bluuebunny/crossref_metadata_2025 huggingface dataset:
Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity
Authors: Araque J. C. , Robert M. A.
Published: March 2016

Because oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.
First-principles study on equation of states and electronic structures of shock compressed Ar up to warm dense regime
Authors: Sun Huayang , Kang Dongdong , Dai Jiayu , Ma Wen , Zhou Liangyuan , Zeng Jiaolong
Published: March 2016

The equation of states (EOS) and electronic structures of argon with temperatures from 0.02 eV to 3 eV and densities from 0.5 g/cm3 to 5.5 g/cm3 are calculated using the pair potential and many-body potential molecular dynamics and the density functional theory (DFT) molecular dynamics with van der Waals (vdW) corrections. First-principles molecular dynamics is implemented above 2.0 g/cm3. For the cases of low densities below 3 g/cm3, we performed pair potential molecular dynamics in order to obtain the ionic configurations, which are used in density functional theory to calculate the EOS and electronic structures. We checked the validity of different methods at different densities and temperatures, showing their behaviors by comparing EOS. DFT without vdW correction works well above 1 eV and 3.5 g/cm3. Below 1 eV and 2.0 g/cm3, it overestimates the pressure apparently and results in incorrect behaviors of the internal energy. With vdW corrections, the semi-empirical force-field correction (DFT-D2) method gives consistent results in the whole density and temperature region, and the vdW density functional (vdW-DF2) method gives good results below 2.5 g/cm3, but it overestimates the pressure at higher densities. The interactions among the atoms are overestimated by the pair potential above 1 eV, and a temperature dependent scaled pair potential can be used to correct the ionic configurations of the pair potential up to 3 eV. The comparisons between our calculations and the experimental multi-shock compression results show that the Hugoniot line of DFT-D2 and DFT tends to give larger pressure than the results of the self-consistent fluid variational theory, and the difference increases with the density. The electronic energy gap exists for all our cases up to 5.5 g/cm3 and 1 eV. The effect of vdW interactions on the electronic structures are also discussed.
Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route
Authors: Benavides A. L. , Aragones J. L. , Vega C.
Published: March 2016

The solubility of NaCl in water is evaluated by using three force field models: Joung–Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.
Dynamic transitions in a model of the hypothalamic-pituitary-adrenal axis
Authors: Čupić Željko , Marković Vladimir M. , Maćešić Stevan , Stanojević Ana , Damjanović Svetozar , Vukojević Vladana , Kolar-Anić Ljiljana
Published: March 2016

Dynamic properties of a nonlinear five-dimensional stoichiometric model of the hypothalamic-pituitary-adrenal (HPA) axis were systematically investigated. Conditions under which qualitative transitions between dynamic states occur are determined by independently varying the rate constants of all reactions that constitute the model. Bifurcation types were further characterized using continuation algorithms and scale factor methods. Regions of bistability and transitions through supercritical Andronov-Hopf and saddle loop bifurcations were identified. Dynamic state analysis predicts that the HPA axis operates under basal (healthy) physiological conditions close to an Andronov-Hopf bifurcation. Dynamic properties of the stress-control axis have not been characterized experimentally, but modelling suggests that the proximity to a supercritical Andronov-Hopf bifurcation can give the HPA axis both, flexibility to respond to external stimuli and adjust to new conditions and stability, i.e., the capacity to return to the original dynamic state afterwards, which is essential for maintaining homeostasis. The analysis presented here reflects the properties of a low-dimensional model that succinctly describes neurochemical transformations underlying the HPA axis. However, the model accounts correctly for a number of experimentally observed properties of the stress-response axis. We therefore regard that the presented analysis is meaningful, showing how in silico investigations can be used to guide the experimentalists in understanding how the HPA axis activity changes under chronic disease and/or specific pharmacological manipulations.
A non-additive repulsive contribution in an equation of state: The development for homonuclear square well chains equation of state validated against Monte Carlo simulation
Authors: Trinh Thi-Kim-Hoang , Passarello Jean-Philippe , de Hemptinne Jean-Charles , Lugo Rafael , Lachet Veronique
Published: March 2016

This work consists of the adaptation of a non-additive hard sphere theory inspired by Malakhov and Volkov [Polym. Sci., Ser. A 49(6), 745–756 (2007)] to a square-well chain. Using the thermodynamic perturbation theory, an additional term is proposed that describes the effect of perturbing the chain of square well spheres by a non-additive parameter. In order to validate this development, NPT Monte Carlo simulations of thermodynamic and structural properties of the non-additive square well for a pure chain and a binary mixture of chains are performed. Good agreements are observed between the compressibility factors originating from the theory and those from molecular simulations.
Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures
Authors: McCarthy Michael C. , Martinez Oscar , McGuire Brett A. , Crabtree Kyle N. , Martin-Drumel Marie-Aline , Stanton John F.
Published: March 2016

HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO2 reaction represents the final step for the production of CO2 in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO2 in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO2. Using isotopically labelled precursors, the OH + C18O reaction predominately yields HOC18O for both isomers, but H18OCO is observed as well, typically at the level of 10%-20% that of HOC18O; the opposite propensity is found for the 18OH + CO reaction. DO + C18O yields similar ratios between DOC18O and D18OCO as those found for OH + C18O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO2, which, at the high pressure of our gas expansion, can readily occur. The large 13C Fermi-contact term (aF) for trans- and cis-HO13CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers.
Microwave spectral taxonomy: A semi-automated combination of chirped-pulse and cavity Fourier-transform microwave spectroscopy
Authors: Crabtree Kyle N. , Martin-Drumel Marie-Aline , Brown Gordon G. , Gaster Sydney A. , Hall Taylor M. , McCarthy Michael C.
Published: March 2016

Because of its structural specificity, rotational spectroscopy has great potential as an analytical tool for characterizing the chemical composition of complex gas mixtures. However, disentangling the individual molecular constituents of a rotational spectrum, especially if many of the lines are entirely new or unknown, remains challenging. In this paper, we describe an empirical approach that combines the complementary strengths of two techniques, broadband chirped-pulse Fourier transform microwave spectroscopy and narrowband cavity Fourier transform microwave spectroscopy, to characterize and assign lines. This procedure, called microwave spectral taxonomy, involves acquiring a broadband rotational spectrum of a rich mixture, categorizing individual lines based on their relative intensities under series of assays, and finally, linking rotational transitions of individual chemical compounds within each category using double resonance techniques. The power of this procedure is demonstrated for two test cases: a stable molecule with a rich spectrum, 3,4-difluorobenzaldehyde, and products formed in an electrical discharge through a dilute mixture of C2H2 and CS2, in which spectral taxonomy has enabled the identification of propynethial, HC(S)CCH.
High temperature breakdown of the Stokes-Einstein relation in a computer simulated Cu-Zr melt
Authors: Han X. J. , Li J. G. , Schober H. R.
Published: March 2016

Transport properties and the Stokes-Einstein (SE) relation in liquid Cu8Zr3 are studied by molecular dynamics simulation with a modified embedded atom potential. The critical temperature Tc of mode coupling theory (MCT) is derived as 930 K from the self-diffusion coefficient D and viscosity η. The SE relation breaks down around TSE = 1900 K, which is far above Tc. At temperatures below TSE, the product of D and η fluctuates around a constant value, similar to the prediction of MCT near Tc. The influence of the microscopic atomic motion on macroscopic properties is investigated by analyzing the time dependent liquid structure and the self-hole filling process. The self-holes for the two components are preferentially filled by atoms of the same component. The self-hole filling dynamics explains the different breakdown behaviors of the SE relation in Zr-rich liquid CuZr2 compared to Cu-rich Cu8Zr3. At TSE, a kink is found in the temperature dependence of both partial and total coordination numbers for the three atomic pair combinations and of the typical time of self-hole filling. This indicates a strong correlation between liquid structure, atomic dynamics, and the breakdown of SE relation. The previously suggested usefulness of the parameter d(D1/D2)/dT to predict TSE is confirmed. Additionally we propose a viscosity criterion to predict TSE in the absence of diffusion data.
Key parameters controlling the performance of catalytic motors
Authors: Esplandiu Maria J. , Afshar Farniya Ali , Reguera David
Published: March 2016

The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential and the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators.
Soft matter dynamics: Accelerated fluid squeeze-out during slip
Authors: Hutt W. , Persson B. N. J.
Published: March 2016

Using a Leonardo da Vinci experimental setup (constant driving force), we study the dependency of lubricated rubber friction on the time of stationary contact and on the sliding distance. We slide rectangular rubber blocks on smooth polymer surfaces lubricated by glycerol or by a grease. We observe a remarkable effect: during stationary contact the lubricant is only very slowly removed from the rubber-polymer interface, while during slip it is very rapidly removed resulting (for the grease lubricated surface) in complete stop of motion after a short time period, corresponding to a slip distance typically of order only a few times the length of the rubber block in the sliding direction. For an elastically stiff material, poly(methyl methacrylate), we observe the opposite effect: the sliding speed increases with time (acceleration), and the lubricant film thickness appears to increase. We propose an explanation for the observed effect based on transient elastohydrodynamics, which may be relevant also for other soft contacts.
Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory
Authors: Schlesinger Daniel , Sellberg Jonas A. , Nilsson Anders , Pettersson Lars G. M.
Published: March 2016

In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.
Influence of ultraviolet irradiation on data retention characteristics in resistive random access memory
Authors: Kimura K. , Ohmi K. , Kishida S. , Kinoshita K.
Published: March 2016

With increasing density of memory devices, the issue of generating soft errors by cosmic rays is becoming more and more serious. Therefore, the irradiation resistance of resistance random access memory (ReRAM) to cosmic radiation has to be elucidated for practical use. In this paper, we investigated the data retention characteristics of ReRAM against ultraviolet irradiation with a Pt/NiO/ITO structure. Soft errors were confirmed to be caused by ultraviolet irradiation in both low- and high-resistance states. An analysis of the wavelength dependence of light irradiation on data retention characteristics suggested that electronic excitation from the valence to the conduction band and to the energy level generated due to the introduction of oxygen vacancies caused the errors. Based on a statistically estimated soft error rates, the errors were suggested to be caused by the cohesion and dispersion of oxygen vacancies owing to the generation of electron-hole pairs and valence changes by the ultraviolet irradiation.
Rephasing invariants of the Cabibbo-Kobayashi- Maskawa matrix
Authors: Pérez R. H. , Kielanowski P. , Juárez W. S. R.
Published: March 2016

The paper is motivated by the importance of the rephasing invariance of the CKM (Cabibbo-Kobayashi-Maskawa) matrix observables. These observables appear in the discussion of the CP violation in the standard model (Jarlskog invariant) and also in the renormalization group equations for the quark Yukawa couplings. Our discussion is based on the general phase invariant monomials built out of the CKM matrix elements and their conjugates. We show that there exist 30 fundamental phase invariant monomials and 18 of them are a product of 4 CKM matrix elements and 12 are a product of 6 CKM matrix elements. In the main theorem we show that a general rephasing invariant monomial can be expressed as a product of at most five factors: four of them are fundamental phase invariant monomials and the fifth factor consists of powers of squares of absolute values of the CKM matrix elements. We also show that the imaginary part of any rephasing invariant monomial is proportional to the Jarlskog’s invariant J or is 0.
Distribution of tunnelling times for quantum electron transport
Authors: Rudge Samuel L. , Kosov Daniel S.
Published: March 2016

In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.
Influence of electron-beam lithography exposure current level on the transport characteristics of graphene field effect transistors
Authors: Kang Sangwoo , Movva Hema C. P. , Sanne Atresh , Rai Amritesh , Banerjee Sanjay K.
Published: March 2016

Many factors have been identified to influence the electrical transport characteristics of graphene field-effect transistors. In this report, we examine the influence of the exposure current level used during electron beam lithography (EBL) for active region patterning. In the presence of a self-assembled hydrophobic residual layer generated by oxygen plasma etching covering the top surface of the graphene channel, we show that the use of low EBL current level results in higher mobility, lower residual carrier density, and charge neutrality point closer to 0 V, with reduced device-to-device variations. We show that this correlation originates from the resist heating dependent release of radicals from the resist material, near its interface with graphene, and its subsequent trapping by the hydrophobic polymer layer. Using a general model for resist heating, we calculate the difference in resist heating for different EBL current levels. We further corroborate our argument through control experiments, where radicals are either intentionally added or removed by other processes. We also utilize this finding to obtain mobilities in excess of 18 000 cm2/V s on silicon dioxide substrates. We believe these results are applicable to other 2D materials such as transition metal dichalcogenides and nanoscale devices in general.
Electrical transport properties of (La,Pr,Ca)MnO3 nanowires investigated using terahertz time domain spectroscopy
Authors: Nguyen T. V. A. , Hattori A. N. , Nagai M. , Nakamura T. , Ashida M. , Tanaka H.
Published: March 2016

The electrical transport properties of a 100-nm-width (La,Pr,Ca)MnO3 nanowire sample were investigated using terahertz (THz) time domain spectroscopy. When the electric field of incident THz pulses was parallel to the nanowires, we obtained their intrinsic THz conductivity. The temperature-dependent dc conductivity and metallic fraction were simultaneously estimated by analyzing the THz conductivity using a metal-insulator composite model. The evaluated dc conductivity closely reproduced that measured by electrical probe measurement. The metallic fraction showed the evolution of electric domains from the metallic state at temperatures below 100 K to the insulating state at temperatures above 150 K through a coexistence region, which was in consistence with the phase-separated scenario.
Imaging coherent transport in chemical vapor deposition graphene wide constriction by scanning gate microscopy
Authors: Chuang Chiashain , Matsunaga Masahiro , Liu Fan-Hung , Woo Tak-Pong , Lin Li-Hung , Oto Kenichi , Ochiai Yuichi , Liang Chi-Te , Aoki Nobuyuki
Published: March 2016

We use a scanning gate microscopy to perturb coherent transport in chemical vapor deposition (CVD) graphene wide constriction. Particularly, we observe conductance oscillations in the wide constriction region (W ∼ 800 nm) characterized by spatial conductance variations, which imply formation of the nanometer-scale ring structure due to the merged domains and intrinsic grain boundaries. Moreover, additional hot charges from high current can suppress the coherent transport, suggesting that the hot carriers with a wide spreading kinetic energy could easily tunnel merged domains and intrinsic grain boundaries in CVD-grown graphene due to the heating effect, a great advantage for applications in graphene-based interference-type nano-electronics.
Achieving all-dielectric metamaterial band-pass frequency selective surface via high-permittivity ceramics
Authors: Li Liyang , Wang Jiafu , Ma Hua , Wang Jun , Feng Mingde , Du Hongliang , Yan Mingbao , Zhang Jieqiu , Qu Shaobo , Xu Zhuo
Published: March 2016

In this paper, we propose the design of all-dielectric metamaterial band-pass frequency selective surfaces (FSSs) using high-permittivity ceramics based on effective medium theory and dielectric resonator theory. The band-pass response can be determined by the permittivity of the dielectric material, the periodicity, and geometrical shape of the dielectric unit cell. As an example, a band-pass FSS composed of H shaped ceramic resonators is demonstrated. Both the simulation and experiment results show that the FSS can achieve a pass band in X-band. Since such FSSs are made of low-loss high-permittivity ceramics, they are of important application values, especially in high-temperature, high-power environments. The design method can be readily extended to the design of FSSs in other frequencies.
Experimental investigation on the energy deposition and morphology of the electrical explosion of copper wire in vacuum
Authors: Shi Zongqian , Shi Yuanjie , Wang Kun , Jia Shenli
Published: March 2016

This paper presents the experimental results of the electrical explosion of copper wires in vacuum using negative nanosecond-pulsed current with magnitude of 1–2 kA. The 20 μm-diameter copper wires with different lengths are exploded with three different current rates. A laser probe is applied to construct the shadowgraphy and interferometry diagnostics to investigate the distribution and morphology of the exploding product. The interference phase shift is reconstructed from the interferogram, by which the atomic density distribution is calculated. Experimental results show that there exist two voltage breakdown modes depending on the amount of the specific energy deposition. For the strong-shunting mode, shunting breakdown occurs, leading to the short-circuit-like current waveform. For the weak-shunting mode with less specific energy deposition, the plasma generated during the voltage breakdown is not enough to form a conductive plasma channel, resulting in overdamped declining current waveform. The influence of the wire length and current rate on the characteristics of the exploding wires is also analyzed.
Growth and characterization of highly tensile strained Ge1−xSnx formed on relaxed InyGa1−yP buffer layers
Authors: Wang Wei , Loke Wan Khai , Yin Tingting , Zhang Zheng , D'Costa Vijay Richard , Dong Yuan , Liang Gengchiau , Pan Jisheng , Shen Zexiang , Yoon Soon Fatt , Tok Eng Soon , Yeo Yee-Chia
Published: March 2016

Ge0.94Sn0.06 films with high tensile strain were grown on strain-relaxed InyGa1−yP virtual substrates using solid-source molecular beam epitaxy. The in-plane tensile strain in the Ge0.94Sn0.06 film was varied by changing the In mole fraction in InxGa1−xP buffer layer. The tensile strained Ge0.94Sn0.06 films were investigated by transmission electron microscopy, x-ray diffraction, and Raman spectroscopy. An in-plane tensile strain of up to 1% in the Ge0.94Sn0.06 was measured, which is much higher than that achieved using other buffer systems. Controlled thermal anneal experiment demonstrated that the strain was not relaxed for temperatures up to 500 °C. The band alignment of the tensile strained Ge0.94Sn0.06 on In0.77Ga0.23P was obtained by high resolution x-ray photoelectron spectroscopy. The Ge0.94Sn0.06/In0.77Ga0.23P interface was found to be of the type I band alignment, with a valence band offset of 0.31 ± 0.12 eV and a conduction band offset of 0.74 ± 0.12 eV.
Large enhancement of bulk spin polarization by suppressing CoMn anti-sites in Co2Mn(Ge0.75Ga0.25) Heusler alloy thin film
Authors: Li S. , Takahashi Y. K. , Sakuraba Y. , Tsuji N. , Tajiri H. , Miura Y. , Chen J. , Furubayashi T. , Hono K.
Published: March 2016

We have investigated the structure and magneto-transport properties of Co2Mn(Ge0.75Ga0.25) (CMGG) Heusler alloy thin films with near-stoichiometric and Mn-rich compositions in order to understand the effect of Co-Mn anti-sites on bulk spin polarization. Anomalous x-ray diffraction measurements using synchrotron radiated x-rays confirmed that CoMn anti-sites easily form in the near-stoichiometric CMGG compound at annealing temperature higher than 400 °C, while it can be suppressed in Mn-rich CMGG films. Accordingly, large enhancement in negative anisotropic magnetoresistance of CMGG films and giant magnetoresistance (GMR) in current-perpendicular-to-plane (CPP) pseudo spin valves were observed in the Mn-rich composition. A large resistance-area product change (ΔRA) of 12.8 mΩ μm2 was demonstrated in the CPP-GMR pseudo spin valves using the Mn-rich CMGG layers after annealing at 600 °C. It is almost twice of the maximum output observed in the CPP-GMR pseudo spin valves using the near-stoichiometric CMGG. These indicate that the spin polarization of CMGG is enhanced in the Mn-rich composition through suppressing the formation of CoMn-antisites in CMGG films, being consistent with first-principle calculation results.
Finite element analysis of surface modes in phononic crystal waveguides
Authors: Guo Yuning , Schubert Martin , Dekorsy Thomas
Published: March 2016

The study of surface modes in phononic crystal waveguides in the hypersonic regime is a burgeoning field with a large number of possible applications. By using the finite element method, the band structure and the corresponding transmission spectrum of surface acoustic waves in phononic crystal waveguides generated by line defects in a silicon pillar-substrate system were calculated and investigated. The bandgaps are caused by the hybridization effect of band branches induced by local resonances and propagating modes in the substrate. By changing the sizes of selected pillars in the phononic crystal waveguides, the corresponding bands shift and localized modes emerge due to the local resonance effect induced by the pillars. This effect offers further possibilities for tailoring the propagation and filtering of elastic waves. The presented results have implications for the engineering of phonon dynamics in phononic nanostructures.
Intrinsic thermal conductivities and size effect of alloys of wurtzite AlN, GaN, and InN from first-principles
Authors: Ma Jinlong , Li Wu , Luo Xiaobing
Published: March 2016

Despite the fact the alloys of wurtzite AlN, GaN, and InN are widely used in electronics, the studies on their thermal conductivities (κ) are inadequate, and the intrinsic limits are still unknown. In this work, the intrinsic κ of alloys and their films are calculated from first-principles within the virtual crystal treatment. The κ of alloys are strongly suppressed even by a small amount of alloying. For instance, with only 1% alloying of Al or In, κ of GaN decreases about 60%. At relatively high alloying, with concentration between 0.2 and 0.8, the κ of alloys are not significantly changed. At room temperature, the minimal a-axis κ are about 18, 22, and 8 W m−1 K−1, while the minimal c-axis κ are about 22, 27, and 10 W m−1 K−1 for AlxGa1−xN, InxGa1−xN, and InxAl1−xN, respectively. The size effect in films can persist up to a few tens of micrometers, and κ can be reduced by half in about 100 nm thick films.
Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment
Authors: Kawai Kotaro , Sakamoto Moritsugu , Noda Kohei , Sasaki Tomoyuki , Kawatsuki Nobuhiro , Ono Hiroshi
Published: March 2016

A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams. These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.
Generation of scalable terahertz radiation from cylindrically focused two-color laser pulses in air
Authors: Kuk D. , Yoo Y. J. , Rosenthal E. W. , Jhajj N. , Milchberg H. M. , Kim K. Y.
Published: March 2016

We demonstrate scalable terahertz (THz) generation by focusing terawatt, two-color laser pulses in air with a cylindrical lens. This focusing geometry creates a two-dimensional air plasma sheet, which yields two diverging THz lobe profiles in the far field. This setup can avoid plasma-induced laser defocusing and subsequent THz saturation, previously observed with spherical lens focusing of high-power laser pulses. By expanding the plasma source into a two-dimensional sheet, cylindrical focusing can lead to scalable THz generation. This scheme provides an energy conversion efficiency of 7 × 10−4, ∼7 times better than spherical lens focusing. The diverging THz lobes are refocused with a combination of cylindrical and parabolic mirrors to produce strong THz fields (>21 MV/cm) at the focal point.
Private general paediatric care availability in Melbourne
Authors: Kunin Marina , Allen Amy R. , Nicolas Caroline , Freed Gary L.
Published: March 2016

Objective The aims of the present study were to determine the actual availability of private general paediatric appointments in the Melbourne metropolitan region for children with non-urgent chronic illnesses and the cost of such care. Methods A ‘secret shopper’ method was used. Telephone calls were made to a random sample of 47 private paediatric clinics. A trained research assistant posed as a parent, requesting the first available appointment with a specific paediatrician. Data regarding appointment availability, total potential charges and net charges after the Medicare rebate were collected. Results Appointments were available in 79% (n = 37) of clinics, with 72% (n = 34) able to offer an appointment with the requested general paediatrician. The number of days until available appointments varied from same day appointments to a wait of 124 days, with an average wait of 33 days. Of practices that provided information about the appointment cost (n = 42), five bulk-billed for the consultation, whereas the remainder (n = 37) were fee-paying clinics. The potential maximum charge for an initial consultation in the fee-paying clinics ranged from A$177 to A$430, with an average cost of A$279. The potential maximum out-of-pocket cost for patients ranged from A$40 to A$222, with an average out-of-pocket cost of A$128. Conclusions Private paediatric care in the Melbourne metropolitan region is generally available. The out-of-pocket cost of private paediatric out-patient care may present a potential economic barrier for some families. What is known about the topic? In Australia, out-of-pocket expenses for private specialist care are not covered by private health insurance. There are no data available on the actual cost of private paediatric consultations that are based on real-time assessments. Data collected in 1998 suggested that the average waiting time for a first standard consultation with a general paediatrician in a private room was 14.1 days. There are no recent empirical data on appointment availability and waiting time for appointments with general paediatricians in Australia. What does this paper add? There is high availability of paediatric consultations in the private sector. Waiting times for an appointment vary considerably from same day appointments to a wait of 124 days, with an average wait of 33 days. The cost of a private paediatric consultation in Australia to the patient is considerable, with an average potential maximum up-front charge for an initial consultation of A$279 and an average potential maximum out-of-pocket cost of A$128. What are the implications for practitioners? Data on the availability and cost of private paediatric consultations are imperative to formulate evidence-informed policy and better understand variations in the availability of public and private care.
The use of walk over weigh to predict calving date in extensively managed beef herds
Authors: Aldridge Michael N. , Lee Stephen J. , Taylor Julian D. , Popplewell Greg I. , Job Fergus R. , Pitchford Wayne S.
Published: March 2016

Beef cattle reproductive rate in northern Australia is low and substantial effort is underway to make improvements. Collection of calf birth date to inform female reproductive rate data is often not practical. Therefore, there is a need to find alternative methods for collecting birth date data. The aim of the project was to trial an automated animal weighing technology (walk over weigh) to estimate calving date for cows in a northern breeding herd grazing in an extensive pasture system. Two-hundred and thirty-two Wagyu cows from a herd of 1195 with confirmed pregnancy tests were stocked in a paddock with a walk over weigh unit at the entry point of the water yard. Each calf born in the paddock was weighed, ear-tagged and a DNA sample collected. After processing, cleaning and smoothing the data, weight profiles of the 232 cows over a 119-day period were analysed. From the weight profiles and confirmed DNA parentage, 96 out of a possible 162 (59%) cows that calved had a correct calving date prediction. It is proposed that improvements in calving date prediction could be increased through engineering changes designed to slow cow movement over the walk over weigh unit. The trial demonstrated with the proposed changes that walk over weigh could be used to estimate calving date in extensive beef herds, with the expectation that this information could be used in genetic evaluation to improve reproductive rate in northern Australia.
Comparison of aquaporin-1 expression between yak (Bos grunniens) and indigenous cattle (Bos taurus) in the Qinghai–Tibetan Plateau
Authors: Zhong C. L. , Kang J. P. , Stewart G. S. , Zhou J. W. , Huang X. D. , Mi J. D. , Liu J. , Yang C. , Zhang Y. , Long R. J.
Published: March 2016

Aquaporins (AQPs) are a large family of integral membrane proteins that facilitate the transport of water through the biomembranes. AQP1, one of the 13 AQPs identified in mammals, is distributed in various tissues and organs, and plays an important role in body water homeostasis. The objectives of the present study were to identify the expression of aquaporin-1 (AQP1) in the kidney, rumen and parotid gland of yaks, and to quantify whether the protein abundance of AQP1 is species specific between yak (Bos grunniens) and indigenous cattle (Bos taurus). Three 3-year-old castrated males (156 ± 6.8 kg of bodyweight) of each of three genotypes, namely, yak, indigenous cattle and the crossbred between the two (Bos taurus♂ × Bos grunniens♀), were used; all animals were grazed in the same autumn pasture of the Qinghai–Tibetan Plateau, China. Western blot results detected (1) 28-kDa unglycosylated AQP1 in the kidney, rumen and parotid gland of all three genotypes, 40-kDa glycosylated AQP1 in renal cortex and medulla. (2) Yaks expressed less 28-kDa AQP1 protein in the outer cortex (P < 0.05), significantly more in the outer medulla (P < 0.01), and slightly more in the ventral rumen (P = 0.088) than did cattle. No difference was observed in the dorsal rumen and parotid gland (P > 0.10). In conclusion, the present study is the first to confirm the presence of AQP1 in bovine rumen and parotid gland and identified its expression in yaks. Abundance of AQP1 protein in yak kidney showed some difference from indigenous cattle. This could provide a new perspective to explain some adaptive mechanisms of yaks to the harsh environment in the Qinghai–Tibetan Plateau.
Differential volume regulation and calcium signaling in two ciliary body cell types is subserved by TRPV4 channels
Authors: Jo Andrew O. , Lakk Monika , Frye Amber M. , Phuong Tam T. T. , Redmon Sarah N. , Roberts Robin , Berkowitz Bruce A. , Yarishkin Oleg , Križaj David
Published: March 2016

Significance

The secretion of aqueous humor from the ciliary body is regulated by osmotic gradients, yet the mechanism through which these cells sense these gradients is still under debate. We have identified the calcium-permeable transient receptor potential vanilloid isoform 4 (TRPV4) ion channel as critical for translating hypotonic stimuli into intracellular signals and linked the activation of this channel to a known proinflammatory lipid signaling pathway. The channel was confined to nonpigmented cells that secrete aqueous fluid and regulate intraocular pressure. Thus, activation of TRPV4 may contribute to vision through metabolic support of anterior eye tissues and regulation of osmotic and tensile homeostasis within the eye.
Assessing the sensitivity of diffusion MRI to detect neuronal activity directly
Authors: Bai Ruiliang , Stewart Craig V. , Plenz Dietmar , Basser Peter J.
Published: March 2016

Significance

Diffusion functional MRI has been proposed as a noninvasive neuroimaging method to detect neuronal activity more directly than current blood-oxygen-level-dependent functional MRI, yet initial findings have proven difficult to interpret and reproduce. Here, we study the direct relationship between water diffusion and neuronal activity by simultaneously imaging intracellular calcium using fluorescence along with diffusion MR acquisitions from organotypic rat brain cortex cultures. Although we found that diffusion MR methods can follow the pathological time course of hyperexcitability, e.g., as those seen in epilepsy, they do not appear to be sensitive or specific enough to detect or follow normal neuronal activity.
Unique coupling of mono- and dioxygenase chemistries in a single active site promotes heme degradation
Authors: Matsui Toshitaka , Nambu Shusuke , Goulding Celia W. , Takahashi Satoshi , Fujii Hiroshi , Ikeda-Saito Masao
Published: March 2016

Significance

Oxygenases are classified into two groups, mono- and dioxygenases, which, respectively, catalyze insertion of one and two oxygen atoms of O2into substrates. These two modes of oxygenation proceed through distinct reaction mechanisms and require totally different active site structures. For more than 60 years, oxygenase enzymes thus far have been found to catalyze either a mono- or dioxygenation reaction. This study has broken this paradigm as it clearly demonstrates that the heme-degrading enzyme fromMycobacterium tuberculosis, MhuD, catalyzes successive mono- and dioxygenation reactions within its single active site. This unprecedented bifunctionality of the single active center rationally explains the unique heme catabolites of MhuD, which have been proposed to meet the physiological demands of the pathogenic bacterium.
Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles
Authors: Julien Olivier , Zhuang Min , Wiita Arun P. , O’Donoghue Anthony J. , Knudsen Giselle M. , Craik Charles S. , Wells James A.
Published: March 2016

Significance

Caspases, a family of 12 proteases involved in irreversible cell state changes including cell death, often cleave common substrates. However, we show here by quantitative N-terminomics MS, for caspase-2 and caspase-6, that the rates of substrate cleavage vary more than 500-fold in cellular lysate. The rates of cleavage show virtually no correlation among common substrates for these two caspases, as well as for three other caspases previously studied: caspase-3, caspase-7, and caspase-8. These global and unbiased studies reveal a greater degree of substrate hierarchy and specialized functions for caspases than previously appreciated. We believe this quantitative approach is of general use to other proteases and enzymes involved in posttranslational modifications to better define their roles.
Putative oncogene
Brachyury
(
T
) is essential to specify cell fate but dispensable for notochord progenitor proliferation and EMT
Authors: Zhu Jianjian , Kwan Kin Ming , Mackem Susan
Published: March 2016

Significance

The notochord is a rod of axial mesoderm that secretes signals that induce formation of vertebrae from somitic mesoderm during embryogenesis. This paper uses genetic approaches in a mouse model to remove function of the
Brachyury
(
T
) transcription factor from notochord precursor cells, which show that T regulates notochord cell fate and is consequently essential for normal spine formation. However, progenitor cells deprived of T survive and adopt neural and mesenchymal fates. They proliferate at a high rate and can adopt a mesenchymal morphology, features associated with aggressive behavior in tumors. These results raise concern about appropriate rationales to therapeutically target T in chordomas, sarcomas that arise from notochord rests, as well as other cancers expressing T.
Development and Evaluation of Two Instruments for Assessing Screening, Brief Intervention, and Referral to Treatment (SBIRT) Competency
Authors: Pringle Janice L. , Seale J. Paul , Shellenberger Sylvia , Grasso Kim M. , Kowalchuk Alicia , Laufman Larry , Bray James H. , Aldridge Arnie
Published: March 2016

Background: Screening, brief intervention, and referral to treatment (SBIRT) is shown to be effective in identifying, intervening with, and making appropriate referrals for patients with unhealthy alcohol use. SBIRT training consists of knowledge-based and skill-based components and has increased the use of screening and intervention skills in clinical settings. This article reports on the development and evaluation of 2 SBIRT proficiency checklists for use across institutions to assess SBIRT skills in both simulated and clinical encounters. Methods: A national panel of 16 experts identified 137 discrete SBIRT skills items for the checklists. From this final list, 2 proficiency checklists were derived: the SBIRT Proficiency Checklist (SPC), composed of 22 questions for videotaped interviews, and the Clinical SBIRT Proficiency Checklist (CSPC), composed of 13 questions for direct clinical observation. An evaluation was conducted to test the reliability of the SPC and to assess the utility of the CSPC. Results: Two checklists for assessing SBIRT proficiency were developed by a collaborative workgroup. Fleiss’ kappa analyses indicated moderate agreement. In addition, faculty recorded satisfaction with the CSPC for assessing residents on their SBIRT performance during clinical encounters. Conclusions: The SPC and the CSPC are practical tools for assessing competence with SBIRT and are easily integrated as standard instruments in a wide range of training settings. Future advancements to the checklists and their evaluation include modification of the SPC rating scale to be consistent with the CSPC, developing a training program for using the checklists, and further testing to improve interrater reliability.