bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil eukaryotic functional diversity, a metatranscriptomic approach
Authors: Bailly Julie , Fraissinet-Tachet Laurence , Verner Marie-Christine , Debaud Jean-Claude , Lemaire Marc , Wésolowski-Louvel Micheline , Marmeisse Roland
Published: September 2007

To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.
The geomicrobiology of gold
Authors: Reith Frank , Lengke Maggy F , Falconer Donna , Craw David , Southam Gordon
Published: September 2007

Microorganisms capable of actively solubilizing and precipitating gold appear to play a larger role in the biogeochemical cycling of gold than previously believed. Recent research suggests that bacteria and archaea are involved in every step of the biogeochemical cycle of gold, from the formation of primary mineralization in hydrothermal and deep subsurface systems to its solubilization, dispersion and re-concentration as secondary gold under surface conditions. Enzymatically catalysed precipitation of gold has been observed in thermophilic and hyperthermophilic bacteria and archaea (for example, Thermotoga maritime, Pyrobaculum islandicum), and their activity led to the formation of gold- and silver-bearing sinters in New Zealand's hot spring systems. Sulphate-reducing bacteria (SRB), for example, Desulfovibrio sp., may be involved in the formation of gold-bearing sulphide minerals in deep subsurface environments; over geological timescales this may contribute to the formation of economic deposits. Iron- and sulphur-oxidizing bacteria (for example, Acidothiobacillus ferrooxidans, A. thiooxidans) are known to breakdown gold-hosting sulphide minerals in zones of primary mineralization, and release associated gold in the process. These and other bacteria (for example, actinobacteria) produce thiosulphate, which is known to oxidize gold and form stable, transportable complexes. Other microbial processes, for example, excretion of amino acids and cyanide, may control gold solubilization in auriferous top- and rhizosphere soils. A number of bacteria and archaea are capable of actively catalysing the precipitation of toxic gold(I/III) complexes. Reductive precipitation of these complexes may improve survival rates of bacterial populations that are capable of (1) detoxifying the immediate cell environment by detecting, excreting and reducing gold complexes, possibly using P-type ATPase efflux pumps as well as membrane vesicles (for example, Salmonella enterica, Cupriavidus (Ralstonia) metallidurans, Plectonema boryanum); (2) gaining metabolic energy by utilizing gold-complexing ligands (for example, thiosulphate by A. ferrooxidans) or (3) using gold as metal centre in enzymes (Micrococcus luteus). C. metallidurans containing biofilms were detected on gold grains from two Australian sites, indicating that gold bioaccumulation may lead to gold biomineralization by forming secondary ‘bacterioform’ gold. Formation of secondary octahedral gold crystals from gold(III) chloride solution, was promoted by a cyanobacterium (P. boryanum) via an amorphous gold(I) sulphide intermediate. ‘Bacterioform’ gold and secondary gold crystals are common in quartz pebble conglomerates (QPC), where they are often associated with bituminous organic matter possibly derived from cyanobacteria. This may suggest that cyanobacteria have played a role in the formation of the Witwatersrand QPC, the world's largest gold deposit.
Stable, high efficiency gyrotron backward-wave oscillator
Authors: Fan C. T. , Chang T. H. , Pao K. F. , Chu K. R. , Chen S. H.
Published: September 2007

Stability issues have been a major concern for the realization of broadband tunability of the gyrotron backward-wave oscillator (gyro-BWO). Multimode, time-dependent simulations are employed to examine the stability properties of the gyro-BWO. It is shown that the gyro-BWO is susceptible to both nonstationary oscillations and axial mode competition in the course of frequency tuning. Regions of nonstationary oscillations and axial mode competition are displayed in the form of stability maps over wide-ranging parameter spaces. These maps serve as a guide for the identification and optimization of stable windows for broadband tuning. Results indicate that a shorter interaction length provides greater stability without efficiency degradation. These theoretical predictions have been verified in a Ka-band gyro-BWO experiment using both short and long interaction lengths. In the case of a short interaction length, continuous and smooth tunability, in magnetic field and in beam voltage, was demonstrated with the high interaction efficiency reported so far. A maximum 3-dB tuning range of 1.3GHz with a peak power of 149kW at 29.8% efficiency was achieved. In a comparative experiment with a longer interaction length, the experimental data are characterized by piecewise-stable tuning curves separated by region(s) of nonstationary oscillations, as predicted by theory.
Observables in the Turaev-Viro and Crane-Yetter models
Authors: Barrett John W. , Faria Martins João , García-Islas J. Manuel
Published: September 2007

We define an invariant of graphs embedded in a 3-manifold and a partition function for 2-complexes embedded in a triangulated 4-manifold by specifying the values of variables in the Turaev-Viro and Crane-yetter state-sum models. In the case of the three-dimensional invariant, we prove a duality formula relating its Fourier transform to another invariant defined via the colored Jones polynomial. In the case of the four-dimensional partition function, we give a formula for it in terms of a regular neighborhood of the 2-complex and the signature of its complement. Some examples are computed which show that the partition function determines an invariant which can detect non locally-flat surfaces in a 4-manifold.
Diffusion model of solute dynamics in a membrane channel: Mapping onto the two-site model and optimizing the flux
Authors: Bezrukov Sergey M. , Berezhkovskii Alexander M. , Szabo Attila
Published: September 2007

The steady-state flux through a singly occupied membrane channel is found for both discrete and continuum models of the solute dynamics in the channel. The former describes the dynamics as nearest-neighbor jumps between N sites, while the latter assumes that the molecule diffuses in a one-dimensional potential of mean force. For both models it is shown that the flux is the same as that for a simple two-site model with appropriately chosen rate constants, which contain all the relevant information about the more detailed dynamics. An interesting consequence of single occupancy is that the flux has a maximum as a function of the channel-solute interaction. If this interaction is too attractive, the molecule will never leave the channel, thus blocking it for the passage of other molecules. If it is too repulsive, the solute molecule will never enter the channel. Thus the flux vanishes in the two limits and, hence, has a maximum somewhere in-between. In the framework of the diffusion model, we find the optimal intrachannel potential of mean force that maximizes the flux using the calculus of variations. For a symmetric channel this potential is flat and occupies the entire channel. In the general case of an asymmetric channel, the optimal potential is obtained by tilting the optimal flat potential for the corresponding symmetric channel around the channel center, so that the solute is driven towards the reservoir with the lower solute concentration by a constant force. This implies that the flux is higher when the solute binding near the channel exit is stronger than that near the entrance.
Picosecond time resolved photoluminescence spectroscopy of a tetracene film on highly oriented pyrolytic graphite: Dynamical relaxation, trap emission, and superradiance
Authors: Voigt M. , Langner A. , Schouwink P. , Lupton J. M. , Mahrt R. F. , Sokolowski M.
Published: September 2007

A detailed time resolved investigation of the photoluminescence of a thin tetracene film deposited on highly oriented pyrolytic graphite is presented. In agreement with Lim et al. [Phys. Rev. Lett. 92, 107402 (2004)], we find strong evidence for superradiance: an increase of the relative intensity of the pure electronic transition with respect to the vibronic sideband and a concomitant decrease of the radiative lifetime from 10to1.83ns upon cooling from 300to4K. For lower temperatures, a redshift (∼200cm−1) of the free exciton is observed. Previously, this shift was attributed to a structural phase transition. Our time resolved spectra reveal that the spectral shift is related to a dynamical relaxation process which occurs within the first 50ps.
Treatment of charge singularities in implicit solvent models
Authors: Geng Weihua , Yu Sining , Wei Guowei
Published: September 2007

This paper presents a novel method for solving the Poisson-Boltzmann (PB) equation based on a rigorous treatment of geometric singularities of the dielectric interface and a Green’s function formulation of charge singularities. Geometric singularities, such as cusps and self-intersecting surfaces, in the dielectric interfaces are bottleneck in developing highly accurate PB solvers. Based on an advanced mathematical technique, the matched interface and boundary (MIB) method, we have recently developed a PB solver by rigorously enforcing the flux continuity conditions at the solvent-molecule interface where geometric singularities may occur. The resulting PB solver, denoted as MIBPB-II, is able to deliver second order accuracy for the molecular surfaces of proteins. However, when the mesh size approaches half of the van der Waals radius, the MIBPB-II cannot maintain its accuracy because the grid points that carry the interface information overlap with those that carry distributed singular charges. In the present Green’s function formalism, the charge singularities are transformed into interface flux jump conditions, which are treated on an equal footing as the geometric singularities in our MIB framework. The resulting method, denoted as MIBPB-III, is able to provide highly accurate electrostatic potentials at a mesh as coarse as 1.2Å for proteins. Consequently, at a given level of accuracy, the MIBPB-III is about three times faster than the APBS, a recent multigrid PB solver. The MIBPB-III has been extensively validated by using analytically solvable problems, molecular surfaces of polyatomic systems, and 24 proteins. It provides reliable benchmark numerical solutions for the PB equation.
Infrared spectroscopy of anionic hydrated fluorobenzenes
Authors: Schneider Holger , Vogelhuber Kristen M. , Weber J. Mathias
Published: September 2007

We investigate the structural motifs of anionic hydrated fluorobenzenes by infrared photodissociation spectroscopy and density functional theory. Our calculations show that all fluorobenzene anions under investigation are strongly distorted from the neutral planar molecular geometries. In the anions, different F atoms are no longer equivalent, providing structurally different binding sites for water molecules and giving rise to a multitude of low-lying isomers. The absorption bands for hexa- and pentafluorobenzene show that only one isomer for the respective monohydrate complexes is populated in our experiment. For C6F6−∙H2O, we can assign these bands to an isomer where water forms a weak double ionic hydrogen bond with two F atoms in the ion, in accord with the results of Bowen et al. [J. Chem. Phys. 127, 014312 (2007), following paper.] The spectroscopic motif of the binary complexes changes slightly with decreasing fluorination of the aromatic anion. For dihydrated hexafluorobenzene anions, several isomers are populated in our experiments, some of which may be due to hydrogen bonding between water molecules.
Time-dependent density functional theory for nonlinear properties of open-shell systems
Authors: Rinkevicius Zilvinas , Jha Prakash Chandra , Oprea Corneliu I. , Vahtras Olav , Ågren Hans
Published: September 2007

This paper presents response theory based on a spin-restricted Kohn-Sham formalism for computation of time-dependent and time-independent nonlinear properties of molecules with a high spin ground state. The developed approach is capable to handle arbitrary perturbations and constitutes an efficient procedure for evaluation of electric, magnetic, and mixed properties. Apart from presenting the derivation of the proposed approach, we show results from illustrating calculations of static and dynamic hyperpolarizabilities of small Si(3n+1)H(6n+3) (n=0,1,2) clusters which mimic Si(111) surfaces with dangling bond defects. The results indicate that the first hyperpolarizability tensor components of Si(3n+1)H(6n+3) have an ordering compatible with the measurements of second harmonic generation in SiO2∕Si(111) interfaces and, therefore, support the hypothesis that silicon surface defects with dangling bonds are responsible for this phenomenon. The results exhibit a strong dependence on the quality of basis set and exchange-correlation functional, showing that an appropriate set of diffuse functions is required for reliable predictions of the first hyperpolarizability of open-shell compounds.
Evaluation of Smagorinsky variants in large-eddy simulations of wall-resolved plane channel flows
Authors: Meyers Johan , Sagaut Pierre
Published: September 2007

In recent years, variational multiscale (VMS) Smagorinsky models have emerged as new models for large-eddy simulations (LES). A common version is the small-small variant, which uses a small-scale extraction of the LES solution, obtained by high-pass filtering the resolved velocity field, to express a Smagorinsky term. The subsequent small-scale extraction of this term is used as a model. In the current work, three formulations of the small-small VMS model are investigated in large-eddy simulations of the plane channel flow. The basic small-small formulation (Model A) is modified to explicitly incorporate effects of the LES filter and the high-pass filter (Model B). A third modification (Model C) is further inertial-range consistent, allowing the use of constant model coefficients for filters widths which are situated in a finite Reynolds-number inertial subrange. We aim to evaluate the performance of these models in the presence of walls. Therefore, channel-flow simulations are performed for Reτ=110, 300, 400, and 650. Further, the effect of changes in the shape of the high-pass filter used for the three models is investigated. A sharp cutoff filter and a Gaussian high-pass filter are considered. In addition, a range of high-pass-filter widths is included in the analysis. Evaluations of the skin-friction, mean-velocity profiles, Reynolds stresses, and spanwise velocity spectra are presented. We show that Model C is most insensitive to changes in Reynolds number and filter shape, closely followed by Model B. Model A is the most sensitive to the considered variations, and simulation quality depends in particular on variations in the filter shape.
Dust structures in cryogenic gas discharges
Authors: Antipov S. N. , Asinovskii E. I. , Fortov V. E. , Kirillin A. V. , Markovets V. V. , Petrov O. F. , Platonov V. I.
Published: September 2007

Results are given of experimental investigations of dust structures of monodisperse particles in a low-pressure dc glow discharge at temperatures of liquid nitrogen (T=77K) and liquid helium (T=4.2K). It is found that the cooling of discharge at invariant discharge current and neutral gas density causes a decrease in the interparticle spacing in structures and an increase in the kinetic energy of dust particles. The forming of a superdense dust structure with free boundaries is observed for the first time at 4.2K.
Impact of attenuator models on computed traveling wave tube performances
Authors: Duan Zhaoyun , Gong Yubin , Wei Yanyu , Wang Wenxiang
Published: September 2007

Radio frequency characteristics of helix traveling wave tubes are analyzed with a one-dimensional numerical model that includes a new, more rigorous, self-consistent attenuator model. The nonlinear properties of the beam-wave interaction, including gain, phase distortion, and intermodulation distortion, are analyzed and compared with simulations using a conventional one-dimensional model of the attenuator. The comparative results show that the small signal gain is about 2–5dB smaller with the new model than with the conventional and wave phase has a difference of 2°–6° between the new and conventional models in the intermediate and large signal regions. The amplitude modulation/phase modulation (AM/PM) conversion from the new model shows a slower reach to maximum than that from the conventional, and when the large input signal is applied, the conventional model’s AM/PM conversion oscillates more quickly compared to the new. Under two-frequency excitation, the fundamental tones are about 5–7dB smaller with the new model than the conventional, while the intermodulation products are approximately 10dB smaller relative to the conventional model.
A numerical investigation of a jet in an oscillating crossflow
Authors: Kremer D. M. , am Ende M. T. , Mustakis J. G. , am Ende D. J.
Published: September 2007

Numerical solutions are presented for a modified form of the canonical jet in crossflow (JICF) in which a steady round jet issues into a crossflow stream oscillating with a sinusoidal velocity profile. The numerical model uses large eddy simulation to simulate turbulent flow and mixing. This system is used to represent the dynamics and flow fields present during subsurface addition of reactants in stirred tanks. Thus, two variables associated with the oscillating crossflow velocity profile were manipulated to simulate the effects of impeller design and operation. Variation of the amplitude of crossflow oscillation had little effect on the trajectory of the jet plume, while variation in the frequency of crossflow oscillation was found to have a significant effect on plume trajectory. Additionally, oscillation of the crossflow affected the contiguity of the plume when compared with a steady crossflow JICF, resulting in mixing enhancement. The numerical solutions were validated using empirical data collected during a previous investigation of a steady crossflow JICF system. This research suggests that mixing during subsurface reagent addition could potentially be enhanced by optimizing impeller operating conditions and draft tube location, and the model presented here may offer a tractable computational method for optimization of these systems.
Analytic gradient for the multireference Brillouin-Wigner coupled cluster method and for the state-universal multireference coupled cluster method
Authors: Pittner Jiří , Šmydke Jan
Published: September 2007

We present the analytic gradient theory and its pilot implementation for the multireference Brillouin-Wigner coupled cluster (BWCC) method and for the state-universal multireference coupled cluster method. The analytic gradient has been derived for three cases: (i) BWCC method without a size-extensivity correction, (ii) BWCC method with the iterative size-extensivity correction, and (iii) for the rigorously size-extensive state-universal method. The pilot implementation is based on full–configuration interaction expansions and is presently limited to single and double excitation levels; however, the resulting equations are general. For BWCC methods, they also do not contain terms explicitly mixing amplitudes of different reference configurations and can thus be implemented in an efficient way. The analytic gradients have been verified with respect to numerically computed ones on the example of CH2 molecule, and geometry optimizations of CH2 and SiH2 have been carried out.
Pulsed electron nuclear double resonance studies of the photoexcited triplet state of pentacene in p-terphenyl crystals at room temperature
Authors: Yago Tomoaki , Link Gerhard , Kothe Gerd , Lin Tien-Sung
Published: September 2007

Pulsed electron nuclear double resonance (ENDOR) using a modified Davies-type [Phys. Lett. 47A, 1 (1974)] sequence is employed to study the hyperfine (HF) structure of the photoexcited triplet state of pentacene dispersed in protonated and deuterated p-terphenyl single crystals. The strong electron spin polarization and long phase memory time of triplet pentacene enable us to perform the ENDOR measurements on the S=1 spin system at room temperature. Proton HF tensor elements and spin density values of triplet pentacene are extracted from a detailed angular-dependent study in which the orientation of the magnetic field is varied systematically in two different pentacene planes. Analysis reveals that the pentacene molecule is no longer planar in the p-terphenyl host lattice. The distortion is more pronounced in the deuterated crystal where the unit cell dimensions are slightly smaller than those of the protonated crystal.
Electronic states of neutral and cationic bis(benzene) titanium and vanadium sandwich complexes studied by pulsed field ionization electron spectroscopy
Authors: Sohnlein Bradford R. , Lei Yuxiu , Yang Dong-Sheng
Published: September 2007

Ti– and V–bz2 (bz=C6H6) sandwich complexes have been prepared in a laser-ablation cluster beam source and studied by pulsed field ionization–zero electron kinetic energy photoelectron spectroscopy and theoretical calculations. The ground electronic states of the neutral Ti– and V–bz2 complexes are determined to be A1g1 and A1g2, and their ionization energies are measured to be 5.732±0.001 and 5.784±0.002eV, respectively. These neutral complexes have η6 binding and are in an eclipsed D6h configuration with flat benzene rings. Ionization of the A1g1 and A1g2 neutral states of Ti– and V–bz2 yields the B1g2 and B1g3 ion states, respectively, in a D2h point group with slightly puckered benzene rings. In addition, the binding and structures of these two complexes are compared with other first-row transition metal bis(benzene) sandwiches.
Modeling of associative ionization reactions in hypersonic rarefied flows
Authors: Boyd Iain D.
Published: September 2007

When vehicles reenter the Earth’s atmosphere from space, the hypersonic conditions are sufficiently energetic to generate ionizing reactions. The production of a thin plasma layer around a hypersonic vehicle can block radio waves sent to and from the vehicle, leading to communications blackout. For Earth entry from orbit, the maximum energy involved in molecular collisions requires only associative ionization of air-species to be considered. In the present study, the modeling of such reactions is considered in detail using the direct simulation Monte Carlo (DSMC) method. For typical Earth entry conditions, with a velocity near 8km∕s, it is shown that the average ionizing reaction probabilities are small. Special numerical techniques must therefore be used in the DSMC technique in order to numerically resolve these reactions. Additional simulation problems arise from the relatively small mass of the electrons in comparison to the other atoms and molecules in these flow fields. Artificially increasing the electron mass greatly increases computational efficiency, and the viability of this approach is investigated. Simulation results are presented for conditions corresponding to the RAM-C II hypersonic flight experiment that gathered measurements of electron number density. It is demonstrated that simulation results for electron number density in this energy regime are relatively insensitive to the mass of the electrons. Direct comparison of DSMC results with the RAM-C II measurements for electron number density shows excellent agreement. These satisfactory comparisons represent the first direct verification of the ability of the DSMC technique to successfully predict the weak plasma generated around a hypersonic vehicle.
Soft x-ray photoreactions of CF3Cl adsorbed on Si(111)-7×7 studied by continuous-time photon-stimulated desorption spectroscopy near F(1s) edge
Authors: Wen C.-R. , Jang C.-Y. , Chou L.-C. , Chen J. , Wu Y.-H. , Chang S.-C. , Tsai W.-C. , Liu C.-C. , Wang S.-K. , Shai Y.
Published: September 2007

The continuous-time core-level photon-stimulated desorption (PSD) spectroscopy was employed to monitor the monochromatic soft x-ray-induced reactions of CF3Cl adsorbed on Si(111)-7×7 near the F(1s) edge (681–704eV). Sequential F+ PSD spectra were measured as a function of photon exposure at the CF3Cl-covered surface (dose=0.3×1015molecules∕cm2, ∼0.75 ML). The F+ PSD and total electron yield (TEY) spectra of molecular solid CF3Cl near the F(1s) edge were also measured. Both F+ PSD and TEY spectra show two features at the energy positions of 690.2 and 692.6eV, and are attributed to the excitations of F(1s) to 11a1[(C–Cl)*] and (8e+12a1)[(C–F)*] antibonding orbitals, respectively. Following Auger decay, two holes are created in the F(2p) lone pair and/or C–F bonding orbitals forming the 2h1e final state which leads to the F+ desorption. This PSD mechanism, which is responsible for the F+ PSD of solid CF3Cl, is employed to interpret the first F+ PSD spectrum in the sequential F+ PSD spectra. The variation of spectrum shapes in the sequential F+ PSD spectra indicates the dissipation of adsorbed CF3Cl molecules and the formation of surface SiF species as a function of photon exposure. From the sequential F+ PSD spectra the photolysis cross section of the adsorbed CF3Cl molecules by photons with varying energy (681–704eV) is determined to be ∼1.0×10−17cm2.
Critical temperature gradient length signatures in heat wave propagation across internal transport barriers in the Joint European Torus
Authors: Casati Alessandro , Mantica P. , Van Eester D. , Hawkes N. , Imbeaux F. , Joffrin E. , Marinoni A. , Ryter F. , Salmi A. , Tala T. , De Vries P. ,   The JET EFDA contributors
Published: September 2007

New results on electron heat wave propagation using ion cyclotron resonance heating power modulation in the Joint European Torus (JET) [P. H. Rebut et al., Nucl. Fusion 25, 1011 (1985)] plasmas characterized by internal transport barriers (ITBs) are presented. The heat wave generated outside the ITB, and traveling across it, always experiences a strong damping in the ITB layer, demonstrating a low level of transport and loss of stiffness. In some cases, however, the heat wave is strongly inflated in the region just outside the ITB, showing features of convective-like behavior. In other cases, a second maximum in the perturbation amplitude is generated close to the ITB foot. Such peculiar types of behavior can be explained on the basis of the existence of a critical temperature gradient length for the onset of turbulent transport. Convective-like features appear close to the threshold (i.e., just outside the ITB foot) when the value of the threshold is sufficiently high, with a good match with the theoretical predictions for the trapped electron mode threshold. The appearance of a second maximum is due to the oscillation of the temperature profile across the threshold in the case of a weak ITB. Simulations with an empirical critical gradient length model and with the theory based GLF23 [R. E. Waltz et al., Phys. Plasmas, 4, 2482 (1997)] model are presented. The difference with respect to previous results of cold pulse propagation across JET ITBs is also discussed.
Hamiltonian theory of adiabatic motion of relativistic charged particles
Authors: Tao Xin , Chan Anthony A. , Brizard Alain J.
Published: September 2007

A general Hamiltonian theory for the adiabatic motion of relativistic charged particles confined by slowly varying background electromagnetic fields is presented based on a unified Lie-transform perturbation analysis in extended phase space (which includes energy and time as independent coordinates) for all three adiabatic invariants. First, the guiding-center equations of motion for a relativistic particle are derived from the particle Lagrangian. Covariant aspects of the resulting relativistic guiding-center equations of motion are discussed and contrasted with previous works. Next, the second and third invariants for the bounce motion and drift motion, respectively, are obtained by successively removing the bounce phase and the drift phase from the guiding-center Lagrangian. First-order corrections to the second and third adiabatic invariants for a relativistic particle are derived. These results simplify and generalize previous works to all three adiabatic motions of relativistic magnetically trapped particles.
Influence of oxygen in atmospheric-pressure argon plasma jet on sterilization of Bacillus atrophaeous spores
Authors: Lim Jin-Pyo , Uhm Han S. , Li Shou-Zhe
Published: September 2007

A nonequilibrium Ar∕O2 plasma discharge at atmospheric pressure was carried out in a coaxial cylindrical reactor with a stepped electrode configuration powered by a 13.56MHz rf power supplier. The argon glow discharge with high electron density produces oxygen reactive species in large quantities. Argon plasma jets penetrate deep into ambient air and create a path for oxygen radicals to sterilize microbes. A sterilization experiment with bacterial endospores indicates that an argon-oxygen plasma jet very effectively kills endospores of Bacillus atrophaeus (ATCC 9372), thereby demonstrating its capability to clean surfaces and its usefulness for reinstating contaminated equipment as free from toxic biological warfare agents. The decimal reduction time (D values) of the Ar∕O2 plasma jet at an exposure distance of 0.5–1.5cm ranges from 5 to 57s. An actinometric comparison of the sterilization data shows that atomic oxygen radicals play a significant role in plasma sterilization. When observed under a scanning electron microscope, the average size of the spores appears to be greatly reduced due to chemical reactions with the oxygen radicals.
Excitonic effects in a time-dependent density functional theory
Authors: Igumenshchev Kirill I. , Tretiak Sergei , Chernyak Vladimir Y.
Published: September 2007

Excited state properties of one-dimensional molecular materials are dominated by many-body interactions resulting in strongly bound confined excitons. These effects cannot be neglected or treated as a small perturbation and should be appropriately accounted for by electronic structure methodologies. We use adiabatic time-dependent density functional theory to investigate the electronic structure of one-dimensional organic semiconductors, conjugated polymers. Various commonly used functionals are applied to calculate the lowest singlet and triplet state energies and oscillator strengths of the poly(phenylenevinylene) and ladder-type (poly)(para-phenylene) oligomers. Local density approximations and gradient-corrected functionals cannot describe bound excitonic states due to lack of an effective attractive Coulomb interaction between photoexcited electrons and holes. In contrast, hybrid density functionals, which include long-range nonlocal and nonadiabatic corrections in a form of a fraction of Hartree-Fock exchange, are able to reproduce the excitonic effects. The resulting finite exciton sizes are strongly dependent on the amount of the orbital exchange included in the functional.
Near-critical swirling flow in a contracting duct: The case of plug axial flow with solid body rotation
Authors: Leclaire Benjamin , Sipp Denis , Jacquin Laurent
Published: September 2007

Rusak and Meder [AIAA J. 42, 2284 (2004)] recently studied the behavior of a near-critical swirling flow in a weakly contracting duct. We investigate the particular inflow condition consisting of plug axial flow with solid body rotation, and introduce a new perturbation expansion specifically suited to that case. We show that the wall recirculation occurring in the exit plane as a result of the nonlinear excitation of the critical wave by the weak contraction is more accurately predicted. We also compute the near-critical flow for strong contractions and show that wall recirculations trapped inside the duct are obtained instead.
Nucleation versus spinodal decomposition in confined binary solutions
Authors: Abyzov Alexander S. , Schmelzer Jürn W. P.
Published: September 2007

Basic features of spinodal decomposition, on one side, and nucleation, on the other side, and the transition between both mechanisms are analyzed within the framework of a generalized thermodynamic cluster model based on the generalized Gibbs approach. Hereby the clusters, representing the density or composition variations in the system, may change with time both in size and in their intensive state parameters (density and composition, for example). In the first part of the analysis, we consider phase separation processes in dependence on the initial state of the system for the case when changes of the state parameters of the ambient system due to the evolution of the clusters can be neglected as this is the case for cluster formation in an infinite system. As a next step, the effect of changes of the state parameters on cluster evolution is analyzed. Such depletion effects are of importance both for the analysis of phase formation in confined systems and for the understanding of the evolution of ensembles of clusters in large (in the limit infinite) systems. The results of the thermodynamic analysis are employed in both cases to exhibit the effect of thermodynamic constraints on the dynamics of phase separation processes.
Speed dependent rotational angular momentum polarization of the O2 (aΔg1) fragment following ozone photolysis in the wavelength range 248–265nm
Authors: Horrocks S. J. , Ritchie G. A. D. , Sharples T. R.
Published: September 2007

The translational anisotropy and rotational angular momentum polarization of a selection of rotational states of the O2 (aΔg1; v=0) photofragment formed from ozone photolysis at 248, 260, and 265nm have been determined using the technique of resonance enhanced multiphoton ionization in combination with time of flight mass spectrometry. At 248nm, the dissociation is well described as impulsive in nature with all rotational states exhibiting similarly large, near-limiting values for the bipolar moments describing their angular momentum alignment and orientation. At 265nm, however, the angular momentum polarization parameters determined for consecutive odd and even rotational states exhibit clear differences. Studies at the intermediate wavelength of 260nm strongly suggest that such a difference in the angular momentum polarization is speed dependent and this proposal is consistent with the angular momentum polarization parameters extracted and reported previously for longer photolysis wavelengths [G. Hancock et al., Phys. Chem. Chem. Phys. 5, 5386 (2003); S. J. Horrocks et al., J. Chem. Phys. 126, 044308 (2007)]. The alternation of angular momentum polarization for successive odd and even J states may be a consequence of the different mechanisms leading to the formation of the two O2 (aΔg1) Λ doublets. Specifically, the involvement of out of plane parent rotational motion is proposed as the origin for the observed depolarization for the Δ− relative to the Δ+ state.
Effect of polymer size and chain length on depletion interactions between two colloids
Authors: Kim Soon-Chul , Suh Soong-Hyuck , Seong Baek-Seok
Published: September 2007

A density functional theory based on the weighted density has been developed to investigate the depletion interactions between two colloids immersed in a bath of the binary polymer mixtures, where the colloids are modeled as hard spheres and the polymers as freely jointed tangent hard-sphere chain mixtures. The theoretical calculations for the depletion forces between two colloids induced by the polymer are in good agreement with the computer simulations. The effects of polymer packing fraction, degree of polymerization, polymer/polymer size ratio, colloid/polymer size ratio on the depletion interactions, and colloid-colloid second virial coefficient B2 due to polymer-mediated interactions have been studied. With increasing the polymer packing fraction, the depletion interaction becomes more long ranged and the attractive interaction near the colloid becomes deeper. The effect of degree polymerization shows that the long chain gives a more stable dispersion for colloids rather than the short chain. The strong effective colloid-colloid attraction appears for the large colloid/polymer and polymer/polymer size ratio. The location of maximum repulsion Rmax is found to appear Rmax∼σc+Rg2 for the low polymer packing fraction and this is shifted to smaller separation Rmax∼σc+σp2 with increasing the polymer packing fraction, where σp2 and Rg2 are the small-particle diameter and the radius of gyration of the polymer with the small-particle diameter, respectively.
Rovibrational energy transfer in ortho-H2+para-H2 collisions
Authors: Panda Aditya N. , Otto Frank , Gatti Fabien , Meyer Hans-Dieter
Published: September 2007

We present the results of a full-dimensional quantum mechanical study of the rovibrational energy transfer in the collision between ortho-H2 and para-H2 in the energy range of 0.1–1.0eV. The multiconfiguration time-dependent Hartree algorithm has been used to propagate the wave packets on the global potential energy surface by Boothroyd et al. [J. Chem. Phys. 116, 666 (2002)] and on a modification of this surface where the short range anisotropy is reduced. State-to-state attributes such as probabilities or integral cross sections are obtained using the formalism of Tannor and Weeks [J. Chem. Phys. 98, 3884 (1993)] by Fourier transforming the correlation functions. The effect of initial rotation of the diatoms on the inelastic and de-excitation processes is investigated.
Relaxation dynamics of a free elongated liquid ligament
Authors: Tong Albert Y. , Wang Zhaoyuan
Published: September 2007

The time-dependent relaxation dynamics of a moderately elongated liquid ligament in air have been numerically studied. The Navier-Stokes equations are solved using a finite-volume formulation with a two-step projection method on a fixed grid. The free surface of the liquid ligament is tracked by a coupled level set and volume-of-fluid method with the surface tension force determined by the continuum surface force model. The relaxation process of the elongated liquid ligament has been simulated and the end-pinching mechanism of the breakup process has been thoroughly examined. It has been found that the formation of a neck is not necessarily a precursor for breakup as inaccurately theorized in the end-pinching mechanism in the literature. The neck may reopen after undergoing an initial development towards pinch-off. In such an instance, droplet pinch-off will not occur. The determining factor for the reopening of a pinching neck has been identified. The experimentally observed restabilization phenomenon, in which further increase of the elongation ratio beyond the critical value would lead to cessation of pinch-off breakup, has also been investigated. Finally, the effects of several parameters on the relaxation mechanism have been examined. The initial end shape and length of the ligament and the Ohnesorge number have been found to play a vital role in the overall relaxation process.
Targeted gold nanorod contrast agent for prostate cancer detection by photoacoustic imaging
Authors: Agarwal A. , Huang S. W. , O’Donnell M. , Day K. C. , Day M. , Kotov N. , Ashkenazi S.
Published: September 2007

A targeted gold nanoparticle has been developed as a contrast agent for photoacoustic medical imaging. We have studied cancer cell targeting by antibody conjugated gold nanorods for high contrast photoacoustic imaging. By changing the aspect ratio of the elongated “rod” shape of the gold nanoparticle, its plasmon peak absorption wavelength can be tuned to the near IR (700–900nm) for an increased penetration depth into biological tissue. Effective cell targeting and sensitive photoacoustic detection of a single layer of cells are demonstrated. Combining ultrasound with contrast agent based photoacoustic imaging is proposed as a visual tool to compound molecular and structural information for early stage prostate cancer detection.
Optimized effective potential method: Is it possible to obtain an accurate representation of the response function for finite orbital basis sets?
Authors: Kollmar Christian , Filatov Michael
Published: September 2007

The optimized effective potential (OEP) equations are solved in a matrix representation using the orbital products of occupied and virtual orbitals for the representation of both the local potential and the response function. This results in a direct relationship between the matrix elements of local and nonlocal operators for the exchange-correlation potential. The effect of the truncation of the number of such products in the case of finite orbital basis sets on the OEP orbital and total energies and on the spectrum of eigenvalues of the response function is examined. Test calculations for Ar and Ne show that rather large AO basis sets are needed to obtain an accurate representation of the response function.
Simple fiber-optic confocal microscopy with nanoscale depth resolution beyond the diffraction barrier
Authors: Ilev Ilko , Waynant Ronald , Gannot Israel , Gandjbakhche Amir
Published: September 2007

A novel fiber-optic confocal approach for ultrahigh depth-resolution (⩽2nm) microscopy beyond the diffraction barrier in the subwavelength nanometric range below 200nm is presented. The key idea is based on a simple fiber-optic confocal microscope approach that is compatible with a differential confocal microscope technique. To improve the dynamic range of the resolving laser power and to achieve a high resolution in the nanometric range, we have designed a simple apertureless reflection confocal microscope with a highly sensitive single-mode-fiber confocal output. The fiber-optic design is an effective alternative to conventional pinhole-based confocal systems and offers a number of advantages in terms of spatial resolution, flexibility, miniaturization, and scanning potential. Furthermore, the design is compatible with the differential confocal pinhole microscope based on the use of the sharp diffraction-free slope of the axial confocal response curve rather than the area around the maximum of that curve. Combining the advantages of ultrahigh-resolution fiber-optic confocal microscopy, we can work beyond the diffraction barrier in the subwavelength (below 200nm) nanometric range exploiting confocal nanobioimaging of single cell and intracellular analytes.
Fringe counting method for synthetic phase with frequency-modulated laser diodes
Authors: Onodera Ribun , Sakuyama Munechika , Ishii Yukihiro
Published: September 2007

Fringe counting method with laser diodes (LDs) for displacement measurement has been constructed. Two LDs are frequency modulated by mutually inverted sawtooth currents on an unbalanced two-beam interferometer. The mutually inverted sawtooth-current modulation of LDs produces interference fringe signals with opposite signs for respective wavelengths. The two fringe signals are fed to an electronic mixer to produce a synthetic fringe signal with a reduced sensitivity to the synthetic wavelength. Synthetic fringe pulses derived from the synthetic fringe signal make a fringe counting system possible for faster movement of the tested mirror.
Simple adaptation of the Bridgman high pressure technique for use with liquid media
Authors: Colombier E. , Braithwaite D.
Published: September 2007

We present a simple novel technique to adapt a standard Bridgman cell for the use of a liquid pressure transmitting medium. The technique has been implemented in a compact cell, able to fit in a commercial Quantum Design PPMS system, and would also be easily adaptable to extreme conditions of very low temperatures or high magnetic fields. Several media have been tested and a mix of fluorinert FC84:FC87 has been shown to produce a considerable improvement over the pressure conditions in the standard steatite solid medium, while allowing a relatively easy setup procedure. For optimized hydrostatic conditions, the success rate is about 80% and the maximum pressure achieved so far is 7.1GPa. Results are shown for the heavy fermion system YbAl3 and for NaV6O15, an insulator showing charge order.
On a viscous critical-stress model of martensitic phase transitions
Authors: Weatherwax John , Vaynblat Dimitri , Bruno Oscar , Rosales Ruben
Published: September 2007

The solid-to-solid phase transitions that result from shock loading of certain materials, such as the graphite-to-diamond transition and the α-ϵ transition in iron, have long been subjects of a substantial theoretical and experimental literature. Recently a model for such transitions was introduced which, based on a CS condition (CS) and without use of fitting parameters, accounts quantitatively for existing observations in a number of systems [Bruno and Vaynblat, Proc. R. Soc. London, Ser. A 457, 2871 (2001)]. While the results of the CS model match the main features of the available experimental data, disagreements in some details between the predictions of this model and experiment, attributable to an ideal character of the CS model, do exist. In this article we present a version of the CS model, the viscous CS model (vCS), as well as a numerical method for its solution. This model and the corresponding solver results in a much improved overall CS modeling capability. The innovations we introduce include: (1) Enhancement of the model by inclusion of viscous phase-transition effects; as well as a numerical solver that allows for a fully rigorous treatment of both, the (2) Rarefaction fans (which had previously been approximated by “rarefaction discontinuities”), and (3) viscous phase-transition effects, that are part of the vCS model. In particular we show that the vCS model accounts accurately for well known “gradual” rises in the α-ϵ transition which, in the original CS model, were somewhat crudely approximated as jump discontinuities.
Defect characterization in GaN: Possible influence of dislocations in the yellow-band features
Authors: Polenta L. , Castaldini A. , Cavallini A.
Published: September 2007

Defects in freestanding gallium nitride were examined in this work. Electron beam induced current mapping evidence a low density of dislocations in the first microns from the upper Ga-terminated surface; correspondingly, deep levels detected by junction spectroscopy exhibit point-like characteristics. Spectral photoconductivity measurements in the poorly dislocated region show the characteristic red, yellow, green, and blue bands, which shift toward higher energies with decreasing temperatures according to Varshni’s law. Spectral photoconductivity measurements carried out in depth evidenced, instead, the quenching of the defect-related yellow band and the prevalence of the green band when temperature increases. This behavior suggests a dislocation-assisted connection between the yellow and green bands, in agreement with theoretical models on their common origin involving complexes VGa-ON.