bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasma startup in the National Spherical Torus Experiment using transient coaxial helicity injection
Authors: Raman R. , Jarboe T. R. , Mueller D. , Nelson B. A. , Bell M. G. , Ono M. , Bigelow T. , Kaita R. , LeBlanc B. , Maqueda R. , Menard J. , Paul S. , Roquemore L. ,   The NSTX Research Team
Published: April 2007

A method of plasma current generation known as coaxial helicity injection (CHI) has been successfully applied in the National Spherical Torus Experiment [M. Ono, S. M. Kaye, Y.-K. M. Peng et al., Nucl. Fusion 40, 3Y–557 (2000)] to form closed, nested magnetic surfaces carrying a plasma current up to 160kA. In some discharges the generated current persists for surprisingly long, ∼400ms. While the CHI method has previously been studied in smaller experiments, such as the Helicity Injected Tokamak (HIT-II) [R. Raman, T. R. Jarboe, B. A. Nelson et al., Phys Rev. Lett. 90, 075005 (2003)] at the University of Washington, the significance of these results are (a) demonstration of the process in a vessel volume thirty times larger than HIT-II on a size scale more comparable to a reactor, (b) a remarkable multiplication factor of 60 between the injected current and the achieved toroidal current, compared to six in previous experiments, and (c) for the first time, fast time scale visible imaging of the entire process that shows discharge formation, disconnection from the injector, and luminous structures consistent with the reconnection of magnetic field lines and closed flux surfaces. These significant results indicate favorable scaling with machine size.
Large-scale synthesis and optical behaviors of ZnO tetrapods
Authors: Zhang Zengxing , Yuan Huajun , Gao Yan , Wang Jianxiong , Liu Dongfang , Shen Jun , Liu Lifeng , Zhou Weiya , Xie Sishen , Wang Xiao , Zhu Xing , Zhao Yuanchun , Sun Lianfeng
Published: April 2007

Zinc oxide tetrapods were synthesized on a large scale through thermal evaporation of zinc powder with a vapor transportation deposition method. Scanning electron microscope images gave clear evidences of twin planes at the junction of the tetrapods. Photoluminescence and waveguide behaviors of a single tetrapod were demonstrated with a near-field scanning optical microscope.
Phase separation in polyisoprene/polystyrene blends by a systematically coarse-grained model
Authors: Sun Qi , Faller Roland
Published: April 2007

The authors have successfully developed a structurally coarse-grained 1,4-cis-polyisoprene–atactic polystyrene blend model by systematic mapping between a detailed atomistic model and a mesoscale model. This is to their best knowledge the first time that a chemically specific polymer blend model has been used to study the phase separation morphology and kinetics in a blend. A structurally optimized force-field model has many advantages over simple bead-spring models in terms of representing the chain microstructure. It keeps the identity of the polymers, particularly the structure through radial distribution functions. Starting from randomly mixed initial configurations, the blends show a clear phase separation for chain lengths around 10 monomers and this separation becomes more pronounced with the increase of chain length. The ensuing morphology is lamellar at equiweight concentrations and cylindrical or spherical at unbalanced concentrations. Morphologies are validated to be stable under increasing system sizes and further characterized quantitatively by density profiles.
Numerical simulation on the mechanical characteristics of double-stranded DNA under axial stretching and lateral unzipping
Authors: Yuan C. A. , Zhang G. Q. , Han C. N. , Chiang K. N. , Cui Y.
Published: April 2007

The mechanical characteristics of the long-chain double-stranded DNA (dsDNA) molecule under the axial stretching and lateral unzipping are studied by the clustered atomistic-continuum method (CACM). The CACM consisted of the clustered atom method (CAM) and the atomistic-continuum method (ACM). The CAM treats the specific atomic group as the superatom, and the ACM describes the chemical binding energies between (super)atoms by virtual elements. The Newtonian based model of the dsDNA includes the superatoms of the backbones∕base pairs and the virtual elements of the stacking energies∕hydrogen bonds. The effective properties of the superatoms are numerically extracted from the single-stranded DNA experiments. Good agreements were achieved between the dsDNA numerical results and the single molecular experimental results. Via the simulation of stretching dsDNA, the mechanical responses, including the twisting of the backbone and variation of the elastic deformation energy and stacking energy, can be elucidated. Moreover, the predictive capability of the dsDNA CACM model is then examined. Furthermore, the dsDNA model with sequential information is subjected to the unzipping loading, and the in silico results reveal that the sliding of the backbones and the sequential dependent mechanical responses.
High-speed tensile test instrument
Authors: Mott P. H. , Twigg J. N. , Roland D. F. , Schrader H. S. , Pathak J. A. , Roland C. M.
Published: April 2007

A novel high-speed tensile test instrument is described, capable of measuring the mechanical response of elastomers at strain rates ranging from 10 to 1600 s−1 for strains through failure. The device employs a drop weight that engages levers to stretch a sample on a horizontal track. To improve dynamic equilibrium, a common problem in high speed testing, equal and opposite loading was applied to each end of the sample. Demonstrative results are reported for two elastomers at strain rates to 588 s−1 with maximum strains of 4.3. At the higher strain rates, there is a substantial inertial contribution to the measured force, an effect unaccounted for in prior works using the drop weight technique. The strain rates were essentially constant over most of the strain range and fill a three-decade gap in the data from existing methods.
Effect of surface roughening on femtosecond laser-induced ripple structures
Authors: Tomita Takuro , Kinoshita Keita , Matsuo Shigeki , Hashimoto Shuichi
Published: April 2007

The effect of surface roughness was studied on the formation of femtosecond laser-induced ripple structures for 4H-SiC. Of the two types of ripple structures, fine and coarse, the threshold fluence for the formation of the fine ripple was remarkably reduced on the surface roughened by intentional rubbing, while the threshold for the formation of the coarse ripple was not affected. The result suggests that the initial surface roughness plays a significant role only for the formation of fine ripples. A brief explanation will be given on the qualitative basis for the specific effect of surface morphology to the fine ripple formation.
Frequency dispersion of dielectric permittivity–voltage hysteresis during field driven ferroelectric-antiferroelectric-ferroelectric transition in antiferroelectric liquid crystal (SmCA*)
Authors: Rahman Muklesur , Mukherjee A. , Chaudhuri B. K. , Yoshizawa A.
Published: April 2007

Dielectric permittivity at different polarizing states during field driven ferroelectric-ferroelectric (F-F) transition and the dielectric relaxation spectra in the antiferroelectric liquid crystal (AFLC) phase have been studied to elucidate the interaction processes involved during the transition. The unwinding process of antiferroelectric helix has been found to be governed by the polar coupling between the applied field and the antiferroelectric polarization vector followed by nonpolar interaction with the dielectric anisotropy of the tilted molecules. Frequency dependence of the permittivity-voltage hysteresis behavior observed during the F-F transitions is concluded to be due to different relaxation processes involved in the AFLC phase.
Magnetoresistance mobility extraction on TiN∕HfO2∕SiO2 metal-oxide-semiconductor field effect transistors
Authors: Thevenod L. , Cassé M. , Desrat W. , Mouis M. , Reimbold G. , Maude D. K. , Boulanger F.
Published: April 2007

The impact of a high-κ material on the carrier mobility in n-channel transistors is studied by magnetoresistance measurements. The mobility is extracted on HfO2∕TiN metal-oxide-semiconductor field effect transistors with this innovative technique. Unlike the CV-split technique, the authors have shown that the measurement of the magnetoresistance allows a reliable mobility extraction down to very low carrier density. They have demonstrated that the use of a hafnium-based oxide as a gate dielectric leads to an additional Coulomb scattering term, well identified at low electron density. These experimental results bring further evidence that the mobility degradation is caused by charges in the HfO2 layer as suggested in previous studies.
Time-resolved Faraday rotation measurements of spin relaxation in InGaAs∕GaAs quantum dots: Role of excess energy
Authors: Robb J. L. , Chen Y. , Timmons A. , Hall K. C. , Shchekin O. B. , Deppe D. G.
Published: April 2007

The authors report measurements of room temperature spin dynamics in InGaAs quantum dots using time-resolved differential transmission and Faraday rotation techniques. They observe an enhancement of the electron spin lifetime by an order of magnitude for direct optical pumping of the quantum dot ground state compared to optical pumping of the GaAs barriers. These findings indicate that the optical excitation conditions can have a critical influence on the spin kinetics, a result which may account for the wide variation of spin lifetimes reported to date. The enhancement in spin lifetime observed here is attributed to the reduction of phonon-mediated spin-flip scattering.
Pt F 6 2 − dianion and its detachment spectrum: A fully relativistic study
Authors: Pernpointner Markus , Cederbaum Lorenz S.
Published: April 2007

In this work we calculate the photoelectron spectrum of the PtF62− dianion by application of the third-order Dirac-Hartree-Fock one-particle propagator technique. Relativistic effects and electron correlation are hereby treated on a consistent theoretical basis which is mandatory for systems containing heavy elements. A PtF62− gas phase photoelectron spectrum is not yet available and our calculations therefore have predictive character. As it is characteristic for dianionic systems a strong dependence on basis set size and molecular geometry is observed. In contrast to the already calculated PtCl62− photoelectron spectrum no valence orbital inversion due to strong interplay of spin-orbit coupling and electron correlation is observed. Furthermore an unusually strong spin-orbit splitting was found for the σ-type subvalence 1t1u molecular spinor despite its very small platinum p population. The double ionization threshold is strongly lowered by relativistic effects now enabling an interatomic Coulombic decay process after ionization from the σ-bonding orbitals. The results stress the importance of spin-orbit coupling for the understanding of the spectral structure which cannot be reproduced by a scalar-relativistic treatment only.
Fine-grained BaZr0.2Ti0.8O3 thin films for tunable device applications
Authors: Ying Z. , Yun P. , Wang D. Y. , Zhou X. Y. , Song Z. T. , Feng S. L. , Wang Y. , Chan H. L. W.
Published: April 2007

A study of the structure and in-plane dielectric properties of BaZr0.2Ti0.8O3 thin film epitaxially grown on (LaAlO3)0.3(Sr2AlTaO6)0.35 (001) single-crystal substrates through pulsed-laser deposition has been carried out. X-ray diffraction measurements revealed a good crystallinity and tensile in-plane stress in the film. Fine grains with an average size of ∼20 nm were observed using atomic force microscopy. Curie temperature of the film was found to be ∼120 °C, which is 100 °C higher than that of the ceramic. Butterfly-shaped C-V curve confirmed the in-plane ferroelectric state in the film. A large dielectric tunability of ∼50% was found in the film.
Si avalanche photodetectors fabricated in standard complementary metal-oxide-semiconductor process
Authors: Kang Hyo-Soon , Lee Myung-Jae , Choi Woo-Young
Published: April 2007

The authors report silicon avalanche photodetectors (APDs) fabricated with 0.18μm standard complementary metal-oxide-semiconductor (CMOS) process without any process modification or a special substrate. When the bias is above the avalanche breakdown voltage, CMOS-compatible APD (CMOS-APD) exhibits negative photoconductance in photocurrent-voltage relationship and rf peaking in the photodetection frequency response. The reflection coefficient measurement of CMOS-APD indicates that rf peaking is due to resonance caused by appearance of inductive components in avalanche region. The rf-peaking frequency increases with the increasing reverse bias voltage.
Detection of shallow inclusions in closed-packed granular beds using mechanical impulses
Authors: Swaminathan Saravanan , Visco Donald P. , Sen Surajit
Published: April 2007

Mechanical energy has been used in the detection of shallow buried objects in granular beds for more than half a century. Here we attempt to answer a fundamental question—at what depths would an object be detectable in an idealized, close-packed, granular bed made of monosized elastic spheres? Systematic particle dynamics based studies reveal the effects of varying the area across which the impulse is generated, object size, and restitution on locating the buried object.
Short-range order of low-coverage Ti∕Al(111): Implications for hydrogen storage in complex metal hydrides
Authors: Muller E. , Sutter E. , Zahl P. , Ciobanu C. V. , Sutter P.
Published: April 2007

Using scanning tunneling microscopy and density functional theory, we characterize the population of low-coverage Ti atoms on Al(111) as a model surface system for transition metal doped alanate hydrogen storage compounds, such as NaAlH4. When deposited at room temperature, Ti is kinetically trapped in first-layer substitutional sites, avoids nearest-neighbor locations, and preferentially forms next-nearest-neighbor pairs, similar to a structure that has been predicted to dissociate H2 with no energy barrier. The results on this well-defined system suggest the presence of a large population of Ti-pair complexes that may catalyze the dissociative chemisorption of hydrogen in Ti-doped alanate storage materials.
Effect of physical aging on the Johari-Goldstein and α relaxations of D-sorbitol: A study by thermally stimulated depolarization currents
Authors: Moura Ramos Joaquim J. , Diogo Hermínio P. , Pinto Susana S.
Published: April 2007

The relaxations in amorphous D-sorbitol have been studied by thermally stimulated depolarization currents during annealing at 255K, which is 17K below its calorimetric glass transition temperature Tg=272K. As the glass structurally relaxes on aging, the features of the α relaxation and of the Johari-Goldstein (JG) relaxation change with time. For the α relaxation (i) the dielectric strength decreases; (ii) the activation energy decreases; and (iii) the relaxation time increases. For the JG relaxation the dielectric strength also decreases but with a different time dependence, and there is no evidence for any modification of the kinetic features of the mobility. The amplitude of response to aging is higher for the higher temperature motional components of the Johari-Goldstein relaxation compared with the lower temperature ones.
Development of bellows and gate valves with a comb-type rf shield for high-current accelerators: Four-year beam test at KEK B-Factory
Authors: Suetsugu Yusuke , Kanazawa Ken-ichi , Shibata Kyo , Shirai Mitsuru , Bondar Aleksander E. , Kuzminykh Victor S. , Gorbovsky Aleksander I. , Sonderegger Kurt , Morii Minoru , Kawada Kakuyu
Published: April 2007

Since a comb-type rf shield was proposed in 2003 as a rf shield for future high-intensity accelerators, various types of bellow chambers and gate valves with this rf shield have been installed in the KEK B-Factory rings in series and tested with beams. Through beam tests to check the performance, a structural simplification has been tried in parallel. The temperatures of the bellow corrugations decreased by a factor of 3–6 compared to those with a conventional finger-type rf shield in most cases. The temperatures of the body of the gate valves also decreased by a factor of 2–5. These results demonstrated the availability of the comb-type rf shield. Although a discharge was observed in one simplified model, the latest model has shown no problem up to a stored beam current of 1.8A (1.3mA/bunch, 6mm bunch length). Experiences with the comb-type rf shield in these four-year beam tests are reviewed here.
Temperature-dependent electroluminescence spectra of organic light emitting diodes based on thermally evaporated bis-imido-phenylene vinylene derivative
Authors: Wantz G. , Hirsch L. , Dautel O. J.
Published: April 2007

This letter reports on the effect of temperature on the electroluminescence spectrum of organic light-emitting diodes based on a low molecular weight compound. Bis-imido-phenylene vinylene derivative has been chosen as green-emitting molecule because of its similarity with poly-phenylene-vinylene derivatives. The electroluminescence spectra are found softly dependent on the degree of crystallinity of the layer and strongly dependent on the temperature. Electroluminescence spectra are fitted with multiple Gaussian peaks corresponding to phonon replica. With increasing temperature a blueshift of the zero-phonon line is observed. This phenomenon, commonly observed with poly-phenylene-vinylene derivatives, is usually explained as a reduction of the effective conjugation length. Such a model cannot be used with small molecules due to a finite conjugation length. A model of thermally activated statistic occupation of excited states is used to fully describe the experimental data. The results definitely rule out any significant role of a reduction of the conjugation length by increasing the temperature. It is also found that increasing the degree of order of the molecular morphology induces a reduction of the width of density of excited states.
Enhanced light extraction of GaN-based light-emitting diodes by using textured n-type GaN layers
Authors: Kim Hyunsoo , Cho Jaehee , Lee Jeong Wook , Yoon Sukho , Kim Hyungkun , Sone Cheolsoo , Park Yongjo , Seong Tae-Yeon
Published: April 2007

The authors report on the enhancement of the light extraction efficiency of GaN-based light-emitting diodes (LEDs) via the texturing of n-type layers. Compared with standard LEDs, LED fabricated with the textured n-type layers produced a significant improvement in the output power, depending on the reflectivity of the n electrode, the etch-pit size, and the chip dimension. The textured LEDs were found to yield the output power enhancement as high as 54%. However, it was also found that the electrical property of the textured LEDs can be degraded when the size of the etch pits is too large, indicating that a well-controlled texturing process is required for the realization of high-efficiency LEDs.
Relationships between plasma methylmalonic acid and ruminal succinate in cobalt-deficient and -repleted sheep
Authors: Wiese S. C. , White C. L. , Williams I. H. , Allen J. G.
Published: April 2007

We measured methylmalonic acid (MMA) in plasma and succinate in the rumen during the depletion of sheep to a state of severe cobalt deficiency and repletion by various forms of supplementation. Groups of 10, cobalt-deficient weaners were allocated to one of 4 treatments: no supplement, 0.1 or 4.0 mg/day of cobalt as a solution of CoSO4.7H2O per os, or intramuscular vitamin B12. Plasma concentrations of MMA were elevated above the normal range (5 µmol/L) after 35 days on the cobalt-deficient diet, before a reduction in feed intake and while liveweights were still increasing. In all 3 supplemented groups of sheep, plasma vitamin B12 concentrations increased to normal levels within 10 days of supplementation (P < 0.001). Plasma MMA concentrations were reduced to normal levels within 10 days with vitamin B12 supplementation but took 31 days with oral cobalt supplementation (P < 0.001). Plasma MMA concentration in the unsupplemented group continued to rise and remain high for the duration of the experiment and did not show the peak and decline to levels indistinguishable from cobalt adequate levels as observed by others. Rumen succinate concentrations were elevated within 6 days of sheep being introduced to a cobalt-deficient diet and in the unsupplemented sheep remained elevated for the duration of measurement. This rise in rumen succinate was seen at a wider range of cobalt intakes than previously reported. In both oral cobalt treatments, vitamin B12 concentrations increased (P < 0.001) and succinate concentrations decreased (P < 0.001) in the rumen to normal levels within 6 days of supplementation. However, the vitamin B12 provided to the sheep by injection was not recycled to the rumen to any effective degree, as demonstrated by the persistence of high rumen succinate concentrations. The ability of the vitamin B12-supplemented sheep to maintain higher rates of wool growth than deficient sheep, while still exhibiting elevated succinate concentrations in the rumen, demonstrates that overcoming the blockage of the methylmalonyl CoA mutase pathway in the rumen is not essential for restoring metabolic pathways such as those responsible for wool growth. This work contributes to the knowledge of plasma MMA and rumen succinate as useful indicators of functional cobalt status and cobalt intake in sheep.
Long-term effects of saline irrigation water on growth, yield, and fruit quality of 'Valencia' orange trees
Authors: Grieve A. M. , Prior L. D. , Bevington K. B.
Published: April 2007

Citrus is regarded as a salt-sensitive crop, but its yield response to salinity is affected by variety, rootstock, duration of salt exposure, irrigation management, soil type, and climate. This study quantified the yield response of mature Valencia [Citrus sinensis (L. Osbeck)] orange trees on sweet orange (C. sinensis) rootstock to increased levels of sodium chloride in irrigation water in the Sunraysia area of the Murray Valley in south-eastern Australia. The orchard was planted on a loamy sand and trees were irrigated and fertilised with a well-managed under-tree microsprinkler system. Four levels of salt, ranging from the river-water control (0.44 dS/m) to 2.50 dS/m, were applied over a 9-year period. Overall yield effects were smaller than expected, and did not conform well to the often used bent-stick model. Relative to the control, yield was initially higher (by up to 9%) in the intermediate salt treatments, and 3% lower in the highest treatment. However, relative yields of salinised trees decreased with time, and in the final year of the experiment, yield of the highest salt treatment was 9% lower than the control. Yield increases in the intermediate treatments resulted from increases in fruit number. All 3 salt treatments decreased average fruit weight by 4% and decreased juice content but increased juice sugar and acid content. Salt treatment strongly reduced trunk growth, and the effect increased with time. Our results show that with appropriate irrigation management, soils, and rootstocks, citrus trees can maintain productivity at salinity levels of 2.0 dS/m or more, but fresh fruit profitability is likely to be lower because of a reduction in average fruit size.
Long-term effects of saline irrigation water on 'Valencia' orange trees: relationships between growth and yield, and salt levels in soil and leaves
Authors: Prior L. D. , Grieve A. M. , Bevington K. B. , Slavich P. G.
Published: April 2007

This study documents changes in yield, growth, soil salinity (ECe) and leaf sodium (Na) and chlorine (Cl) concentrations in mature Valencia orange [Citrus sinensis (L.Osbeck)] trees on sweet orange (Citrus sinensis) rootstock in response to increased levels of Na and Cl in irrigation water. Four levels of salt, ranging from the river-water control (0.44 dS/m) to 2.50 dS/m, were applied over a 9-year period through an under-tree microsprinkler system to trees in the Sunraysia area of the Murray Valley in south-eastern Australia. A salt-balance model showed that evapotranspiration was reduced by salinity, whereas leaching fractions increased from an average 24% in the control to 51% in the most saline treatment. The high leaching fractions were achieved as a result of freely draining soils and good irrigation management, and allowed us to maintain low to moderate levels of soil salinity throughout the trial and minimised the effect of salt treatment on fruit yield. Soil salinity increased almost linearly in response to irrigation-water salinity during the first year, and fluctuated seasonally thereafter; however, very few readings exceeded 3 dS/m, even in the highest treatments. By contrast, leaf Na and Cl concentrations in the highest salt treatment continued to increase over the first 4 years. The relationship between yield and soil salinity was extremely weak, but yield did decrease as foliar concentrations of Na and Cl increased: in Year 9, leaf Na in the highest treatment relative to the control was associated with a predicted reduction of 17% in yield and 59% in annual trunk-diameter growth.
Seasonal variation in milk production and cheese yield from commercial dairy farms located in northern Victoria is associated with pasture and grazing management and supplementary feeding practices
Authors: Walker G. P. , Williams R. , Doyle P. T. , Dunshea F. R.
Published: April 2007

A study of irrigated pasture-based commercial dairy farms that made use of split calving (two distinct periods of calving; autumn and spring) was undertaken between April 2001 and March 2002 in northern Victoria, to examine associations between herd nutrition, time of year and season of calving and the production and composition of milk. On average, herds that had access to higher digestibility pasture or were fed more cereal grain-based concentrates produced more milk. However, the average marginal yield of 4% fat corrected milk/kg cereal grain-based concentrates was less than responses achieved under experimental conditions in northern Victoria. Herds that calved in autumn had different production characteristics to those that calved in spring, in that they did not show an early lactation peak in milk yield and produced milk with lower average concentrations of crude protein, casein and fat. Despite this, herds that calved in autumn had greater persistency of milk yield in mid to late lactation, when they tended to be better fed on pasture, so that yields of milk solids over a notional 310-day lactation were similar for both calving groups (523 v. 529 kg fat + protein; autumn v. spring, respectively), but herds that calved in autumn produced milk with a lower potential to yield cheddar cheese (10.2 v. 10.6 kg cheese/100 kg milk; P < 0.01). Farms that produced milk in the lowest quartile for potential to yield cheddar cheese differed from the top quartile in that they: (i) milked fewer cows (175 v. 250); (ii) fed less supplements (5.6 v. 9.4 kg DM/cow.day); (iii) walked their herds shorter distances between pasture and the dairy (2.2 v. 3.2 km/day); (iv) allocated lower herbage allowances (33 v. 43 kg DM/cow.day); and (v) grazed pastures at a mass low enough to have restricted pasture intake (< 3 t DM/ha), about twice the frequency of farms (0.40 v. 0.17) in the top quartile. Greater productivity of the dairy industry in northern Victoria could be achieved through better grazing and pasture management and supplementary feeding practices on farms.
Structures and spectral signatures of protonated water networks in bacteriorhodopsin
Authors: Mathias Gerald , Marx Dominik
Published: April 2007

Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H
+
·(H
2
O)
3
and H
+
·(H
2
O)
4
, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H
+
·(H
2
O)
4
network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.
Intravesicular and intervesicular interaction by orthogonal multivalent host–guest and metal–ligand complexation
Authors: Lim Choon Woo , Crespo-Biel Olga , Stuart Marc C. A. , Reinhoudt David N. , Huskens Jurriaan , Ravoo Bart Jan
Published: April 2007

Host vesicles composed of amphiphilic β-cyclodextrin CD1 recognize metal-coordination complexes of the adamantyl-functionalized ethylenediamine ligand L via hydrophobic inclusion in the β-cyclodextrin cavities at the vesicle surface. In the case of Cu(II) and L, the resulting coordination complex was exclusively CuL
2
, and the interaction with the host vesicles was intravesicular, unless the concentration of metal complex and vesicles was high (>0.1 mM). In the case of Ni(II) and L, a mixture was formed consisting of mainly NiL and NiL
2
, the interaction with the host vesicles was effectively intervesicular, and addition of the guest–metal complex resulted in aggregation of the vesicles into dense, multilamellar clusters even in dilute solution [1 μM Ni(II)]. The metal–L complex could be eliminated by a strong chelator such as EDTA, and the intervesicular interaction could be suppressed by a competitor such as unmodified β-cyclodextrin. The result from this investigation is that the strongest metal-coordination complex [Cu(II) with L] binds exclusively intravesicularly, whereas the weakest metal-coordination complex [Ni(II) with L] binds predominantly intervesicularly and is the strongest interfacial binder. These experimental observations are confirmed by a thermodynamic model that describes multivalent orthogonal interactions at interfaces.
HIV controllers exhibit potent CD8 T cell capacity to suppress HIV infection
ex vivo
and peculiar cytotoxic T lymphocyte activation phenotype
Authors: Sáez-Cirión Asier , Lacabaratz Christine , Lambotte Olivier , Versmisse Pierre , Urrutia Alejandra , Boufassa Faroudy , Barré-Sinoussi Françoise , Delfraissy Jean-François , Sinet Martine , Pancino Gianfranco , Venet Alain
Published: April 2007

Some rare HIV-1-infected individuals, referred to as HIV controllers (HIC), have persistently undetectable plasma viral load in the absence of therapy. This control of HIV-1 replication has been associated with a strong, multifunctional specific CD8
+
T cell response. However, no direct link between this immune response and the control of viremia has so far been provided. We investigated parameters of specific CD8
+
T cell response and
in vitro
susceptibility to HIV-1 infection in 11 HIC. We found high frequencies of HIV-specific CD8
+
T cells. Interestingly, these cells expressed the activation marker HLA-DR but not CD38. This unique phenotype differentiates HIV-specific CD8
+
T cells from HIC and noncontroller subjects and likely reflects a high potential to expand upon exposure to antigen and a capacity to exert effector functions. Accordingly, although CD4
+
T cells from HIC were fully susceptible to HIV-1 superinfection, their CD8
+
T cells effectively suppressed HIV-1 infection. Remarkably, this potent anti-HIV activity was observed without prior stimulation of CD8
+
T cells. This activity was not mediated by secreted inhibitory factors but was due to the elimination of infected CD4
+
T cells and was observed only with autologous CD4
+
T cells, indicating an HLA-restricted cytotoxic mechanism. This constitutive antiviral capacity of CD8
+
T cells could account for the control of viral replication in HIC.
Optimal prediction and the rate of decay for solutions of the Euler equations in two and three dimensions
Authors: Hald Ole H. , Stinis Panagiotis
Published: April 2007

The “
t
-model” for dimensional reduction is applied to the estimation of the rate of decay of solutions of the Burgers equation and of the Euler equations in two and three space dimensions. The model was first derived in a statistical mechanics context, but here we analyze it purely as a numerical tool and prove its convergence. In the Burgers case, the model captures the rate of decay exactly, as was previously shown. For the Euler equations in two space dimensions, the model preserves energy as it should. In three dimensions, we find a power law decay in time and observe a temporal intermittency.
Connecting protein structure with predictions of regulatory sites
Authors: Morozov Alexandre V. , Siggia Eric D.
Published: April 2007

A common task posed by microarray experiments is to infer the binding site preferences for a known transcription factor from a collection of genes that it regulates and to ascertain whether the factor acts alone or in a complex. The converse problem can also be posed: Given a collection of binding sites, can the regulatory factor or complex of factors be inferred? Both tasks are substantially facilitated by using relatively simple homology models for protein–DNA interactions, as well as the rapidly expanding protein structure database. For budding yeast, we are able to construct reliable structural models for 67 transcription factors and with them redetermine factor binding sites by using a Bayesian Gibbs sampling algorithm and an extensive protein localization data set. For 49 factors in common with a prior analysis of this data set (based largely on phylogenetic conservation), we find that half of the previously predicted binding motifs are in need of some revision. We also solve the inverse problem of ascertaining the factors from the binding sites by assigning a correct protein fold to 25 of the 49 cases from a previous study. Our approach is easily extended to other organisms, including higher eukaryotes. Our study highlights the utility of enlarging current structural genomics projects that exhaustively sample fold structure space to include all factors with significantly different DNA-binding specificities.
Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling
Authors: Grigorenko Bella L. , Rogov Alexander V. , Topol Igor A. , Burt Stanley K. , Martinez Hugo M. , Nemukhin Alexander V.
Published: April 2007

The intrinsic chemical reaction of adenosine triphosphate (ATP) hydrolysis catalyzed by myosin is modeled by using a combined quantum mechanics and molecular mechanics (QM/MM) methodology that achieves a near
ab initio
representation of the entire model. Starting with coordinates derived from the heavy atoms of the crystal structure (Protein Data Bank ID code
1VOM
) in which myosin is bound to the ATP analog ADP·VO
4
−
, a minimum-energy path is found for the transformation ATP + H
2
O → ADP + P
i
that is characterized by two distinct events: (
i
) a low activation-energy cleavage of the P
γ

O
βγ
bond and separation of the γ-phosphate from ADP and (
ii
) the formation of the inorganic phosphate as a consequence of proton transfers mediated by two water molecules and assisted by the Glu-459–Arg-238 salt bridge of the protein. The minimum-energy model of the enzyme–substrate complex features a stable hydrogen-bonding network in which the lytic water is positioned favorably for a nucleophilic attack of the ATP γ-phosphate and for the transfer of a proton to stably bound second water. In addition, the P
γ

O
βγ
bond has become significantly longer than in the unbound state of the ATP and thus is predisposed to cleavage. The modeled transformation is viewed as the part of the overall hydrolysis reaction occurring in the closed enzyme pocket after ATP is bound tightly to myosin and before conformational changes preceding release of inorganic phosphate.
GABAergic inhibition at dendrodendritic synapses tunes γ oscillations in the olfactory bulb
Authors: Lagier Samuel , Panzanelli Patrizia , Russo Raúl E. , Nissant Antoine , Bathellier Brice , Sassoè-Pognetto Marco , Fritschy Jean-Marc , Lledo Pierre-Marie
Published: April 2007

In the olfactory bulb (OB), odorants induce oscillations in the γ range (20–80 Hz) that play an important role in the processing of sensory information. Synaptic transmission between dendrites is a major contributor to this processing. Glutamate released from mitral cell dendrites excites the dendrites of granule cells, which in turn mediate GABAergic inhibition back onto mitral cells. Although this reciprocal synapse is thought to be a key element supporting oscillatory activity, the mechanisms by which dendrodendritic inhibition induces and maintains γ oscillations remain unknown. Here, we assessed the role of the dendrodendritic inhibition, using mice lacking the GABAAreceptor α1-subunit, which is specifically expressed in mitral cells but not in granule cells. The spontaneous inhibitory postsynaptic current frequency in these mutants was low and was consistent with the reduction of GABAAreceptor clusters detected by immunohistochemistry. The remaining GABAAreceptors in mitral cells contained the α3-subunit and supported slower decaying currents of unchanged amplitude. Overall, inhibitory-mediated interactions between mitral cells were smaller and slower in mutant than in WT mice, although the strength of sensory afferent inputs remained unchanged. Consequently, both experimental and theoretical approaches revealed slower γ oscillations in the OB network of mutant mice. We conclude, therefore, that fast oscillations in the OB circuit are strongly constrained by the precise location, subunit composition and kinetics of GABAAreceptors expressed in mitral cells.
Unique germ-line organelle, nuage, functions to repress selfish genetic elements in
Drosophila melanogaster
Authors: Lim Ai Khim , Kai Toshie
Published: April 2007

The nuage is an electron-dense perinuclear structure that is known to be a hallmark of animal germ-line cells. Although the conservation of the nuage throughout evolution accentuates its essentiality, its role(s) and the exact mechanism(s) by which it functions in the germ line still remain unknown. Here, we report a nuage component, Krimper (KRIMP), in
Drosophila melanogaster
and show that it ensures the repression of the selfish genetic elements in the female germ line. The
Krimp
loss-of-function allele exhibited female sterility, defects in karyosome formation and oocyte polarity, and precocious
osk
translation. These phenotypes are commonly observed in the other nuage component mutants,
vasa
(
vas
) and
maelstrom
(
mael
), and the RNA-silencing component mutants,
spindle-E
(
spn-E
) and
aubergine
(
aub
), suggesting a shared underlying defect that uses RNA silencing. Moreover, we demonstrated that the localization of the nuage components depends on both SPN-E and AUB and that the selfish genetic elements were derepressed to different extents in the nuage component mutants, as well as in
aub
and
armitage
(
armi
) mutants. In the nuage component mutants,
vas, krimp
, and
mael
, the levels of
roo, I-element
, and
HeT-A
repeat-associated small interfering RNAs were greatly reduced. Hence, our data suggest that the nuage functions as a specialized center that protects the genome in the germ-line cells via gene regulation mediated by repeat-associated small interfering RNAs.
Four domains of p300 each bind tightly to a sequence spanning both transactivation subdomains of p53
Authors: Teufel Daniel P. , Freund Stefan M. , Bycroft Mark , Fersht Alan R.
Published: April 2007

The transcriptional coactivator p300 binds to and mediates the transcriptional functions of the tetrameric tumor suppressor p53. Both proteins consist of independently folded domains linked by intrinsically disordered sequences. A well studied short sequence of the p53 transactivation domain, p53(15–29), binds weakly to four folded domains of p300 [Taz1/cysteine–histidine-rich region 1 (CH1), Kix, Taz2/CH3, IBiD], with dissociation constants (
K
D
) in the 100 μM region. However, we found that a longer N-terminal transactivation domain construct p53(1–57) bound tightly to each p300 domain. Taz2/CH3 had the greatest affinity (
K
D
= 27 nM) and competes with the N-terminal domain of Mdm2 for the p53 N terminus. p300 thus can protect the N terminus of p53 against the binding of other proteins. Mutations of p53 that abrogate transactivation (L22Q/W23S, W53Q/F54S) greatly weakened binding to each p300 domain, linking phenotypic defects to weakened coactivator binding. We propose a complex between tetrameric p53 and p300 in which four domains of p300 wrap around the four transactivation domains of p53.
Role of group-conserved residues in the helical core of β
2
-adrenergic receptor
Authors: Chelikani Prashen , Hornak Viktor , Eilers Markus , Reeves Phillip J. , Smith Steven O. , RajBhandary Uttam L. , Khorana H. Gobind
Published: April 2007

G protein-coupled receptors (GPCRs) belonging to class A contain several highly conserved (>90%) amino acids in their transmembrane helices. Results of mutational studies of these highly conserved residues suggest a common mechanism for locking GPCRs in an inactive conformation and for their subsequent activation upon ligand binding. Recently, a second set of sites in the transmembrane helices has been identified in which amino acids with small side chains, such as Gly, Ala, Ser, Thr, and Cys, are highly conserved (>90%) when considered as a group. These group-conserved residues have not been recognized as having essential structural or functional roles. To determine the role of group-conserved residues in the β
2
-adrenergic receptor (β
2
-AR), amino acid replacements guided by molecular modeling were carried out at key positions in transmembrane helices H2–H4. The most significant changes in receptor expression and activity were observed upon replacement of the amino acids Ser-161 and Ser-165 in H4. Substitution at these sites by larger residues lowered the expression and activity of the receptor but did not affect specific binding to the antagonist ligand dihydroalprenolol. A second site mutation, V114A, rescued the low expression of the S165V mutant. Substitution of other group-conserved residues in H2–H4 by larger amino acids lowered receptor activity in the order Ala-128, Ala-76, Ser-120, and Ala-78. Together these data provide comprehensive analysis of group-conserved residues in a class A GPCR and allow insights into the roles of these residues in GPCR structure and function.
Induction of Vascular Permeability: βPIX and GIT1 Scaffold the Activation of Extracellular Signal-regulated Kinase by PAK
Authors: Stockton Rebecca , Reutershan Jörg , Scott David , Sanders John , Ley Klaus , Schwartz Martin Alexander
Published: April 2007

Increased permeability of blood vessels is an important component of inflammation, but in some circumstances it contributes to tissue injury and organ failure. Previous work showed that p21-activated kinase (PAK) is a critical regulator of endothelial cell–cell junctions through effects on myosin light chain phosphorylation and cell contractility. We now show that blocking PAK function inhibits fluid leak in a mouse model of acute lung injury. In cultured endothelial cells, induction of myosin light chain phosphorylation by PAK is mediated by mitogen-activated protein kinase kinase and extracellular signal-regulated kinase (Erk). Erk in lipopolysaccharide (LPS)-treated mouse lung is activated in a PAK-dependent manner in several cell types, most prominently vascular endothelium. Activation of Erk requires the integrity of the complex between PAK, PIX, and GIT1. Several means of disrupting this complex inhibit stimulation of vascular permeability in vitro. A cell-permeant peptide that blocks binding of PAK to PIX inhibits LPS-induced fluid leak in the mouse lung injury model. We conclude that the PAK–PIX–GIT1 complex is critical for Erk-dependent myosin phosphorylation and vascular permeability.
The RING Finger Domain of MDM2 Is Essential for MDM2-mediated TGF-β Resistance
Authors: Kannemeier Christian , Liao Rong , Sun Peiqing
Published: April 2007

In this study, we attempt to gain insights into the molecular mechanism underlying MDM2-mediated TGF-β resistance. MDM2 renders cells refractory to TGF-β by overcoming a TGF-β–induced G1 cell cycle arrest. Because the TGF-β resistant phenotype is reversible upon removal of MDM2, MDM2 likely confers TGF-β resistance by directly targeting the cellular machinery involved in the growth inhibition by TGF-β. Investigation of the structure-function relationship of MDM2 reveals three elements essential for MDM2 to confer TGF-β resistance in both mink lung epithelial cells and human mammary epithelial cells. One of these elements is the C-terminal half of the p53-binding domain, which at least partially retained p53-binding and inhibitory activity. Second, the ability of MDM2 to mediate TGF-β resistance is disrupted by mutation of the nuclear localization signal, but is restored upon coexpression of MDMX. Finally, mutations of the zinc coordination residues of the RING finger domain abrogates TGF-β resistance, but not the ability of MDM2 to inhibit p53 activity or to bind MDMX. These data suggest that RING finger-mediated p53 inhibition and MDMX interaction are not sufficient to cause TGF-β resistance and imply a crucial role of the E3 ubiquitin ligase activity of this domain in MDM2-mediated TGF-β resistance.
Analysis of P-Body Assembly inSaccharomyces cerevisiae
Authors: Teixeira Daniela , Parker Roy
Published: April 2007

Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), that contain untranslating mRNAs in conjunction with proteins involved in translation repression and mRNA decapping and degradation. However, the order of protein assembly into P-bodies and the interactions that promote P-body assembly are unknown. To gain insight into how yeast P-bodies assemble, we examined the P-body accumulation of Dcp1p, Dcp2p, Edc3p, Dhh1p, Pat1p, Lsm1p, Xrn1p, Ccr4p, and Pop2p in deletion mutants lacking one or more P-body component. These experiments revealed that Dcp2p and Pat1p are required for recruitment of Dcp1p and of the Lsm1-7p complex to P-bodies, respectively. We also demonstrate that P-body assembly is redundant and no single known component of P-bodies is required for P-body assembly, although both Dcp2p and Pat1p contribute to P-body assembly. In addition, our results indicate that Pat1p can be a nuclear-cytoplasmic shuttling protein and acts early in P-body assembly. In contrast, the Lsm1-7p complex appears to primarily function in a rate limiting step after P-body assembly in triggering decapping. Taken together, these results provide insight both into the function of individual proteins involved in mRNA degradation and the mechanisms by which yeast P-bodies assemble.
Expanding benzene to giant graphenes: towards molecular devices
Authors: Müller Sibylle , Müllen Klaus
Published: April 2007

Phenylene-based conjugated materials provide versatile platforms for the development of molecular devices. Architectures of one- and two-dimensional polyphenylenes, which self-assemble into three-dimensional objects with advantageous electronic properties, have been investigated. Systematic relations between the size, substitution and shape with function were found, which enabled the further optimization of the materials. Hand in hand with the development of suitable methods for visualization and processing, promising results were obtained for performance of nanoscale electronic devices.