the absence of Ca2+ influx when Ca2+ stores are depleted by inhibitors of SERCA (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase). Previous studies found that Ca2+-store depletion does not produce a CIF (Ca2+ influx factor) activity in 401L cells. These observations have prompted the question whether 401L cells possess the signalling machinery that permits non-voltage-gated Ca2+ influx to occur. We tested the hypothesis that ryanodine-sensitive Ca2+ pools and activation of RyRs (ryanodine receptors) constitute a signalling pathway capable of inducing Ca2+ influx in 401L cells. We found that 401L cells express mRNA for RyR1 and RyR2 and that RyR activators induced Ca2+ release. Activation of RyRs robustly couples with Ca2+ influx responses in 401L cells, in sharp contrast with absence of Ca2+ influx when cells are treated with SERCA inhibitors. Thus it is clear that 401L cells, despite lacking depletion-induced Ca2+ influx pathways, express the functional components of a Ca2+ influx pathway under the control of RyR function. These findings further support the importance of the 401L cell line as an important cell phenotype for deciphering Ca2+ influx regulation.
Anomalous pH-dependence of the activity of human matrilysin (matrix metalloproteinase-7) as revealed by nitration and amination of its tyrosine residues
Authors: MUTA Yuko , ONEDA Hiroshi , INOUYE Kuniyo
Published: February 2005

Matrilysin activity exhibits a broad bell-shaped pH-dependence profile, with pKa values of 4.0 and 9.8. A maximum of five out of eight tyrosine residues in matrilysin were nitrated with tetranitromethane. On nitration of between one and five tyrosines, pKa at the alkaline side (pKe2) was shifted from 9.8 to 10.3–10.6, while that at the acidic side (pKe1) was not altered. The pKe2 that was shifted by nitration to 10.3–10.6 was restored to 9.4–9.7 by subsequent amination, suggesting that the shift in pKe2 is induced by a negative charge introduced on the most reactive tyrosine, Tyr-150. The Michaelis constant (Km) observed at pH 10 was decreased by nitration as a result of the increase in pKe2, suggesting that the residue with pKe2 may play a role in the recognition of substrate. When four or five tyrosines were nitrated, the activity at pH <7 decreased significantly, while that at pH 7–10 was unchanged, and thus the pH-dependence was not bell-shaped, but anomalous, with a third pKa (pKe3) of 6.2–6.4 in addition to pKe1 and pKe2. This suggests the possibility that a newly introduced nitrotyrosine residue has a strong influence on the activity as an ionizable group.
The roles of Sp1, Sp3, USF1/USF2 and NRF-1 in the regulation and three-dimensional structure of the Fragile X mental retardation gene promoter
Authors: KUMARI Daman , GABRIELIAN Andrei , WHEELER David , USDIN Karen
Published: February 2005

Expansion of a CGG·CCG-repeat tract in the 5′-untranslated region of the FMR1 (Fragile X mental retardation 1) gene causes its aberrant transcription. This produces symptoms ranging from premature ovarian failure and Fragile X associated tremor and ataxia syndrome to FMR syndrome, depending on the size of the expansion. The promoter from normal alleles shows four protein-binding regions in vivo. We had previously shown that in mouse brain extracts two of these sites are bound by USF1/USF2 (upstream stimulatory factors 1 and 2) heterodimers and NRF-1 (nuclear respiratory factor-1). We also showed that these sites are involved in the positive regulation of FMR1 transcription in neuronally derived cells. In the present study, we show that Sp1 (specificity protein 1) and Sp3 are also strong positive regulators of FMR1 promoter activity. We also show that, like Sp1 and E-box-binding proteins such as USF1 and USF2, NRF-1 causes DNA bending, in this case producing a bend of 57° towards the major groove. The combined effect of the four protein-induced bends on promoter geometry is the formation of a highly compact arch-like structure in which the 5′ end of the promoter is brought in close proximity to the 3′ end. We had previously shown that while point mutations in the GC-boxes decrease promoter activity, deletion of either one of them leads to an increase in promoter activity. We can reconcile these observations with the positive effect of Sp1 and Sp3 if protein-induced bending acts, at least in part, to bring together distally spaced factors important for transcription initiation.
Quantitative determination of the binding of β2-glycoprotein I and prothrombin to phosphatidylserine-exposing blood platelets
Authors: BEVERS Edouard M. , JANSSEN Marie P. , COMFURIUS Paul , BALASUBRAMANIAN Krishnakumar , SCHROIT Alan J. , ZWAAL Robert F. A. , WILLEMS George M.
Published: February 2005

The plasma protein β2GPI (β2-glycoprotein I) has been proposed to mediate phagocytosis of apoptotic cells and to play a role in the antiphospholipid syndrome. This suggestion is based mainly on the presumption that β2GPI has an appreciable interaction with PS (phosphatidylserine)-exposing cell membranes. However, quantitative data on the binding of β2GPI to PS-exposing cells under physiologically relevant conditions are scarce and conflicting. Therefore we evaluated the binding of β2GPI to PS-expressing blood platelets. Flow cytometry showed that binding of β2GPI is negligible at physiological ionic strength, in contrast with significant binding occurring at low ionic strength. Binding parameters of β2GPI and (for comparison) prothrombin were quantified by ellipsometric measurement of protein depletion from the supernatant following incubation with platelets. At low ionic strength (20 mM NaCl, no CaCl2), a dissociation constant (Kd) of 0.2 μM was found for β2GPI, with 7.4×105 binding sites per platelet. Under physiologically relevant conditions (120 mM NaCl and 3 mM CaCl2), binding of β2GPI was not detectable (extrapolated Kd>80 μM). Prothrombin binding (at 3 mM CaCl2) was much less affected by ionic strength: Kd values of 0.5 and 1.4 μM were observed at 20 and 120 mM NaCl respectively. The low affinity and the presence of many lipid-binding proteins in plasma that can compete with the binding of β2GPI suggest that only a small fraction (<5%) of the binding sites on PS-exposing blood cells are likely to be occupied by β2GPI. These findings are discussed in relation to the alleged (patho-)physiological functions of β2GPI.
Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
Authors: XU Zheng , AU Shannon W. N.
Published: February 2005

SUMO (small ubiquitin-related modifier) is a member of the ubiquitin-like protein family that regulates cellular function of a variety of target proteins. SUMO proteins are expressed as their precursor forms. Cleavage of the residues after the ‘GG’ region of these precursors by SUMO-specific proteases in maturation is a prerequisite for subsequent sumoylation. To understand further this proteolytic processing, we expressed and purified SENP1 (sentrin-specific protease 1), one of the SUMO-specific proteases, using an Escherichia coli expression system. We show that SENP1 is capable of processing all SUMO-1, -2 and -3 in vitro; however, the proteolytic efficiency of SUMO-1 is the highest followed by SUMO-2 and -3. We demonstrate further that the catalytic domain of SENP1 (SENP1C) alone can determine the substrate specificity towards SUMO-1, -2 and -3. Replacement of the C-terminal fragments after the ‘GG’ region of SUMO-1 and -2 precursors with that of the SUMO-3, indicates that the C-terminal fragment is essential for efficient maturation. In mutagenesis analysis, we further map two residues immediately after the ‘GG’ region, which determine the differential maturation. Distinct patterns of tissue distribution of SENP1, SUMO-1, -2 and -3 are characterized. Taken together, we suggest that the observed differential maturation process has its physiological significance in the regulation of the sumoylation pathway.
Subtype-specific regulation of equilibrative nucleoside transporters by protein kinase CK2
Authors: STOLK Meaghan , COOPER Elizabeth , VILK Greg , LITCHFIELD David W. , HAMMOND James R.
Published: February 2005

Two subtypes of equilibrative transporters, es (equilibrative inhibitor-sensitive) and ei (equilibrative inhibitor-insensitive), are responsible for the majority of nucleoside flux across mammalian cell membranes. Sequence analyses of the representative genes, ENT1 {equilibrative nucleoside transporter 1; also known as SLC29A1 [solute carrier family 29 (nucleoside transporters), member 1]} and ENT2 (SLC29A2), suggest that protein kinase CK2-mediated phosphorylation may be involved in the regulation of es- and ei-mediated nucleoside transport. We used human osteosarcoma cells transfected with catalytically active or inactive α′ and α subunits of CK2 to assess the effects of CK2 manipulation on nucleoside transport activity. Expression of inactive CK2α′ (decreased CK2α′ activity) increased the number of binding sites (∼1.5-fold) for the es-specific probe [3H]NBMPR ([3H]nitrobenzylthioinosine), and increased (∼1.8-fold) the Vmax for 2-chloro[3H]adenosine of the NBMPR-sensitive (es) nucleoside transporter. There was a concomitant decrease in the Vmax of the NBMPR-resistant (ei-mediated) uptake of 2-chloro[3H]adenosine. This inhibition of CK2α′ activity had no effect, however, on either the KD of [3H]NBMPR binding or the Km of 2-chloro[3H]adenosine uptake. Quantitative PCR showed a transient decrease in the expression of both hENT1 (human ENT1) and hENT2 mRNAs within 4–12 h of induction of the inactive CK2α′ subunit, but both transcripts had returned to control levels by 24 h. These data suggest that inhibition of CK2α′ reduced ei activity by attenuation of hENT2 transcription, while the increase in es/hENT1 activity was mediated by post-translational action of CK2. The observed modification in es activity was probably due to a CK2α′-mediated change in the phosphorylation state of the ENT1 protein, or an interacting protein, effecting an increase in the plasma membrane lifetime of the transport proteins.
PAK and other Rho-associated kinases – effectors with surprisingly diverse mechanisms of regulation
Authors: ZHAO Zhou-shen , MANSER Ed
Published: February 2005

The Rho GTPases are a family of molecular switches that are critical regulators of signal transduction pathways in eukaryotic cells. They are known principally for their role in regulating the cytoskeleton, and do so by recruiting a variety of downstream effector proteins. Kinases form an important class of Rho effector, and part of the biological complexity brought about by switching on a single GTPase results from downstream phosphorylation cascades. Here we focus on our current understanding of the way in which different Rho-associated serine/threonine kinases, denoted PAK (p21-activated kinase), MLK (mixed-lineage kinase), ROK (Rho-kinase), MRCK (myotonin-related Cdc42-binding kinase), CRIK (citron kinase) and PKN (protein kinase novel), interact with and are regulated by their partner GTPases. All of these kinases have in common an ability to dimerize, and in most cases interact with a variety of other proteins that are important for their function. A diversity of known structures underpin the Rho GTPase–kinase interaction, but only in the case of PAK do we have a good molecular understanding of kinase regulation. The ability of Rho GTPases to co-ordinate spatial and temporal phosphorylation events explains in part their prominent role in eukaryotic cell biology.
Compartmental oxidation of thiol–disulphide redox couples during epidermal growth factor signalling
Authors: HALVEY Patrick J. , WATSON Walter H. , HANSEN Jason M. , GO Young-Mi , SAMALI Afshin , JONES Dean P.
Published: February 2005

Exogenously added ROS (reactive oxygen species) cause generalized oxidation of cellular components, whereas endogenously generated ROS induced by physiological stimuli activate discrete signal transduction pathways. Compartmentation is an important aspect of such pathways, but little is known about its role in redox signalling. We measured the redox states of cytosolic and nuclear Trx1 (thioredoxin-1) and mitochondrial Trx2 (thioredoxin-2) using redox Western blot methodologies during endogenous ROS production induced by EGF (epidermal growth factor) signalling. The glutathione redox state was measured by HPLC. Results showed that only cytosolic Trx1 undergoes significant oxidation. Thus EGF signalling involves subcellular compartmental oxidation of Trx1 in the absence of a generalized cellular oxidation.
Hepatically derived selenoprotein P is a key factor for kidney but not for brain selenium supply
Authors: SCHWEIZER Ulrich , STRECKFUß Florian , PELT Paco , CARLSON Bradley A. , HATFIELD Dolph L. , KÖHRLE Josef , SCHOMBURG Lutz
Published: February 2005

Liver-specific inactivation of Trsp, the gene for selenocysteine tRNA, removes SePP (selenoprotein P) from plasma, causing serum selenium levels to fall from 298 μg/l to 50 μg/l and kidney selenium to decrease to 36% of wild-type levels. Likewise, glutathione peroxidase activities decreased in plasma and kidney to 43% and 18% respectively of wild-type levels. This agrees nicely with data from SePP knockout mice, supporting a selenium transport role for hepatically expressed SePP. However, brain selenium levels remain unaffected and neurological defects do not occur in the liver-specific Trsp knockout mice, while SePP knockout mice suffer from neurological defects. This indicates that a transport function in plasma is exerted by hepatically derived SePP, while in brain SePP fulfils a second, hitherto unexpected, essential role.
More roles for selenoprotein P: local selenium storage and recycling protein in the brain
Authors: RICHARDSON Des R.
Published: February 2005

How is the essential micronutrient, selenium (Se), transported in the serum and then donated to tissues? In this issue of the Biochemical Journal, Schweizer and colleagues demonstrate, using conditional and total mouse knockout models, that SePP (selenoprotein P) is the major transporter of Se in the serum. Moreover, in the sanctuary area of the brain, SePP was shown to play a hitherto unexpected role as a local Se storage and recycling protein that directly maintains brain Se levels. Considering the function of Se in normal brain metabolism, these results are crucial for our understanding of the role of selenoproteins in redox regulation, antioxidant defences, thyroid hormone metabolism and the development of neurodegenerative conditions.
Observation of recombination enhanced defect annealing in 4H–SiC
Authors: Storasta L. , Carlsson F. H. C. , Bergman J. P. , Janzén E.
Published: February 2005

We report observation of recombination enhanced defect annealing in 4H–SiC detected by capacitance transient spectroscopy and low temperature photoluminescence (PL). Intrinsic defect centers, created by 160keV electron irradiation, reduce in concentration after illumination at temperatures much lower than previously reported annealing temperatures of 400 and 800°C. The effect is observed after both external intense above band gap laser excitation, and with recombination in a forward biased pin diode. PL measurements show that several lines, normally detected after electron irradiation, have almost or entirely disappeared by recombination enhanced annealing at room temperature. From capacitance transient measurements, the annealing enhancement is found to be largest for the HS2 hole trap, while the EH1 and EH3 electron traps also anneal out by recombination enhanced reaction but at a lower rate.
Axisymmetric motion of a file of red blood cells through capillaries
Authors: Pozrikidis C.
Published: February 2005

The axisymmetric, pressure-driven motion of red blood cells through cylindrical capillaries is investigated by numerical simulation. The mathematical formulation takes into consideration the nearly incompressible and elastic properties of the cell membrane with respect to shearing and bending deformation from the unstressed shape of the biconcave disk. In the theoretical model, the cells are arranged in a periodic file that is coaxial with the capillaries, and the evolution from the equilibrium to a highly deformed steady shape is computed using a boundary-integral method for axisymmetric Stokes flow. The results illustrate the significance of the capillary radius and cell spacing on the discharge hematocrit and apparent viscosity of the one-dimensional suspension, and validate the assumptions of approximate solutions based on the lubrication approximation for tightly fitting cells developed by previous authors.
The method of regularized Stokeslets in three dimensions:  Analysis, validation, and application to helical swimming
Authors: Cortez Ricardo , Fauci Lisa , Medovikov Alexei
Published: February 2005

The method of regularized Stokeslets is a Lagrangian method for computing Stokes flow driven by forces distributed at material points in a fluid. It is based on the superposition of exact solutions of the Stokes equations when forces are given by a cutoff function. We present this method in three dimensions, along with an analysis of its accuracy and performance on the model problems of flow past a sphere and the steady state rotation of rigid helical tubes. Predicted swimming speeds for various helical geometries are compared with experimental data for motile spirochetes. In addition, the regularized Stokeslet method is readily implemented in conjunction with an immersed boundary representation of an elastic helix that incorporates passive elastic properties as well as mechanisms of internal force generation.
A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties
Authors: Steinhauser Martin Oliver
Published: February 2005

This paper investigates the conformational and scaling properties of long linear polymer chains. These investigations are done with the aid of Monte Carlo (MC) and molecular dynamics (MD) simulations. Chain lengths that comprise several orders of magnitude to reduce errors of finite size scaling, including the effect of solvent quality, ranging from the athermal limit over the θ-transition to the collapsed state of chains are investigated. Also the effect of polydispersity on linear chains is included which is an important issue in the real fabrication of polymers. A detailed account of the hybrid MD and MC simulation model and the exploited numerical methods is given. Many results of chain properties in the extrapolated limit of infinite chain lengths are documented and universal properties of the chains within their universality class are given. An example of the difference between scaling exponents observed in actual solvents and those observed in the extremes of “good solvents” and “θ-solvents” in simulations is provided by comparing simulation results with experimental data on low density polyethylene. This paper is concluded with an outlook on the extension of this study to branched chain systems of many different branching types.
Experiments and quantum-chemical calculations on Rydberg states of H2CS in the region 5.6–9.5 eV
Authors: Chiang Su-Yu , Lin I-Feng
Published: February 2005

Absorption spectrum of H2CS in the region 5.6–9.5 eV was recorded with a continuously tunable light source of synchrotron radiation. After we subtracted absorption bands of CS2, our spectrum clearly shows vibrational progressions associated with transitions A11(π,π*)–XA11 and B21(n,4s)–XA11 in the region 5.6–6.7 eV. A spectrum from which absorption of C2H4 and CS2 are subtracted shows several discrete bands in the region 6.9–9.5 eV. A Rydberg state B21(n,4pz) lying below Rydberg state A11(n,4py) is confirmed, and the C–H symmetric stretching (ν1) and CH out-of-plane bending (ν4) modes for a transition B21(n,4s)–XA11 are identified. New transitions to Rydberg states associated with excitation to 5s-11s,5pz-7pz,5py-7py, and 3d-6d are identified based on quantum defects and comparison with vertical excitation energies predicted with time-dependent density-functional theory (TD-DFT) and outer-valence Green’s-function (OVGF) methods. For lower excited states predictions from these TD-DFT∕6-31+G calculations agree satisfactorily with experimental values, but for higher Rydberg states the OVGF method using aug-cc-pVTZ basis set augmented with extra diffuse functions yields more accurate predictions of excitation energies.
Absolute vibrational and electronic cross sections for low-energy electron (2–12 eV) scattering from condensed pyrimidine
Authors: Levesque P. L. , Michaud M. , Sanche L.
Published: February 2005

Low-energy vibrational and electronic electron-energy-loss (EEL) spectra of pyrimidine condensed on a thin film of solid argon held at 18 K are reported for the incident-energy range of 2–12 eV. Sensitivity to symmetry and spin forbidden transitions as well as correlations to the triplet states of benzene make it possible to ascribe the main features, below 7 eV in the electronic part of the EEL spectrum, to triplet transitions. The lowest EEL feature with an energy onset at 3.5 eV is attributed to a transition to the B13(n→π*) valence electronic state and the next triplet n→π* transition to a A23 state located around 4.5 eV. The remaining EEL features at 4.3, 5.2, 5.8, and 6.5 eV are all assigned to π→π* transitions to states of symmetry B23, A13, B23, and B23+A13, respectively. The most intense maximum at 7.6 eV is found to correspond to both B21 and A11 transitions, as in the vacuum ultraviolet spectra. Absolute inelastic cross sections per scatterer are derived from a single collision treatment described herein. Their values are found to lie within the 10−17cm2 range for both the electronic and the vibrational excitations. Features in the energy dependence of the cross sections are discussed, whenever possible, by comparison with data and mechanisms found in the gas phase. A maximum over the 4–5 eV range is attributed to a B̃B12 shape resonance and another one observed in the 6–7 eV range is ascribed to either or both σ* shape resonances of A12 and B22 symmetries.
Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries
Authors: Berk Usta O. , Ladd Anthony J. C. , Butler Jason E.
Published: February 2005

A numerical method to simulate the dynamics of polymer solutions in confined geometries has been implemented and tested. The method combines a fluctuating lattice-Boltzmann model of the solvent [Ladd, Phys. Rev. Lett. 70, 1339 (1993)] with a point-particle model of the polymer chains. A friction term couples the monomers to the fluid [Ahlrichs and Dünweg, J. Chem. Phys. 111, 8225 (1999)], providing both the hydrodynamic interactions between the monomers and the correlated random forces. The coupled equations for particles and fluid are solved on an inertial time scale, which proves to be surprisingly simple and efficient, avoiding the costly linear algebra associated with Brownian dynamics. Complex confined geometries can be represented by a straightforward mapping of the boundary surfaces onto a regular three-dimensional grid. The hydrodynamic interactions between monomers are shown to compare well with solutions of the Stokes equations down to distances of the order of the grid spacing. Numerical results are presented for the radius of gyration, end-to-end distance, and diffusion coefficient of an isolated polymer chain, ranging from 16 to 1024 monomers in length. The simulations are in excellent agreement with renormalization group calculations for an excluded volume chain. We show that hydrodynamic interactions in large polymers can be systematically coarse-grained to substantially reduce the computational cost of the simulation. Finally, we examine the effects of confinement and flow on the polymer distribution and diffusion constant in a narrow channel. Our results support the qualitative conclusions of recent Brownian dynamics simulations of confined polymers [Jendrejack et al., J. Chem. Phys. 119, 1165 (2003) and Jendrejack et al., J. Chem. Phys. 120, 2513 (2004)].
Stress anisotropy induced by periodic boundary conditions
Authors: González-Melchor Minerva , Orea Pedro , López-Lemus Jorge , Bresme Fernando , Alejandre José
Published: February 2005

Finite size effects due to periodic boundary conditions are investigated using computer simulations in the canonical ensemble. We study liquids with densities corresponding to typical liquid coexistence densities, and temperatures between the triple and critical points. The components of the pressure tensor are computed in order to analyze the finite size effects arising from the size and geometry of the simulation box. Two different box geometries are considered: cubic and parallelepiped. As expected the pressure tensor is isotropic in cubic boxes, but it becomes anisotropic for small noncubic boxes. We argue this is the origin of the anomalous behavior observed recently in the computation of the surface tension of liquid-vapor interfaces. Otherwise, we find that the bulk pressure is sensitive to the box geometry when small simulation boxes are considered. These observations are general and independent of the model liquid considered. We report results for liquids interacting through short range forces, square well and Lennard-Jones, and also long range Coulombic interactions. The effect that small surface areas have on the surface tension is discussed, and some preliminary results at the liquid vapor-interface for the square well potential are given.
Exciton migration in a polythiophene: Probing the spatial and energy domain by line-dipole Förster-type energy transfer
Authors: Westenhoff Sebastian , Daniel Clément , Friend Richard H. , Silva Carlos , Sundström Villy , Yartsev Arkady
Published: February 2005

We study exciton migration in low molecular weight poly[3-(2,5-dioctylphenyl)thiophene] in dilute solution by means of ultrafast spectroscopy and Monte Carlo simulations of resonance energy transfer using the line-dipole Förster approach. The model includes the build-up of polymer chains, site-selective exciton generation, and diffusion through incoherent energy transfer. Time-resolved, ensemble-averaged experimental data are reproduced, namely photoluminescence spectral migration and stimulated emission anisotropy decays measured by streak camera and femtosecond transient absorption spectroscopy under site-selective excitation conditions. Importantly, the relatively simple line-dipole Förster-type approach beyond the point-dipole approximation reproduces both experiments quantitatively. Since explicit chain conformations are used in the model, the simulations yield a descriptive microscopic picture of exciton migration. The effective conjugation length (lseg=2.9nm, 7.4 monomer units) and the disorder of the chains (Ω=0.8) are yielded as the only fitting parameters. We find an extra component that is not covered by our fits in anisotropy decays at early times for high excitation energies. This is interpreted within the context that the effective conjugation is limited by conformational disorder.
Restricted orientational motion of nitroxides in molecular glasses: Direct estimation of the motional time scale basing on the comparative study of primary and stimulated electron spin echo decays
Authors: Dzuba S. A. , Kirilina E. P. , Salnikov E. S. , Kulik L. V.
Published: February 2005

A comparative study of anisotropic relaxation in two-pulse primary and three-pulse stimulated electron spin echo decays provides a direct way to distinguish fast (correlation time τc<10−6s) and slow (τc>10−6s) motions. Anisotropic relaxation is detected as a difference of the decay rates for different resonance field positions in anisotropic electron paramagnetic resonance spectra. For fast motion anisotropic relaxation influences the primary echo decay and does not influence the stimulated echo decay. For slow motion it is seen in both two-pulse echo and three-pulse stimulated echo decays. For nitroxide spin probes dissolved in glassy glycerol only fast motion was found below 200K. Increase of temperature above 200K results in the appearance of slow motion. Its amplitude increases rapidly with temperature increase. While in glycerol glass slow motion appears above glass transition temperature Tg, in ethanol glass it is observable below Tg. The scenario of motional dynamics in glasses is proposed which involves the broadening of the correlation time distribution with increasing temperature.
Charge-transfer Zn-porphyrin derivatives with very large two-photon absorption cross sections at 1.3–1.5 μm fundamental wavelengths
Authors: Luo Yi , Rubio-Pons Oscar , Guo Jing-Dong , Ågren Hans
Published: February 2005

A series of charge-transfer Zn-porphyrin derivatives with large two-photon absorption cross sections at 1.3–1.5 μm fundamental wavelengths are designed using time-dependent hybrid density functional theory. The fluorescence of these chromospheres is expected to be in the region of 700–900 nm. These unique features make them suitable for a variety of biophotonic and telecommunication applications.
Photoisomerization of azobenzene from first-principles constrained density-functional calculations
Authors: Tiago Murilo L. , Ismail-Beigi Sohrab , Louie Steven G.
Published: February 2005

Despite considerable work in the field, the precise mechanism for the photoisomerization of azobenzene, C12H10N2, is still an open issue. Early theoretical studies of the problem indicated that isomerization occurs through an in-plane inversion path, and this has been used to explain recent time-resolved UV-visible spectroscopy measurements. On the other hand, a number of recent theoretical studies have concluded that a torsion of the N–N bond (“rotation path”) is probably the most favorable mechanism for photoisomerization involving the first excited state. We have performed first-principles calculations using constrained density-functional theory (DFT) and time-dependent DFT in the local-density approximation, with results that also favor the rotation path mechanism. Our results are compared with other analyses, primarily based on configuration interaction.
Electron correlation in Hooke’s law atom in the high-density limit
Authors: Gill P. M. W. , O’Neill D. P.
Published: February 2005

Closed-form expressions for the first three terms in the perturbation expansion of the exact energy and Hartree–Fock energy of the lowest singlet and triplet states of the Hooke’s law atom are found. These yield elementary formulas for the exact correlation energies (−49.7028 and −5.80765mEh) of the two states in the high-density limit and lead to a pair of necessary conditions on the exact correlation kernel G(w) in Hartree–Fock–Wigner theory.
Computer simulations of the collapse of a granular column
Authors: Zenit Roberto
Published: February 2005

Recently, two independent groups reported experimental results on the process of collapse of a cylindrical granular column. It was found that the shape of the final deposit depended mostly on column aspect ratio; surprisingly, the frictional properties of the material appeared not to influence the results significantly. In this investigation, making use of discrete element code, simulations of an equivalent two-dimensional system were carried out. The numerical results qualitatively reproduce the behavior observed in experiments. Performing an energy balance of the system, the different deposit regimes can be discerned.
Axial stretching and vortex definition
Authors: Wu J.-Z. , Xiong A.-K. , Yang Y.-T.
Published: February 2005

Four existing invariant criteria for defining a vortex are diagnosed analytically and demonstrated by the Burgers and Sullivan vortices. Two of the criteria are found disqualified as generally applicable, and one underestimates the core radius. The diagnosis leads to a general requirement for any possible criterion: it should be able to identify the vortex axis and allow for arbitrary axial strain.
Magneto-rotation of nonmagnetic micro-crystals caused by diamagnetic anisotropy
Authors: Uyeda Chiaki , Takashima Ryoichi , Tanaka Kenta
Published: February 2005

Preferential alignments of magnetically stable axes of diamagnetic micro-crystals dispersed in liquid ethanol were observed at a low field of 1 T for basic inorganic oxides without the use of a superconducting magnet; alignments were newly observed for corundum, forsterite, gypsum, orthoclase, KDP, and Al(OH)3. Diamagnetic anisotropy (Δχ)dia of the material was the cause of alignment. Most of the inorganic oxides, other than the above-mentioned materials, are expected to show alignment at similar field intensities. This is because their calculated (Δχ)dia values exceed 1×10−9emu∕g; it was assumed in the calculation that (Δχ)dia values originate from individual bonding orbital.
Adsorption-induced conversion of the carbon nanotube field effect transistor from ambipolar to unipolar behavior
Authors: Kang Donghun , Park Noejung , Hyun Jaewoong , Bae Eunju , Ko Juhye , Kim Jujin , Park Wanjun
Published: February 2005

We investigate ambipolar to unipolar transition by the effect of ambient air on the carbon nanotube field-effect transistor. A unipolar transport property of the double-walled nanotube field-effect transistor and its conversion from ambipolar behavior are observed. We suggest that adsorptions of oxygen molecules, whose lowest-unoccupied-molecular-orbital state is around the midgap of the carbon nanotube, could suppress the electron channel formation and, consequently, result in the unipolar transport behavior.
Effects of WO3 dopant on the structure and electrical properties of Pb0.97La0.03(Zr0.52Ti0.48)O3 thin films
Authors: Shannigrahi Santiranjan , Yao Kui
Published: February 2005

Pb 0.97 La 0.03 ( Zr 0.52 Ti 0.48 ) O 3 + x WO 3 at % (x=0, 0.2, 0.5, 1, and 2) (PLWZT) thin films are deposited on Pt–Ti–SiO2–Si substrates using a sol-gel process. We demonstrate that WO3 dopant plays a significant role on the structure and electrical properties of the PLWZT films. X-ray diffraction (XRD) analyses show that the PLWZT films undergo a dramatic tetragonal–to–cubic crystalline phase transformation with a small amount of WO3 additives. X-ray photoelectron spectroscopy (XPS) study shows that the chemical state of W changes with varying concentration of WO3 in the films. Moreover, PLWZT films with a small amount of WO3 doping (0.2 at %) show a decreased conductivity with an improved remnant polarization value of 30μC∕cm2. In addition, compared to the base (PLZT) film, such doping concentration also leads to significantly improved fatigue characteristics. A defect chemistry mechanism indicating the reduction of oxygen vacancies by the substitution of W for Ti at different doping concentrations has been proposed to explain the observed experimental results.
230% room-temperature magnetoresistance in CoFeB∕MgO∕CoFeB magnetic tunnel junctions
Authors: Djayaprawira David D. , Tsunekawa Koji , Nagai Motonobu , Maehara Hiroki , Yamagata Shinji , Watanabe Naoki , Yuasa Shinji , Suzuki Yoshishige , Ando Koji
Published: February 2005

Magnetoresistance (MR) ratio up to 230% at room temperature (294% at 20 K) has been observed in spin-valve-type magnetic tunnel junctions (MTJs) using MgO tunnel barrier layer fabricated on thermally oxidized Si substrates. We found that such a high MR ratio can be obtained when the MgO barrier layer was sandwiched with amorphous CoFeB ferromagnetic electrodes. Microstructure analysis revealed that the MgO layer with (001) fiber texture was realized when the MgO layer was grown on amorphous CoFeB rather than on polycrystalline CoFe. Since there have been no theoretical studies on the MTJs with a crystalline tunnel barrier and amorphous electrodes, the detailed mechanism of the huge tunneling MR effect observed in this study is not clear at the present stage. Nevertheless, the present work is of paramount importance in realizing high-density magnetoresistive random access memory and read head for ultra high-density hard-disk drives into practical use.
Strongly localized exciton luminescence in Cr-doped GaN
Authors: Shanthi S. , Hashimoto M. , Zhou Y. K. , Kimura S. , Emura S. , Hasegawa S. , Hasuike N. , Harima H. , Asahi H.
Published: February 2005

Low-temperature photoluminescence spectrum of the transition metal Cr-doped GaN (GaCrN) shows unusual high-intensity emission lines at 3.365 and 3.311 eV. The spectrum also contains a weak neutral donor bound excitonic transition of wurtzite GaN at 3.47 eV, free excitonic transition of GaCrN at 3.29 eV, and two low-intensity lines at 3.24 and 3.17 eV. From our investigations, we attribute these high-intensity lines to the stacking faults which can bind excitons and are due to the coexistence of wurtzite and zinc blende phases of GaN. The 3.24 and 3.17 eV lines are interpreted as phonon replica lines of the 3.31 eV emission line.
Effect of electrical bias on metastability in hydrogenated nanocrystalline silicon solar cells
Authors: Yue Guozhen , Yan Baojie , Yang Jeffrey , Guha Subhendu
Published: February 2005

The effect of electrical bias on metastability in hydrogenated nanocrystalline silicon (nc-Si:H) solar cells is studied. We find that forward bias current injection in the dark does not cause any degradation in nc-Si:H solar cells, while light soaking under reverse bias enhances the light-induced degradation in the cell performance. These phenomena are contrary to those found in hydrogenated amorphous silicon solar cells. We argue that the forward injected carriers mainly transport through the nanocrystallites where carrier recombination does not create metastable defects. The increased degradation under reverse bias is explained in terms of the heterogeneity of the material structure.
Efficient polymer-nanocrystal quantum-dot photodetectors
Authors: Qi Difei , Fischbein Michael , Drndić Marija , Šelmić Sandra
Published: February 2005

We have realized highly efficient photodetectors based on composites of the semiconducting polymer poly[2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene] and PbSe nanocrystal quantum dots. The external quantum efficiency in these devices is greater than 1 for electric fields E∼7×105V∕cm. The observed photocurrent gain could be attributed to the carrier multiplication in PbSe nanocrystal quantum dots via multiple exciton generation, and the efficient charge conduction through the host polymer material. This photocurrent gain is observed only when the PbSe nanocrystal band gap is at least three times smaller than the optical energy gap of the active polymer material.
Piezoresistance of carbon nanotubes on deformable thin-film membranes
Authors: Grow Randal J. , Wang Qian , Cao Jien , Wang Dunwei , Dai Hongjie
Published: February 2005

Carbon nanotubes have interesting electromechanical properties that may enable a new class of nanoscale mechanical sensors. We fabricated two-terminal nanotube devices on silicon nitride membranes, measured their electronic transport versus strain, and estimated their band gaps and the strain-induced changes in them. We found band-gap increases and decreases among both semiconducting and small-gap semiconducting (SGS) tubes. The SGS band gaps exceeded the predicted curvature-induced gaps for their diameter. Some of the band-gap changes for both types of tubes exceeded the predicted maxima. These anomalies are likely caused by interaction with the rough silicon nitride surface.
Flux pinning enhancement in melt-processed YBa2Cu3O7 with extended nanodefects
Authors: Shlyk L. , Krabbes G. , Fuchs G. , Nenkov K.
Published: February 2005

Melt-processed YBa2Cu3O7 (YBCO), containing a random array of Y–Ba–Cu–Ir–O nanostructures (about 20–150nm in diameter and several μm in length) has been grown. The pinning efficiency of the resulting YBCO nanocomposite is superior to Li-doped or undoped melt-processed YBCO at higher magnetic fields. At 77K, the irreversibility field increases more than 8T in the presence of the extended nanodefects. The increase of the effective activation energy of the YBCO nanocomposite is nearly twice that of the Li-doped material.
Work function uniformity of Al–Ni alloys obtained by scanning Maxwell-stress microscopy as an effective tool for evaluating metal transistor gates
Authors: Matsukawa Takashi , Yasumuro Chiaki , Yamauchi Hiromi , Masahara Meishoku , Suzuki Eiichi , Kanemaru Seigo
Published: February 2005

Work function control of metal transistor gates was implemented with Al–Ni alloys. In addition to obtaining conventional capacitance-voltage (C-V) measurements to evaluate the work function, we microscopically characterized the work function distribution through scanning Maxwell-stress microscopy (SMM). The C-V curves of the Al–Ni alloys that we investigated exhibited work functions approximately between those of Al and Ni. The SMM analysis revealed that an Al–Ni alloy fabricated by the interdiffusion of a Ni∕Al stack had a significant nonuniformity of the work function. This nonuniformity correlated with degradation of the C-V characteristics for interdiffused Al–Ni alloys.