bluuebunny/crossref_metadata_2025 huggingface dataset:
Contributions of natural and anthropogenic forcing to changes in temperature extremes over the United States
Authors: Meehl Gerald A. , Arblaster Julie M. , Tebaldi Claudia
Published: October 2007

Observations averaged over the U.S. for the second half of the 20th century have shown a decrease of frost days, an increase in growing season length, an increase in the number of warm nights, and an increase in heat wave intensity. For the first three, a nine member multi‐model ensemble shows similar changes over the U.S. in 20th century experiments that combine anthropogenic and natural forcings, though the relative contributions of each are unclear. Here we show results from two global coupled climate models run with anthropogenic and natural forcings separately. Averaged over the continental U.S., they show that the observed changes in the four temperature extremes are accounted for with anthropogenic forcings, but not with natural forcings (even though there are some differences in the details of the forcings). This indicates that most of the changes in temperature extremes over the U.S. are likely due to human activity.
Postseismic deformation of the Andaman Islands following the 26 December, 2004 Great Sumatra–Andaman earthquake
Authors: Paul J. , Lowry A. R. , Bilham R. , Sen S. , Smalley R.
Published: October 2007

Two years after the Great Sumatra‐Andaman earthquake the 3.1 m WSW coseismic displacement at Port Blair, Andaman Islands, had increased by 32 cm. Postseismic uplift initially exceeded 1 cm per week and decreased to <1 mm/week. By 2007 points near Port Blair had risen more than 20 cm, a 24% reversal of coseismic subsidence. Uplift at eight GPS sites suggests a gradual eastward shift of the coseismic neutral axis separating subsidence from uplift. Simulations of the GPS postseismic displacements as viscoelastic relaxation of coseismic stress change and as slip on the plate interface indicate that slip down‐dip of the seismic rupture dominates near‐field deformation during the first two years. Postseismic slip beneath the Andaman Islands released moment equivalent to a magnitude Mw ≥ 7.5 earthquake, and the distribution suggests deep slip in the stable frictional regime accelerated to catch up to the coseismic rupture.
Soil moisture variability across climate zones
Authors: Lawrence Justin E. , Hornberger George M.
Published: October 2007

Variability in soil moisture is controlled by temporal variability in atmospheric conditions and spatial variability in land‐surface conditions. Observations of soil moisture have revealed a variety of patterns – generally, in semiarid regions variance increased as mean soil moisture content increased, in humid regions variance decreased as mean soil moisture content increased, and in temperate regions variance peaked at intermediate moisture contents. We collected soil moisture data at Big Meadows, an upland wetland in Shenandoah National Park, Virginia, and we observed peak variance at intermediate moisture contents, consistent with other sites in temperate climate zones. A modified soil moisture dynamics model was used to examine how soil moisture patterns evolve through time, how topography, soil, and vegetation affect these patterns, and how the trends observed across climate zones can be explained. The trends observed relate to theoretical bounds on soil moisture distributions, i.e., the wilting point and the porosity.
Imaging of Polar Mesosphere Summer Echoes with the 450 MHz Poker Flat Advanced Modular Incoherent Scatter Radar
Authors: Nicolls M. J. , Heinselman C. J. , Hope E. A. , Ranjan S. , Kelley M. C. , Kelly J. D.
Published: October 2007

Polar Mesosphere Summer Echoes (PMSE) occur near the mesopause during the polar summer months. PMSE are primarily studied at VHF, however there have been some detections at higher frequencies. Here, we report on some of the first detections of PMSE with the 450 MHz (67 cm) Poker Flat Advanced Modular Incoherent Scatter Radar (PFISR). Echoes were observed with volume reflectivities (radar scattering cross section per unit volume) near 2–3 × 10−17 m−1. On 11 June 2007, PFISR was operating in a 26‐beam position mode, with look directions spread over an approximately 80 by 80 km2 region at 85 km altitude with elevation angles as low as ∼50°. The measurements showed patchy (tens of kilometer) irregularity regions drifting in from the north, in addition to smaller, more localized structures. There was no evidence for strong aspect sensitivity of these UHF echoes, as PMSE was observed in all look directions with relatively uniform intensity. The observations indicate the presence of fossilized irregularities drifting with the background wind field as well as areas of developing irregularities possibly associated with the presence of active neutral air turbulence.
Thinning and stretching of the plasma sheet
Authors: Petrukovich A. A. , Baumjohann W. , Nakamura R. , Runov A. , Balogh A. , Rème H.
Published: October 2007

With Cluster observations in the magnetotail we study dynamics of plasma sheet thinning and stretching during 39 intervals associated with substorm growth phases. The cross‐tail current density and normal magnetic field generally scale as Bn ∼ TpNp1/2/J0, but with frequent transient variations. Typical pre‐onset values are Bz ∼ 1–2 nT, J0 ∼ 4–8 nA/m2, thickness (Harris estimate) >3000 km. A current density increase in each particular event is not accompanied with a corresponding number density increase. About 30% of the events are characterized by a large (>5 nT) field component parallel to the current (in most of cases equal to By), implying adiabatic particle dynamics even with small Bz. Most local onsets, associated with the ends of thin sheet intervals, were accompanied with tailward plasma flows. In some cases embedded current sheet structure was detected and, therefore, estimation of thickness requires caution.
Directional distribution of the short wave estimated from HF ocean radars
Authors: Hisaki Yukiharu
Published: October 2007

Short‐wave directional distributions estimated using HF (high‐frequency) radar are compared with model predictions. The short‐wave directional distributions are estimated on the basis of HF radar using two‐ and four‐parameter parametric models to describe short‐wave directional distributions. The model‐predicted short‐wave directional distributions are computed using the energy balance equation. The nonlinear interaction source function in the energy balance equation is calculated from both the exact computation and the discrete interaction approximation (DIA). The predicted short‐wave directional distributions from the exact computation and the DIA are compared with those estimated using HF radar. The energy balance equation is simplified by neglecting the propagation term, and the validity of the simplification is investigated. It is found that the four‐parameter model is more accurate than the two‐parameter model to estimate short‐wave directional distribution using HF radar. The model‐predicted mean short‐wave directions with respect to wind directions are correlated with those estimated from the HF radar. The short‐wave direction change associated with a sudden wind shift can be reproduced both from the exact computation and the DIA. The predicted second‐order moments of short‐wave directional distributions are also correlated with those estimated from the HF radar. This result shows that the model can reproduce transient short‐wave directional distributions associated with changes of wind direction. The short‐wave directional distributions predicted by the exact computation are narrower than those predicted by the DIA and estimated using the HF radar. The simplification of the energy balance equation is not the main source of the short‐wave prediction error.
A novel member of the SAF (scaffold attachment factor)-box protein family inhibits gene expression and induces apoptosis
Authors: Chan Ching Wan , Lee Youn-Bok , Uney James , Flynn Andrea , Tobias Jonathan H. , Norman Michael
Published: October 2007

The SLTM [SAF (scaffold attachment factor)-like transcription modulator] protein contains a SAF-box DNA-binding motif and an RNA-binding domain, and shares an overall identity of 34% with SAFB1 {scaffold attachment factor-B1; also known as SAF-B (scaffold attachment factor B), HET [heat-shock protein 27 ERE (oestrogen response element) and TATA-box-binding protein] or HAP (heterogeneous nuclear ribonucleoprotein A1-interacting protein)}. Here, we show that SLTM is localized to the cell nucleus, but excluded from nucleoli, and to a large extent it co-localizes with SAFB1. In the nucleus, SLTM has a punctate distribution and it does not co-localize with SR (serine/arginine) proteins. Overexpression of SAFB1 has been shown to exert a number of inhibitory effects, including suppression of oestrogen signalling. Although SLTM also suppressed the ability of oestrogen to activate a reporter gene in MCF-7 breast-cancer cells, inhibition of a constitutively active β-galactosidase gene suggested that this was primarily the consequence of a generalized inhibitory effect on transcription. Measurement of RNA synthesis, which showed a particularly marked inhibition of [3H]uridine incorporation into mRNA, supported this conclusion. In addition, analysis of cell-cycle parameters, chromatin condensation and cytochrome c release showed that SLTM induced apoptosis in a range of cultured cell lines. Thus the inhibitory effects of SLTM on gene expression appear to result from generalized down-regulation of mRNA synthesis and initiation of apoptosis consequent upon overexpressing the protein. While indicating a crucial role for SLTM in cellular function, these results also emphasize the need for caution when interpreting phenotypic changes associated with manipulation of protein expression levels.
Regulation of stress-induced intracellular sorting and chaperone function of Hsp27 (HspB1) in mammalian cells
Authors: Bryantsev Anton L. , Kurchashova Svetlana Yu. , Golyshev Sergey A. , Polyakov Vladimir Yu. , Wunderink Herman F. , Kanon Bart , Budagova Karina R. , Kabakov Alexander E. , Kampinga Harm H.
Published: October 2007

In vitro, small Hsps (heat-shock proteins) have been shown to have chaperone function capable of keeping unfolded proteins in a form competent for Hsp70-dependent refolding. However, this has never been confirmed in living mammalian cells. In the present study, we show that Hsp27 (HspB1) translocates into the nucleus upon heat shock, where it forms granules that co-localize with IGCs (interchromatin granule clusters). Although heat-induced changes in the oligomerization status of Hsp27 correlate with its phosphorylation and nuclear translocation, Hsp27 phosphorylation alone is not sufficient for effective nuclear translocation of HspB1. Using firefly luciferase as a heat-sensitive reporter protein, we demonstrate that HspB1 expression in HspB1-deficient fibroblasts enhances protein refolding after heat shock. The positive effect of HspB1 on refolding is completely diminished by overexpression of Bag-1 (Bcl-2-associated athanogene), the negative regulator of Hsp70, consistent with the idea of HspB1 being the substrate holder for Hsp70. Although HspB1 and luciferase both accumulate in nuclear granules after heat shock, our results suggest that this is not related to the refolding activity of HspB1. Rather, granular accumulation may reflect a situation of failed refolding where the substrate is stored for subsequent degradation. Consistently, we found 20S proteasomes concentrated in nuclear granules of HspB1 after heat shock. We conclude that HspB1 contributes to an increased chaperone capacity of cells by binding unfolded proteins that are hereby kept competent for refolding by Hsp70 or that are sorted to nuclear granules if such refolding fails.
FRET studies with Factor X mutants provide insight into the topography of the membrane-bound Factor X/Xa
Authors: Qureshi Shabir H. , Yang Likui , Yegneswaran Subramanian , Rezaie Alireza R.
Published: October 2007

FRET (fluorescence resonance energy transfer) studies have shown that the vitamin K-dependent coagulation proteases bind to membrane surfaces perpendicularly, positioning their active sites above the membrane surfaces. To investigate whether EGF (epidermal growth factor) domains of these proteases play a spacer function in this model of the membrane interaction, we used FRET to measure the distance between the donor fluorescein dye in the active sites of Fl–FPR (fluorescein–D-Phe-Pro-Arg-chloromethane)-inhibited fXa (activated Factor Xa) and its N-terminal EGF deletion mutant (fXa-desEGF1), and the acceptor OR (octadecylrhodamine) dye incorporated into phospholipid vesicles composed of 80% phosphatidylcholine and 20% phosphatidylserine. The average distance of closest approach (L) between fluorescein in the active site and OR at the vesicle surface was determined to be 56±1 Å (1 Å=0.1 nm) and 63±1 Å for fXa-desEGF1 compared with 72±2 Å and 75±1 Å for fXa, in the absence and presence of fVa (activated Factor V) respectively, assuming κ2=2/3. In comparison, an L value of 95±6 Å was obtained for a S195C mutant of fXa in the absence of fVa in which fluorescein was attached directly to Cys195 of fXa. These results suggest that (i) EGF1 plays a spacer function in holding the active site of fXa above the membrane surface, (ii) the average distance between fluorescein attached to Fl–FPR in the active site of fXa and OR at the vesicle surface may not reflect the actual distance of the active-site residue relative to the membrane surface, and (iii) fVa alters the orientation and/or the height of residue 195 above the membrane surface.
Characterization of the DNA- and dNTP-binding activities of the human cytomegalovirus DNA polymerase catalytic subunit UL54
Authors: Picard-Jean Frédéric , Bougie Isabelle , Bisaillon Martin
Published: October 2007

The catalytic subunit of the human cytomegalovirus DNA polymerase is critical for the replication of the virus. In the present study, we report the expression and purification of a recombinant catalytic subunit of the human cytomegalovirus DNA polymerase expressed in bacteria which retains polymerase activity. As a first step towards elucidating the nature of the interaction between the enzyme, DNA and dNTPs, we have utilized endogenous tryptophan fluorescence to evaluate the binding of ligands to the enzyme. Using this technique, we demonstrate that the minimal DNA-binding site of the enzyme is 6 nt. We also report the first detailed study of the binding kinetics and thermodynamic parameters involved in the interaction between the enzyme, DNA and dNTPs. Our thermodynamic analyses indicate that the initial formation of the enzyme–DNA binary complex is driven by a favourable entropy change, but is also clearly associated with an unfavourable enthalpic contribution. In contrast, the interaction of dNTPs to the binary complex was shown to depend on a completely different mode of binding that is dominated by a favourable enthalpy change and associated with an unfavourable entropy change. In order to provide additional insights into the structural modifications that occur during catalysis, we correlated the effect of DNA and dNTP binding on protein structure using CD. Our results indicate that the enzyme undergoes a first conformational change upon the formation of the protein–DNA binary complex, which is followed by a second structural modification upon dNTP binding. The present study provides a better understanding of the molecular basis of DNA and dNTP recognition by the catalytic subunit of the human cytomegalovirus DNA polymerase.
Methionine sulfoxide reductases: selenoprotein forms and roles in antioxidant protein repair in mammals
Authors: Kim Hwa-Young , Gladyshev Vadim N.
Published: October 2007

Msrs (methionine sulfoxide reductases), MsrA and MsrB, are repair enzymes that reduce methionine sulfoxide residues in oxidatively damaged proteins to methionine residues in a stereospecific manner. These enzymes protect cells from oxidative stress and have been implicated in delaying the aging process and progression of neurodegenerative diseases. In recent years, significant efforts have been made to explore the catalytic properties and physiological functions of these enzymes. In the current review, we present recent progress in this area, with the focus on mammalian MsrA and MsrBs including their roles in disease, evolution and function of selenoprotein forms of MsrA and MsrB, and the biochemistry of these enzymes.
Management of initial orthostatic hypotension: lower body muscle tensing attenuates the transient arterial blood pressure decrease upon standing from squatting
Authors: Krediet C. T. Paul , Go-Schön Ingeborg K. , Kim Yu-Sok , Linzer Mark , Van Lieshout Johannes J. , Wieling Wouter
Published: October 2007

IOH (initial orthostatic hypotension) comprises symptoms of cerebral hypoperfusion caused by an abnormally large transient MAP (mean arterial pressure) decrease 5–15 s after arising from a supine, sitting or squatting position. Few treatment options are available. In the present study, we set out to test the hypothesis that LBMT (lower body muscle tensing) attenuates IOH after rising from squatting and its symptoms in daily life. A total of 13 IOH patients (nine men; median age, 27 years) rose from squatting twice, once with LBMT and once without. In addition, seven healthy volunteers (five men; median age, 27 years) were studied in a cross-over study design. They stood up from the squatting position three times, once combined with LBMT. Blood pressure (Finometer) was measured continuously, and CO (cardiac output) by Modelflow and TPR (total peripheral resistance) were computed. MAP, CO and TPR were compared without and with LBMT. Using a questionnaire, the perceived effectiveness of LBMT in the patients' daily lives was evaluated. With LBMT, the minimal MAP after standing up was higher in both groups (19 mmHg in patients and 13 mmHg in healthy subjects). In healthy subjects, the underlying mechanism was a blunted TPR decrease (to 47% compared with 60%; P<0.05), whereas in the patients no clear CO or TPR pattern was discernible. During follow-up, eight out of ten patients using LBMT reported fewer IOH symptoms. In conclusion, LBMT is a new intervention to attenuate the transient blood pressure decrease after standing up from squatting, and IOH patients should be advised about the use of this manoeuvre.
Maternal fish oil supplementation in pregnancy modifies neonatal leukotriene production by cord-blood-derived neutrophils
Authors: Prescott Susan L. , Barden Anne E. , Mori Trevor A. , Dunstan Janet A.
Published: October 2007

Fish oil supplementation has been shown to reduce neutrophil production of inflammatory LTB4 (leukotriene B4) in adults. The present study is the first to examine the effects on neonatal neutrophil function following supplementation in pregnancy. Pregnant women with allergic disease (n=98) were randomized to receive either fish oil [3.7 g of n−3 long-chain PUFAs (polyunsaturated fatty acids)/day] or a placebo supplement for the final 20 weeks of pregnancy. Leukotriene production by neonatal neutrophils was measured after stimulation with the calcium ionophore A23187. This was examined in relation to supplementation, cell membrane fatty acid levels and mononuclear cytokine production. Neutrophil LTB4 production was significantly reduced in neonates whose mothers had received fish oil in pregnancy. This was most evident for isomer 2 of LTB4 (P=0.031), although this was also observed for total LTB4 (P=0.051) and isomer 1 (P=0.088). There was also a trend for lower production of other PUFA metabolites, namely 5-HETE (5-hydroxyeicosatetraenoic acid; P=0.054) in the fish oil group. Accordingly, LTB4 levels were inversely related to membrane n−3 PUFA levels. Less inflammatory products (LTB5) were only produced at very low levels, although there was a trend for higher levels of this metabolite in the fish oil group. Consistent with this, LTB5 levels were positively correlated with n−3 PUFA membrane levels, particularly EPA (eicosapentanoic acid) and negatively correlated with n−6 PUFAs. Neonates with lower neutrophil LTB4 production also had lower production of pro-inflammatory IL (interleukin)-6 responses (r=0.35, P=0.005) and regulatory IL-10 responses (r=0.37, P=0.003) by LPS (lipopolysaccharide)-stimulated neonatal mononuclear cells. In conclusion, maternal dietary changes can modify neonatal neutrophil function. This has implications for the early immune programming, which can be influenced by the inflammatory milieu of local tissues during initial antigen encounter. It also provides evidence of another pathway through which long-chain PUFAs status can influence early immune development.
Increasing the fat-to-carbohydrate ratio in a high-fat diet prevents the development of obesity but not a prediabetic state in rats
Authors: Sinitskaya Natalia , Gourmelen Sylviane , Schuster-Klein Carole , Guardiola-Lemaitre Béatrice , Pévet Paul , Challet Etienne
Published: October 2007

Metabolic disorders induced by high-fat feeding in rodents evoke some, if not all, of the features of human metabolic syndrome. The occurrence and severity of metabolic disorders, however, varies according to rodent species, and even strain, as well as the diet. Therefore, in the present study, we investigated the long-term obesogenic and diabetogenic effects of three high-fat diets differing by their fat/carbohydrate ratios. Sprague–Dawley rats were fed a control high-carbohydrate and low-fat diet [HCD; 3:16:6 ratio of fat/carbohydrate/protein; 15.48 kJ/g (3.7 kcal/g)], a high-fat and medium-carbohydrate diet [HFD1; 53:30:17 ratio of fat/carbohydrate/protein; 19.66 kJ/g (4.7 kcal/g)], a very-high-fat and low-carbohydrate diet [HFD2; 67:9:24 ratio of fat/carbohydrate/protein; 21.76 kJ/g (5.2 kcal/g)] or a very-high-fat and carbohydrate-free diet [HFD3; 75:0:25 ratio of fat/carbohydrate/protein; 24.69 kJ/g (5.9 kcal/g)] for 10 weeks. Compared with the control diet (HCD), rats fed with high-fat combined with more (HFD1) or less (HFD2) carbohydrate exhibited higher BMI (body mass index; +13 and +10% respectively; P<0.05) and abdominal fat (+70% in both HFD1 and HFD2; P<0.05), higher plasma leptin (+130 and +135% respectively; P<0.05), lower plasma adiponectin levels (−23 and −30% respectively; P<0.05) and impaired glucose tolerance. Only the HFD1 group had insulin resistance. By contrast, a very-high-fat diet devoid of carbohydrate (HFD3) led to impaired glucose tolerance, insulin resistance and hypoadiponectinaemia (−50%; P<0.05), whereas BMI, adiposity and plasma leptin did not differ from respective values in animals fed the control diet. We conclude that increasing the fat-to-carbohydrate ratio to the uppermost (i.e. carbohydrate-free) in a high-fat diet prevents the development of obesity, but not the prediabetic state (i.e. altered glucose tolerance and insulin sensitivity).
Tunable absorption resonance in electromechanical one-dimensional metallodielectric photonic band gap structures
Authors: Cappeddu M. G. , Savalli N. , Baglio S. , Scalora M. , Davenport W. , Bloemer M. J. , Larciprete M. C.
Published: October 2007

We present the results of an experimental study of an electromechanical, one-dimensional, metallodielectric photonic band gap structure. We monitor the reflectance as a function of the thickness of an air gap located inside the stack. The results suggest that, by changing the thickness of the air gap by approximately 20 nm, a large contrast can be achieved between high- and low-reflectance states, as reflectance switches from a fraction of a percent to about 70%. Using this approach, we are able to selectively remove a relatively narrow but tunable wavelength range from the reflected spectrum, thus making possible applications to accelerometers, linear optical switches, modulators, and other specialized filters in the visible range. The characteristic absorption spectrum can be controlled by varying air gap and dielectric layer thicknesses.
Kinetic energy density study of some representative semilocal kinetic energy functionals
Authors: García-Aldea David , Alvarellos J. E.
Published: October 2007

There is a number of explicit kinetic energy density functionals for noninteracting electron systems that are obtained in terms of the electron density and its derivatives. These semilocal functionals have been widely used in the literature. In this work, we present a comparative study of the kinetic energy density of these semilocal functionals, stressing the importance of the local behavior to assess the quality of the functionals. We propose a quality factor that measures the local differences between the usual orbital-based kinetic energy density distributions and the approximated ones, allowing us to ensure if the good results obtained for the total kinetic energies with these semilocal functionals are due to their correct local performance or to error cancellations. We have also included contributions coming from the Laplacian of the electron density to work with an infinite set of kinetic energy densities. For all but one of the functionals, we have found that their success in the evaluation of the total kinetic energy is due to global error cancellations, whereas the local behavior of their kinetic energy density becomes worse than that corresponding to the Thomas-Fermi functional.
Geometries and stabilities of Ag-doped Sin (n=1–13) clusters: A first-principles study
Authors: Chuang Feng-Chuan , Hsieh Yun-Yi , Hsu Chih-Chiang , Albao Marvin A.
Published: October 2007

The structures of AgSin (n=1–13) clusters are investigated using first-principles calculations. Our studies suggest that AgSin clusters with n=7 and 10 are relatively stable isomers and that these clusters prefer to be exohedral rather than endohedral. Moreover, doping leaves the inner core structure of the clusters largely intact. Additionally, the plot of fragmentation energies as a function of silicon atoms shows that the AgSin are favored to dissociate into one Ag atom and Sin clusters. Alternative pathways exist for n>7 (except n=11) in which the Ag–Si cluster dissociates into a stable Si7 and a smaller fragment AgSin−7. The AgSi11 cluster dissociates into a stable Si10 and a small fragment AgSi. Lastly, our analysis indicates that doping of Ag atom significantly decreases the gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital for n>7.
Study of statistical properties of edge turbulence in the National Spherical Torus Experiment with the gas puff imaging diagnostic
Authors: Agostini M. , Zweben S. J. , Cavazzana R. , Scarin P. , Serianni G. , Maqueda R. J. , Stotler D. P.
Published: October 2007

An investigation is presented of the edge turbulence in the National Spherical Torus Experiment [M. Ono, M. G. Bell, R. E. Bell et al., Plasma Phys. Control. Fusion, 45, A335 (2003)] based on the optical gas puff imaging (GPI) diagnostic. First of all, the edge fluctuations are characterized for the low confinement mode (L-mode) discharges as a function of the radius. The probability distribution function of the fluctuations is shown to be non-Gaussian for all the radial positions studied, but the deviation from the normal distribution is greater outside the separatrix; in this region the area occupied by the edge structures (“blobs”) is greater than inside the separatrix, and this is correlated with the decrease of the logarithmic radial derivative of the pressure gradient. Then the difference between the L-mode and the high confinement mode (H-mode) is studied. With the continuous wavelet transform technique the intense bursts in the GPI signal can be detected; their number decreases in the H-mode with respect to the L-mode, with no significant change in the poloidal velocities. The difference between the two regimes is also observed in the poloidal wavenumber spectra: L-mode and H-mode have two different injection scales for the energy, and different cascades take place. Only in the L-mode the energy flows toward the small wavenumber feeding the bigger blobs.
Pathways to folding, nucleation events, and native geometry
Authors: Travasso Rui D. M. , Telo da Gama Margarida M. , Faísca Patrícia F. N.
Published: October 2007

We perform extensive Monte Carlo simulations of a lattice model and the Gō potential [N. Gɵ and H. Taketomi, Proc. Natl. Acad. Sci. U.S.A. 75, 559563 (1978)] to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e., that with more nonlocal contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.
Effects of low surfactant Sb coverage on Zn and C incorporation in GaP
Authors: Howard A. D. , Stringfellow G. B.
Published: October 2007

The use of surfactants during the vapor phase growth of III-V materials to control fundamental characteristics of epitaxial layers is becoming increasingly important. We have investigated the remarkable effects of Sb, from triethylantimony (TESb) pyrolysis, on the Zn doping during the organometallic vapor phase epitaxial growth (OMVPE) of GaP. Antimony is isoelectronic with the P host; therefore it is not a dopant in this material. It is also much larger than P so little incorporation occurs. We used secondary ion mass spectroscopy (SIMS) to investigate in detail the effects of TESb flow rate (Sb surface coverage) on the incorporation of the dopant Zn, as well as the background impurities C and H in GaP. The doping efficiency of Zn increased by as much as a factor of 2 when Sb was added during growth. Importantly, the observed effect was steady throughout the entire range of Sb levels from an Sb/III ratio of 0.01–0.05. Previous studies indicate that this would yield Sb surface coverages of 0.3 (for Sb/III=0.01) to 0.65 (for Sb/III=0.05). Thus, the Sb surface coverage is not saturated. Other results indicate that Sb coverage may be higher at the step edge, which suggests that the surfactant effect on Zn doping occurs at the step edge. Additionally, Sb caused an increase in the hydrogen concentration and a reduction in the carbon contamination. We propose a simple mechanism for the surfactant effect on Zn doping due to an increase of Sb coverage near the step edge.
Topological effects for nonsymmetrical configurations: The C2H2+ as a case study
Authors: Halász G. J. , Vibók Á. , Baer M.
Published: October 2007

During the last decade the study of topological effects formed by molecular systems became a routine but it was always carried out for configurations that were limited by symmetry conditions. To be more specific this applied to the Jahn-Teller (JT) effect formed by molecular configurations of planar symmetry [see, e.g., Baer et al., Faraday Discuss. 127, 337 (2004)] and the Renner-Teller effect formed by configurations of axial symmetry [see, e.g., Halász et al., J. Chem. Phys. 126, 154309 (2007)]. In this article we consider for the first time molecular configurations that avoid any symmetry conditions or, in other words, are characterized by the C1 point group. We report on a detailed study of topological effects formed by such a molecular system. The study concentrates on both, the two-state (Abelian) case and the multistate (non-Abelian) case. It is shown that the theory that was originally developed to treat topological effects due the JT intersection and also applies for the study of topological effects in the most general case. The study is accompanied with numerical results.
Collisionality and magnetic geometry effects on tokamak edge turbulent transport. II. Many-blob turbulence in the two-region model
Authors: Russell D. A. , Myra J. R. , D’Ippolito D. A.
Published: October 2007

A two-region model, coupling the outboard midplane and the X-point region, was proposed in Paper I [J. R. Myra, D. A. Russell, and D. A. D’Ippolito, Phys. Plasmas 13, 112502 (2006)] to study the effects of collisionality and magnetic geometry on electrostatic turbulent transport in the edge and scrape-off layer of a diverted tokamak plasma by filamentary coherent structures or “blobs.” Attention was focused on the properties of isolated blobs. That study is extended here to the many-blob, turbulent saturated state driven by a linearly unstable density profile. The evolution of the density profile is included. It is demonstrated that turbulent density transport increases with collisionality but decreases with enhanced magnetic field-line fanning and shear in this model. Field-line shear induces poloidal velocity in isolated blob propagation and de-correlates the electrostatic potentials in the two regions in the turbulent regime. Probability density functions of density flux resemble those of experimental probe data: both are insensitive to magnetic field geometry and collisionality. It is shown that blobs are born where the skewness of density fluctuations vanishes and the logarithmic pressure gradient is maximized. The simulations show increased particle fluxes with increased plasma resistivity, which are due to increases in both blob velocity and creation rate (or spatial “packing fraction”). A wavelet-type Gaussian-fitting analysis is used to study the dependence of blob velocity on blob size. It is found that streamers, which dominate the simulations, move faster than circular blobs when the two regions are electrically disconnected.
Optical properties upon vacuum ultraviolet excitation of sol-gel based Y3Al5O12:Tb3+, Ce3+ powders
Authors: Potdevin A. , Chadeyron G. , Boyer D. , Mahiou R.
Published: October 2007

Optical properties in the vacuum ultraviolet (VUV) region of cerium and terbium activated Y3Al5O12 powders obtained by the sol-gel process were investigated at room and low temperatures. Both Tb3+ and Ce3+ doped samples exhibited a broad absorption band within the conventional Xe-Ne plasma emission range (140–190 nm). Optimal doping rates have been determined for both rare-earth ions. Emission spectra from cerium doped samples were recorded at 8.2 K and uncovered the splitting of the ground state of Ce3+ ions. Decay times of Ce3+ fluorescence can be fitted by double exponential curves, which can be ascribed to a retrapping phenomenon. Eventually, optical characteristics of codoped Y3Al5O12:(Tb,Ce) and Y3Al5O12:(Tb,Gd) were studied.
Extended storage time of poly(3-hexylthiophene) field-effect transistors via immersion in common solvents
Authors: Majewski L. A. , Song A. M.
Published: October 2007

The influence of storage in three different commonly used solvents on the stability of bottom-contact organic field-effect transistors (OFETs) using poly(3-hexylthiophene)-2,5-diyl (P3HT) as the active layer was studied. It is demonstrated that the immersion in a nonpolar solvent, cyclohexane, caused the devices to degrade rapidly. In contrast, the immersion of the devices in two polar solvents, acetone and water, did not significantly affect the performance of these OFETs for periods as long as 20h. Due to the significantly extended device stability in comparison with that in ambient air, de-ionized water might be a convenient storage medium for P3HT OFETs during device fabrication if a temporary isolation from ambient atmosphere is required.
Fast electron temperature measurements using a “multicolor” optical soft x-ray array
Authors: Delgado-Aparicio L. F. , Stutman D. , Tritz K. , Finkenthal M. , Bell R. , Hosea J. , Kaita R. , LeBlanc B. , Roquemore L. , Wilson J. R.
Published: October 2007

A fast (⩽0.1ms) and compact “multicolor” scintillator-based optical soft x-ray (OSXR) array has been developed for time- and space-resolved measurements of the electron temperature [Te(R,t)] profiles in magnetically confined fusion plasmas. The 48-channel tangential multicolor OSXR prototype was tested on the National Spherical Torus Experiment. Each sight line views the same plasma volume at the midplane (0⩽r∕a⩽1), in three distinct energy ranges determined by beryllium foils with different thicknesses. A tangential view of the toroidally (circular) symmetric plasma allows an Abel inversion of the line-integrated SXR brightness to obtain the x-ray emissivity profiles which are then used to constrain the reconstruction of the fast Te(R,t). The first assessment of the electron temperature is obtained by modeling the slope of the continuum radiation with the ideal double-foil method using both the line-integrated intensity measurements as well as the inverted SXR emissivity profiles.
Ab initio electron propagator calculations in molecular transport junctions: Predictions of negative differential resistance
Authors: Kletsov Aleksey , Dahnovsky Yuri
Published: October 2007

In this work we study current-voltage characteristics in transport molecular junctions with a 1,4-benzene dithiol molecule as a bridge by using different ab initio electron propagator methods such as OVGF and P3 which are both programs in a Gaussian software package. The current-voltage characteristics are calculated for different values of Fermi energy in various basis sets such as 6-311++G(p,d) and cc-pVDZ and are compared with the experimental data. A good agreement is found in almost the entire voltage range. In addition, the results of our calculations indicate that the accuracy of ab initio electron propagator methods is in the range of 0.2–0.3eV. Since the computational methods are truly ab initio, implying no adjustable parameters, functions, or functionals, the theoretical predictions can be improved only by changing the model of a transport device. The current-voltage characteristics predict peaks, i.e., negative differential resistances, for the various values of Fermi energy. As shown, the origin of the negative differential resistances is related to the voltage dependences of overlap integrals for the active terminal orbitals, expansion coefficients of partial atomic wavefunctions in Dyson orbitals, and the voltage dependences of Dyson poles (ionization potentials). We find that two peak behavior in the current-voltage characteristics can be explained by the anharmonicity of potential energy surfaces. As a result of our studies, we predict that negative differential resistances can be experimentally found by changing a position of Fermi level, i.e., by using different metal electrodes coated by a gold atomic monolayer.
Governing equations of the terminal current Green’s functions and their application to derivation of the Nyquist theorem for multiterminal semiconductor devices
Authors: Hong Sung-Min , Min Hong Shick , Park Young June , Park Chan Hyeong
Published: October 2007

This paper presents the governing equations of the Green’s functions for the short-circuit terminal noise currents of semiconductor devices under the drift-diffusion scheme. Using these equations, the Nyquist theorem is derived for multiterminal bipolar semiconductor devices at nonzero frequencies with generation-recombination processes considered. It is explicitly shown that generation-recombination noise sources play an essential role in canceling out part of terminal noise contributions from diffusion noise sources to finally obtain the equilibrium thermal noise.
Control of carbon nanostructure: From nanofiber toward nanotube and back
Authors: Melechko A. V. , Klein K. L. , Fowlkes J. D. , Hensley D. K. , Merkulov I. A. , McKnight T. E. , Rack P. D. , Horton J. A. , Simpson M. L.
Published: October 2007

The unique properties of carbon nanofibers (CNFs) make them attractive for numerous applications ranging from field emitters to biological probes. In particular, it is the deterministic synthesis of CNFs, which requires precise control over geometrical characteristics such as location, length, diameter, and alignment, that enables the diverse applications. Catalytic plasma enhanced chemical vapor deposition of vertically aligned CNFs is a growth method that offers substantial control over the nanofiber geometry. However, deterministic synthesis also implies control over the nanofiber’s physical and chemical properties that are defined by internal structure. Until now, true deterministic synthesis has remained elusive due to the lack of control over internal graphitic structure. Here we demonstrate that the internal structure of CNFs can be influenced by catalyst preparation and ultimately defined by growth conditions. We have found that when the growth rate is increased by 100-fold, obtained through maximized pressure, plasma power, and temperature, the resulting nanofibers have an internal structure approaching that of multiwalled nanotubes. We further show that the deliberate modulation of growth parameters results in modulation of CNF internal structure, and this property has been used to control the CNF surface along its length for site specific chemistry and electrochemistry.
Smectic ordering in athermal systems of rodlike triblock copolymers
Authors: Varga Szabolcs , Fraden Seth
Published: October 2007

The phase behavior of the system of parallel rigid triblock copolymers is examined using the second virial density functional theory. The triblock particle consists of two identical infinitely thin hard rods of finite lengths on the opposite ends of one central hard cylinder with nonzero length and diameter. Stability analyses and free energy calculations show that the system of parallel particles can form not only uniform nematic and smectic A phases but also a smectic C phase. The stability and structure of the tilted structure are controlled by only the diameter and the length of the central cylinder segment. Interestingly, the diameter affects only the layer tilting and the periodicity, but not the packing fraction of the nematic to smectic–C transition. For all values of cylinder length the usual smectic A and smectic C transitions compete with each other and no nematic-columnar transition is observed. At low and high cylinder lengths the smectic A phase is stabilized first, while the smectic C is the most stable for intermediate length values.
Linear and nonlinear optical properties of one-dimensional photonic crystals containing ZnO defects
Authors: Lee Geon Joon , Lee Young Pak , Jung Sung Goo , Hwangbo Chang Kwon , Kim Sunman , Park Inkyu
Published: October 2007

The linear and nonlinear optical properties of one-dimensional photonic crystals containing ZnO defects were studied by linear absorption spectroscopy and the femtosecond Z-scan technique. Photonic crystals containing ZnO defects, (Ta2O5∕SiO2)5∕ZnO∕(SiO2∕Ta2O5)5, were prepared using electron-beam deposition and magnetron sputtering. The transmission spectra of these photonic crystals revealed a defect mode resonance and a broad photonic band gap. The observed transmission spectra could be described by applying the optical transfer matrix formalism to the multilayer structure. When compared with the Z-scan curve of the ZnO film, that of the resonant photonic crystal exhibited a larger transmittance dip. The enhancement of the nonlinear absorption in the resonant photonic crystal is due to the strong confinement of the optical field.
Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration
Authors: Jayaraman Arthi , Hall Carol K. , Genzer Jan
Published: October 2007

We use lattice Monte Carlo simulations to study the thermodynamics of hybridization of single-stranded “target” genes in solution with complementary “probe” DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8–24 segments. The segments on the probe and target are distinct, with each segment representing a sequence of nucleotides that interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how surface density (number of probes per unit surface area) and concentration of target molecules affect the extent of hybridization. For short probe lengths, as the surface density increases, the probability of binding long stretches of target segments increases at low surface density, reaches a maximum at an intermediate surface density, and then decreases at high surface density. Furthermore, as the surface density increases, the target is less likely to bind completely to one probe; instead, it binds simultaneously to multiple probes. At short probe lengths, as the target concentration increases, the fraction of targets binding completely to the probes (specificity) decreases. At long probe lengths, varying the target concentration does not affect the specificity. At all target concentrations as the probe length increases, the fraction of target molecules bound to the probes by at least one segment (sensitivity) increases while the fraction of target molecules completely bound to the probes (specificity) decreases. This work provides general guidelines to maximizing microarray sensitivity and specificity. Our results suggest that the sensitivity and specificity can be maximized by using probes 130–180 nucleotides long at a surface density in the range of 7×10−5–3×10−4probemoleculespernm2.
In
As
∕
Al
As
Sb
based quantum cascade lasers
Authors: Marcadet X. , Renard C. , Carras M. , Garcia M. , Massies J.
Published: October 2007

The advantages and drawbacks of the different semiconductor materials which can be used for the fabrication of quantum cascade laser (QCL) emitting in the 3–4μm wavelength range bring us to propose a material combination which can be lattice matched to InAs substrate. It is shown that using InAs quantum wells and AlAsSb barriers, it is possible to balance the strain in QCL structures made on InAs whatever the active region design and the wavelength targeted. A first InAs∕AlAsSb QCL structure has been grown and fully characterized by x-ray diffraction. The devices emit at 3.5μm at 300K in pulsed mode.
Observable consequences of formation of Au anions from deposition of Au atoms on ultrathin oxide films
Authors: Giordano Livia , Martinez Umberto , Sicolo Sabrina , Pacchioni Gianfranco
Published: October 2007

Charging of metal atoms or clusters on oxide surfaces has important consequences on their chemical and physical properties. Recently it is has been shown that negatively charged gold atoms and clusters form spontaneously from neutral Au atoms deposited on ultrathin MgO films. The formation of anions on the surface remains difficult to prove experimentally. Also theoretically, the discrimination between neutral and charged adsorbed species is not straightforward. In this paper we perform an accurate analysis of the observable consequences of the formation of Au anions on an oxide surface. To this end we consider the following properties: spin distribution, density of states, Bader charges, substrate relaxation, simulated scanning tunneling microscopy images, work function changes, CO vibrational frequency, electric field effects, and core level shifts. Most of these properties are accessible experimentally, at least in principle. Taken individually, these properties do not necessarily provide conclusive evidence about the charged nature of the adsorbate. Taken together, they offer a complete and unambiguous characterization of the formation of Au anions.