bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of storm surge, wave, currents, and inundation in the Outer Banks and Chesapeake Bay during Hurricane Isabel in 2003: The importance of waves
Authors: Sheng Y. Peter , Alymov Vadim , Paramygin Vladimir A.
Published: April 2010

This paper investigates the effects of waves on storm surge, currents, and inundation in the Outer Banks and Chesapeake Bay during Hurricane Isabel in 2003 through detailed comparison between observed wind, wave, surge, and inundation data and results from an integrated storm surge modeling system, CH3D‐SSMS. CH3D‐SSMS, which includes coupled coastal and basin‐scale storm surge and wave models, successfully simulated measured winds, waves, storm surge, currents, and inundation during Isabel. Comprehensive modeling and data analysis revealed noticeable effects of waves on storm surge, currents, and inundation. Among the processes that represent wave effects, radiation stress (outside the estuaries) and wave‐induced stress (outside and inside the estuaries) are more important than wave‐induced bottom stress in affecting the water level. Maximum surge was 3 m, while maximum wave height was 20 m offshore and 2.5 m inside the Chesapeake Bay, where the maximum wave‐induced water level reached 1 m. Significant waves reached 3.5 m and 16 s at Duck Pier, North Carolina, and 1.6 m and 5 s at Gloucester, Virginia. At Duck, wave effects accounted for ∼36 cm or 20% of the peak surge elevation of 1.71 m. Inside the Chesapeake Bay, wave effects account for 5–10% of observed peak surge level. A two‐layer flow is found at Kitty Hawk, North Carolina, during the peak of storm surge owing to the combined effects of wind and wave breaking. Higher surge elevations result when the 3‐D surge model, instead of the 2‐D surge model, is coupled with the 2‐D wave model owing to its relatively lower bottom friction. Wave heights obtained with 3‐ and 2‐D surge models show little difference.
Circulation at the entrance of the Gulf of California from satellite altimeter and hydrographic observations
Authors: Godínez Victor M. , Beier E. , Lavín M. F. , Kurczyn J. A.
Published: April 2010

The surface circulation around the entrance to the Gulf of California is described from satellite altimetry supported by 10 conductivity‐temperature‐depth (CTD) surveys. The sea surface height calculated from the 1/4° World Ocean Database 2001 climatology plus the Archiving, Validation, and Interpretation of Satellite Oceanographic altimeter data (October 1992 to January 2008) were RMS adjusted to the dynamic height calculated from CTD data; the 27.0 kg m−3 isopycnal provided the optimum reference. In the mean, the surface circulation shows a branch of the California Current heading landward toward the Gulf of California entrance, where it splits into two subbranches; these are separated by a cyclonic circulation attached to the coast south of Cabo Corrientes. This feature is produced by Sverdrup dynamics and is the first observational indication that the Mexican Coastal Current is generated locally by the wind stress curl, as previously suggested by numerical models. The global variance of the surface circulation can be separated into seasonal (explained variance 35%), interannual (explained variance 35%), and mesoscale (explained variance 30%) components. The seasonal signal, which shows the interplay of the poleward Mexican Coastal Current and the equatorward branch of the California Current, can be explained by a long Rossby wave model forced by the annual wind and by radiation from the coast. The interannual component is dominated by the El Niño‐Southern Oscillation, which induces in the gulf entrance an anticyclonic (cyclonic) circulation during El Niño (La Niña); this circulation includes a poleward‐flowing branch (during El Niño) parallel to the Pacific coast of the Baja California peninsula. The mesoscale variability is caused by intense eddy activity.
Modeling the effects of methane source changes on the seasonal cycles of methane mixing ratio and δ13C in Southern Hemisphere midlatitudes
Authors: Allan W. , Struthers H. , Lowe D. C. , Mikaloff Fletcher S. E.
Published: April 2010

The apparent kinetic isotope effect (ɛA) inferred from measurements of methane (CH4) and δ13CH4 in the extratropical Southern Hemisphere (ETSH) is significantly larger than expected if the sink were caused by hydroxyl radical (OH•) alone. If the OH• sink were the primary driver for the observed seasonal cycles in CH4 and δ13CH4 in the ETSH, published laboratory data suggest an ɛA of the order −3.9‰. However, a value of the order −11‰ has been inferred from measurements in the background troposphere. Atomic chlorine (Cl•) in the marine boundary layer (MBL) could explain the difference, but an alternative hypothesis is that the large ɛA in the ETSH is due to seasonally varying CH4 emissions. We test this by sequentially omitting or doubling CH4 emissions from each seasonally varying source in the UMeth model (Unified Model with Methane) and evaluating the corresponding effects on ɛA at Baring Head (41.40°S). If only the OH• sink is included, the maximum change in ɛA is about 1.7‰. When both OH• and a mean Cl• concentration of 18 × 103 atoms cm−3 in the MBL are included, the maximum change in ɛA is about 1.1‰. For realistic changes in the CH4 sources over a few years (∼10% of the simulated changes), we estimate that changes in ɛA are of the same order as the uncertainties in the derivation of ɛA from time series of CH4 and δ13CH4 over a comparable period. We conclude that realistic changes in seasonally varying CH4 sources do not significantly affect ɛA or previously derived estimates of the MBL Cl• sink using ɛA.
Convective vortices and dust devils at the Phoenix Mars mission landing site
Authors: Ellehoj M. D. , Gunnlaugsson H. P. , Taylor P. A. , Kahanpää H. , Bean K. M. , Cantor B. A. , Gheynani B. T. , Drube L. , Fisher D. , Harri A.‐M. , Holstein‐Rathlou C. , Lemmon M. T. , Madsen M. B. , Malin M. C. , Polkko J. , Smith P. H. , Tamppari L. K. , Weng W. , Whiteway J.
Published: April 2010

The Phoenix Mars Lander detected a larger number of short (∼20 s) pressure drops that probably indicate the passage of convective vortices or dust devils. Near‐continuous pressure measurements have allowed for monitoring the frequency of these events, and data from other instruments and orbiting spacecraft give information on how these pressure events relate to the seasons and weather phenomena at the Phoenix landing site. Here 502 vortices were identified with a pressure drop larger than 0.3 Pa occurring in the 151 sol mission (Ls 76 to 148). The diurnal distributions show a peak in convective vortices around noon, agreeing with current theory and previous observations. The few events detected at night might have been mechanically forced by turbulent eddies caused by the nearby Heimdal crater. A general increase with major peaks in the convective vortex activity occurs during the mission, around Ls = 111. This correlates with changes in midsol surface heat flux, increasing wind speeds at the landing site, and increases in vortex density. Comparisons with orbiter imaging show that in contrast to the lower latitudes on Mars, the dust devil activity at the Phoenix landing site is influenced more by active weather events passing by the area than by local forcing.
Scale‐wise evolution of rainfall probability density functions fingerprints the rainfall generation mechanism
Authors: Molini Annalisa , Katul Gabriel G. , Porporato Amilcare
Published: April 2010

The cross‐scale probabilistic structure of rainfall intensity records collected over time scales ranging from hours to decades at sites dominated by both convective and frontal systems is investigated. Across these sites, intermittency build‐up from slow to fast time‐scales is analyzed in terms of heavy tailed and asymmetric signatures in the scale‐wise evolution of rainfall probability density functions (pdfs). The analysis demonstrates that rainfall records dominated by convective storms develop heavier‐tailed power law pdfs toward finer scales when compared with their frontal systems counterpart. Also, a concomitant marked asymmetry build‐up emerges at such finer time scales. A scale‐dependent probabilistic description of such fat tails and asymmetry appearance is proposed based on a modified q‐Gaussian model, able to describe the cross‐scale rainfall pdfs in terms of the nonextensivity parameter q, a lacunarity (intermittency) correction and a tail asymmetry coefficient, linked to the rainfall generation mechanism.
Radiative signature of increasing atmospheric carbon dioxide in HIRS satellite observations
Authors: Chung Eui‐Seok , Soden Brian J.
Published: April 2010

We examine the cause and implications of decadal trends observed in the High‐Resolution Infrared Radiation Sounder (HIRS) CO2 channels over the period 1980–1999 in conjunction with Microwave Sounding Unit (MSU) O2 channel measurements and climate model simulations. Simulated HIRS brightness temperatures (TBs) from the climate model with constant carbon dioxide indicate a global warming trend (∼0.2 K/decade) consistent with the corresponding MSU observations. By contrast, simulations with observed time‐varying CO2 concentration result in a global decreasing TB trend (∼−0.3 K/decade), indicating a greater influence of increased CO2 on the HIRS radiances compared to the tropospheric warming. Moreover, comparison between observation and simulations suggests that there may be important regional variations in the CO2 trends, particularly over the northern hemisphere midlatitudes downstream from major CO2 sources (U.S. and China). Thus the HIRS CO2 radiances may provide one opportunity to supplement existing surface networks by constraining regional patterns of decadal CO2 variability.
Hemoglobin-Induced Oxidative Stress Contributes to Matrix Metalloproteinase Activation and Blood–Brain Barrier Dysfunction in vivo
Authors: Katsu Masataka , Niizuma Kuniyasu , Yoshioka Hideyuki , Okami Nobuya , Sakata Hiroyuki , Chan Pak H
Published: April 2010

Hemoglobin (Hb) released from extravasated erythrocytes is implicated in brain edema after intracerebral hemorrhage (ICH). Hemoglobin is a major component of blood and a potent mediator of oxidative stress after ICH. Oxidative stress and matrix metalloproteinases (MMPs) are associated with blood–brain barrier (BBB) dysfunction. This study was designed to elucidate whether Hb-induced oxidative stress contributes to MMP-9 activation and BBB dysfunction in vivo. An intracerebral injection of Hb into rat striata induced increased hydroethidine (HEt) signals in parallel with MMP-9 levels. In situ gelatinolytic activity colocalized with oxidized HEt signals in vessel walls, accompanied by immunoglobulin G leakage and a decrease in immunoactivity of endothelial barrier antigen, a marker of endothelial integrity. Administration of a nonselective MMP inhibitor prevented MMP-9 levels and albumin leakage in injured striata. Moreover, reduction in oxidative stress by copper/zinc-superoxide dismutase (SOD1) overexpression reduced oxidative stress, MMP-9 levels, albumin leakage, and subsequent apoptosis compared with wild-type littermates. We speculate that Hb-induced oxidative stress may contribute to early BBB dysfunction and subsequent apoptosis, partly through MMP activation, and that SOD1 overexpression may reduce Hb-induced oxidative stress, BBB dysfunction, and apoptotic cell death.
Impact of Arginase II on CBF in Experimental Cortical Impact Injury in Mice Using MRI
Authors: Bitner Brittany R , Brink Danielle C , Mathew Leela C , Pautler Robia G , Robertson Claudia S
Published: April 2010

Traumatic brain injury (TBI) results in reduced cerebral blood flow (CBF) and low levels of the vasodilator nitric oxide (NO) may be involved. Arginase II negatively regulates NO production through competition for the substrate L-arginine. We determined whether arginase II-deficient (ArgII−/−) mice would show improved CBF after TBI through arterial spin-labeling magnetic resonance imaging (MRI). The ArgII−/− mice exhibit a significantly improved CBF recovery after trauma in the perilesional brain ( P=0.0015) and in various other brain regions. In conclusion, arginase II deficiency leads to a better CBF recovery after TBI and implicates arginase II in hemodynamic processes.
Vascular dysfunction in cerebrovascular disease: mechanisms and therapeutic intervention
Authors: Miller Alyson A. , Budzyn Klaudia , Sobey Christopher G.
Published: April 2010

The endothelium plays a crucial role in the control of vascular homoeostasis through maintaining the synthesis of the vasoprotective molecule NO• (nitric oxide). Endothelial dysfunction of cerebral blood vessels, manifested as diminished NO• bioavailability, is a common feature of several vascular-related diseases, including hypertension, hypercholesterolaemia, stroke, subarachnoid haemorrhage and Alzheimer's disease. Over the past several years an enormous amount of research has been devoted to understanding the mechanisms underlying endothelial dysfunction. As such, it has become apparent that, although the diseases associated with impaired NO• function are diverse, the underlying causes are similar. For example, compelling evidence indicates that oxidative stress might be an important mechanism of diminished NO• signalling in diverse models of cardiovascular ‘high-risk’ states and cerebrovascular disease. Although there are several sources of vascular ROS (reactive oxygen species), the enzyme NADPH oxidase is emerging as a strong candidate for the excessive ROS production that is thought to lead to vascular oxidative stress. The purpose of the present review is to outline some of the mechanisms thought to contribute to endothelial dysfunction in the cerebral vasculature during disease. More specifically, we will highlight current evidence for the involvement of ROS, inflammation, the RhoA/Rho-kinase pathway and amyloid β-peptides. In addition, we will discuss currently available therapies for improving endothelial function and highlight future therapeutic strategies.
Language and Literacy Curriculum Supplement for Preschoolers Who Are Academically At Risk: A Feasibility Study
Authors: Justice Laura M. , McGinty Anita S. , Cabell Sonia Q. , Kilday Carolyn R. , Knighton Kathy , Huffman Ginger
Published: April 2010

Purpose

The potential benefit that a low-cost scripted language and literacy supplemental curriculum titled
Read It Again!
(RIA; L. M. Justice, A. S. McGinty, A. R. Beckman, & C. R. Kilday, 2006) may have on preschool-age children’s skills was explored. RIA was developed to meet the needs of preschool educators who may not have access to current commercially available high-cost language and literacy curricula, which often require ongoing intensive professional development. RIA involves implementing 60 large-group lessons over a 30-week period that feature repeated use of 15 commercial storybooks.

Method

Using a quasi-experimental pre–post research design, 11 preschool teachers implemented RIA in their classrooms for an academic year, and 9 teachers working in comparable preschool programs served as comparisons. Language and literacy measures were collected in the fall and spring of the year.

Results

Children whose teachers implemented RIA had higher scores in the spring on measures of language (i.e., grammar and vocabulary) and measures of literacy (i.e., rhyme, alliteration, and print). Effect-size estimates were consistent with medium- to large-size effects.

Conclusions

RIA may be a viable means of enhancing the language and literacy instruction that is delivered within preschool classrooms and, therefore, a means of enhancing children’s language and literacy learning. Future directions for continued evaluation of RIA are discussed.
What Makes a Caseload (Un)Manageable? School-Based Speech-Language Pathologists Speak
Authors: Katz Lauren A. , Maag Abby , Fallon Karen A. , Blenkarn Katie , Smith Megan K.
Published: April 2010

Purpose

Large caseload sizes and a shortage of speech-language pathologists (SLPs) are ongoing concerns in the field of speech and language. This study was conducted to identify current mean caseload size for school-based SLPs, a threshold at which caseload size begins to be perceived as unmanageable, and variables contributing to school-based SLPs' feelings of caseload manageability.

Method

Approximately 2,000 public-school-based SLPs from across the country were solicited to participate in an online, Web-based survey between April and May of 2007. Of those SLPs who were contacted, 634 full-time SLPs from 49 states completed the survey. The data were evaluated using descriptive statistics and logistic regression.

Results

The mean caseload size for SLPs in this study was 49 students. At the caseload range of 41–50 students, approximately 60% of the SLPs perceived their caseload size as unmanageable. Logistic regression revealed caseload size, years of experience, and extent of collaboration as significant predictors of an SLP’s likelihood of feeling that his or her caseload size is manageable.

Conclusions

Caseload size continues to be an area of concern for school-based SLPs, and efforts to address this problem must continue in order to prevent long-term struggles with SLPs' dissatisfaction, shortages, and turnover. Policy, research, and clinical implications are discussed.
Ion and electron irradiation-induced effects in nanostructured materials
Authors: Krasheninnikov A. V. , Nordlund K.
Published: April 2010

A common misconception is that the irradiation of solids with energetic electrons and ions has exclusively detrimental effects on the properties of target materials. In addition to the well-known cases of doping of bulk semiconductors and ion beam nitriding of steels, recent experiments show that irradiation can also have beneficial effects on nanostructured systems. Electron or ion beams may serve as tools to synthesize nanoclusters and nanowires, change their morphology in a controllable manner, and tailor their mechanical, electronic, and even magnetic properties. Harnessing irradiation as a tool for modifying material properties at the nanoscale requires having the full microscopic picture of defect production and annealing in nanotargets. In this article, we review recent progress in the understanding of effects of irradiation on various zero-dimensional and one-dimensional nanoscale systems, such as semiconductor and metal nanoclusters and nanowires, nanotubes, and fullerenes. We also consider the two-dimensional nanosystem graphene due to its similarity with carbon nanotubes. We dwell on both theoretical and experimental results and discuss at length not only the physics behind irradiation effects in nanostructures but also the technical applicability of irradiation for the engineering of nanosystems.
Dynamical equation for an electron-hole pair condensate in a system of two graphene layers
Authors: Bezuglyĭ A. I.
Published: April 2010

In bilayer graphene n-p systems the electron-hole pairs with spatially separated components at low temperatures transition into a superfluid state. A microscopic derivation of the dynamical equation for the wave function of the electron-hole pair condensate in a strong perpendicular magnetic field is given for low pair density. The temperature of the transition into a superfluid state is calculated in a wide interval of interlayer distances and magnetic fields on the basis of the elementary excitation spectrum.
Monte Carlo simulation of a two-dimensional electron gas on a disordered host lattice
Authors: Slavin V. V.
Published: April 2010

The low-temperature thermodynamic properties of a two-dimensional electron gas on a disordered host lattice are studied in the limit of low electron concentration. A novel Monte Carlo simulation algorithm making it possible to study the properties of this system effectively is proposed. Nonzero residual entropy per particle is found and its value is determined. It is shown on the basis of the proposed model that a cusp characteristic for spin-glass systems is present in the low-temperature dependence of the dielectric susceptibility as a function of the external electric field.
Mean-field theory of orientational ordering in rigid rotor models with identical atoms: spin conversion and thermal equilibration
Authors: Hetényi Balázs
Published: April 2010

In coupled rotor models which describe identical rotating nuclei the nuclear spin states restrict the possible angular momenta of each molecule. There are two mean-field approaches to determining the orientational phase diagrams in such systems. In one the nuclear spin conversion times are assumed to be instantaneous and in the other infinite. In this paper the intermediate case, when the spin conversion times are significantly slower than those of rotational time scales but are not infinite on the time-scale of the experiment, is investigated. Via incorporation of the configurational degeneracy it is shown that in the thermodynamic limit the mean-field approach in the intermediate case is identical to the instantaneous spin conversion time approximation. The total entropy can be split into configurational and rotational terms. The mean-field phase diagram of a model of coupled rotors of three-fold symmetry is also calculated in the two approximations. It is shown that the configurational entropy has a maximum as a function of temperature which shifts to lower temperatures with increasing order.
Poisson–Vlasov in a strong magnetic field: A stochastic solution approach
Authors: Vilela Mendes R.
Published: April 2010

Stochastic solutions are obtained for the Maxwell–Vlasov equation in the approximation where magnetic field fluctuations are neglected and the electrostatic potential is used to compute the electric field. This is a reasonable approximation for plasmas in a strong external magnetic field. Both Fourier and configuration space solutions are constructed.
Periodic local Møller–Plesset second order perturbation theory method applied to molecular crystals: Study of solid NH3 and CO2 using extended basis sets
Authors: Maschio Lorenzo , Usvyat Denis , Schütz Martin , Civalleri Bartolomeo
Published: April 2010

We have calculated the equilibrium geometry, formation energy, and bulk modulus of two molecular bulk crystals, NH3 and CO2, at the periodic post-Hartree–Fock correlated level. The dependence of the results on the basis set has been analyzed, by employing basis sets up to aug-cc-pVQZ quality. In the calculations, we used the periodic local Møller–Plesset second order perturbation theory (LMP2), implemented in the CRYSCOR program. Multipolar expansion techniques, as well as density fitting, are employed in this code to reduce the number of and to factorize the required electron repulsion integrals; as a consequence of that, the computational cost for the correlation part of the calculations is comparable to that of the Hartree–Fock. Auxiliary calculations performed on molecular dimers are also reported to verify the accuracy of the LMP2 approach and of the basis sets used. Furthermore, the effect of spin-component scaling has been investigated for the two crystals. One intention of the present paper is also to lay out and specify the computational setup, which is generally applicable for accurate CRYSCOR calculations on molecular crystals.
Lattice-Boltzmann simulations of repulsive particle-particle and particle-wall interactions: Coughing and choking
Authors: Başağaoğlu Hakan , Succi Sauro
Published: April 2010

We propose and numerically investigate a new particle retention mechanism for particle entrapment in creeping flows in a constricted section of a saturated rough-walled narrow flow channel. We hypothesize that particles, whose size is smaller than channel width, can be temporarily or permanently immobilized in a flow channel away from channel walls due to particle-particle and particle-wall repulsive potentials, and, consequently, the flow field is clogged temporarily (coughing) or permanently (choking). Two mathematically simplified repulsive particle-particle and particle-wall interaction potentials are incorporated into a two-dimensional colloidal lattice-Boltzmann model. These potentials are two-body Lennard-Jones 12 and screened electrostatic repulsive potentials. Numerical simulations reveal that unlike in smooth-walled flow channels, particles are entrapped away from rough-walled channel walls and subsequently clog the flow field if fluid-drag and repulsive forces on particles are in balance. Off-balance forces, however, could result in temporary clogging if repulsive forces are stronger on the advancing edge of a particle than on its trailing edge. The new conceptualization and two-particle numerical simulations successfully captured (i) temporary entrapment of two particles (coughing), (ii) temporary entrapment of one of the particles with permanent entrapment of the other particle (coughing-choking), and (iii) permanent entrapment of both particles (choking) as a function of repulsive interaction strength.
A route to explain water anomalies from results on an aqueous solution of salt
Authors: Corradini D. , Rovere M. , Gallo P.
Published: April 2010

In this paper we investigate the possibility to detect the hypothesized liquid-liquid critical point of water in supercooled aqueous solutions of salts. Molecular dynamics computer simulations are conducted on bulk TIP4P water and on an aqueous solution of sodium chloride in TIP4P water, with concentration c=0.67 mol/kg. The liquid-liquid critical point is found both in the bulk and in the solution. Its position in the thermodynamic plane shifts to higher temperature and lower pressure for the solution. Comparison with available experimental data allowed us to produce the phase diagrams of both bulk water and the aqueous solution as measurable in experiments. Given the position of the liquid-liquid critical point in the solution as obtained from our simulations, the experimental determination of the hypothesized liquid-liquid critical point of water in aqueous solutions of salts appears possible.
Epitaxial growth of Co2MnSi thin films at the vicinal surface of n-Ge(111) substrate
Authors: Nahid M. A. I. , Oogane M. , Naganuma H. , Ando Y.
Published: April 2010

The structure and magnetic properties of Co2MnSi films on n-Ge(111) substrate were investigated for the motivation of spin injection. The 50-nm-thick Co2MnSi films were fabricated on n-Ge(111) substrates by dc sputtering and postannealed about 1 h at the various temperatures ranging from 200–500 °C. In the annealing temperature range of 300–400 °C, the Co2MnSi were grown epitaxially at the vicinal surface of n-Ge(111) substrates. The epitaxial layer of Co2MnSi films was about 18 nm thick at 350 °C and exhibited ferromagnetic behavior. Interestingly, there was no diffusion of Ge inside the epitaxial layer and atomically flat interface was obtained.
Ferromagnetic and antiferromagnetic properties of the semihydrogenated SiC sheet
Authors: Xu B. , Yin J. , Xia Y. D. , Wan X. G. , Liu Z. G.
Published: April 2010

The intriguing electronic and magnetic properties of the semihydrogenated SiC sheet are investigated by means of the first-principles calculations. The semihydrogenated SiC sheet exhibits diverse electronic and magnetic properties: a ferromagnetic semiconductor when Si atoms are hydrogenated, while an antiferromagnetic semiconductor with C atoms hydrogenated. The semihydrogenated SiC sheet with the C atoms hydrogenated is found to be more stable than the sheet with the Si atoms hydrogenated. Thus, controlling the hydrogenation on the different atom sites can precisely modulate the electronic and magnetic properties of the semihydrogenated SiC sheet, which endues the semihydrogenated SiC sheet great potential applications in the future functional nanodevices.
Threshold effects in I−⋅CH3CN and I−⋅H2O cluster anion detachment: The angular distribution as an indicator of electronic autodetachment
Authors: Mbaiwa Foster , Wei Jie , Van Duzor Matthew , Mabbs Richard
Published: April 2010

I − ⋅ H 2 O and I−⋅CH3CN cluster anion photodetachment properties (photoelectron spectra and angular distributions) are recorded via velocity mapped photoelectron imaging for wavelengths between 270 and 340 nm, in small energy increments. These are compared with free I− detachment results and reveal the presence of a sharp change in the angular distribution for the P23/2 spin orbit channel in the vicinity of the P21/2 threshold. The effect is seen at this threshold in the I−⋅H2O cluster anion and just below threshold for I−⋅CH3CN. The effect is attributed to an electronic autodetachment process, which is dependent on electronic energy transfer mediated by the electron-neutral complex produced in the excitation process. These results highlight the potential of cluster anion detachment as a probe of electron-molecule interactions and in particular the sensitivity of the angular distributions to intracluster electron transfer processes.
The Voronoi volume and molecular representation of molar volume: Equilibrium simple fluids
Authors: Hunjan Jagtar Singh , Eu Byung Chan
Published: April 2010

The Voronoi volume of simple fluids was previously made use of in connection with volume transport phenomena in nonequilibrium simple fluids. To investigate volume transport phenomena, it is important to develop a method to compute the Voronoi volume of fluids in nonequilibrium. In this work, as a first step to this goal, we investigate the equilibrium limit of the nonequilibrium Voronoi volume together with its attendant related molar (molal) and specific volumes. It is proved that the equilibrium Voronoi volume is equivalent to the molar (molal) volume. The latter, in turn, is proved equivalent to the specific volume. This chain of equivalences provides an alternative procedure of computing the equilibrium Voronoi volume from the molar volume/specific volume. We also show approximate methods of computing the Voronoi and molar volumes from the information on the pair correlation function. These methods may be employed for their quick estimation, but also provide some aspects of the fluid structure and its relation to the Voronoi volume. The Voronoi volume obtained from computer simulations is fitted to a function of temperature and pressure in the region above the triple point but below the critical point. Since the fitting function is given in terms of reduced variables for the Lennard-Jones (LJ) model and the kindred volumes (i.e., specific and molar volumes) are in essence equivalent to the equation of state, the formula obtained is a reduced equation state for simple fluids obeying the LJ model potential in the range of temperature and pressure examined and hence can be used for other simple fluids.
Anelastic anomalies and negative Poisson’s ratio in tetragonal BaTiO3 ceramics
Authors: Dong Liang , Stone Donald S. , Lakes Roderic S.
Published: April 2010

Anelastic anomalies (sharp variations in modulus and damping with temperature) were observed in tetragonal BaTiO3 via broadband viscoelastic spectroscopy after aging at 50 °C for 15 h. The effect was most pronounced under electrical short circuit condition, at low frequency and under small excitation strain (10−6). Softening in bulk modulus and negative Poisson’s ratio were observed near 60 °C. Effects are attributed to an oxygen vacancy mechanism. A relaxational model cannot account for sharp response at smaller strains. Heterogeneity of negative stiffness is considered as a cause.
Electron attachment to chlorine azide at 298 and 400 K
Authors: Freel Keith , Friedman Jeffrey F. , Miller Thomas M. , Heaven Michael C. , Viggiano A. A.
Published: April 2010

Electron attachment to chlorine azide (ClN3) was studied using a flowing-afterglow Langmuir-probe apparatus. Electron attachment rates were measured to be 3.5×10−8 and 4.5×10−8 cm3 s−1 at 298 and 400 K, respectively, with an estimated 35% absolute accuracy. Cl− was the sole ion product of the attachment reaction; weak ion signals were observed for other anions and attributed to impurities and secondary ion-molecule reactions. Assuming a relative uncertainty of ±10% for these data, an activation energy for the attachment reaction may be given as 24±10 meV.
Stabilization of ideal pressure gradient driven edge modes during pulsed parallel current drive in reversed field pinch
Authors: Svidzinski V.A. , Li H.
Published: April 2010

Significant improvement of plasma confinement in the Madison Symmetric Torus reversed field pinch (RFP) has been routinely achieved by applying an inductive electric field at the plasma boundary in the direction parallel to the equilibrium magnetic field at the plasma edge. An auxiliary edge current is driven by this electric field with the goal of replacing the dynamo-driven current and modifying the parallel current profile to reduce current-driven instabilities. This current-drive technique is called pulsed parallel current drive (PPCD) in RFP. During PPCD plasma fluctuations are reduced everywhere resulting in tokamak-like confinement parameters, while the edge density profile steepens significantly and plasma beta increases. A steep edge plasma pressure profile, a relatively high plasma beta and a strong unfavourable curvature of equilibrium magnetic field near the edge in RFP could excite pressure-driven fluid turbulence near the edge and worsen plasma confinement, opposite to the experimental observations. In this study stability analysis of edge pressure gradient driven ideal modes in standard-like and in PPCD-like plasma equilibria is performed. An ideal magnetohydrodynamic plasma model in cylindrical RFP equilibrium with a step function plasma pressure profile and a vacuum layer between the plasma boundary and the conducting shell is used. Standard-like and PPCD-like plasma equilibria in the model are defined by the direction of the surface current at the plasma–vacuum interface. The results show that while in standard-like equilibrium the edge pressure gradient driven modes are highly unstable in this model, the transition to PPCD-like equilibrium completely stabilizes these modes. The modes stabilization is primarily due to strengthening of magnetic shear at the location of the pressure gradient during the drive and due to the proximity of this location to the conducting wall. This stabilization mechanism is not specific to RFPs, making PPCD a general method of stabilization of the edge pressure gradient driven instabilities which could be applied in other magnetic confinement systems. Application of PPCD to stabilize the edge localized modes in tokamaks is proposed.
Compact complete minimal immersions in ℝ³
Authors: Alarcón Antonio
Published: April 2010

In this paper we find, for any arbitrary finite topological type, a compact Riemann surface

M

,

\mathcal {M},

an open domain

M
⊂

M

M\subset \mathcal {M}

with the fixed topological type, and a conformal complete minimal immersion

X
:
M
→

R

3

X:M\to \mathbb {R}^3

which can be extended to a continuous map

X
:

M
¯

→

R

3

,

X:\overline {M}\to \mathbb {R}^3,

such that

X

|

∂
M

X_{|\partial M}

is an embedding and the Hausdorff dimension of

X
(
∂
M
)

X(\partial M)

is

1.
1.

We also prove that complete minimal surfaces are dense in the space of minimal surfaces spanning a finite set of closed curves in

R

3

\mathbb {R}^3

, endowed with the topology of the Hausdorff distance.
Convexity and horizontal second fundamental forms for hypersurfaces in Carnot groups
Authors: Capogna Luca , Pauls Scott , Tyson Jeremy
Published: April 2010

We use a Riemannian approximation scheme to give a characterization for smooth convex functions on a Carnot group (in the sense of Danielli–Garofalo–Nhieu or Lu–Manfredi–Stroffolini) in terms of the positive semidefiniteness of the horizontal second fundamental form of their graph.
Complete reducibility and separability
Authors: Bate Michael , Martin Benjamin , Röhrle Gerhard , Tange Rudolf
Published: April 2010

Let

G
G

be a reductive linear algebraic group over an algebraically closed field of characteristic

p
>
0

p > 0

. A subgroup of

G
G

is said to be separable in

G
G

if its global and infinitesimal centralizers have the same dimension. We study the interaction between the notion of separability and Serre’s concept of

G
G

-complete reducibility for subgroups of

G
G

. A separability hypothesis appears in many general theorems concerning

G
G

-complete reducibility. We demonstrate that some of these results fail without this hypothesis. On the other hand, we prove that if

G
G

is a connected reductive group and

p
p

is very good for

G
G

, then any subgroup of

G
G

is separable; we deduce that under these hypotheses on

G
G

, a subgroup

H
H

of

G
G

is

G
G

-completely reducible provided Lie

G
G

is semisimple as an

H
H

-module.

Recently, Guralnick has proved that if

H
H

is a reductive subgroup of

G
G

and

C
C

is a conjugacy class of

G
G

, then

C
∩
H

C\cap H

is a finite union of

H
H

-conjugacy classes. For generic

p
p

— when certain extra hypotheses hold, including separability — this follows from a well-known tangent space argument due to Richardson, but in general, it rests on Lusztig’s deep result that a connected reductive group has only finitely many unipotent conjugacy classes. We show that the analogue of Guralnick’s result is false if one considers conjugacy classes of

n
n

-tuples of elements from

H
H

for

n
>
1

n > 1

.
Homogenization of one-phase Stefan-type problems in periodic and random media
Authors: Kim Inwon , Mellet Antoine
Published: April 2010

We investigate the homogenization of Stefan-type problems with oscillating diffusion coefficients. Both cases of periodic and random (stationary ergodic) mediums are considered. The proof relies on the coincidence of viscosity solutions and weak solutions (which are the time derivatives of the solutions of an obstacle problem) for the Stefan problem. This coincidence result is of independent interest.
Lyapunov exponents of hyperbolic measures and hyperbolic periodic orbits
Authors: Wang Zhenqi , Sun Wenxiang
Published: April 2010

Lyapunov exponents of a hyperbolic ergodic measure are approximated by Lyapunov exponents of hyperbolic atomic measures on periodic orbits.
The cluster category of a canonical algebra
Authors: Barot M. , Kussin D. , Lenzing H.
Published: April 2010

We study the cluster category of a canonical algebraAAin terms of the hereditary category of coherent sheaves over the corresponding weighted projective lineX\mathbb {X}. As an application we determine the automorphism group of the cluster category and show that the cluster-tilting objects form a cluster structure in the sense of Buan, Iyama, Reiten and Scott. The tilting graph of the sheaf category always coincides with the tilting or exchange graph of the cluster category. We show that this graph is connected if the Euler characteristic ofX\mathbb {X}is non-negative, or equivalently, ifAAis of tame (domestic or tubular) representation type.
Combinatorics and geometry of power ideals
Authors: Ardila Federico , Postnikov Alexander
Published: April 2010

We investigate ideals in a polynomial ring which are generated by powers of linear forms. Such ideals are closely related to the theories of fat point ideals, Cox rings, and box splines.

We pay special attention to a family of power ideals that arises naturally from a hyperplane arrangement

A

\mathcal {A}

. We prove that their Hilbert series are determined by the combinatorics of

A

\mathcal {A}

and can be computed from its Tutte polynomial. We also obtain formulas for the Hilbert series of certain closely related fat point ideals and zonotopal Cox rings.

Our work unifies and generalizes results due to Dahmen-Micchelli, Holtz-Ron, Postnikov-Shapiro-Shapiro, and Sturmfels-Xu, among others. It also settles a conjecture of Holtz-Ron on the spline interpolation of functions on the lattice points of a zonotope.
A generalized Mazur’s theorem and its applications
Authors: Tan Ki-Seng
Published: April 2010

We generalize a theorem of Mazur concerning the universal norms of an abelian variety over a

Z

p
d

\mathbb {Z}_p^d

-extension of a complete local field. Then we apply it to the proof of a control theorem for abelian varieties over global function fields.
Equivariant spectral triples and Poincaré duality for 𝑆𝑈_{𝑞}(2)
Authors: Chakraborty Partha , Pal Arupkumar
Published: April 2010

Let

A

\mathcal {A}

be the

C
∗

C^*

-algebra associated with

S

U
q

(
2
)

SU_q(2)

, let

π
\pi

be the representation by left multiplication on the

L
2

L_2

space of the Haar state and let

D
D

be the equivariant Dirac operator for this representation constructed by the authors earlier. We prove in this article that there is no operator other than the scalars in the commutant

π
(

A

)
′

\pi (\mathcal {A})’

that has bounded commutator with

D
D

. This implies that the equivariant spectral triple under consideration does not admit a rational Poincaré dual in the sense of Moscovici, which in particular means that this spectral triple does not extend to a

K
K

-homology fundamental class for

S

U
q

(
2
)

SU_q(2)

. We also show that a minor modification of this equivariant spectral triple gives a fundamental class and thus implements Poincaré duality.
Alignment-free local structural search by writhe decomposition
Authors: Zhi Degui , Shatsky Maxim , Brenner Steven E.
Published: April 2010

Motivation: Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residue-level structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities.

Results: We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizing scop domains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test.

Availability: The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/

Contact:  dzhi@compbio.berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Payao: a community platform for SBML pathway model curation
Authors: Matsuoka Yukiko , Ghosh Samik , Kikuchi Norihiro , Kitano Hiroaki
Published: April 2010

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members.

Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported.

Contact:  kitano@sbi.jp
Temperature-Dependent Expression of Type III Secretion System Genes and Its Regulation in Bradyrhizobium japonicum
Authors: Wei Min , Takeshima Keisuke , Yokoyama Tadashi , Minamisawa Kiwamu , Mitsui Hisayuki , Itakura Manabu , Kaneko Takakazu , Tabata Satoshi , Saeki Kazuhiko , Omori Hirofumi , Tajima Shigeyuki , Uchiumi Toshiki , Abe Mikiko , Ishii Satoshi , Ohwada Takuji
Published: April 2010

The genome-wide expression profiles of Bradyrhizobium japonicum in response to soybean (Glycine max (L.) Merr.) seed extract (SSE) and genistein were monitored with time at a low temperature (15°C). A comparison with the expression profiles of the B. japonicum genome previously captured at the common growth temperature (30°C) revealed that the expression of SSE preferentially induced genomic loci, including a large gene cluster encoding the type III secretion system (T3SS), were considerably delayed at 15°C, whereas most nodulation (nod) gene loci, including nodD1 and nodW, were rapidly and strongly induced by both SSE and genistein. Induction of the T3SS genes was progressively activated upon the elevation of temperature to 30°C and positively responded to culture population density. In addition, genes nolA and nodD2 were dramatically induced by SSE, concomitantly with the expression of T3SS genes. However, the deletion mutation of nodD2 but not nolA led to elimination of the T3SS genes expression. These results indicate that the expression of the T3SS gene cluster is tightly regulated with integration of environmental cues such as temperature and that NodD2 may be involved in its efficient induction in B. japonicum.
An In Planta Method for Assessing the Role of Basidiospores in Rhizoctonia Foliar Disease of Tomato
Authors: Bartz Faith E. , Cubeta Marc A. , Toda Takeshi , Naito Shigeo , Ivors Kelly L.
Published: April 2010

A tomato (Solanum lycopersicum) foliar blight disease of unknown etiology was observed in North Carolina (NC) during 2005 to 2006. Symptoms included necrotic lesions and blighted leaves, with signs of white mycelial growth on abaxial leaf surfaces. The morphology of isolates from symptomatic leaves was consistent with that of Rhizoctonia solani. Because the pattern of symptom expression suggested that basidiospores were the primary inoculum source, Koch's postulates were fulfilled using a method to generate basidiospores in planta. Isolates were characterized by morphology, DNA sequence analysis, hyphal anastomosis, and somatic hyphal interactions. Phylogenetic analyses and hyphal anastomosis criteria support placement of the isolates in R. solani anastomosis group 3 (AG-3). Tomato foliar blight isolates from NC form a single phylogenetic group with tomato isolates of R. solani AG-3 from Japan and are more closely related to R. solani AG-3 isolates from potato than tobacco. Isolates exhibited both compatible and incompatible hyphal interactions when paired in vitro. To our knowledge, this is the first detailed report of tomato foliar blight caused by R. solani AG-3 in North America. A comprehensive description of the technique employed for producing basidiospores is presented with potential utility for understanding foliar disease etiology in other Rhizoctonia pathosystems.