bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation
Authors: Zhao Guang-Jiu , Han Ke-Li , Lei Yi-Bo , Dou Yu-Sheng
Published: September 2007

Detailed simulation study is reported for the excited-state dynamics of photoisomerization of cis-tetraphenylethylene (TPE) following excitation by a femtosecond laser pulse. The technique for this investigation is semiclassical dynamics simulation, which is described briefly in the paper. Upon photoexcitation by a femtosecond laser pulse, the stretching motion of the ethylenic bond of TPE is initially excited, leading to a significant lengthening of ethylenic bond in 300fs. Twisting motion about the ethylenic bond is activated by the energy released from the relaxation of the stretching mode. The 90° twisting about the ethylenic bond from an approximately planar geometry to nearly a perpendicular conformation in the electronically excited state is completed in 600fs. The torsional dynamics of phenyl rings which is temporally lagging behind occurs at about 5ps. Finally, the twisted TPE reverts to the initial conformation along the twisting coordinate through nonadiabatic transitions. The simulation results provide a basis for understanding several spectroscopic observations at molecular levels, including ultrafast dynamic Stokes shift, multicomponent fluorescence, viscosity dependence of the fluorescence lifetime, and radiationless decay from electronically excited state to the ground state along the isomerization coordinate.
Protein elasticity determined by pressure tuning of the tyrosine residue of ubiquitin
Authors: Somoza Mark M. , Wiedersich Johannes , Friedrich Josef
Published: September 2007

We determined the isotropic, isothermal compressibility of ubiquitin by pressure tuning spectral holes burnt into the red edge of the absorption spectrum of the single tyrosine residue. The pressure shift is perfectly linear with burn frequency. From these data, a compressibility of 0.086GPa−1 in the local environment of the tyrosine residue could be determined. This value fits nicely into the range known for proteins. Although the elastic behavior at low temperatures does not show any unusual features, the pressure tuning behavior at room temperature is quite surprising: the pressure-induced spectral shift is close to zero, even up to very high pressure levels of 0.88GPa, well beyond the denaturation point. The reason for this behavior is attributed to equally strong blue as well as red spectral pressure shifts resulting in an average pressure-induced solvent shift that is close to zero.
Vaporization Enthalpy: Corresponding-States Correlations Versus DIPPR Database
Authors: Cachadiña I. , Mulero A.
Published: September 2007

Data for the vaporization enthalpy accepted in the Design Institute for Physical Property Data® (DIPPR®) database are compared with those given by general correlations based on the corresponding-states method. In particular, four analytical predictive correlations were used. Three of them require as input the critical temperature and the acentric factor. The fourth requires a molecular Lennard-Jones parameter and the acentric factor. Results obtained for 1576 fluids indicate that the recommended model for an overall use, in order to reproduce the DIPPR data, is the one proposed by Sivaraman et al. [Ind. Eng. Chem. Fundam. 23, 97 (1984)].
Large-area photonic structures in freestanding films
Authors: Vita Francesco , Lucchetta Daniele E. , Castagna Riccardo , Criante Luigino , Simoni Francesco
Published: September 2007

The authors report the fabrication of freestanding two-dimensional photonic crystals in organic materials. Large-area patterned structures, with submicrometric spatial resolution, have been recorded in spin-coated polymer-dispersed liquid crystals via holographic photolithography. After the removal of the liquid crystal, the polymeric film is peeled off from the substrate. Scanning electron microscope images show the high homogeneity of the structure in any spatial direction. These films can be conveniently used in a wide range of applications, from templates for high-refractive index photonic crystals to flexible photonic elements.
Contact measurement of internal fluid flow within poly(n-isopropylacrylamide) gels
Authors: Lin Wei-Chun , Shull Kenneth R. , Hui Chung-Yuen , Lin Yu-Yun
Published: September 2007

A technique is presented that is ideally suited for characterizing the mechanical and transport properties of polymer gels at small strains. A flat, circular punch and a flat, rectangular punch are used to probe the response of gels under oscillatory loading conditions. Solvent transport within the gel is driven by gradients in hydrostatic pressure, giving rise to a dissipative response quantified by the phase lag between the punch displacement and the resulting load. By comparing results for different punch sizes, it is possible to differentiate between dissipation resulting from internal solvent flow and dissipation due to the viscoelastic character of the polymer network itself. Use of the technique is illustrated with poly(n-isopropylacrylamide) gels, which undergo a reversible structural transition just above room temperature. We show that heterogeneous structure formed above the transition temperature is not conducive to internal solvent flow within these gels.
Molecular dynamics simulation study of erbium induced devitrification in vitreous PbF2
Authors: Dantelle Géraldine , Mortier Michel , Monteil André , Chaussedent Stéphane , Silva Mauricio A. P.
Published: September 2007

Molecular dynamics simulations of the devitrification process of a lead fluoride glass doped with Er3+ ions were carried out. This technique appears to be a relevant way to perform systematic analysis of the system structure and to study the influence of defects on PbF2 crystallization. We modeled the total enthalpy, the radial distribution functions, and the diffracted intensities of systems containing different amounts of Er3+ ions. We demonstrated by means of different simulations that Er3+ ions lowered the devitrification temperature of PbF2, in good agreement with the experimental results. The genuine role of Er3+ ions in the devitrification process of PbF2 has been investigated. Er3+ ions have an unquestionable influence of the crystallization of PbF2. Although the latter does not start in the nearest neighborhood of Er3+ ions, the presence of Er3+ ions in a close environment may favor the lead fluoride crystallization.
An energy principle for the stability of charged dust cloud
Authors: Avinash K.
Published: September 2007

The stability of a charged dust cloud embedded in a quasineutral plasma background is studied using an energy principle. In this equilibrium, the electric fields arising due to the inhomogeneous dust distribution within the plasma background balances its self-gravity. The perturbed equation for the normal modes is obtained in terms of the Lagrangian displacement of the dust fluid ξ⃗ with a Hermitian operator. Hence, the square of the eigenvalue is real. The total potential energy (gravitational and electrostatic) integral is expressed as a quadratic in ξ⃗. The compression due to the electrostatic field (or equivalently the acoustic modes) and the gravity due to the plasma background is shown to make a stabilizing contribution, while the gravity of the dust makes a destabilizing contribution to the potential energy integral. The stabilizing contribution due to the plasma background, which is missed in analysis based on Jean’s swindle, is a new effect and appears in our stability analysis due to a proper treatment of the equilibrium. This stability theory is applied to the study of the gravitational stability of one-dimensional spherically symmetric dust clouds. The equation for the radial oscillations is shown to be of the Sturm-Liouville form; hence the stability of the fundamental mode decides the overall stability of the configuration. A simple trial function is used to obtain the eigenvalue of the fundamental mode. The low dust density branch of the equilibrium is shown to be robustly stable mainly due to the electric field compression. At high dust densities, the charge reduction effects weaken the field compression. This destabilizes the fundamental mode and the over all configuration. A spherically symmetric collapse of the dust cloud sets in as the eigenvalue of the fundamental mode crosses zero. The radial oscillations of the low density dust cloud, the collapse at high densities, and the resulting mass limit has been predicted earlier and seen in recent numerical simulations.
Structural and electrical properties of high-κ Bi2Mg2∕3Nb4∕3O7 pyrochlore films on silicon for possible gate dielectric applications
Authors: Sahu B. S. , Ahn Jun-Ku , Seong Nak-Jin , Yoon Soon-Gil
Published: September 2007

Bi 2 Mg 2 ∕ 3 Nb 4 ∕ 3 O 7 pyrochlore films were deposited on p-type Si (100) substrates using radio frequency reactive magnetron sputtering technique. Rapid thermal annealing (RTA) in O2 ambient followed by RTA in N2 ambient was carried out. The structural, morphological, and chemical bonding features of these films were studied by x-ray diffraction, scanning electron microscopy, atomic force microscopy, and x-ray photoelectron spectroscopy. All the films exhibit smooth, homogeneous, continuous, crack free, and dense films surfaces with root-mean-square roughness values in the range of 1.91−4.16 Å. The films show high crystallization temperature at about 900 °C. High temperature annealing gives rise to more oxygen incorporation in the films with probable formation of silicate type bonding at the interface. Effective oxide charge density, flatband voltage, hysteresis, oxide trap charge density, and interface state density values are comparable to those of some of the most widely investigated high-k gate dielectrics. The values decrease with increasing annealing temperature. A minimum leakage current density of the order of ∼10−6 A∕cm2 at a bias voltage of −1 V has been obtained even after annealing at 800 °C. All the annealed films show high breakdown field values of more than 5 MV/cm.
Epitaxial lateral overgrowth of a-plane GaN by metalorganic chemical vapor deposition
Authors: Ni X. , Özgür Ü. , Morkoç H. , Liliental-Weber Z. , Everitt H. O.
Published: September 2007

We report on epitaxial lateral overgrowth (ELO) of (112¯0) a-plane GaN by metalorganic chemical vapor deposition. Different growth rates of Ga- and N-polar wings together with wing tilt create a major obstacle for achieving a smooth, fully coalesced surface in ELO a-plane GaN. To address this issue a two-step growth method was employed to provide a large aspect ratio of height to width in the first growth step followed by enhanced lateral growth in the second by controlling the growth temperature. By this method, the average ratio of Ga- to N-polar wing growth rate has been reduced from 4–6 to 1.5–2, which consequently reduced the wing-tilt induced height difference between the two approaching wings at the coalescence front, thereby making their coalescence much easier. Transmission electron microscopy showed that the threading dislocation density in the wing regions was 1.0×108 cm−2, more than two orders of magnitude lower than that in the window regions (4.2×1010 cm−2). However, a relatively high density of basal stacking faults of 1.2×104 cm−1 was still present in the wing regions as compared to c -plane GaN, where they are rarely observed away from the substrate. Atomic force microscopy (AFM) measurements showed two orders of magnitude higher density of surface pits in the window than in the wing regions, which were considered to be terminated by dislocations (partial ones related to stacking faults and full ones) on the surface. The existence of basal stacking faults was also revealed by AFM measurements on the a-plane ELO sample after wet chemical etching in hot H3PO4∕H2SO4 (1:1). The extensions of Ga-polar wings near the meeting fronts were almost free of stacking faults. The improvement of crystalline quality in the overgrown layer by ELO was also verified by near field scanning optical microscopy and time-resolved photoluminescence measurements; the former showing strongly enhanced luminescence from the wing regions, and the latter indicating longer decay times (0.25 ns) compared to a standard a-plane GaN template (40 ps).
Temperature dependence of the magnetic and electrical properties of Permalloy∕gadolinium∕Permalloy thin films
Authors: Ranchal R. , Aroca C. , Maicas M. , López E.
Published: September 2007

The magnetic and electrical properties of Permalloy∕gadolinium∕Permalloy (Py∕Gd∕Py) trilayers have been studied as a function of temperature by using vibrating sample magnetometer and transport measurements with current in plane configuration. The observed dependence of the magnetic moment with temperature can be explained by a paramagnetic contribution. Electrical measurements show that this contribution is originated by the formation of Gd1−xNix alloys at the Py∕Gd interfaces because of the Ni diffusion. Despite the Ni diffusion, we find no evidence of amorphization from either the Py layer or the Py∕Gd interfaces. We also obtain the Curie temperature of the Gd1−xNix alloys by the position of inflexion points in the resistance versus temperature curve.
Adaptive control of force microscope cantilever dynamics
Authors: Jensen S. E. , Dougherty W. M. , Garbini J. L. , Sidles J. A.
Published: September 2007

Magnetic resonance force microscopy (MRFM) and other emerging scanning probe microscopies entail the detection of attonewton-scale forces. Requisite force sensitivities are achieved through the use of soft force microscope cantilevers as high resonant-Q micromechanical oscillators. In practice, the dynamics of these oscillators are greatly improved by the application of force feedback control computed in real time by a digital signal processor (DSP). Improvements include increased sensitive bandwidth, reduced oscillator ring up/down time, and reduced cantilever thermal vibration amplitude. However, when the cantilever tip and the sample are in close proximity, electrostatic and Casimir tip-sample force gradients can significantly alter the cantilever resonance frequency, foiling fixed-gain narrow-band control schemes. We report an improved, adaptive control algorithm that uses a Hilbert transform technique to continuously measure the vibration frequency of the thermally-excited cantilever and seamlessly adjust the DSP program coefficients. The closed-loop vibration amplitude is typically 0.05 nm. This adaptive algorithm enables narrow-band formally-optimal control over a wide range of resonance frequencies, and preserves the thermally-limited signal to noise ratio (SNR).
Crystal and electronic structure of Li15Si4
Authors: Kubota Yoshiyuki , Escaño Mary Clare Sison , Nakanishi Hiroshi , Kasai Hideaki
Published: September 2007

Silicon is one of the most promising anode materials for future rechargeable batteries because of its high theoretical capacity. New crystalline Li15Si4 was found as the fully electrochemical lithiated phase of crystalline Si or amorphous Si. Density functional theory was used to study the crystal and electronic structure of Li15Si4. Li15Si4 is formed by the unit figure in which six Li atoms surround a Si atom with two different Li–Si bond lengths. The Li atom has negative charge of 0.56–0.63 in Li15Si4. The average intercalation voltage for the lithium intercalation reaction from crystalline Si to Li15Si4 is 0.303 V, which is in good agreement with that predicted by the Coulometric titration experiment result for Li–Si alloys.
Noise suppression and stabilization of an ion beam extracted from dense plasma
Authors: Dorf M. A. , Sidorov A. V. , Zorin V. G. , Bohanov A. F. , Vodopyanov A. V. , Izotov I. V. , Razin S. V. , Skalyga V. A.
Published: September 2007

The dynamics of an ion beam formed in a two-electrode extraction system with a long puller is studied. The dependence of the extracted beam current on the plasma density is investigated numerically and experimentally. It is found that the dependence is weak (the “plateau regime”), when the density greatly exceeds the optimal value corresponding to the maximum current that can be extracted. Beam formation in the plateau regime ensures noise suppression, as well as stability of the extracted current, even at appreciable density fluctuations in the emitting plasma; it also significantly enhances the brightness of the beam. The proposed technique of noise suppression and ion beam stabilization using the two-electrode extraction system may find application in sources with dense plasmas (MEVVA, laser sources, etc.). The efficiency of the technique was demonstrated in experiments with gas-dynamic electron cyclotron resonance source of multicharged ions SMIS 37.
Hard x-ray response of a CdZnTe ring-drift detector
Authors: Owens A. , den Hartog R. , Quarati F. , Gostilo V. , Kondratjev V. , Loupilov A. , Kozorezov A. G. , Wigmore J. K. , Webb A. , Welter E.
Published: September 2007

We present the results of an experimental study of a special type of CdZnTe detector of hard x and γ rays—a ring-drift detector. The device consists of a double ring electrode structure surrounding a central point anode with a guard plane surrounding the outer anode ring. The detector can be operated in two distinctively different modes of charge collection—pseudohemispherical and pseudodrift. We study the detector response profiles obtained by scanning the focused x-ray beam over the whole detector area, specifically the variations in count rate, peak position, and energy resolution for x rays from 10 to 100 keV. In addition, at 662 keV the energy resolution was shown to be 4.8 keV, more than a factor of 2 better than for CdZnTe coplanar grid detectors. To interpret the experimental data, we derive an analytical expression for the spatial distribution of the electric field inside the detector and neglecting carrier diffusion, and identify carrier collection patterns for both modes of operation within the drift model approximation. We show that this model provides a good understanding of measured profiles.
Synchrotron x-ray microscopy studies on electromigration of a two-phase material
Authors: Lee A. , Liu W. , Ho C. E. , Subramanian K. N.
Published: September 2007

Basic issues involving movement of conductive constituents and microstructural evolution from high current density in single phase materials are well documented. Recently, electromigration of conductive constituents in multiphase materials has gained attention due to the necessity of employing such alloys for interconnects in microelectronics. Reported studies on these alloys using complicated industrial geometry suffer from contributions such as current crowding. Hence a basic understanding on operative mechanisms during electromigration in multiphase alloys cannot be gained from these studies. Consequently, several mechanisms proposed from these studies involve fitting parameters and not well-understood complex diffusional processes. A joint configuration designed to avoid current crowding and associated local Joule heating is suitable for evaluating electromigration induced microstructural events. Synchrotron x-ray microscopy has provided information regarding two- and three-dimensional crystallographic orientations and strain fields in such joints, aiding the development of a basic understanding of electromigration in two-phase alloys.
Illumination induced charge separation at tetraphenyl-porphyrin/metal oxide interfaces
Authors: Zidon Y. , Shapira Yoram , Dittrich Th.
Published: September 2007

Charge separation processes were studied at tetraphenyl-porphyrin (H2TPP)/metal oxide interfaces by surface photovoltage spectroscopy. The thickness of the depleted Ti and Sn oxide layers was about 2nm. Acceptorlike interface states play a crucial role in the steady-state light-induced negative charging of H2TPP surface layers as well as in tunneling or light-induced discharging. The results indicate that steady-state negative charging of the H2TPP layer is induced by preferential recombination of holes at the (H2TPP)/metal oxide interface and depends only weakly on temperature. The modulated surface photovoltage is dominated by hole transport at low temperatures and by electron transport at higher temperatures. The activation energy of the latter is of the order of 0.4eV.
Mechanical response of freestanding Au nanopillars under compression
Authors: Zepeda-Ruiz Luis A. , Sadigh Babak , Biener Juergen , Hodge Andrea M. , Hamza Alex V.
Published: September 2007

We employ molecular dynamics simulations of defect-free nanopillars with realistic cylindrical geometries to obtain an atomic-level picture of their deformation behavior under compression. We find that dislocations are nucleated in the two outermost surface layers. Furthermore, plastic yield depends crucially on the particular arrangement of steps and facets at the surface of the nanopillars. We show that different facet orientations can differ dramatically in their response to external stresses. Freestanding nanopillars exhibit a highly nonuniform distribution of stresses along their height. This causes an elastic deformation that leads to a barrel-like shape attained by the nanopillars under compression. The stress concentration at the center of the pillars due to barreling causes dislocations to preferentially nucleate in this region.
Soft x-ray coherent scattering: Instrument and methods at ESRF ID08
Authors: Beutier Guillaume , Marty Alain , Livet Frédéric , van der Laan Gerrit , Stanescu Stefan , Bencok Peter
Published: September 2007

An experimental setup has been developed to perform soft x-ray coherent scattering at beamline ID08 of the European Synchrotron Radiation Facility. An intense coherent beam was obtained by filtering the primary beam with the monochromator and a circular pinhole. A pinhole holder with motorized translations was installed inside the UHV chamber of the diffractometer. The scattered intensity was recorded in reflection geometry with a back-illuminated charge coupled device camera. As a demonstration we report experimental results of resonant magnetic scattering using coherent beam. The degree of coherence is evaluated, and it is shown that, while the vertical coherence is much higher than the horizontal one at the source, the situation is reversed at the diffractometer. The intensity of the coherent beam is also discussed.
Low-resistance Ohmic contact on undoped AlGaN∕GaN heterostructure with surface treatment using CCl2F2 reactive ion etching
Authors: Zhou X. J. , Qiu K. , Ji C. J. , Zhong F. , Li X. H. , Wang Y. Q.
Published: September 2007

The effects of the surface treatments on the performance of Ti∕Al∕Ti∕Au Ohmic contacts to undoped AlGaN∕GaN heterostructure are investigated. Contact resistance and specific contact resistivity as low as 0.25Ωmm and 5.85×10−7Ωcm2, respectively, have been achieved through pretreatment in CCl2F2 plasma followed by buffered oxide etch solution, with rapid thermal annealing at 900°C for 30s in a N2 ambient. The electrical quality and annealing temperature dependence of the metallization scheme are illustrated. Furthermore, excellent edge acuity is also demonstrated for this annealed Ti∕Al∕Ti∕Au Ohmic contact.
Integrated optical readout for miniaturization of cantilever-based sensor system
Authors: Nordström Maria , Zauner Dan A. , Calleja Montserrat , Hübner Jörg , Boisen Anja
Published: September 2007

The authors present the fabrication and characterization of an integrated optical readout scheme based on single-mode waveguides for cantilever-based sensors. The cantilever bending is read out by monitoring changes in the optical intensity of light transmitted through the cantilever that also acts as a waveguide. The complete system is fabricated in the photosensitive polymer SU-8. They show theoretical calculations on the expected sensitivity both when operated in air and liquid and compare these with experimental characterization of the system in air where the cantilever is deflected mechanically. The experimental results compare well with the results obtained from the theoretical calculations.
Gas damping of carbon nanotube oscillators
Authors: Martin Michael James , Houston Brian H.
Published: September 2007

Previous experimental results suggest that gas damping is a significant loss mechanism for carbon-nanotube-based mechanical resonators operating in low vacuum conditions. Using free-molecular flow theory for the gas and a continuum-based model for the nanotube resonator, a model for gas damping of single-wall carbon nanotube bridges and cantilevers is proposed. When compared to experimental data for a single-wall carbon nanotube bridge oscillator, the model agrees to within the limits of the known experimental geometry.
Ballistic quantum transport in a nanoscale metal-oxide-semiconductor field effect transistor
Authors: Arora Vijay K. , Tan Michael L. P. , Saad Ismail , Ismail Razali
Published: September 2007

The ballistic saturation velocity in a nanoscale metal-oxide-semiconductor field effect transistor (MOSFET) is revealed to be limited to the Fermi velocity in a degenerately induced channel appropriate for the quasi-two-dimensional nature of the inverted channel. The saturation point drain velocity is shown to rise with the increasing drain voltage approaching the intrinsic Fermi velocity, giving the equivalent of channel-length modulation. Quantum confinement effect degrades the channel mobility to the confining gate electric field as well as increases the effective thickness of the gate oxide. When the theory developed is applied to an 80nm MOSFET, excellent agreement to the experimental data is obtained.
Fabrication of InAs composite channel high electron mobility transistors by utilizing Ne-based atomic layer etching
Authors: Kim T.-W. , Song J.-I. , Jang J. H. , Kim D.-H. , Park S. D. , Bae J. W. , Yeom G. Y.
Published: September 2007

High electron mobility transistors (HEMTs) with InAs∕InGaAs composite channel were fabricated by employing low damage, highly selective Ne-based atomic layer etching (ALET) for the dry gate recess process. Ne-based ALET exhibited very high etch selectivity of InP over InAlAs which is suitable for dry gate recess process removing InP etch stop layer on top of InAlAs Schottky barrier layer. The plasma induced damage on the exposed InAlAs surface due to the ALET was much lower than that due to the conventional Ar-based reactive ion etching (RIE), which was verified by atomic force microscopy and Hall measurements. For further comparison, dc characteristics were compared for the two types of 0.3μm HEMTs fabricated by utilizing ALET and conventional RIE during the dry gate recess processes.
Identification of defects in Y3Al5O12 crystals by positron annihilation spectroscopy
Authors: Selim F. A. , Solodovnikov D. , Weber M. H. , Lynn K. G.
Published: September 2007

Positron annihilation, thermoluminescence, and optical absorption measurements were applied with the aid of several annealing and diffusion procedures to investigate the nature of point defects in Y3Al5O12 (YAG) single crystals. By annealing at 1500°C in air or O, and diffusing Al into a Ce doped YAG single crystal, a reduction of nearly two orders of magnitude in vacancy concentration was observed. Scintillation measurements showed a significant improvement in energy resolution after Al diffusion. This study revealed the presence of vacancy-defect complexes, most likely associated with cation antisites in YAG crystals.
Detection of THz radiation with semiconductor diode lasers
Authors: Brenner C. , Hoffmann S. , Hofmann M. R. , Salhi M. , Koch M. , Klehr A. , Erbert G. , Tränkle G. , Steiner J. T. , Kira M. , Koch S. W.
Published: September 2007

As a consequence of the strong many-body interactions in the electron-hole plasma, a semiconductor laser efficiently interacts with terahertz radiation. The injection of terahertz laser radiation into the active region of a diode laser induces a measurable variation of the voltage over the p-n junction, indicating the potential of a semiconductor laser to act as a terahertz detector.
Self-assembled biomimetic antireflection coatings
Authors: Linn Nicholas C. , Sun Chih-Hung , Jiang Peng , Jiang Bin
Published: September 2007

The authors report a simple self-assembly technique for fabricating antireflection coatings that mimic antireflective moth eyes. Wafer-scale, nonclose-packed colloidal crystals with remarkable large hexagonal domains are created by a spin-coating technology. The resulting polymer-embedded colloidal crystals exhibit highly ordered surface modulation and can be used directly as templates to cast poly(dimethylsiloxane) (PDMS) molds. Moth-eye antireflection coatings with adjustable reflectivity can then be molded against the PDMS master. The specular reflection of replicated nipple arrays matches the theoretical prediction using a thin-film multilayer model. These biomimetic films may find important technological application in optical coatings and solar cells.
Investigation of the structural transformation behavior of Ge2Sb2Te5 thin films using high resolution electron microscopy
Authors: Kim Eun Tae , Lee Jeong Yong , Kim Yong Tae
Published: September 2007

Structural transformation of the Ge2Sb2Te5 was investigated by a high resolution transmission electron microscopy (HRTEM). It was found that Ge atoms undergo umbrella-flip motion from a tetrahedral site into an octahedral site in transforming from the amorphous to the metastable phase of Ge2Sb2Te5. The presence of a twin boundary between fcc and hexagonal structured Ge2Sb2Te5 was also confirmed through the HRTEM observations. These results support the umbrella-flip model proposed by Kolobov et al. [Nat. Mater. 3, 703 (2004)] and the epitaxial growth model proposed by Park et al. [Appl. Surf. Sci. 256, 8102 (2006)].
Determining the diet of cryptic folivores: an assessment of diet analysis techniques using the green ringtail possum (Pseudochirops archeri) as a case study
Authors: Jones Katherine M. W. , Krockenberger Andrew K.
Published: September 2007

The dietary requirements of folivores affect many aspects of their ecology, including home range, potential for social interaction, abiotic/climatic requirements and habitat choice at the landscape and local scale. The purpose of this study was to investigate the advantages and disadvantages of three techniques commonly used to determine the diet of rainforest folivores. Many folivores are arboreal, nocturnal and cryptic, causing a variety of problems for determining their diet. The largely folivorous green ringtail possum (Pseudochirops archeri) is all of these, inhabiting complex rainforest and often displaying particularly cryptic or evasive behaviour. No single technique produced a comprehensive dietary list for P. archeri, and each had different biases in the diet composition determined. As the actual diet of P. archeri was unknown and not measurable, it was impossible to determine which technique most accurately described its diet. Direct observations were time-consuming and difficult within dense forest, faecal analysis underestimated the importance of species with fragile cuticles, and tree selection was not directly related to food intake. However, direct observation produced the highest diversity of diet from a single method, faecal analysis required the least time in the field, and tree selection allowed intraspecific measures of preference to be determined. Thus, multiple dietary analysis techniques were required to meet the aim of this study, which was to provide the most comprehensive estimation of dietary diversity in a cryptic, arboreal folivore.
Ecological and human dimensions of management of feral horses in Australia: a review
Authors: Nimmo Dale Graeme , Miller Kelly K.
Published: September 2007

In Australia, the management of feral horse populations is a contentious issue, owing to their pluralistic status as an introduced pest and a national icon. In this review, we synthesise current knowledge of the ecological effects of feral horses and the human dimensions of feral horse management, using case studies from around the world to illustrate contentious and successful management practices. We highlight gaps in the literature and suggest that more peer-reviewed research would be beneficial in reducing the current public controversy surrounding management of feral horses.
Aspects of the biology of the European rabbit (Oryctolagus cuniculus) and rabbit haemorrhagic disease virus (RHDV) in coastal eastern Australia
Authors: Richardson B. J. , Phillips S. , Hayes R. A. , Sindhe S. , Cooke B. D.
Published: September 2007

A population of wild rabbits in a high-rainfall area near Sydney, New South Wales, was studied for 8 years to investigate the population biology of the rabbit in a high-rainfall area, to examine factors affecting the length of the breeding season, and to describe the biology of RHDV and a RHDV-like virus in the population. The breeding season was short, starting in June and ending in October, though some conceptions occurred in every month of the year. Supplementary feeding with grain, germinated wheat or high-protein rabbit pellets did not extend the breeding season, so predictions that the length of the breeding season and occurrence of anaemia were influenced by a lack of protein in the diet were not upheld. Myxomatosis appeared in late summer each year as in inland southern Australia. Studies of the immunostatus of the population showed that, even in the years before RHDV was released in Australia, 80–100% of adult animals were seropositive when tested with ELISA specifically designed to detect antibodies to RHDV, arguably owing to the presence of a RHDV-like virus. The proportion of seropositive animals fell when annual rainfall was below 600 mm and rose when it was above 700 mm. Presumably, in areas where rainfall is usually low the proportion of the population infected with the putative RHDV-like virus would slowly drop to a low level, providing a possible basis for the different epidemiological patterns found for RHDV in different parts of Australia.
Use of Xanthorrhoea semiplana (grass-trees) for refuge by Rattus fuscipes (southern bush rat)
Authors: Frazer Deborah S. , Petit Sophie
Published: September 2007

This study investigated the use of the grass-tree, Xanthorrhoea semiplana F.Muell. (family Xanthorrhoeaceae), for shelter by Rattus fuscipes (southern bush rat) in South Australia. Eight bush rats were radio-tracked for 4–8 days each. To identify the understorey shelters available to each animal, surveys were conducted using point-intercept sampling at 2-m intervals along transect lines. Grass-tree density was calculated in each area used by the radio-tracked animals, and canopy thickness of grass-trees selected for refuge was assigned a score; the availability of other potential shelters was also calculated. The results indicated that (1) R. fuscipes preferentially selected grass-trees over other understorey shelter; (2) the grass-trees chosen had thick canopy covers; (3) areas with high grass-tree densities were preferred for cover over areas with fewer grass-trees; and (4) grass-trees provided dense cover and, therefore, concealed burrows and nest sites.
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding
Authors: Chahine Jorge , Oliveira Ronaldo J. , Leite Vitor B. P. , Wang Jin
Published: September 2007

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.
Spectroscopic validation of the pentameric structure of phospholamban
Authors: Traaseth Nathaniel J. , Verardi Raffaello , Torgersen Kurt D. , Karim Christine B. , Thomas David D. , Veglia Gianluigi
Published: September 2007

Phospholamban (PLN) regulates calcium translocation within cardiac myocytes by shifting sarco(endo)plasmic reticulum Ca
2+
-ATPase (SERCA) affinity for calcium. Although the monomeric form of PLN (6 kDa) is the principal inhibitory species, recent evidence suggests that the PLN pentamer (30 kDa) also is able to bind SERCA. To date, several membrane architectures of the pentamer have been proposed, with different topological orientations for the cytoplasmic domain: (
i
) extended from the bilayer normal by 50–60°; (
ii
) continuous α-helix tilted 28° relative to the bilayer normal; (
iii
) pinwheel geometry, with the cytoplasmic helix perpendicular to the bilayer normal and in contact with the surface of the bilayer; and (
iv
) bellflower structure, in which the cytoplasmic domain helix makes ≈20° angle with respect to the membrane bilayer normal. Using a variety of cell membrane mimicking systems (i.e., lipid vesicles, oriented lipid bilayers, and detergent micelles) and a combination of multidimensional solution/solid-state NMR and EPR spectroscopies, we tested the different structural models. We conclude that the pinwheel topology is the predominant conformation of pentameric PLN, with the cytoplasmic domain interacting with the membrane surface. We propose that the interaction with the bilayer precedes SERCA binding and may mediate the interactions with other proteins such as protein kinase A and protein phosphatase 1.
Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism
Authors: Taneja Bhupesh , Schnurr Bernhard , Slesarev Alexei , Marko John F. , Mondragón Alfonso
Published: September 2007

Topoisomerase V is a type I topoisomerase without structural or sequence similarities to other topoisomerases. Although it belongs to the type I subfamily of topoisomerases, it is unrelated to either type IA or IB enzymes. We used real-time single-molecule micromechanical experiments to show that topoisomerase V relaxes DNA via events that release multiple DNA turns, employing a constrained swiveling mechanism similar to that for type IB enzymes. Relaxation is powered by the torque in the supercoiled DNA and is constrained by friction between the protein and the DNA. Although all type IB enzymes share a common structure and mechanism and type IA and type II enzymes show marked structural and functional similarities, topoisomerase V represents a different type of topoisomerase that relaxes DNA in a similar overall manner as type IB molecules but by using a completely different structural and mechanistic framework.
Disrupted cardiac development but normal hematopoiesis in mice deficient in the second CXCL12/SDF-1 receptor, CXCR7
Authors: Sierro Frederic , Biben Christine , Martínez-Muñoz Laura , Mellado Mario , Ransohoff Richard M. , Li Meizhang , Woehl Blanche , Leung Helen , Groom Joanna , Batten Marcel , Harvey Richard P. , Martínez-A Carlos , Mackay Charles R. , Mackay Fabienne
Published: September 2007

Chemotactic cytokines (chemokines) attract immune cells, although their original evolutionary role may relate more closely with embryonic development. We noted differential expression of the chemokine receptor CXCR7 (RDC-1) on marginal zone B cells, a cell type associated with autoimmune diseases. We generated
Cxcr7
−/−
mice but found that CXCR7 deficiency had little effect on B cell composition. However, most
Cxcr7
−/−
mice died at birth with ventricular septal defects and semilunar heart valve malformation. Conditional deletion of
Cxcr7
in endothelium, using
Tie2-Cre
transgenic mice, recapitulated this phenotype. Gene profiling of
Cxcr7
−/−
heart valve leaflets revealed a defect in the expression of factors essential for valve formation, vessel protection, or endothelial cell growth and survival. We confirmed that the principal chemokine ligand for CXCR7 was CXCL12/SDF-1, which also binds CXCR4. CXCL12 did not induce signaling through CXCR7; however, CXCR7 formed functional heterodimers with CXCR4 and enhanced CXCL12-induced signaling. Our results reveal a specialized role for CXCR7 in endothelial biology and valve development and highlight the distinct developmental role of evolutionary conserved chemokine receptors such as CXCR7 and CXCR4.
Recent transcontinental sweep of
Toxoplasma gondii
driven by a single monomorphic chromosome
Authors: Khan A. , Fux B. , Su C. , Dubey J. P. , Darde M. L. , Ajioka J. W. , Rosenthal B. M. , Sibley L. D.
Published: September 2007

Toxoplasma gondii
is a highly prevalent protozoan parasite that infects a wide range of animals and threatens human health by contaminating food and water. A markedly limited number of clonal parasite lineages have been recognized as predominating in North American and European populations, whereas strains from South America are comparatively diverse. Here, we show that strains from North America and Europe share distinct genetic polymorphisms that are mutually exclusive from polymorphisms in strains from the south. A striking exception to this geographic segregation is a monomorphic version of one chromosome (Chr1a) that characterizes virtually all northern and many southern isolates. Using a combination of molecular phylogenetic and phenotypic analyses, we conclude that northern and southern parasite populations diverged from a common ancestor in isolation over a period of ≈10
6
yr, and that the monomorphic Chr1a has swept each population within the past 10,000 years. Like its definitive feline hosts,
T. gondii
may have entered South America and diversified there after reestablishment of the Panamanian land bridge. Since then, recombination has been an infrequent but important force in generating new
T. gondii
genotypes. Genes unique to a monomorphic version of a single parasite chromosome may have facilitated a recent population sweep of a limited number of highly successful
T. gondii
lineages.
Plant disease susceptibility conferred by a “resistance” gene
Authors: Lorang Jennifer M. , Sweat Teresa A. , Wolpert Thomas J.
Published: September 2007

The molecular nature of many plant disease resistance (R) genes is known; the largest class encodes nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins that are structurally related to proteins involved in innate immunity in animals. Few genes conferring disease susceptibility, on the other hand, have been identified. Recent identification of susceptibility to the fungusCochliobolus victoriaeinArabidopsis thalianahas enabled our cloning ofLOV1, a disease susceptibility gene that, paradoxically, is a member of the NBS-LRR resistance gene family. We foundLOV1mediates responses associated with defense, but mutations in known defense response pathways do not prevent susceptibility toC. victoriae. These findings demonstrate that NBS-LRR genes can condition disease susceptibility and resistance and may have implications forRgene deployment.
Distinct thermal behavior of GeO
2
glass in tetrahedral, intermediate, and octahedral forms
Authors: Shen Guoyin , Liermann Hanns-Peter , Sinogeikin Stanislav , Yang Wenge , Hong Xinguo , Yoo Choong-Shik , Cynn Hyunchae
Published: September 2007

One fascinating high-pressure behavior of tetrahedral glasses and melts is the local coordination change with increasing pressure, which provides a structural basis for understanding numerous anomalies in their high-pressure properties. Because the coordination change is often not retained upon decompression, studies must be conducted
in situ
. Previous
in situ
studies have revealed that the short-range order of tetrahedrally structured glasses and melts changes above a threshold pressure and gradually transforms to an octahedral form with further pressure increase. Here, we report a thermal effect associated with the coordination change at given pressures and show distinct thermal behaviors of GeO
2
glass in tetrahedral, octahedral, and their intermediate forms. An unusual thermally induced densification, as large as 16%, was observed on a GeO
2
glass at a pressure of 5.5 gigapascal (GPa), based on
in situ
density and x-ray diffraction measurements at simultaneously high pressures and high temperatures. The large thermal densification at high pressure was found to be associated with the 4- to 6-fold coordination increase. Experiments at other pressures show that the tetrahedral GeO
2
glass displayed small thermal densification at 3.3 GPa arising from the relaxation of intermediate range structure, whereas the octahedral glass at 12.3 GPa did not display any detectable thermal effects.
Real-time observations of single bacteriophage λ DNA ejections
in vitro
Authors: Grayson Paul , Han Lin , Winther Tabita , Phillips Rob
Published: September 2007

The physical, chemical, and structural features of bacteriophage genome release have been the subject of much recent attention. Many theoretical and experimental studies have centered on the internal forces driving the ejection process. Recently, Mangenot
et al.
[Mangenot S, Hochrein M, Rädler J, Letellier L (2005)
Curr Biol
15:430–435.] reported fluorescence microscopy of phage T5 ejections, which proceeded stepwise between DNA nicks, reaching a translocation speed of 75 kbp/s or higher. It is still unknown how high the speed actually is. This paper reports real-time measurements of ejection from phage λ, revealing how the speed depends on key physical parameters such as genome length and ionic state of the buffer. Except for a pause before DNA is finally released, the entire 48.5-kbp genome is translocated in ≈1.5 s without interruption, reaching a speed of 60 kbp/s. The process gives insights particularly into the effects of two parameters: a shorter genome length results in lower speed but a shorter total time, and the presence of divalent magnesium ions (replacing sodium) reduces the pressure, increasing ejection time to 8–11 s. Pressure caused by DNA–DNA interactions within the head affects the initiation of ejection, but the close packing is also the dominant source of friction: more tightly packed phages initiate ejection earlier, but with a lower initial speed. The details of ejection revealed in this study are probably generic features of DNA translocation in bacteriophages and have implications for the dynamics of DNA in other biological systems.