bluuebunny/crossref_metadata_2025 huggingface dataset:
Funneling and frustration in the energy landscapes of some designed and simplified proteins
Authors: Truong Ha H. , Kim Bobby L. , Schafer Nicholas P. , Wolynes Peter G.
Published: July 2013

We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans. Natural proteins have evolved to function as well as fold, and this is a source of energetic frustration. The sequence of Top7, on the other hand, was designed with architecture alone in mind using only native state stability as the optimization criterion. Its topology had not previously been observed in nature. Experimental studies show that the folding kinetics of Top7 is more complex than the kinetics of folding of otherwise comparable naturally occurring proteins. In this paper, we use structure prediction tools, frustration analysis, and free energy profiles to illustrate the folding landscapes of Top7 and two other proteins designed by Takada. We use both perfectly funneled (structure-based) and predictive (transferable) models to gain insight into the role of topological versus energetic frustration in these systems and show how they differ from those found for natural proteins. We also study how robust the folding of these designs would be to the simplification of the sequences using fewer amino acid types. Simplification using a five amino acid type code results in comparable quality of structure prediction to the full sequence in some cases, while the two-letter simplification scheme dramatically reduces the quality of structure prediction.
Body-fixed relativistic molecular Hamiltonian and its application to nuclear spin-rotation tensor: Linear molecules
Authors: Xiao Yunlong , Liu Wenjian
Published: July 2013

The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]10.1063/1.4797496. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR.
Exact solutions of the Navier-Stokes equations with spiral or elliptical oscillation between two infinite planes
Authors: Zhang Ming-Jie , Su Wei-Dong
Published: July 2013

Exact solutions of the Navier-Stokes equations between two infinite planes are considered, where the velocity components parallel to the planes depend linearly on two spatial coordinates, and the third component depends only on the coordinate perpendicular to the planes. A class of unsteady exact solutions is found in this form with spiral or elliptical oscillation as an eigenmode of exponential time dependence, which can be arbitrarily superposed, while the pressure and boundary conditions remain unchanged. As a specific case, the flow between two infinite rotating disks is considered, and the corresponding eigenvalue problems are numerically investigated. Multiple solutions have been taken into account under axisymmetric and non-axisymmetric distributions of pressure. The eigenvalues, which are dependent on the Reynolds number, the rotation ratio, and the pressure parameter ratio, are calculated, and the phase diagrams containing neutral curves are presented. It is shown that some axisymmetric flows between two parallel rotating disks can be associated with an added periodic oscillation at low frequency proportional to the rotation ratio and with arbitrarily large amplitude.
Dependence of the most probable and average bond rupture force on the force loading rate: First order correction to the Bell–Evans model
Authors: Sekatskii S. K. , Benedetti F. , Dietler G.
Published: July 2013

The Bell–Evans model which predicts the linear dependence of the most probable intermolecular bond rupture force on the logarithm of stretching force loading rate is usually used to discuss the dynamic force spectroscopy experiment data. This model is consistent with the Kramers' theory of the bond dissociation rate only if one presupposes an independence of the pre-exponential factors in the Kramers relation on the acting force and a linear decrease of the dissociation barrier height on this same force, and for this to be true rather special shape of the interaction landscape is required. Here, we present a first order correction to this model (first terms of corresponding Taylor expansions are taken into account), discuss its implication for the interpretation of dynamic force spectroscopy experiment data and compare our model with the Monte Carlo simulation of a specially designed single molecule dynamic force spectroscopy experiment. In addition to the most probable bond rupture force, an average rupture force values are also calculated. All approximations made and the range of applicability of the obtained results are carefully described and compared with those for some other models in the field.
On the origin of intense luminescence at 0.93 eV from multi-crystalline silicon
Authors: Krause Christoph , Mankovics Daniel , Krause Hans-Michael , Arguirov Tzanimir , Kittler Martin
Published: July 2013

Strong luminescence emission at 0.93 eV appears on some specific grain boundaries in multicrystalline silicon. The emission is generated on spots, forming irregular pattern along those grain boundaries. The spots show also strong non-radiative recombination. Fitting the temperature dependence using an Arrhenius plot indicates a level of 120 meV in the silicon band gap involved in that transition. We relate the appearance of the center to a specific dislocation network formed at slightly misoriented local Σ3 grain boundary parts.
Thermomagnetic energy harvesting with first order phase change materials
Authors: Post Alexander , Knight Chris , Kisi Erich
Published: July 2013

Two cycles of thermomagnetic generation have been compared, one with a conventional ferromagnetic material and one using a Heusler alloy undergoing a first order phase transformation. The two have been analytically compared in terms of overall thermal-to-magnetic energy conversion efficiency. In addition, a state-space model of a thermomagnetic generator has been developed and analyzed in order to compare the performance of the two in terms of response to decreased thermal difference and changes in plate separation. Both analytical calculations and simulation indicated a large difference in operational behavior between the two materials, with the Heusler alloy's behavior being characterized by latent heat and large changes in magnetism, and the ferromagnet being characterized by a smaller heat input and more gradual magnetic change. The theoretical energy conversion efficiency of the Heusler alloy was calculated to be 0.2% under an external field of 3kOe, increasing to 0.8% under a field of 15kOe. These values corresponded to 15.9% and 63.8% of the Carnot limit, respectively, and compare favorably with the conversion efficiencies of ferromagnetic materials previously used in thermomagnetic generation.
Near infrared photoluminescence from bismuth-doped nanoporous silica thin films
Authors: rong gui Sa chu , Imakita Kenji , Fujii Minoru , Bai Zhenhua , Hayashi Shinji
Published: July 2013

Photoluminescence (PL) properties of bismuth (Bi) doped porous silica thin films annealed at various temperatures and in different atmospheres were studied. The near infrared (NIR) luminescence depended strongly on the annealing atmosphere and temperature. To reveal the origin of the NIR luminescence, we performed comprehensive PL studies including steady state and time-resolved PL measurements at 8–300 K in wide excitation (250–500 nm) and detection (400–1550 nm) wavelength ranges. It was revealed that multiple Bi luminescence centers, such as Bi3+, Bi2+, Bi+, and Bi dimer, are stabilized in porous silica.
Orientation dependence of electron and phonon thermal conduction and its correlation with mechanical strength in aluminum interfaces
Authors: Samvedi Vikas , Tomar Vikas
Published: July 2013

This work presents an understanding of orientation dependence of electronic and phononic thermal conduction in Al interfaces. Focus is on quantifying the effect of interface orientation, the effect of tensile strain, and the effect of temperature on electronic and phononic thermal conduction across examined Al interfaces at temperatures ranging from 300 K to 900 K. Al being metal has free electrons as the primary source of heat carriers. Analyses indicate that the Al strength reduction with increase in temperature occurs in combination with phonon and electron thermal conductivity change. Single crystalline Al shows a direct correlation among the temperature increase, strength reduction, phonon thermal conductivity decrease, and electron thermal conductivity increase. The anisotropy and mismatch in thermal expansion at examined interfaces contributes to reduction in temperature increase associated material softening and to reductions in associated electron thermal conductance and phonon thermal conductance changes. Analyses further indicate that thermal conductivity reduction at a material interface due to tensile straining is attributed to phonon frequency range reduction caused by selective passage of long wavelength phonon through material interfaces. On the other hand, thermal conductivity reduction due to temperature increase can be attributed to anisotropy in thermal expansion and to phonon dispersion relation shape change. Based on physical observations a relation describing thermal conductivity of examined interfaces as a function of interface area and interface atom density as a function of interface orientation is proposed.
Spatio-temporal profiling of cluster mass fraction in a pulsed supersonic gas jet by frequency-domain holography
Authors: Gao Xiaohui , Arefiev Alexey V. , Korzekwa Richard C. , Wang Xiaoming , Shim Bonggu , Downer Michael C.
Published: July 2013

We present an in-depth study of a rapid, noninvasive, single-shot optical method of determining cluster mass fraction fc(r, t) at specified positions r within, and at time t after opening the valve of, a pulsed high-pressure pulsed supersonic gas jet. A ∼2 mJ, 40 fs pump pulse ionizes the monomers, causing an immediate drop in the jet's refractive index njet proportional to monomer density, while simultaneously initiating hydrodynamic expansion of the clusters. The latter leads to a second drop in njet that is proportional to cluster density and is delayed by ∼1 ps. A temporally stretched probe pulse measures the 2-step index evolution in a single shot by frequency-domain holography, enabling recovery of fc. We present a model for recovering fc from fs-time-resolved phase shifts. We also present extensive measurements of spatio-temporal profiles fc(r,t) of cluster mass fraction in a high-pressure supersonic argon jet for various values of backing pressure P0 and reservoir temperature T0.
Dielectric response of transformer oil based ferrofluid in low frequency range
Authors: Rajnak M. , Kurimsky J. , Dolnik B. , Marton K. , Tomco L. , Taculescu A. , Vekas L. , Kovac J. , Vavra I. , Tothova J. , Kopcansky P. , Timko M.
Published: July 2013

In this article, our experimental study of the dynamic dielectric behaviour of transformer oil-based ferrofluid with magnetite nanoparticles is presented. Frequency-dependent dielectric permittivity and dissipation factor were measured within the frequency range from 20 Hz to 2 MHz by a capacitance method. The ferrofluid samples were placed in a liquid crystal cell, and experiments were carried out in an electromagnetically anechoic chamber. Two polarization processes and corresponding relaxations were revealed within the applied frequency range. Schwarz theory of electric double layer polarization is used to explain the low frequency relaxation maximum. Moreover, the shift of the maximum position towards higher frequencies is observed as the magnetic volume fraction in the ferrofluid increases. The related decrease in relaxation time due to higher counterion mobility is analysed. Reduced electric field intensity due to depolarization field, which is dependent on the particle concentration, is proposed as the reason for the maxima shift. This assumption is wholly supported by a complementary experiment.
Control of silicon nanoparticle size embedded in silicon oxynitride dielectric matrix
Authors: Ehrhardt F. , Ferblantier G. , Muller D. , Ulhaq-Bouillet C. , Rinnert H. , Slaoui A.
Published: July 2013

In this study, silicon rich silicon oxynitride layers containing more than 15% nitrogen were deposited by electron cyclotron resonance assisted plasma enhanced vapor deposition in order to form silicon nanoparticles after a high temperature thermal annealing. The effect of the flows of the precursor gases on the composition and the structural properties of the layers was assessed by Rutherford backscattering spectroscopy, elastic recoil detection analysis, and infrared spectroscopic measurements. The morphological and crystallinity properties were investigated by energy filtered transmission electron microscopy and Raman spectroscopy. We show that the excess of silicon in the silicon oxynitride layer controls the silicon nanoparticles size. On the other hand, the crystalline fraction of particles is found to be strongly correlated to the nanoparticle size. Finally, the photoluminescence measurements show that it is also possible to tune the photoluminescence peak position between 400 and 800 nm and its intensity by changing the silicon excess in the silicon rich silicon oxynitride matrix.
Tuning the formation of p-type defects by peroxidation of CuAlO2 films
Authors: Luo Jie , Lin Yow-Jon , Hung Hao-Che , Liu Chia-Jyi , Yang Yao-Wei
Published: July 2013

p-type conduction of CuAlO2 thin films was realized by the rf sputtering method. Combining with Hall, X-ray photoelectron spectroscopy, energy dispersive spectrometer, and X-ray diffraction results, a direct link between the hole concentration, Cu vacancy (VCu), and interstitial oxygen (Oi) was established. It is shown that peroxidation of CuAlO2 films may lead to the increased formation probability of acceptors (VCu and Oi), thus, increasing the hole concentration. The dependence of the VCu density on growth conditions was identified for providing a guide to tune the formation of p-type defects in CuAlO2. Understanding the defect-related p-type conductivity of CuAlO2 is essential for designing optoelectronic devices and improving their performance.
Elastic and elasto-optical properties of triglycine-zinc chloride crystal
Authors: Tylczyński Z. , Trzaskowska A.
Published: July 2013

The behaviours of bulk phonons propagating in triglycine-zinc chloride (Gly3-ZnCl2) single crystal for different polarizations of the incident and scattered beams were studied by Brillouin spectroscopy. All components of the elastic and elasto-optical tensors were determined at room temperature. Dependences of the velocities of quasi-longitudinal, transverse, and quasi-transverse phonons propagating in the planes (110), (101), and (011) on the direction of propagation are presented.
Characterization of Fe-N nanocrystals and nitrogen–containing inclusions in (Ga,Fe)N thin films using transmission electron microscopy
Authors: Kovács A. , Schaffer B. , Moreno M. S. , Jinschek J. R. , Craven A. J. , Dietl T. , Bonanni A. , Dunin-Borkowski R. E.
Published: July 2013

Nanometric inclusions filled with nitrogen, located adjacent to FenN (n = 3 or 4) nanocrystals within (Ga,Fe)N layers, are identified and characterized using scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). High-resolution STEM images reveal a truncation of the Fe-N nanocrystals at their boundaries with the nitrogen-containing inclusions. A controlled electron beam hole drilling experiment is used to release nitrogen gas from an inclusion in situ in the electron microscope. The density of nitrogen in an individual inclusion is measured to be 1.4 ± 0.3 g/cm3. These observations provide an explanation for the location of surplus nitrogen in the (Ga,Fe)N layers, which is liberated by the nucleation of FenN (n > 1) nanocrystals during growth.
Work function modulation of bilayer MoS2 nanoflake by backgate electric field effect
Authors: Li Yang , Xu Cheng-Yan , Zhang Bao-You , Zhen Liang
Published: July 2013

We report the work function modulation of bilayer MoS2 nanoflake induced by backgate electric filed. The Fermi level of bilayer MoS2 increased by 115 meV with the backgate bias larger than the threshold voltage. Carrier doping induced by the electric filed was responsible for the variation of work function of MoS2 nanoflake. Meanwhile, asymmetric contact potential drops at electrical contacts were observed, which was consistent with the asymmetric electrical output characteristics. Thermonic field emission theory was used to explain the carrier transport mechanism between Pt and bilayer MoS2, and the larger contact barriers led to the lower carrier mobility.
AlN-based piezoelectric micromachined ultrasonic transducer for photoacoustic imaging
Authors: Chen Bingzhang , Chu Futong , Liu Xingzhao , Li Yanrong , Rong Jian , Jiang Huabei
Published: July 2013

We report on the fabrication of a piezoelectric micromachined ultrasonic transducer (pMUT) and its application to photoacoustic imaging. With c-axis orientation, AlN was grown on a 300 nm-thick SiO2 film and a 200 nm-thick bottom electrode at room temperature. The device consists of SiO2, bottom electrode, AlN films, upper electrode, and polyimide protective layer. An area ratio of 0.45 was used between the upper electrode and the vibration area of the pMUT to provide an optimal sensitivity of transducer. Its resonant frequency was measured to be 2.885 MHz, and the coupling coefficient in the range of 2.38%–3.71%. The fabricated pMUT was integrated with a photoacoustic imaging system and photoacoustic image of a phantom was obtained. The resolution of the system was measured to be about 240 μm.
Role of point defects and HfO2/TiN interface stoichiometry on effective work function modulation in ultra-scaled complementary metal–oxide–semiconductor devices
Authors: Pandey R. K. , Sathiyanarayanan Rajesh , Kwon Unoh , Narayanan Vijay , Murali K. V. R. M.
Published: July 2013

We investigate the physical properties of a portion of the gate stack of an ultra-scaled complementary metal-oxide-semiconductor (CMOS) device. The effects of point defects, such as oxygen vacancy, oxygen, and aluminum interstitials at the HfO2/TiN interface, on the effective work function of TiN are explored using density functional theory. We compute the diffusion barriers of such point defects in the bulk TiN and across the HfO2/TiN interface. Diffusion of these point defects across the HfO2/TiN interface occurs during the device integration process. This results in variation of the effective work function and hence in the threshold voltage variation in the devices. Further, we simulate the effects of varying the HfO2/TiN interface stoichiometry on the effective work function modulation in these extremely-scaled CMOS devices. Our results show that the interface rich in nitrogen gives higher effective work function, whereas the interface rich in titanium gives lower effective work function, compared to a stoichiometric HfO2/TiN interface. This theoretical prediction is confirmed by the experiment, demonstrating over 700 meV modulation in the effective work function.
Formation of nickel-platinum silicides on a silicon substrate: Structure, phase stability, and diffusion from ab initio computations
Authors: Christensen M. , Eyert V. , Freeman C. , Wimmer E. , Jain A. , Blatchford J. , Riley D. , Shaw J.
Published: July 2013

The formation of Ni(Pt)silicides on a Si(001) surface is investigated using an ab initio approach. After deposition of a Ni overlayer alloyed with Pt, the calculations reveal fast diffusion of Ni atoms into the Si lattice, which leads initially to the formation of Ni2Si. At the same time, Si atoms are found to diffuse into the metallic overlayer. The transformation of Ni2Si into NiSi is likely to proceed via a vacancy-assisted diffusion mechanism. Silicon atoms are the main diffusing species in this transformation, migrating from the Si substrate through the growing NiSi layer into the Ni2Si. Pt atoms have a low solubility in Ni2Si and prefer Si-sites in the NiSi lattice, thereby stabilizing the NiSi phase. The diffusivity of Pt is lower than that of Ni. Furthermore, Pt atoms have a tendency to segregate to interfaces, thereby acting as diffusion barriers.
Quasi-equilibrium size distribution of subcritical nuclei in amorphous phase change AgIn-Sb2Te
Authors: Darmawikarta Kristof , Lee Bong-Sub , Shelby Robert M. , Raoux Simone , Bishop Stephen G. , Abelson John R.
Published: July 2013

We investigate the effect of low temperature annealing or of extended storage at room temperature on the subsequent nucleation behavior of amorphous AgIn-incorporated Sb2Te (AIST), a material for phase change memories. Time-resolved reflectivity measurements during pulsed laser crystallization reveal the rates of solid-phase transformation, while fluctuation transmission electron microscopy detects the nanoscale order in the amorphous phase prior to crystallization. The nanoscale order is postulated to consist of subcritical nuclei that coarsen upon annealing at temperatures ranging from 25 °C (for months) or 100 °C (for hours). Samples that have been annealed remain fully amorphous as evaluated by conventional diffraction experiments. Shorter nucleation times are consistently associated with the observation of increased nanoscale order. The effect of annealing is observed to saturate: there is no further reduction in nucleation time or increase in nanoscale order for annealing at 100 °C beyond three hours. This result supports the general prediction of classical nucleation theory that the size distribution of subcritical nuclei increases from the as-deposited state to a quasi-equilibrium.
Electronic properties of doped magnesium thioindate ternary spinel in the normal and in the inverse structure
Authors: Tablero C.
Published: July 2013

We present a theoretical study of the structural and electronic properties of the M-doped MgIn2S4 ternary spinel semiconductor with M = V, Cr, and Mn. All substitutions, in the normal and in the inverse structure, are analyzed. Some of these possible substitutions present intermediate-band states in the band gap with a different occupation for a spin component. It increases the possibilities of inter-band transitions and could be interesting for applications in optoelectronic devices. The contribution to, and the electronic configuration of, these intermediate bands for the octahedral and tetrahedral sites is analyzed and discussed. The study of the substitutional energies indicates that these substitutions are favorable. Comparison between the pure and doped host's absorption coefficients shows that this deeper band opens up more photon absorption channels and could therefore increase the solar-light absorption with respect to the host.
In situ laser annealing during growth of Pb(Zr0.52Ti0.48)O3 thin films
Authors: Rajashekhar Adarsh , Fox Austin , Bharadwaja S. S. N. , Trolier-McKinstry Susan
Published: July 2013

A pulsed laser deposition system with in situ laser annealing was utilized to grow Pb(Zr0.52Ti0.48)O3 thin films on a laser crystallized Pb(Zr0.20Ti0.80)O3 seed layer, at a temperature of ∼370 °C. Polycrystalline 1.1 μm thick films exhibited columnar grains with small grain sizes (∼30 nm). The films showed well-saturated hysteresis loops (with ∼25 μC/cm2 remanent polarization, ∼50 kV/cm coercive field) and exhibited loss tangents <2.5% with a permittivity of ∼730. Film orientation could be controlled via the substrate choice; {111} Pb(Zr0.52Ti0.48)O3 films were grown on oriented (111) Pb(Zr0.30Ti0.70)O3 sol-gel seed layers, while {001} films were prepared on (100) SrTiO3 single crystals.
Columns formed by multiple twinning in nickel layers—An approach of grain boundary engineering by electrodeposition
Authors: Alimadadi Hossein , Bastos Fanta Alice , Somers Marcel A. J. , Pantleon Karen
Published: July 2013

Complementary microscopic and diffraction based methods revealed a peculiar microstructure of electrodeposited nickel. For the as-deposited layer, thus, without any additional treatment, multiple twinning yields a high population of Σ3n boundaries, which interrupts the network of normal high angle grain boundaries. A peculiar arrangement of Σ3 boundaries forming five-fold junctions is observed. The resulting microstructure meets the requirements for grain boundary engineering. Twinning induced effects on the crystallographic orientation of grains result in one major texture component being a ⟨210⟩ fiber axis and additional minor orientations originating from first and second generation twins of ⟨210⟩, i.e., ⟨542⟩ and ⟨20 2 1⟩.
Effects of graphene thickness on the electrical properties of carbon nanotube field effect transistors with graphene contacts
Authors: Tamaoki Masato , Kishimoto Shigeru , Mizutani Takashi
Published: July 2013

We have studied the effects of the thickness of the graphene on the current-voltage characteristics of the carbon nanotube field effect transistors (CNT-FETs) with graphene contacts. It was shown that the CNT-FETs with thin graphene contacts showed larger drain ON current and transconductance than those of the devices with the thick graphene contacts. The result was explained by the inter-graphene resistance which dominates the contact resistance of the CNT-FETs with the graphene contacts. The inter-graphene resistance was estimated to be 2.2 Ω · cm2 from the extrinsic transconductance of the devices.
Dynamics of photoexcited carriers in the presence of disorder in radial heterostructured GaAs/AlGaAs/GaAs nanowires
Authors: Guimarães F. E. G. , Caface R. A. , Arakaki H. , de Souza C. A. , Pusep Yu. A.
Published: July 2013

Time-resolved photoluminescence was employed to study electron-hole dynamics in radial heterostructured GaAs/AlGaAs/GaAs core/inner shell/outer shell nanowires. It was found that impurity random potential results in a red shift of the recombination time maximum with respect to the photoluminescence peak energy.
Evanescently coupled optomechanical system with SiN nanomechanical oscillator and deformed silica microsphere
Authors: Oo Thein , Dong Chunhua , Fiore Victor , Wang Hailin
Published: July 2013

An evanescently coupled optomechanical system is developed, in which a SiN nanomechanical oscillator couples to the evanescent field of whispering gallery optical modes in a slightly deformed silica microsphere. The evanescent optomechanical coupling length varies strongly along the whispering gallery optical path, with the maximum coupling length nearly three times that of a regular optical resonator. The deformed resonator also allows efficient free-space evanescent excitation of whispering gallery optical modes. These unique features enable a relatively simple and robust implementation of evanescently coupled optomechanical systems.
Graphitization of amorphous carbon and its transformation pathways
Authors: Loh G. C. , Baillargeat D.
Published: July 2013

The graphitic ordering of the amorphous state of carbon has been a long-standing challenge. Whilst there are numerous transformation methodologies, including the high-temperature-pressure approach, there are still many unclear elements concerning the mechanism. By employing classical molecular dynamics simulations, the process of graphitization of amorphous carbon is modelled and analyzed. A systematic study of various schemes of loading conditions suggests that (1) axial strain is a vital ingredient in the transformation, and (2) there exists a close relationship between the mean layer atomic density of the amorphous carbon structure and the graphitization process. Furthermore, the non-simultaneity (i.e., in a delayed manner) of structure loading (by high-temperature annealing and straining) promotes a greater extent of graphitization, as compared to a concurrent means. More interestingly, edge and non-edge bonds behave dissimilarly in response to a change in the atomic density, and graphitization prevails at different stages of the fast and slow loading schemes. Virial pressure calculations validate the structural stability.
Bomb radiocarbon dating of the endangered white abalone (Haliotis sorenseni): investigations of age, growth and lifespan
Authors: Andrews Allen H. , Leaf Robert T. , Rogers-Bennett Laura , Neuman Melissa , Hawk Heather , Cailliet Gregor M.
Published: July 2013

Understanding basic life-history characteristics of white abalone (Haliotis sorenseni), such as estimated lifespan, is critical to making informed decisions regarding the recovery of this endangered species. All predictive modelling tools used to forecast the status and health of populations following restoration activities depend on a validated estimate of adult lifespan. Of the seven Haliotis species in California, white abalone is considered to have the highest extinction risk and was the first marine invertebrate listed as an endangered species under the Federal Endangered Species Act (ESA). Lifespan was previously estimated from observations of early growth; however, no study has generated ages for the largest white abalone. To address questions of age and growth, bomb radiocarbon (Δ14C) dating was used on shells from large white abalone. Measured bomb Δ14C levels were compared to regional Δ14C reference records to provide estimates of age, growth and lifespan. Bomb radiocarbon dating indicated that growth was variable among individuals, with a maximum estimated age of 27 years. The findings presented here provide support for previous age and growth estimates and an estimated lifespan near 30 years. These age data support the perception of a critical need for restoring the remnant aging and potentially senescent population.
Learning from the implementation of inter-organisational web-based care planning and coordination
Authors: Walker Rae , Blacker Vivian , Pandita Linda , Close Jacky , Mason Wendy , Watson Julie
Published: July 2013

In Victoria, despite strong policy support, e-care planning and coordination is poorly developed. The action research project discussed here was developed to overcome organisational and worker-level barriers to change. The project outcomes highlighted the need for work on the building blocks of e-care coordination that enhance workers’ knowledge and skills, and provide permission and support for appropriate collaborative system and services coordination practices.
Proton transfer through the water gossamer
Authors: Hassanali Ali , Giberti Federico , Cuny Jérôme , Kühne Thomas D. , Parrinello Michele
Published: July 2013

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.
SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules
Authors: Maier Josef , Adzhubei Alexei A. , Egge-Jacobsen Wolfgang
Published: July 2013

Summary: Functional modules within protein sequences are often extracted by consensus sequence patterns representing a linear motif; however, other functional regions may only be described by combined features such as amino acid composition, profiles of amino acid properties and randomly distributed short sequence motifs. If only a small number of functional examples are well characterized, the researcher needs a tool to extract similar sequences for further investigation.

Availability and Implementation: We provide the web application ‘SAPA tool’, which allows the user to search with combined properties, ranks the extracted target regions by an integrated score, estimates false discovery rates by using decoy sequences and provides them as a sequence file or spreadsheet. Source code, user manual and the web application implemented in Perl, HTML, CSS and JavaScript and running on Apache are freely available at http://sapa-tool.uio.no/sapa/

Contact:  josef.maier@istls.de or w.m.egge-jacobsen@imbv.uio.no

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tiki, at the head of a new superfamily of enzymes
Authors: Sanchez-Pulido Luis , Ponting Chris P.
Published: July 2013

Summary: Tiki proteins appear to antagonize Wnt signalling pathway by acting as Wnt proteases, thereby affecting Wnt solubility by its amino-terminal cleavage. Tiki1 protease activity was shown to be metal ion-dependent and was inhibited by chelating agents and thus was tentatively proposed to be a metalloprotease. Nevertheless, Tiki proteins exhibit no detectable sequence similarity to previously described metalloproteases, but instead have been reported as being homologues of TraB proteins (Pfam ID: PF01963), a widely distributed family of unknown function and structure. Here, we show that Tiki proteins are members of a new superfamily of domains contained not just in TraB proteins, but also in erythromycin esterase (Pfam ID: PF05139), DUF399 (domain of unknown function 399; Pfam ID: PF04187) and MARTX toxins that contribute to host invasion and pathogenesis by bacteria. We establish the core fold of this enzymatic domain and its catalytic residues.

Contact:  luis.sanchezpulido@dpag.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
ATR phosphorylates SMARCAL1 to prevent replication fork collapse
Authors: Couch Frank B. , Bansbach Carol E. , Driscoll Robert , Luzwick Jessica W. , Glick Gloria G. , Bétous Rémy , Carroll Clinton M. , Jung Sung Yun , Qin Jun , Cimprich Karlene A. , Cortez David
Published: July 2013

The DNA damage response kinase ataxia telangiectasia and Rad3-related (ATR) coordinates much of the cellular response to replication stress. The exact mechanisms by which ATR regulates DNA synthesis in conditions of replication stress are largely unknown, but this activity is critical for the viability and proliferation of cancer cells, making ATR a potential therapeutic target. Here we use selective ATR inhibitors to demonstrate that acute inhibition of ATR kinase activity yields rapid cell lethality, disrupts the timing of replication initiation, slows replication elongation, and induces fork collapse. We define the mechanism of this fork collapse, which includes SLX4-dependent cleavage yielding double-strand breaks and CtIP-dependent resection generating excess single-stranded template and nascent DNA strands. Our data suggest that the DNA substrates of these nucleases are generated at least in part by the SMARCAL1 DNA translocase. Properly regulated SMARCAL1 promotes stalled fork repair and restart; however, unregulated SMARCAL1 contributes to fork collapse when ATR is inactivated in both mammalian and Xenopus systems. ATR phosphorylates SMARCAL1 on S652, thereby limiting its fork regression activities and preventing aberrant fork processing. Thus, phosphorylation of SMARCAL1 is one mechanism by which ATR prevents fork collapse, promotes the completion of DNA replication, and maintains genome integrity.
Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states
Authors: Pontvianne Frederic , Blevins Todd , Chandrasekhara Chinmayi , Mozgová Iva , Hassel Christiane , Pontes Olga M.F. , Tucker Sarah , Mokroš Petr , Muchová Veronika , Fajkus Jiří , Pikaard Craig S.
Published: July 2013

Eukaryotes can have thousands of 45S ribosomal RNA (rRNA) genes, many of which are silenced during development. Using fluorescence-activated sorting techniques, we show that active rRNA genes in Arabidopsis thaliana are present within sorted nucleoli, whereas silenced rRNA genes are excluded. DNA methyltransferase (met1), histone deacetylase (hda6), or chromatin assembly (caf1) mutants that disrupt silencing abrogate this nucleoplasmic–nucleolar partitioning. Bisulfite sequencing data indicate that active nucleolar rRNA genes are nearly completely demethylated at promoter CGs, whereas silenced genes are nearly fully methylated. Collectively, the data reveal that rRNA genes occupy distinct but changeable nuclear territories according to their epigenetic state.
GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination
Authors: Ginno Paul A. , Lim Yoong Wearn , Lott Paul L. , Korf Ian , Chédin Frédéric
Published: July 2013

Strand asymmetry in the distribution of guanines and cytosines, measured by GC skew, predisposes DNA sequences toward R-loop formation upon transcription. Previous work revealed that GC skew and R-loop formation associate with a core set of unmethylated CpG island (CGI) promoters in the human genome. Here, we show that GC skew can distinguish four classes of promoters, including three types of CGI promoters, each associated with unique epigenetic and gene ontology signatures. In particular, we identify a strong and a weak class of CGI promoters and show that these loci are enriched in distinct chromosomal territories reflecting the intrinsic strength of their protection against DNA methylation. Interestingly, we show that strong CGI promoters are depleted from the X chromosome while weak CGIs are enriched, a property consistent with the acquisition of DNA methylation during dosage compensation. Furthermore, we identify a third class of CGI promoters based on its unique GC skew profile and show that this gene set is enriched for Polycomb group targets. Lastly, we show that nearly 2000 genes harbor GC skew at their 3′ ends and that these genes are preferentially located in gene-dense regions and tend to be closely arranged. Genomic profiling of R-loops accordingly showed that a large proportion of genes with terminal GC skew form R-loops at their 3′ ends, consistent with a role for these structures in permitting efficient transcription termination. Altogether, we show that GC skew and R-loop formation offer significant insights into the epigenetic regulation, genomic organization, and function of human genes.
Two polymorphs of tris(ethylenediamine)cobalt(III) tetrathioantimonate(V)
Authors: Wang Ming-Feng , Yue Cheng-Yang , Yuan Zhuang-Dong , Lei Xiao-Wu
Published: July 2013

Details of the structures of two polymorphs of tris(ethylenediamine)cobalt(III) tetrathioantimonate(V), [Co(C2H8N2)3][SbS4], are reported. The first polymorph crystallizes in the orthorhombic space groupPna21, whereas the second polymorph belongs to the tetragonal space groupP42bc. Both structures contain octahedral [Co(en)3]3+cations (en is ethylenediamine) and tetrahedral [SbS4]3−anions, which are interconnectedviavarious N—H...S hydrogen bonds to form two different types of three-dimensional network.
The zwitterionic structure of 2-hydroxy-4-[(2-hydroxybenzylidene)amino]benzoic acid
Authors: Júnior Anderson A. B. C. , De Carvalho Gustavo S. G. , Marques Lippy F. , Corrêa Charlane C. , Da Silva Adilson D. , Machado Flávia C.
Published: July 2013

The title compound, C14H11NO4, exists in the solid phase in the zwitterionic form, 2-{[(4-carboxy-3-hydroxyphenyl)iminiumyl]methyl}phenolate, with the H atom from the phenol group on the 2-hydroxybenzylidene ring transferred to the imine N atom, resulting in a strong intramolecular N—H...O hydrogen bond between the iminium H atom and the phenolate O atom, forming a six-membered hydrogen-bonded ring. In addition, there is an intramolecular O—H...O hydrogen bond between the carboxylic acid group and the adjacent hydroxy group of the other ring, and an intermolecular C—H...O contact involving the phenol group and the C—H group adjacent to the imine bond, connecting the molecules into a two-dimensional network in the (10\overline{3}) plane. π–π stacking interactions result in a three-dimensional network. This study is important because it provides crystallographic evidence, supported by IR data, for the iminium zwitterionic form of Schiff bases.
Three transition-metal complexes with the macrocyclic ligandmeso-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane (L): [Cu(ClO4)2(L)], [Zn(NO3)2(L)] and [CuCl(L)(H2O)]Cl
Authors: Yasmin Sabina , Suarez Sebastián , Doctorovich Fabio , Roy Tapashi G. , Baggio Ricardo
Published: July 2013

The three transition-metal complexes, (meso-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N)bis(perchlorato-κO)copper(II), [Cu(ClO4)2(C18H40N4)], (I), (meso-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N)bis(nitrato-κO)zinc(II), [Zn(NO3)2(C18H40N4)], (II), and aquachlorido(meso-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N)copper(II) chloride, [CuCl(C18H40N4)(H2O)]Cl, (III), are described. The molecules display a very similarly distorted 4+2 octahedral environment for the cation [located at an inversion centre in (I) and (II)], defined by the macrocycle N4group in the equatorial sites and two further ligands intrans-axial positions [two O–ClO3ligands in (I), two O–NO2ligands in (II) and one chloride and one aqua ligand in (III)]. The most significant difference in molecular shape resides in these axial ligands, the effect of which on the intra- and intermolecular hydrogen bonding is discussed. In the case of (I), all strong hydrogen-bond donors are saturated in intramolecular interactions, while weak intermolecular C—H...O contacts result in a three-dimensional network. In (II) and (III), instead, there are N—H and O—H donors left over for intermolecular interactions, giving rise to the formation of strongly linked but weakly interacting chains.
Poly[bis[μ2-3-(pyridin-4-yl)benzoato-κ3N:O,O′]lead(II)]
Authors: Guo Yi-Ping , Wang Hui , Li Guo-Ting
Published: July 2013

In the title compound, [Pb(C12H8NO2)2]n, the Pb atom sits on a crystallographicC2axis and is six-coordinate, ligated by two chelating carboxylate groups from two 3-(pyridin-4-yl)benzoate (L) ligands and by two N atoms from another two ligands. Each ligand bridges two PbIIcentres, extending the structure into a corrugated two-dimensional (4,4) net. The ligandLis conformationally chiral, with a torsion angle of 27.9 (12)° between the planes of its two rings. The torsion angle has the same sense throughout the structure, so that the extended two-dimensional polymer is homochiral. Investigation of the thermal stability shows that the network is stable up to 613 K. In the absence of any stereoselective factor in the preparation of the compound, the enantiomeric purity of the crystal studied, based only on the torsional conformation of the ligand, implies that the bulk sample is a racemic conglomerate.
Recovery strategy for group service failures
Authors: Zhou Yuanyuan , Huang Minxue , S.L. Tsang Alex , Zhou Nan
Published: July 2013

Purpose

– Consumers use cues to assess whether a recovery is effective. Prior literature on service recovery has focused mainly on individual-related factors. This paper aims to study how other consumers in the same failure and recovery influence an individual consumer to evaluate the firm
'
s recovery efforts.

Design/methodology/approach

– Two experiments were conducted. Experiment 1 tested the interaction effects between recovery modes (public vs private) and recovery dimensions (economic vs social) on an individual consumer
'
s evaluation of a recovery strategy for a group service failure. Experiment 2 investigated the complementary role of social recovery on economic compensation.

Findings

– Experiment 1 identified a significant interaction effect. Results suggest that an individual in a group service failure responds more favorably to public economic recovery than to private recovery. However, an individual
'
s reaction to social recovery follows the opposite pattern. Furthermore, in experiment 2 a complementary effect between economic recovery and social recovery was found.

Originality/value

– One potential contribution is that the paper sheds light on the issue related to the influence from other affected consumers in the same service failure and recovery situation in affected consumers
'
recovery evaluation. An individual will consider the recovery other individuals receive when he or she evaluates the recovery
'
s strategy. The paper also provides insight into the complementary use of economic and social recoveries to enhance a consumer
'
s evaluation of a firm
'
s overall recovery at a reduced cost.
The moderating effects of need for cognition on drivers of customer loyalty
Authors: Hansen Håvard , M. Samuelsen Bendik , E. Sallis James
Published: July 2013

Purpose

– While satisfaction, value, image, and credibility are commonly assumed to drive customer loyalty, there is nevertheless reason to question whether their effects vary across groups of consumers. This paper seeks to explore how individuals with contrasting need-for-cognition (NFC) levels differ in using memory-based information when forming behavioral intentions towards a current service provider.

Design/methodology/approach

– The authors tested the hypotheses by means of survey data from customers of retail banks, and applied two-group analysis using structural equation modeling (SEM) to test the moderating effects of NFC.

Findings

– Satisfaction positively affects loyalty for high NFCs, but not for low NFCs. Image is insignificant in both groups. Value positively affects loyalty for low NFCs, but not for high NFCs. Credibility has a positive effect for low NFCs, but not for high NFCs.

Research limitations/implications

– The limited sample size affects the power of the test methodology, but Chow-tests of regression models gave similar results. Further research should test the model in other contexts to enhance external validity.

Practical Implications

– To develop more effective customer strategies, both researchers and practitioners need to understand how different types of consumers attend to and utilize information when forming behavioral intentions. The standard practice of surveying customer satisfaction and loyalty typically requires the consumer to make a memory-based judgment.

Originality/value

– Previous research has primarily focused on how consumer demographics moderate satisfaction-loyalty links. This paper includes additional drivers of loyalty, and assesses moderation by a personality trait (NFC) not previously used in satisfaction-loyalty research. The results indicate that a consumer
'
s dispositional tendency to think and elaborate (more or less) can bias survey results.