bluuebunny/crossref_metadata_2025 huggingface dataset:
Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm
Authors: Thomsen Bo , Hansen Mikkel Bo , Seidler Peter , Christiansen Ove
Published: March 2012

We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations. The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene, and uracil illustrate the usefulness of the new VCC based method.
Universal state-selective corrections to multi-reference coupled-cluster theories with single and double excitations
Authors: Brabec Jiří , van Dam Hubertus J. J. , Pittner Jiří , Kowalski Karol
Published: March 2012

The recently proposed universal state-selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] to approximate multi-reference coupled-cluster (MRCC) energies can be commonly applied to any type of MRCC theory based on the Jeziorski-Monkhorst [B. Jeziorski and H. J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] exponential ansatz. In this paper we report on the performance of a simple USS correction to the Brillouin-Wigner and Mukherjee's MRCC approaches employing single and double excitations (USS-BW-MRCCSD and USS-Mk-MRCCSD). It is shown that the USS-BW-MRCCSD correction, which employs the manifold of single and double excitations, can be related to a posteriori corrections utilized in routine BW-MRCCSD calculations. In several benchmark calculations we compare the USS-BW-MRCCSD and USS-Mk-MRCCSD results with the results obtained with the full configuration interaction method.
Note: Volume errors and equimolar surfaces
Authors: Floris Franca Maria
Published: March 2012

Excess volumes related to the process of forming a spherical cavity in water were used to obtain the excess number of solvent molecules at the accessible surface. The expression presented in a previous work to describe the scaling of this property with the cavity radius has been revised. In particular, changes were introduced in order to agree with results from scaled particle theory in the limit of very small cavities. This expression enables one to obtain equimolar radii and, after free energy calculations, the surface tension at the equimolar surfaces. The effect of the excess volume errors on these properties is discussed.
Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules
Authors: Fyta Maria , Netz Roland R.
Published: March 2012

Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.
Highly uniform periodic inverse quantum dots arrays
Authors: Dias N. L. , Garg A. , Reddy U. , Choi U. , Coleman J. J.
Published: March 2012

We demonstrate high density, periodic arrays of inverse quantum dots with ±1 nm (σd/d = 0.025) variation of the critical dimension. Finite element calculations are performed to determine the effect of this size variation on the energy dispersion and intersubband gap. The subband gap is smeared for size variations greater than 1 nm for all lattice constants. This establishes an upper bound on the fabrication tolerances required to realize devices based on inverse quantum dot lattices. The quantum well wet etching step is found to be the limiting step to achieving greater pore to pore uniformity.
Plasma flow structures as analytical solution of a magneto-hydro-dynamic model with pressure
Authors: Paccagnella R.
Published: March 2012

In this work starting from a set of magnetohydrodynamic (MHD) equations that describe the dynamical evolution for the pressure driven resistive/interchange modes in a magnetic confinement system, global solutions for the plasma flow relevant for toroidal pinches like tokamaks and reversed field pinches (RFPs) are derived. Analytical solutions for the flow stream function associated with the dominant modes are presented.
Enhanced superbanana transport caused by chaotic scattering across an asymmetric separatrix
Authors: Dubin Daniel H. E. , Kabantsev A. A. , Driscoll C. F.
Published: March 2012

This paper discusses a novel “chaotic” form of superbanana transport and compares the theory to experiments on non-neutral plasmas. Superbanana transport is caused by particles that cross local trapping separatrices (magnetic or electric ripples) in the presence of field “errors” such as toroidal magnetic curvature. Traditionally, collisions (at rate ν) cause separatrix crossings, with resulting transport that scales as ν1/2B-1/2. The “chaotic” transport of interest here occurs when the separatrix is “ruffled” in the direction of plasma drift; then, collisionless particle orbits give random trapping and detrapping. Prior theory assumed a “stellarator symmetry” and suggested that these orbits give reduced transport scaling as νp with p∼1. Here, we fully characterize chaotic transport and show that the transport is enhanced rather than reduced, scaling as ν0B-1. Experiments on pure electron plasmas provide quantitative transport measurements, with precise control of the overall field error, and of the trapping separatrix with and without ruffles. The experiments show close agreement with theory over a decade in B, for both collisional neoclassical transport, and for the distinctive chaotic transport. At low magnetic fields, transport scaling as B-p with p>rsim2 becomes dominant, showing preliminary agreement with bounce-resonant theory.
Characterizing counter-streaming interpenetrating plasmas relevant to astrophysical collisionless shocks
Authors: Ross J. S. , Glenzer S. H. , Amendt P. , Berger R. , Divol L. , Kugland N. L. , Landen O. L. , Plechaty C. , Remington B. , Ryutov D. , Rozmus W. , Froula D. H. , Fiksel G. , Sorce C. , Kuramitsu Y. , Morita T. , Sakawa Y. , Takabe H. , Drake R. P. , Grosskopf M. , Kuranz C. , Gregori G. , Meinecke J. , Murphy C. D. , Koenig M. , Pelka A. , Ravasio A. , Vinci T. , Liang E. , Presura R. , Spitkovsky A. , Miniati F. , Park H.-S.
Published: March 2012

A series of Omega experiments have produced and characterized high velocity counter-streaming plasma flows relevant for the creation of collisionless shocks. Single and double CH2 foils have been irradiated with a laser intensity of ∼ 1016 W/cm2. The laser ablated plasma was characterized 4 mm from the foil surface using Thomson scattering. A peak plasma flow velocity of 2000 km/s, an electron temperature of ∼ 110 eV, an ion temperature of ∼ 30 eV, and a density of ∼ 1018 cm−3 were measured in the single foil configuration. Significant increases in electron and ion temperatures were seen in the double foil geometry. The measured single foil plasma conditions were used to calculate the ion skin depth, c/ωpi∼0.16 mm, the interaction length, ℓint, of ∼ 8 mm, and the Coulomb mean free path, λmfp∼27mm. With c/ωpi≪ℓint≪λmfp, we are in a regime where collisionless shock formation is possible.
Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme
Authors: Roy Susmita , Jana Biman , Bagchi Biman
Published: March 2012

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10–15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15–20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations.
Shock and mechanical response of 2139-T8 aluminum
Authors: Casem Daniel T. , Dandekar Dattatraya P.
Published: March 2012

Planar shock wave experiments were performed on 2139-T8 aluminum to determine its response to dynamic loading. A Hugoniot was determined to 12 GPa. Lateral stress measurements along with a study of the release behavior indicate that this material retains its shear strength to at least 8 GPa. Spall strength was measured for ∼1 μs compressive pulse durations and found to be approximately constant at 1.45 GPa up to shock stresses of 10 GPa. Beyond 10 GPa, spall strength decreases considerably. Uniaxial stress compression tests were conducted with a servo-hydraulic load frame and the Kolsky bar method to obtain stress-strain curves at strain-rates from 0.001/s to 85k/s. This data shows the material is rate independent. The shock experiments were simulated using a Lagrangian finite element code using a polynomial equation of state, the Johnson-Cook strength law, and the Cochran and Banner spall model. The ability of the simulations to reproduce the experimentally measured data is mixed, with significant deviations in modeling the plastic wave front, plastic release, and the spall pull-back signals.
Hybrid molecular dynamics simulations of living filaments
Authors: Caby Mathieu , Hardas Priscilla , Ramachandran Sanoop , Ryckaert Jean-Paul
Published: March 2012

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.
Dynamic response of a polymer-stabilized blue-phase liquid crystal
Authors: Yan Jin , Chen Yuan , Wu Shin-Tson , Liu Shih-Hsien , Cheng Kung-Lung , Shiu Jyh-Wen
Published: March 2012

Fast response time is the most attractive feature of polymer-stabilized blue phase liquid crystals (PS-BPLCs). We have investigated the dynamic response of a PS-BPLC under various electric fields and found that the response time becomes slower as the applied electric field exceeds a critical field. Further analyses of experimental data reveal that two relaxation processes are involved. Possible mechanism is proposed to explain the behavior of each process. These results provide useful guidelines for achieving fast response time without hysteresis.
Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents
Authors: Hezaveh Samira , Samanta Susruta , Milano Giuseppe , Roccatano Danilo
Published: March 2012

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O–C–C–O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.
High-pressure behavior of dense hydrogen up to 3.5 TPa from density functional theory calculations
Authors: Geng Hua Y. , Song Hong X. , Li J. F. , Wu Q.
Published: March 2012

Structural behavior and equation of state (EOS) of atomic and molecular crystal phases of dense hydrogen at pressures up to 3.5 TPa are systematically investigated with density functional theory. The results indicate that the Vinet EOS model that fitted to low-pressure experimental data overestimates the compressibility of dense hydrogen drastically when beyond 500 GPa. Metastable multi-atomic molecular phases with weak covalent bonds are observed. When compressed beyond about 2.8 TPa, these exotic low-coordinated phases become competitive with the ground state and other high-symmetry atomic phases. Using nudged elastic band method, the transition path and the associated energy barrier between these high-pressure phases are evaluated. In particular for the case of dissociation of diatomic molecular phase into the atomic metallic Cs-IV phase, the existent barrier might raise the transition pressure about 200 GPa at low temperatures. Plenty of flat and broad basins on the energy surface of dense hydrogen have been discovered, which should take a major responsibility for the highly anharmonic zero point vibrations of the lattice, as well as the quantum structure fluctuations in some extreme cases. At zero pressure, our analysis demonstrates that all of these atomic phases of dense hydrogen known so far are unquenchable.
Lifetime measurements in an electrostatic ion beam trap using image charge monitoring
Authors: Rahinov Igor , Toker Yoni , Heber Oded , Strasser Daniel , Rappaport Michael , Schwalm Dirk , Zajfman Daniel
Published: March 2012

A technique for mass-selective lifetime measurements of keV ions in a linear electrostatic ion beam trap is presented. The technique is based on bunching the ions using a weak RF potential and non-destructive ion detection by a pick-up electrode. This method has no mass-limitation, possesses the advantage of inherent mass-selectivity, and offers a possibility of measuring simultaneously the lifetimes of different ion species with no need for prior mass-selection.
Classification, selection rules, and symmetry properties of the Clebsch- Gordan coefficients of symmetric group
Authors: Doma S. B. , Hammad M. M.
Published: March 2012

New analytical expressions for Clebsch-Gordan coefficients (CGCs) of symmetric group are formulated based on the Racah factorization lemma. As examples, CGCs for the coupling [ f − 1, 1] · [ f − 1, 1] and [ f − 1, 1] · [ f − 2, 2] are tabulated. We have introduced a new technique called the Clebsch-Gordan sequences (CGSs). CGSs provide a partial understanding of vanishing of CGCs and an explanation of new symmetry properties of multiplicity-free CGCs.
Square spiral photonic crystal with visible bandgap
Authors: Krabbe Joshua D. , Leontyev Viktor , Taschuk Michael T. , Kovalenko Andriy , Brett Michael J.
Published: March 2012

Nanoimprint lithography was combined with glancing angle deposition (GLAD) of titanium dioxide to fabricate a square spiral columnar film with a bandgap in the visible spectral range. Nanoimprint stamps were fabricated with seed spacing ranging from 80 to 400 nm, and four periods of square spiral film were deposited on top of the 320 nm array of seeds. The ratio of lattice spacing, vertical pitch and spiral arm swing was chosen as a : P : A = 1 : 1.35 : 0.7 and the deposition angle was fixed at 86° to maximize the square spiral film’s bandgap. Reflectivity measurements show that the fabricated structure exhibit a pseudo-gap centered at around 600 nm wavelength, in good agreement with finite difference electromagnetic simulations. The absence of a full 3D bandgap is due the deviation of GLAD columns’ cross-section from the optimal one, which has to be highly elongated in the deposition plane. However, simulations show that a geometry close to the fabricated one will produce a full 3D bandgap, if the structure is inverted. The material refractive index in such an inverted photonic crystal can be as low as n = 2.15.
Characterization of phosphorus-doped multiwalled carbon nanotubes
Authors: Larrude D. G. , Maia da Costa M. E. H. , Monteiro F. H. , Pinto A. L. , Freire F. L.
Published: March 2012

Phosphorus-doped multiwalled carbon nanotubes (P-MWNTs) have been successfully synthesized by spray pyrolysis methods using a solution of ferrocene and triphenylphosphine in toluene. Electron microscopy images reveal corrugated tubes with a special morphology, similar to a carbon necklace. P-MWNTs are shorter compared to undoped tubes grown in the same conditions using ferrocene and toluene as precursors. Raman spectroscopy characterization suggests the formation of more defective tubes as the phosphorus in the precursor solution was increased. X-ray photoelectron spectroscopy (XPS) revealing the chemical environment of the phosphorus atoms clearly indicates the presence of substitutional phosphorus in the nanotubes.
RbxBayMn[3-(x + 2y)]/2[Fe(CN)6]·zH2O prussian blue analogues: Controlling magnetic ordering by alkaline earth metal cation substitution and magnetic field
Authors: Thakur N. , Yusuf S. M. , Paulose P. L. , Keller L.
Published: March 2012

We have controlled the nature of magnetic ordering in RbxBayMn[3-(x + 2y)]/2[Fe(CN)6]·zH2O prussian blue analogues by alkaline earth metal cation (Ba2+) substitution and application of an external magnetic field. Structural analysis, by employing Rietveld refinement of X-ray and neutron diffraction patterns, reveals a tetragonal crystal structure for all these compounds. The presence of Fe3+-C ≡ N-Mn2+ chains in the structure, and absence of both cyanide flipping (Mn2+-C ≡ N-Fe3+) and charge transfer from Mn2+ to Fe3+ (Fe2+-C ≡ N-Mn3+) have been confirmed by infrared and Mössbauer studies. The analysis of the low temperature neutron powder diffraction data reveals a long-range antiferromagnetic ordering in these compounds. The magnetic structure is layered, consisting of an antiparallel stacking of ferromagnetic sheets along the crystallographic c-direction. Within each sheet in the ab plane, the ordered moments of Mn2+ [5.04(1) μB for (x = 0.84, y = 0) and 4.99(7) μB for (x = 0.19, y = 0.3) sample at 1.5 K] and Fe3+ [0.98(3) μB for (x = 0.84, y = 0) and 0.99(3) μB for (x = 0.19, y = 0.3) sample at 1.5 K] are aligned ferromagnetically along the c-axis. Interestingly, dc magnetization study indicates that on application of an external magnetic field, an antiferromagnetic to ferrimagnetic-like phase transition occurs below ∼5 K. This phase transition becomes more and more prominent with increasing magnetic field as well as for higher Ba substitution. The role of a number of factors (such as ionic radius of Ba2+ ion and change in net ligand strength around Mn due to chemical insertion of Ba2+ ions) on the affecting nature of magnetic ordering has been discussed. The observed magnetism in these compounds is seen in light of the orbital model of superexchange interaction between magnetic ions (Mn2+ and Fe3+) mediated by cyanide ligands.
Modeling plastic deformation effect on magnetization in ferromagnetic materials
Authors: Li Jianwei , Xu Minqiang , Leng Jiancheng , Xu Mingxiu
Published: March 2012

Based on the Sablik-Landgraf model, an integrated model has been developed which provides a description of the effect of plastic deformation on magnetization. The modeling approach is to incorporate the effect of plastic deformation on the effective field and that on the model parameters. The effective field incorporates the contributions of residual stress, stress demagnetization term, and the plastic deformation. We also consider the effect of plastic deformation on the model parameters: pinning coefficient, the scaling constant and the interdomain coupling coefficient. The computed magnetization exhibits sharp change in the preliminary stage of plastic deformation, and then decreases slowly with the increase of plastic strain, in agreement with experimental results.
Capacitive tunnels in single-walled carbon nanotube networks on flexible substrate
Authors: Iqbal M. Z. , Iqbal M. W. , Eom Jonghwa , Ahmad Muneer , Ferrer-Anglada Núria
Published: March 2012

We report the analysis of single-walled carbon nanotube networks, which are expected to be suitable as miniaturized flexible radio frequency RC filters and also have important implications for high frequency devices. The surface morphology obtained by atomic force microscopy shows that most of the growth on polypropylene carbonate substrate is homogeneous. The large value of peak intensity ratio of G and D band in Raman spectra indicates the high purity network. Nyquist plots of carbon nanotube networks on a flexible substrate are close to real circles, indicating that the material is conducting, and suggest a simple equivalent circuit having a resistor in parallel with a capacitor. The Bode plots give the dependence of real and imaginary impedances on frequency. While at high frequency, the impedance decreases, due to generation of capacitance between a single-walled carbon nanotube; at low frequency, it shows the normal behavior, having constant value. The tunnels among different carbon nanotubes are capable of storing electric charge. The accumulative capacitances of tunnels for three varied concentrations are calculated by electrochemical impedance spectroscopy simulations to fit the observed Nyquist plots.
Compressed microtubules: Splitting or buckling
Authors: Jin M. Z. , Ru C. Q.
Published: March 2012

Microtubule (MT) is the mechanically strongest cytoskeletal element in eukaryotic cells and plays a key role in maintaining cell’s geometrical shape by bearing compressive forces. MTs are highly dynamic, and “dynamic instability” is referred to the switch between polymerization and depolymerization phases (the latter is characterized by splitting of protofilaments at the plus end). A micromechanics model is proposed here to study whether an axially compressed microtubule, protected by a “cap” consisted of a few layers of strongly bonded GTP dimers at the plus end, can split prior to overall buckling. Our basic conclusion is that compression-driven splitting of a capped microtubule can happen prior to overall buckling when the microtubule is very short (typically shorter than few hundreds of nanometers). For example, compression-driven splitting from middle of a capped microtubule can happen prior to buckling when the length of microtubule is shorter than a few hundreds of nanometers. In addition, for capped microtubules shorter than 125−180 nm (depending on specific values of axial Young’s modulus and adhesion energy between protofilaments), mechanical compression will cause splitting of the microtubule at its plus end prior to overall buckling. On the other hand, however, for microtubules of length longer than 0.3−0.75 micron (depending on specific values of axial Young’s modulus and adhesion energy between protofilaments), the present model shows that a cap composed of even one single layer of GTP dimers is sufficient to prevent compression-driven splitting prior to buckling, in agreement with the known observations that dynamic instability or splitting of moderately long microtubules could happen only when the cap is completely lost at the plus end.
Restoring mode degeneracy in H1 photonic crystal cavities by uniaxial strain tuning
Authors: Luxmoore I. J. , Ahmadi E. D. , Luxmoore B. J. , Wasley N. A. , Tartakovskii A. I. , Hugues M. , Skolnick M. S. , Fox A. M.
Published: March 2012

We demonstrate a uniaxial strain technique to tune the mode wavelengths of planar photonic crystal cavities. With experiments and numerical simulations, we show that it is possible to use an externally applied strain to control the splitting of the modes of the H1 cavity with high precision. By using this technique, we restore degeneracy to the fundamental modes of an H1 cavity which are initially split by ∼0.5 nm, thus demonstrating unpolarized emission at ∼950 nm with a quality factor of ∼3300.
Enhanced atomic corrugation in dynamic force microscopy—The role of repulsive forces
Authors: Lichtenstein L. , Büchner C. , Stuckenholz S. , Heyde M. , Freund H.-J.
Published: March 2012

Full range two dimensional (2D) force mapping was performed by means of low temperature dynamic force microscopy (DFM) on a highly complex surface structure. For this purpose, we used a thin film of vitreous silica on a Ru(0001)-support, which is a 2D structural equivalent to silica glass. The 2D spectroscopy shows that the contrast generating shift in vertical distance between two sites on the surface is twice as large on the repulsive branch of the frequency shift-distance curve as compared to the attractive branch. The results give insight into the origin of the formation of atomic resolution in DFM.
Structural properties and quasiparticle band structures of Cu-based quaternary semiconductors for photovoltaic applications
Authors: Zhang Yubo , Sun Xiudong , Zhang Peihong , Yuan Xun , Huang Fuqiang , Zhang Wenqing
Published: March 2012

Cu-based quaternary chalcogenide semiconductors (Cu2-II-IV-VI4) are a large group of materials that hold great promises for a variety of applications, especially as thin-film solar cell absorbers. However, despite intensive research activities, a systematic understanding of the evolution of the electronic and structural properties with chemical compositions of these materials is still lacking. In this paper, we present first-principles calculations of the structural and electronic properties of eight such semiconductors (Cu2-II-IV-VI4, with II = Zn and Cd; IV = Ge and Sn; VI = S and Se). The variation of the structural parameters with chemical compositions, investigated using the HSE06 hybrid functional, follows a few interesting trends. The quasiparticle bandgap, calculated using the state-of-the-art GW approximation, also varies systematically with chemical compositions. Effects of cation disordering on the band gaps are also investigated. This systematic understanding of the structural parameters and quasiparticle band gaps would be useful for future structural characterization and material design.
Spectroscopic evaluation of band alignment of atomic layer deposited BeO on Si(100)
Authors: Lei Ming , Yum J. H. , Price J. , Hudnall Todd W. , Bielawski C. W. , Banerjee S. K. , Lysaght P. S. , Bersuker G. , Downer M. C.
Published: March 2012

We report optical characterization of the conduction band offset (CBO) between atomic-layer-deposited single crystal BeO and Si using internal photoemission (IPE) and internal multi-photon photoemission (IMPE), and of the valence band offset (VBO) using synchrotron x-ray photoelectron spectroscopy. The IPE/IMPE measurements indicate a CBO of 2.31 ± 0.1 eV for 10 nm thick as-deposited oxides. For samples subjected to post-deposition anneal in N2 at 600 °C and 900 °C, it increases to 2.54 ± 0.1 eV and 2.61 ± 0.1 eV, respectively. The VBO is stable at 4.14 ± 0.2 eV for both as-deposited and annealed samples.
Note: Programmable data acquisition system for research measurements from meteorological radiosondes
Authors: Harrison R. G. , Nicoll K. A. , Lomas A. G.
Published: March 2012

A programmable data acquisition system to allow novel use of meteorological radiosondes for atmospheric science measurements is described. In its basic form it supports four analogue inputs at 16 bit resolution, and up to two further inputs at lower resolution, configurable instead for digital instruments. It also provides multiple instrument power supplies (+8 V, +16 V, +5 V, and −8 V) from the 9 V radiosonde battery. During a balloon flight encountering air temperatures from +17 °C to −66 °C, the worst case voltage drift in the 5 V unipolar digitisation circuitry was 20 mV. The system liberates a new range of low cost atmospheric research measurements, by utilising radiosondes routinely launched internationally for weather forecasting purposes. No additional receiving equipment is required. Comparisons between the specially instrumented and standard meteorological radiosondes show negligible effect of the additional instrumentation on the standard meteorological data.
Note: A method to isolate and detect a large number of single molecules by microdroplet fluorescence spectroscopy
Authors: Ng K. C. , Heredia K. H. , Kliewer D.
Published: March 2012

A laser induced fluorescence system, in combination with a glass-frit nebulizer and a photo-voltaic cell detector, is described for single molecule detection. The glass-frit nebulizer continuously generates a large number of droplets with an average droplet size of three micrometers in diameter. Rhodamine 6G molecules were detected at the 10−12 M level. Concentrations 10−12–10−10 M would provide mostly single molecules (0, 1, 2, 3, …) in the individual droplets, as determined by Poisson distribution.
Anomalous wetting on a superhydrophobic graphite surface
Authors: Hong Siang-Jie , Li Yueh-Feng , Hsiao Mu-Jou , Sheng Yu-Jane , Tsao Heng-Kwong
Published: March 2012

A superhydrophobic graphite surface has been fabricated through two facile physical steps, peeling and ultrasonicating. Peeling yields micron-scale roughening, and thus a highly hydrophobic surface is obtained. Further ultrasonicating results in a superhydrophobic surface with nanostructure embedded in microstructure. The nanostructure leads to networklike pores on the superhydrophobic film and convective Ostwald ripening is observed. Owing to their distinct resistance to liquid imbibition, contact angle hysteresis on hydrophobic and superhydrophobic surfaces is fundamentally different. Moreover, the adhesive force on a superhydrophobic surface grows with the contact time, and such aging effect is absent on hydrophobic graphite surface.
Biogas fuel reforming for solid oxide fuel cells
Authors: Murphy Danielle M. , Richards Amy E. , Colclasure Andrew , Rosensteel Wade A. , Sullivan Neal P.
Published: March 2012

In this paper, strategies for biogas reforming and their ensuing effects on solid oxide fuel cell (SOFC) performance are explored. Synthesized biogas (65% CH4 + 35% CO2) fuel streams are reformed over a rhodium catalyst supported on a porous α-alumina foam. Reforming approaches include steam reforming and catalytic partial oxidation (CPOX) utilizing either air or pure oxygen as the oxidant. A computational model is developed and utilized to guide the specification of reforming conditions that maximize both CH4 and CO2 conversions. Model predictions are validated with experimental measurements over a wide range of biogas-reforming conditions. Higher reforming temperatures are shown to activate the biogas-borne CO2 to enable significant methane dry-reforming chemistry. Dry reforming minimizes the oxidant-addition needs for effective biogas conversion, potentially decreasing the thermal requirements for reactant heating and improving system efficiency. Such high-temperature reforming conditions are prevalent during CPOX with a pure-O2 oxidant. While CPOX-with-O2 reforming is highly exothermic, the endothermicity of dry-reforming chemistry can be exploited to ensure that catalyst temperatures do not reach levels which cause catalyst sintering and degradation. SOFC electrochemical performance under biogas reformate is shown to vary substantially with reforming approach. Cell operation under CPOX-with-O2 reformate is found to be comparable to that under humidified hydrogen.
Intrinsic thermoelectric power of group VB metals
Authors: Okram Gunadhor Singh
Published: March 2012

We have reinvestigated the thermopower of group VB metals in polycrystalline forms in the temperature range of 6-300K, taking into account the critical nature of the sample surface and heat treatment especially for niobium. Strikingly small magnitude, negative sign, phonon drag dip and superconductivity not reported previously were observed in surface-cleaned single crystalline Nb. However, while thermopower magnitudes are small, mixed signs were found in the polycrystalline V, Nb and Ta samples. These properties were therefore interpreted as their intrinsic properties and were briefly discussed taking into account of the existing theory by fitting also the data that give the Fermi energies of 10.94 eV, 5.08 eV and 1.86eV, respectively.
Physics of cancer propagation: A game theory perspective
Authors: Cleveland Chris , Liao David , Austin Robert
Published: March 2012

This is a theoretical paper which examines at a game theoretical perspective the dynamics of cooperators and cheater cells under metabolic stress conditions and high spatial heterogeneity. Although the ultimate aim of this work is to understand the dynamics of cancer tumor evolution under stress, we use a simple bacterial model to gain fundamental insights into the progression of resistance to drugs under high competition and stress conditions.
Rationality, Stability, and Endogenous Price Formation in Spatially Interdependent Markets
Authors: Plummer Paul , Sheppard Eric , Haining Robert
Published: March 2012

Spatial competition between firms is standard fare for traditional location theory and contemporary geographical economics. In this paper we examine the implications of modeling spatial competition using an approach grounded in geographical political economy, using mathematics as the language of theory. We make no presumptions about the existence of, or agents' prior knowledge about, equilibrium; utilizing methodologies from nonlinear dynamics appropriate to this situation. For competition between equally spaced retailers along an unbounded linear market, selling a homogeneous commodity to uniformly dispersed consumers we show that Nash equilibrium, which rationalizes the existence and persistence of spatial price equilibria, need not hold. Depending on behavioral parameters, out-of-equilibrium dynamics may not converge toward equilibrium, displaying instead limit-cycle or aperiodic behavior. Further, even for cases that do converge, it can be rational for firms in equilibrium to set prices which depart from it, thereby increasing their profits. The presumptions of geographical economics concerning equilibrium are not adequate to make sense of capitalist spatial price competition.
The Anticipated Emotional Consequences of Adaptive Behaviour—Impacts on the Take-up of Household Flood-Protection Measures
Authors: Harries Tim
Published: March 2012

When considering householder responses to flood risk, researchers and policy makers have perhaps focused too much on the influence of risk perceptions and concerns about material costs and benefits. Using secondary analysis of survey data from UK households who had experienced flooding or who were at risk of flooding, this paper presents evidence to suggest that protective behaviour may be influenced less by material and financial considerations than by concerns about feelings of anxiety and insecurity. It also looks at the role of beliefs about protection and flooding in mediating the impacts of flood experience and suggests that experience reduces confidence in the ameliorative capacity of insurance and promotes the belief that protective measures increase anxiety about flooding. The paper concludes that more research should be carried out on the role of anticipated emotions in risk response and that policy makers and the designers of protection products should pay more attention to the emotional barriers and incentives to adaptation.
Perennial ryegrass breeding in New Zealand: A dairy industry perspective
Authors: Lee Julia M. , Matthew Cory , Thom Errol R. , Chapman David F.
Published: March 2012

Genetic improvement programs for livestock and pasture plants have been central to the development of the New Zealand (NZ) pastoral industry. Although genetic improvement of livestock is easily shown to improve animal production on-farm, the link between genetic improvement of pasture plants and animal production is less direct. For several reasons, gains in farm output arising from improved plant performance are more difficult to confirm than those arising from livestock improvement, which has led to some debate in the livestock industries about which plant traits to prioritise in future breeding programs to deliver the greatest benefit. This review investigates this situation, with the aim of understanding how genetic improvement of perennial ryegrass (Lolium perenne L.), the predominant pasture grass, may more directly contribute towards increased productivity in the NZ dairy industry. The review focuses on the dairy industry, since it is the largest contributor to the total value of NZ agricultural exports. Also, because rates of pasture renewal are greater in the dairy industry compared with the sheep and beef industries, genetic gain in pasture plants is likely to have the greatest impact if the correct plant traits are targeted. The review highlights that many aspects of ryegrass growth and ecology have been manipulated through breeding, with evidence to show that plant performance has been altered as a result. However, it is not clear to what extent these gains have contributed to the economic development of the NZ dairy industry. There are opportunities for breeders and scientists to work together more closely in defining economic traits that positively influence pasture performance and to translate this information to objectives for breeding programs, systematically linking information on the measured traits of ryegrass cultivars to economic values for those traits to assist farmer decision-making regarding the most appropriate cultivars to use in their farm system, and better defining genotype × environment interactions in key productivity traits of modern ryegrass cultivars. Changes in priorities for investment of public- and industry-good funds in forage improvement research and development will be needed if these opportunities are to be captured.
Non-climacteric ripening in strawberry fruit is linked to ABA, FaNCED2 and FaCYP707A1
Authors: Ji Kai , Chen Pei , Sun Liang , Wang Yanping , Dai Shengjie , Li Qian , Li Ping , Sun Yufei , Wu Yan , Duan Chaorui , Leng Ping
Published: March 2012

To study the role of ABA in development and ripening of strawberry fruit, two ABA key synthetase genes FaNCED1, FaNCED2 and one ABA key degradation enzyme gene FaCYP707A1 were cloned from strawberry cultivar ‘Ablion’. The three genes and putative amino acid sequences, respectively, had high similarities with their homologues in other plants. In strawberry pulp, expression of FaNCED2 rose in two stages that corresponded with increases in ABA levels. The expression of FaNCED1 was much lower and increased continually. The expression of FaCYP707A1 increased as fruit changed from bright green to white, then decreased as it ripened. Auxin reduced expression of these three genes. Analysis of expression of these genes in different organs and tissues showed that FaNCED2 was abundant in mature achenes and the pulp (receptacle) had high expression of FaNCED1 and FaCYP707A1. ABA may play a regulation role in strawberry fruit development and ripening. The content of ABA was regulated by its key synthetase gene NCED2 and degradation gene CYP707A1.
Comparative use of active searches and artificial refuges to survey reptiles in temperate eucalypt woodlands
Authors: Michael Damian R. , Cunningham Ross B. , Donnelly Christine F. , Lindenmayer David B.
Published: March 2012

Context
In many parts of the world, artificial refuges (ARs) are increasingly used to survey different kinds of herpetofauna. Despite gaining popularity, the merit of using ARs compared with standardised active searches remains poorly known, as does their application in regions that support species exhibiting varied life-form strategies.

Aims
We examined the effectiveness of using two survey methods, active searches and ARs (corrugated steel, roof tiles and three different timber refuges), to detect herpetofauna in a range of eucalypt-woodland communities in south-eastern Australia.

Methods
We collected count data over a 12-year period from three independent long-term biodiversity monitoring programs in southern New South Wales. We used generalised linear models to compare detection probabilities among survey methods (active searches versus ARs) and among ARs, for each study area.

Key results
In all study areas, active searches detected the highest mean species richness per site. However, both methods provided complimentary species, thereby maximising species inventory at a regional scale. Species more likely to be detected in active searches included diurnally active, terrestrial and arboreal heliotherms, whereas species detected more frequently using ARs included nocturnal thigmotherms.

Conclusions
A combination of active searches and AR types is required to provide regional-scale representative reptile assemblages, although more than five consecutive surveys may be needed before species accumulation curves reach plateaux. In future studies, we recommend using stacks of corrugated steel to detect heliothermic Scincidae and arboreal Gekkonidae, roof tiles to detect thigmothermic Pygopodidae and railway sleepers to detect cryptozoic Elapidae and tunnel-dwelling Gekkonidae.

Implications
Using a combination of ARs and active searches will increase the chance of detecting both common and cryptic species and deploying corrugated steel provides a cost-effective method for surveying reptiles in long-term studies.
Co-transplantation of pure blood stem cells with antigen-specific but not bulk T cells augments functional immunity
Authors: Müller Antonia M. S. , Shashidhar Sumana , Küpper Natascha J. , Kohrt Holbrook E. K. , Florek Mareike , Negrin Robert S. , Brown Janice M. , Shizuru Judith A.
Published: March 2012

Impaired immunity is a fundamental obstacle to successful allogeneic hematopoietic cell transplantation. Mature graft T cells are thought to provide protection from infections early after transplantation, but can cause life-threatening graft-vs.-host disease. Human CMV is a major pathogen after transplantation. We studied reactivity against the mouse homologue, murine CMV (MCMV), in lethally irradiated mice given allogeneic purified hematopoietic stem cells (HSCs) or HSCs supplemented with T cells or T-cell subsets. Unexpectedly, recipients of purified HSCs mounted superior antiviral responses compared with recipients of HSC plus unselected bulk T cells. Furthermore, supplementation of purified HSC grafts with CD8
+
memory or MCMV-specific T cells resulted in enhanced antiviral reactivity. Posttransplantation lymphopenia promoted massive expansion of MCMV-specific T cells when no competing donor T cells were present. In recipients of pure HSCs, naive and memory T cells and innate lymphoid cell populations developed. In contrast, the lymphoid pool in recipients of bulk T cells was dominated by effector memory cells. These studies show that pure HSC transplantations allow superior protective immunity against a viral pathogen compared with unselected mature T cells. This reductionist transplant model reveals the impact of graft composition on regeneration of host, newly generated, and mature transferred T cells, and underscores the deleterious effects of bulk donor T cells. Our findings lead us to conclude that grafts composed of purified HSCs provide an optimal platform for in vivo expansion of selected antigen-specific cells while allowing the reconstitution of a naive T-cell pool.