bluuebunny/crossref_metadata_2025 huggingface dataset:
Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11)
Authors: Viegas Aldino , Sardinha João , Freire Filipe , Duarte Daniel F. , Carvalho Ana L. , Fontes Carlos M. G. A. , Romão Maria J. , Macedo Anjos L. , Cabrita Eurico J.
Published: January 2013

Non-catalytic cellulosomal CBMs (carbohydrate-binding modules) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligo-saccharides) and enzyme into close contact. In the present study we carried out an atomistic rationalization of the molecular determinants of ligand specificity for a family 11 CBM from thermophilic Clostridium thermocellum [CtCBM11 (C. thermocellum CBM11)], based on a NMR and molecular modelling approach. We have determined the NMR solution structure of CtCBM11 at 25°C and 50°C and derived information on the residues of the protein that are involved in ligand recognition and on the influence of the length of the saccharide chain on binding. We obtained models of the CtCBM11–cellohexaose and CtCBM11–cellotetraose complexes by docking in accordance with the NMR experimental data. Specific ligand–protein CH-π and Van der Waals interactions were found to be determinant for the stability of the complexes and for defining specificity. Using the order parameters derived from backbone dynamics analysis in the presence and absence of ligand and at 25°C and 50°C, we determined that the protein's backbone conformational entropy is slightly positive. This data in combination with the negative binding entropy calculated from ITC (isothermal titration calorimetry) studies supports a selection mechanism where a rigid protein selects a defined oligosaccharide conformation.
Palmitoylation and the trafficking of peripheral membrane proteins
Authors: Chamberlain Luke H. , Lemonidis Kimon , Sanchez-Perez Maria , Werno Martin W. , Gorleku Oforiwa A. , Greaves Jennifer
Published: January 2013

Palmitoylation, the attachment of palmitate and other fatty acids on to cysteine residues, is a common post-translational modification of both integral and peripheral membrane proteins. Dynamic palmitoylation controls the intracellular distribution of peripheral membrane proteins by regulating membrane–cytosol exchange and/or by modifying the flux of the proteins through vesicular transport systems.
Insights into the molecular evolution of oxytocin receptor ligand binding
Authors: Koehbach Johannes , Stockner Thomas , Bergmayr Christian , Muttenthaler Markus , Gruber Christian W.
Published: January 2013

The design and development of selective ligands for the human OT (oxytocin) and AVP (arginine vasopressin) receptors is a big challenge since the different receptor subtypes and their native peptide ligands display great similarity. Detailed understanding of the mechanism of OT's interaction with its receptor is important and may assist in the ligand- or structure-based design of selective and potent ligands. In the present article, we compared 69 OT- and OT-like receptor sequences with regards to their molecular evolution and diversity, utilized an in silico approach to map the common ligand interaction sites of recently published G-protein-coupled receptor structures to a model of the human OTR (OT receptor) and compared these interacting residues within a selection of different OTR sequences. Our analysis suggests the existence of a binding site for OT peptides within the common transmembrane core region of the receptor, but it appears extremely difficult to identify receptor or ligand residues that could explain the selectivity of OT to its receptors. We remain confident that the presented evolutionary overview and modelling approach will aid interpretation of forthcoming OTR crystal structures.
Coxsackievirus B transmission and possible new roles for extracellular vesicles
Authors: Inal Jameel M. , Jorfi Samireh
Published: January 2013

Coxsackievirus B1, a member of the Picornaviridae family is a non-enveloped single-stranded RNA virus associated with human diseases including myocarditis and pancreatitis. Infection of the intestinal mucosa, lined by polarized epithelial cells, requires interaction of coxsackievirus with apically located DAF (decay-accelerating factor) before transport to the basolaterally located CAR (coxsackie and adenovirus receptor), where entry is mediated by endocytosis. As with many other non-enveloped viruses, coxsackievirus has to induce lysis of host cells in order to perpetuate infection. However, recent evidence indicates that virus spread to secondary sites is not only achieved by a lytic mechanism and a non-lytic cell–cell strategy has been suggested for coxsackievirus B3. A physical interaction between infected and non-infected cells has been shown to be an efficient mechanism for retroviral transmission and one type of extracellular vesicle, the exosome, has been implicated in HIV-1 transmission. HIV-1 also takes advantage of depolymerization of actin for spread between T-cells. Calpain-mediated depolymerization of the actin cytoskeleton, as a result of increases in intracellular calcium concentration during coxsackievirus infection, would result in a release of host cell-derived microvesicles. If so, we speculate that maybe such microvesicles, increasingly recognized as major vehicles mediating intercellular communication, could play a role in the intercellular transmission of non-enveloped viruses.
Attack from both ends: mRNA degradation in the crenarchaeon Sulfolobus solfataricus
Authors: Evguenieva-Hackenberg Elena , Bläsi Udo
Published: January 2013

RNA stability control and degradation are employed by cells to control gene expression and to adjust the level of protein synthesis in response to physiological needs. In all domains of life, mRNA decay can commence in the 5′–3′ as well as in the 3′–5′-direction. Consequently, mechanisms are in place conferring protection on mRNAs at both ends. Upon deprotection, dedicated enzymes/enzyme complexes access either end and trigger 5′–3′ or 3′–5′-directional decay. In the present paper, we first briefly review the general mRNA decay pathways in Bacteria and Eukarya, and then focus on 5′–3′ and 3′–5′-directional decay in the crenarchaeon Sulfolobus solfataricus, which is executed by a RNase J-like ribonuclease and the exosome complex respectively. In addition, we describe mechanisms that stabilize mRNAs at the 5′- as well as at the 3′-end.
Chemical proteomics: a powerful tool for exploring protein lipidation
Authors: Storck Elisabeth M. , Serwa Remigiusz A. , Tate Edward W.
Published: January 2013

The study of post-translational modifications such as protein lipidation is a non-trivial challenge of the post-genomic era. In recent years the field of chemical proteomics has greatly advanced our ability to identify and quantify protein lipidation. In the present review, we give a brief overview of the tools available to study protein acylation, prenylation and cholesterylation, and their application in the identification and quantification of protein lipidation in health and disease.
Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes
Authors: Zhang Changyi , Tian Bin , Li Suming , Ao Xiang , Dalgaard Kevin , Gökce Serkan , Liang Yunxiang , She Qunxin
Published: January 2013

Recently, a novel gene-deletion method was developed for the crenarchaeal model Sulfolobus islandicus, which is a suitable tool for addressing gene essentiality in depth. Using this technique, we have investigated functions of putative DNA repair genes by constructing deletion mutants and studying their phenotype. We found that this archaeon may not encode a eukarya-type of NER (nucleotide excision repair) pathway because depleting each of the eukaryal NER homologues XPD, XPB and XPF did not impair the DNA repair capacity in their mutants. However, among seven homologous recombination proteins, including RadA, Hel308/Hjm, Rad50, Mre11, HerA, NurA and Hjc, only the Hjc nuclease is dispensable for cell viability. Sulfolobus encodes redundant BER (base excision repair) enzymes such as two uracil DNA glycosylases and two putative apurinic/apyrimidinic lyases, but inactivation of one of the redundant enzymes already impaired cell growth, highlighting their important roles in archaeal DNA repair. Systematically characterizing these mutants and generating mutants lacking two or more DNA repair genes will yield further insights into the genetic mechanisms of DNA repair in this model organism.
Modern biophysical approaches probe transcription-factor-induced DNA bending and looping
Authors: Gietl Andreas , Grohmann Dina
Published: January 2013

The genetic information of every living organism is stored in its genomic DNA that is perceived as a chemically stable and robust macromolecule. But at the same time, to fulfil its functions properly, it also needs to be highly dynamic and flexible. This includes partial melting of the double helix or compaction and bending of the DNA often brought about by protein factors that are able to interact with DNA stretches in a specific and non-specific manner. The conformational changes in the DNA need to be understood in order to describe biological systems in detail. As these events play out on the nanometre scale, new biophysical approaches have been employed to monitor conformational changes in this regime at the single-molecule level. Focusing on transcription factor action on promoter DNA, we discuss how current biophysical techniques are able to quantitatively describe this molecular process.
Thermococcus kodakarensis DNA replication
Authors: Li Zhuo , Kelman Lori M. , Kelman Zvi
Published: January 2013

DNA replication plays an essential role in all life forms. Research on archaeal DNA replication began approximately 20 years ago. Progress was hindered, however, by the lack of genetic tools to supplement the biochemical and structural studies. This has changed, however, and genetic approaches are now available for several archaeal species. One of these organisms is the thermophilic euryarchaeon Thermococcus kodakarensis. In the present paper, the recent developments in the biochemical, structural and genetic studies on the replication machinery of T. kodakarensis are summarized.
Lytic viruses infecting organisms from the three domains of life
Authors: Snyder Jamie C. , Young Mark J.
Published: January 2013

It is probably a biological constant that viruses are found associated with all known life and that they play an essential role in the ecology and evolution of all lifeforms. Lytic viruses have now been discovered that infect organisms from each of the three domains of life. Recently, a new lysis system has been described for two archaeal viruses. This lysis system appears to be novel and distinct from previously described virus-encoded lysis systems. A comparison of lytic viruses from each of the three domains may provide insights concerning the evolution of viruses.
G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms
Authors: Chini Bice , Parenti Marco , Poyner David R. , Wheatley Mark
Published: January 2013

The papers resulting from the recent Biochemical Society Focused Meeting ‘G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms’ held in Prato in September 2012 are introduced in the present overview. A number of future goals for GPCR (G-protein-coupled receptor) research are considered, including the need to develop biophysical and computational methods to explore the full range of GPCR conformations and their dynamics, the need to develop methods to take this into account for drug discovery and the importance of relating observations on isolated receptors or receptors expressed in model systems to receptor function in vivo.
New classes of spin chains from $(S\widehat{O}_{(q)}(N)$(SÔ(q)(N), $S\widehat{p }_{(q)}(N))$Sp̂(q)(N)) Temperley-Lieb algebras: Data transmission and (q, N) parametrized entanglement entropies
Authors: Chakrabarti Amitabha , Chakraborti Anirban , Hidalgo Esteban Guevara
Published: January 2013

A Temperley-Lieb algebra is extracted from the operator structure of a new class of N2×N2 braid matrices presented and studied in previous papers and designated as \documentclass[12pt]{minimal}\begin{document}$S\widehat{O}_{(q)}(N)$\end{document}SÔ(q)(N), \documentclass[12pt]{minimal}\begin{document}$S\widehat{p} _{(q)}(N)$\end{document}Sp̂(q)(N) for the q-deformed orthogonal and symplectic cases, respectively. Spin chain Hamiltonians are derived from such braid matrices and the corresponding chains are studied. Time evolutions of the chains and the possibility of transition of data encoded in the parameters of mixed states from one end to the other are analyzed. The entanglement entropies S(q, N) of eigenstates of the crucial operator, namely, the q-dependent N2×N2 projector P0 appearing in the corresponding Hamiltonian are obtained. Study of entanglements generated under the actions of \documentclass[12pt]{minimal}\begin{document}$S\widehat{O}(N)$\end{document}SÔ(N), \documentclass[12pt]{minimal}\begin{document}$S\widehat{p}(N)$\end{document}Sp̂(N) braid operators, unitarized with imaginary rapidities (spectral parameters) is presented as a perspective.
Bubble motion and size variation during thermal migration with phase change
Authors: Nurse A. K. , McFadden G. B. , Coriell S. R.
Published: January 2013

An analysis of the motion of a spherical bubble in a two-phase (fluid-fluid), single component system with a vertical linear temperature gradient is presented. The model for the migration of an immiscible bubble under the effects of buoyancy and thermocapillarity, considered by Young et al. [“The motion of bubbles in a vertical temperature gradient,” J. Fluid Mech. 6, 350–356 (1959)], is modified to allow for phase change at the bubble surface. We allow the possibility of both translation of the bubble in the vertical direction and the change of bubble radius with time. Depending on the material parameters, the thermocapillary and buoyancy effects that govern the migration of an immiscible bubble can be overwhelmed by the effects of latent heat generation, resulting in a change in the mechanism driving the motion. For a water-steam system, conditions are determined for a stationary bubble in which the effects of buoyancy and thermal migration are balanced. The linear stability of the bubble is considered, and conditions are determined that correspond to small-amplitude oscillations of the position and radius of the bubble. A weakly nonlinear analysis of the solution in the vicinity of the unstable solution is performed, and the results are compared with a numerical solution of the nonlinear equations.
Electronic interferometers in the quantum Hall effect regime
Authors: Devyatov E. V.
Published: January 2013

The paper describes and conceptualizes results of an experimental study of a new class of interferometers, electronic analogues of known optical interference schemes, in the quantum Hall effect regime, which are based on co-propagating edge states.
Sound wave excitation of spin current
Authors: Lyapilin I. I.
Published: January 2013

The kinetics of conduction electrons interacting with the field of sound waves in a constant magnetic field is studied. Macroscopic balance equations for macroscopic spin components are derived to describe nonlinear acoustic resonance regime. It is shown that such an interaction may give rise to a spin current.
Temperature dependence of the bandwidth of delocalized states for n-InGaAs/GaAs in the quantum Hall effect regime
Authors: Arapov Yu. G. , Gudina S. V. , Neverov V. N. , Novokshonov S. G. , Klepikova A. S. , Kharus G. I. , Shelushinina N. G. , Yakunin M. V.
Published: January 2013

Temperature and magnetic-field dependences of longitudinal ρxx(B,T) and Hall ρxy(B,T) resistivities of n-InxGa1−xAs/GaAs nanostructures with single and double quantum wells are investigated in the quantum Hall regime at B = 0–16 Т and T = 0.05–70 K, before and after IR illumination. The temperature dependence of the QHE plateau-plateau transition width is analyzed and information about temperature dependences of the bandwidth of delocalized states in the center of Landau subbands is obtained.
An electrical injection metallic cavity nanolaser with azimuthal polarization
Authors: Ding Kang , Yin Leijun , Hill Martin T. , Liu Zhicheng , van Veldhoven Peter J. , Ning C. Z.
Published: January 2013

We demonstrated for the first time an azimuthally polarized laser source from an electrically driven metallic cavity nanolaser with a physical cavity volume of 0.146 λ3 (λ = 1416 nm). Single TE01 mode lasing at 78 K was achieved by taking the advantages of the large free spectral range in such nanoscale lasers and the azimuthal polarization of lasing emission was verified experimentally. Mode shift controlled by device cavity radius was observed over a large wavelength range from 1.37 μm to 1.53 μm. Such metallic cavity nanolaser provides a compact electrically driven laser source for azimuthally polarized beam.
Superconducting properties of new heterofullerides
Authors: Kulbachinskii V. A. , Lunin R. A. , Kachan I. P. , Velikodnyi Yu. A. , Bulychev B. M. , Tarasov V. P.
Published: January 2013

Superconducting properties of new heterofullerides synthesized for the first time AnMmHgxC60 (A = K, Rb, Cs; M = Be, Mg, B, Al, Ga, In; n = 1, 2; m = 1, 2; x ≪ 1) were investigated at low temperatures. The low frequency inductive method was used to detect a superconducting transition. All the samples were studied by X-ray diffraction (XRD), solid state nuclear magnetic resonance (NMR), electron spin resonance (ESR), and Raman scattering. It is found that most of the superconducting heterofullerides are potassium heterofullerides. For the fulleride K2GaHgxC60 the critical temperature of the superconducting transition is Tc = 20 K. Indium and boron heterofullerides are not superconductors. The synthesis of heterofullerides via amalgams (Hg–K–Mg, Hg–Rb–Al) gives rise to two different superconducting phases.
Evaluation of heterogeneity measures and their relation to the glass transition
Authors: Di Xiaojun , McKenna Gregory B.
Published: January 2013

For most phase transitions, dynamic slowdown is accompanied by a static structure change. However, in the case of the supercooled liquid, which is a special liquid state below the melting temperature, one observes pronounced dynamic slowdown, i.e., diffusion coefficient, relaxation time, and viscosity change 10–14 orders of magnitude within a relatively small temperature range. This occurs without the pronounced static structure change observed in other phase transitions. Over the past several decades, there has been extensive research aimed to understand why the glass transition occurs, to establish what the glass transition exactly is, and to improve our understanding of how molecules move near to the glass transition. In the present work, we have examined the idea that the dramatic reduction in molecular mobility or dynamic slowdown in a supercooled liquid during cooling from above Tg occurs because of the increasing length scale of heterogeneous subregions, or the cooperatively rearranging regions (CRR) proposed by Adam and Gibbs. Although there is little doubt about the existence of microscopic heterogeneous regions, the absence of the “universal” parameters to characterize the temperature dependent heterogeneity data and type of temperature divergence among different parameters over the same temperature range suggests the possibility that the heterogeneity itself may not relate to the CRR directly and thus may not be the key cause of the glass transition phenomenon. It remains an important research challenge to identify which, if any, of the heterogeneity parameters relates in a causal manner to the glass transition.
Contraction of completeness-optimized basis sets: Application to ground-state electron momentum densities
Authors: Lehtola Susi , Manninen Pekka , Hakala Mikko , Hämäläinen Keijo
Published: January 2013

Completeness-optimization is a novel method for the formation of one-electron basis sets. Contrary to conventional methods of basis set generation that optimize the basis set with respect to ground-state energy, completeness-optimization is a completely general, black-box method that can be used to form cost-effective basis sets for any wanted property at any level of theory. In our recent work [J. Lehtola, P. Manninen, M. Hakala, and K. Hämäläinen, J. Chem. Phys. 137, 104105 (2012)]10.1063/1.4749272 we applied the completeness-optimization approach to forming primitive basis sets tuned for calculations of the electron momentum density at the Hartree-Fock (HF) level of theory. The current work extends the discussion to contracted basis sets and to the post-HF level of theory. Contractions are found to yield significant reductions in the amount of functions without compromising the accuracy. We suggest polarization-consistent and correlation-consistent basis sets for the first three rows of the periodic table, which are completeness-optimized for electron momentum density calculations.
Atom probe study of Cu2ZnSnSe4 thin-films prepared by co-evaporation and post-deposition annealing
Authors: Schwarz T. , Cojocaru-Mirédin O. , Choi P. , Mousel M. , Redinger A. , Siebentritt S. , Raabe D.
Published: January 2013

We use atom probe tomography (APT) for resolving nanometer scale compositional fluctuations in Cu2ZnSnSe4 (CZTSe) thin-films prepared by co-evaporation and post-deposition annealing. We detect a complex, nanometer–sized network of CZTSe and ZnSe domains in these films. Some of the ZnSe domains contain precipitates having a Cu- and Sn-rich composition, where the composition cannot be assigned to any of the known equilibrium phases. Furthermore, Na impurities are found to be segregated at the CZTSe/ZnSe interface. The insights given by APT are essential for understanding the growth of CZTSe absorber layers for thin-film solar cells and for optimizing their optoelectronic properties.
Quantitative analysis of anisotropic edge retraction by solid-state dewetting of thin single crystal films
Authors: Hyun Kim Gye , Zucker Rachel V. , Ye Jongpil , Craig Carter W. , Thompson Carl V.
Published: January 2013

When single crystal thin films undergo solid state dewetting, film edges retract at a rate that is strongly affected by their crystallographic orientations. Lithographically patterned macroscopic edges with a limited number of specific in-plane crystallographic orientations remain straight as they retract. Macroscopic edges with other crystallographic orientations develop in-plane facets, whose in-plane normals are the same as those of kinetically stable edges. Therefore, a quantitative understanding of the retraction of kinetically stable edges can serve as the basis for understanding the retraction of edges with all other in-plane orientations. Measurements of the rates of retraction of kinetically stable edges for single crystal (100) and (110) Ni films on MgO are reported. Retracting edges develop out-of-plane facets that are generally consistent with the facets expected from the equilibrium Wulff shape. To capture the observed anisotropic character of the edge retraction rate, edge retraction through surface diffusion driven by the surface Laplacian of the weighted mean curvature of fully faceted edges has been modeled. The 2-dimensional model and experiments show a similar time scaling for the edge retraction distance (∼tn, with n ∼ 0.4) and the rim height and width (n ∼ 0.2). Also, they are consistent with the specific observed retraction rate anisotropy, within the range of known error of the surface energies and diffusivities used in the model. However, formation of valleys ahead of the rims is observed in the experiments on (110) films but not in the simulation.
Continuous wave ultraviolet-laser sintering of ZnO and TiO2 nanoparticle thin films at low laser powers
Authors: Sandmann Alice , Notthoff Christian , Winterer Markus
Published: January 2013

In this work, continuous wave UV-laser sintering of ZnO and TiO2 nanoparticle (NP) thin films at different laser powers from 10–80 mW focused to a spot size of 10 μm are studied. We show that laser sintering can be observed even at laser powers as low as 30 mW, using an UV-laser at 325 nm. Compared to these results, laser sintering of ZrO2 nanoparticles is not observed within the laser power range under investigation. Furthermore, we describe the laser heating process numerically using an iterative finite element algorithm, which couples the heat equation with a simplified sintering model. The numerical and experimental results match well and reveal two key parameters responsible for the effective heating and sintering process: The laser wavelength in relation to the wavelength corresponding to the band gap of the material and the initial porosity of the film.
Optimized unrestricted Kohn–Sham potentials from ab initio spin densities
Authors: Boguslawski Katharina , Jacob Christoph R. , Reiher Markus
Published: January 2013

The reconstruction of the exchange–correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn–Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange–correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011)10.1063/1.3670414] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.
Three-dimensional transition of vortex shedding flow around a circular cylinder at right and oblique attacks
Authors: Zhao Ming , Thapa Jitendra , Cheng Liang , Zhou Tongming
Published: January 2013

Vortex shedding from an inclined circular cylinder at low values of Reynolds number (Re) is investigated numerically. The aim of the study is to investigate the effect of cylinder oblique angle on the transition from two-dimensionality (2D) to three-dimensionality (3D) of the wake flow. The Navier-Stokes equations are solved by the Petrov-Galerkin finite element method for Reynolds numbers ranging from 100 to 1000 and the flow attack angles of α = 0° and 45°. For the right attack angle case (α = 0°), the predicted wavy spanwise vortices in the early stage of the transition mode A, the vortex dislocation in the late stage of the transition mode A and the streamwise-vortex dominant wake flow structure in the transition mode B are found to agree well with independent experimental observations and measurements. The transition from 2D to 3D at α = 45° was found distinctively different from that at α = 0°. For α = 45°, no clear-cut transition modes are observed. The wake is characterized by wavy spanwise vortices close to the lower boundary of the transition Reynolds number regime, which are similar to those in the early stage of the transition mode A at α = 0°. The vortex-dislocation in the transition mode A was not observed at α = 45°. It appears that the fluid flow in the spanwise direction in the primary vortices at α = 45° does not allow the instability to sustain at a specific spanwise location and trigger the vortex dislocation. Although the wake flow structure is different, the variation of the normal Strouhal number with the normal Reynolds number (both based on the velocity component perpendicular to the cylinder span) at α = 45° is close to that at α = 0° in the transitional Reynolds number regime. The root mean square of the lift coefficient normalized by the velocity component perpendicular to the axial direction of the cylinder at α = 45° is about 20% to 25% larger than that at α = 0° in the Reynolds number regime between 250 and 500.
A 4 MA, 500 ns pulsed power generator CQ-4 for characterization of material behaviors under ramp wave loading
Authors: Wang Guiji , Luo Binqiang , Zhang Xuping , Zhao Jianheng , Sun Chengwei , Tan Fuli , Chong Tao , Mo Jianjun , Wu Gang , Tao Yanhui
Published: January 2013

A pulsed power generator CQ-4 was developed to characterize dynamic behaviors of materials under ramp wave loading, and to launch high velocity flyer plates for shock compression and hypervelocity impact experiments of materials and structures at Institute of Fluid Physics, China Academy of Engineering Physics. CQ-4 is composed of twenty capacitor and primary discharge switch modules with total capacitance of 32μF and rated charging voltage of 100 kV, and the storage energy is transmitted by two top and bottom parallel aluminum plates insulated by twelve layers of polyester film with total thickness of 1.2 mm. Between capacitor bank and chamber, there are 72 peaking capacitors with total capacitance of 7.2 μF and rated voltage of 120 kV in parallel, which are connected with the capacitor bank in parallel. Before the load, there is a group of seven secondary self-breaking down switches connected with the total circuit in series. The peaking capacitors and secondary switches are used to shape the discharging current waveforms. For short-circuit, the peak current of discharging can be up to 3 ∼ 4 MA and rise time varies from 470 ns to 600 ns when the charging voltages of the generator are from 75 kV to 85 kV. With CQ-4 generator, some quasi-isentropic compression experiments under ramp wave loadings are done to demonstrate the ability of CQ-4 generator. And some experiments of launching high velocity flyer plates are also done on CQ-4. The experimental results show that ramp wave loading pressure of several tens of GPa on copper and aluminum samples can be realized and the velocity of aluminum flyer plate with size of 10 mm × 6 mm × 0.35 mm can be accelerated to about 11 km/s and the velocity of aluminum flyer plate with size of 10 mm × 6 mm × 0.6 mm can be up to about 9 km/s, which show that CQ-4 is a good and versatile tool to realize ramp wave loading and shock compression for shock physics.
Ultrafast optical technique for measuring the electrical dependence of the elasticity of piezoelectric thin film: Demonstration on AlN
Authors: Devos A. , Emery P. , Defay E. , Hassine N. Ben , Parat G.
Published: January 2013

We present a technique based on ultrafast acoustics which permits us to measure the electrical dependence of the elastic properties of a thin piezoelectric layer. Ultrafast acoustics offers a unique way of measuring elastic properties of thin-layer in a non-destructive way using ultrashort optical pulses. We apply this technique to a thin layer to which a dc voltage is simultaneously applied. Both the film thickness and the sound velocity are affected. The two effects can be separated by use of a semi-transparent top electrode. A demonstration is made on a thin aluminum nitride (AlN). From that the d33 piezoelectric coefficient and the stiffness variation induced by the bias in AlN are measured.
A test stand for off-line laser ion source development at TRIUMF
Authors: Lavoie J. P. , Li R. , Bricault P. , Lassen J. , Chachkova O. , Teigelhöfer A.
Published: January 2013

A test stand for ion source development and laser resonance ionization spectroscopy was built and commissioned at TRIUMF. The test stand is needed to develop efficient ion sources that can function reliably in the hostile, high temperature, high radiation environment of TRIUMF's isotope separator on-line (ISOL) production target ion source. In addition, it enables laser resonance ionization spectroscopy to develop laser excitation schemes suitable for the solid-state laser systems used with TRIUMF's resonant ionization laser ion source . Also, it allows for possible improvement of current ion sources and validation of new designs. The test stand employs a copy of the ion optics used on-line, so that results can be transferred directly to radioactive ion beam production. Due to space restrictions and the need for rapid mass scans, a quadrupole mass spectrometer is used as a mass separator. One of the first experiments conducted on the laser ion source test stand (LIS STAND) was resonant ionization spectroscopy of gallium to improve on the ionization scheme previously used on-line, so that low yield isotopes (e.g., 62Ga) become available for experiments. Different Rydberg series in gallium were observed and autoionizing states were searched for. The overall LIS STAND system performance, characteristics, and the first resonant ionization spectroscopy are described.
Comparative study of transparent rectifying contacts on semiconducting oxide single crystals and amorphous thin films
Authors: Lajn Alexander , von Wenckstern Holger , Grundmann Marius , Wagner Gerald , Barquinha Pedro , Fortunato Elvira , Martins Rodrigo
Published: January 2013

We demonstrate fully transparent, highly rectifying contacts (TRC) on amorphous GaInZnO and compare them to TRC fabricated on single crystalline bulk ZnO and heteroepitaxial ZnO thin films. The contacts’ transparency in the visible spectral range exceeds 70%. From numerical simulations, we conclude that thermionic emission is the dominating transport mechanism, however, for several samples with low net doping density diffusion theory must be applied. The detailed investigation of the rectification properties of the TRC using temperature-dependent current-voltage and capacitance-voltage measurements reveals that barrier inhomogeneities govern the IV-characteristics of all diodes irrespective of the sample crystallinity. Assuming a Gaussian barrier height distribution, the extracted mean barrier heights typically range between 1.1 and 1.3 V. The width of the barrier distribution correlates with the mean barrier height and ranges from 110 to 130 mV. By compiling literature data, we found that this correlation holds also true for Schottky diodes on elemental and III-V semiconductors.
Mild hydration of didecyldimethylammonium chloride modified DNA by 1H-nuclear magnetic resonance and by sorption isotherm
Authors: Harańczyk H. , Kobierski J. , Nizioł J. , Hebda E. , Pielichowski J. , Zalitacz D. , Marzec M. , El-Ghayoury A.
Published: January 2013

The gaseous phase hydration of deoxyribonucleic acid and didecyldimethylammonium chloride (C19H42ClN) complexes (DNA-DDCA) was observed using hydration kinetics, sorption isotherm, and high power nuclear magnetic resonance. Three bound water fractions were distinguished: (i) a very tightly bound water not removed by incubation over silica gel, (ii) a tightly bound water saturating with the hydration time t1h = (0.59 ± 0.04) h, and a loosely bound water fraction, (iii) with the hydration time t2h = (20.9 ± 1.3) h. Proton free induction decay was decomposed into the signal associated with the solid matrix of DNA-DDCA complex (T2S∗≈ 30 μs) and two liquid signal components coming from tightly bound (T2L1∗≈ 100 μs) and from loosely bound water fraction (T2L2∗≈ 1000 μs).
Magnetism and stability of noncompensated anion-cation codoped ZnO
Authors: Pan Jing , Wang Shudong , Zhang Daoyu , Hu Jingguo , Chen Qian , Wang Jinlan
Published: January 2013

The magnetism and stability of monodoped and codoped ZnO with transition metal (TM = Sc, Ti, V, Cr) or light element (LE = C, N) and their compensated (Sc+N, Ti+C) or noncompensated n-p (Sc+C, Ti+N, V+C, V+N, Cr+C, Cr+N) pairs are studied via spin-polarized density functional theory calculations. The ferromagnetic ordering is observed in the doped systems except for the Sc-, (Sc+N), (Ti+C), and (Ti+N) doping. The noncompensated (V+N) and (Cr+N)-codoped ZnO may be the best candidates for ZnO-based spintronics due to their good ferromagnetism and reliable stability. Additionally, the noncompensated (Sc+C)-codoped ZnO is a net p-type ferromagnetic semiconductor. More importantly, the noncompensated codoping enhances the thermodynamic and kinetic solution of the dopants due to the strong electrostatic attraction between the n- and p-type dopants. These findings suggest that the noncompensated codoping might be a possible way to achieve good and stable dilute magnetic devices.
Precise measurement of the transverse piezoelectric coefficient for thin films on anisotropic substrate
Authors: Chun Doo-Man , Sato Masashi , Kanno Isaku
Published: January 2013

In this study, we propose a reliable measurement method for the effective transverse piezoelectric coefficient for thin films especially on anisotropic substrate. This coefficient for piezoelectric Pb(Zr, Ti)O3 (PZT) thin films was calculated by measuring the electric field-induced tip displacement of unimorph cantilevers composed of PZT thin films and Si substrates. We evaluated the reliability of the proposed measurement method by comparing it with numerical analysis and confirmed that the relative error of the piezoelectric coefficient (e31, f) was less than 1%. We prepared 16 different unimorph cantilevers composed of identical PZT films on different Si beam geometries that had various substrate thicknesses and cantilever widths. Although the effective transverse piezoelectric coefficient e31, f of PZT thin films ranged from −6.5 to −14 C/m2 as a function of the applied voltage, the difference among the 16 samples with an applied voltage of 25 V was within 10%. These results demonstrate that the proposed measurement method has sufficient reliability and can be used to evaluate the effective transverse piezoelectric coefficient e31, f of thin films.
Structure induced conductivity enhancement in metal-doped molybdenum oxide thin films
Authors: Cheyns David , Kam Benjamin , Vasseur Karolien , Heremans Paul , Rand Barry P.
Published: January 2013

We study doped molybdenum oxide (MoO3) thin films as thickness-tunable transport layers in organic photovoltaics. In an illustrative device, we show that the introduction of thick pristine MoO3 layers is unfavorable for device operation due to an increased series resistance, but this can be overcome by doping the transport layer with small amounts of metal. However, as opposed to a conventional doping mechanism, we ascribe the doping-induced conductivity enhancement to originate from an improved crystallinity of MoO3. This latter effect appears to be an example of metal induced crystallization. These flat, transparent, and conductive MoO3 layers are ideal candidates for high work function transport layers in several architectures of organic or other thin film optoelectronic devices and we demonstrate this by its use in tandem organic photovoltaics.
High mobility ambipolar MoS2 field-effect transistors: Substrate and dielectric effects
Authors: Bao Wenzhong , Cai Xinghan , Kim Dohun , Sridhara Karthik , Fuhrer Michael S.
Published: January 2013

We fabricate MoS2 field effect transistors on both SiO2 and polymethyl methacrylate (PMMA) dielectrics and measure charge carrier mobility in a four-probe configuration. For multilayer MoS2 on SiO2, the mobility is 30–60 cm2/Vs, relatively independent of thickness (15–90 nm), and most devices exhibit unipolar n-type behavior. In contrast, multilayer MoS2 on PMMA shows mobility increasing with thickness, up to 470 cm2/Vs (electrons) and 480 cm2/Vs (holes) at thickness ∼50 nm. The dependence of the mobility on thickness points to a long-range dielectric effect of the bulk MoS2 in increasing mobility.
Competition of circularly polarized laser modes in the modulation instability of hot magnetoplasma
Authors: Sepehri Javan N.
Published: January 2013

The present study is aimed to investigate the problem of modulation instability of an intense laser beam in the hot magnetized plasma. The propagation of intense circularly polarized laser beam along the external magnetic field is considered using a relativistic fluid model. The nonlinear equation describing the interaction of laser pulse with magnetized hot plasma is derived in the quasi-neutral approximation, which is valid for hot plasma. Nonlinear dispersion equation for hot plasma is obtained. For left- and right-hand polarizations, the growth rate of instability is achieved and the effect of temperature, external magnetic field, and kind of polarization on the growth rate is considered. It is observed that for the right-hand polarization, increase of magnetic field leads to the increasing of growth rate. Also for the left-hand polarization, increase of magnetic field inversely causes decrease of the growth rate.
Polyimide/nanosized CaCu3Ti4O12 functional hybrid films with high dielectric permittivity
Authors: Yang Yang , Zhu Ben-Peng , Lu Zhi-Hong , Wang Zi-Yu , Fei Chun-Long , Yin Di , Xiong Rui , Shi Jing , Chi Qing-Guo , Lei Qing-Quan
Published: January 2013

This work reports the high dielectric permittivity of polyimide (PI) embedded with CaCu3Ti4O12 (CCTO) nanoparticles. The dielectric behavior has been investigated over a frequency of 100 Hz-1 MHz. High dielectric permittivity (ε = 171) and low dielectric loss (tan δ = 0.45) at 100 Hz have been observed near the percolation threshold. The experimental results fit well with the Percolation theory. We suggest that the high dielectric permittivity originates from the large interface area and the remarkable Maxwell-Wagner-Sillars effect at percolation in which nomadic charge carriers are blocked at internal interfaces between CCTO nanoparticles and the polyimide matrix.
Dual threshold diode based on the superconductor-to-insulator transition in ultrathin TiN films
Authors: Baturina Tatyana I. , Kalok David , Bilušić Ante , Vinokur Valerii M. , Baklanov Mikhail R. , Gutakovskii Anton K. , Latyshev Alexander V. , Strunk Christoph
Published: January 2013

We investigate transport properties of superconducting TiN films in the vicinity of the superconductor-insulator transition (SIT). We show that the current-voltage (I-V) characteristics are mirror-symmetric with respect to the SIT and can be switched to each other by the applied magnetic field. In both superconducting and insulating states, the low-temperature I-V characteristics have pronounced diode-like threshold character, demonstrating voltage/current jumps over several orders of magnitude at the corresponding critical current or threshold voltage. We have found that for both states, the theory developed for Josephson junction arrays offers a quantitative description of the experimental results.
Time-resolved electroluminescence of bulk Ge at room temperature
Authors: Terada Yosuke , Yasutake Yuhsuke , Fukatsu Susumu
Published: January 2013

Time-resolved spectroscopy of bulk Ge at room temperature allows to differentiate direct-gap electroluminescence (EL) from indirect-gap EL. The results indicate that there exists strong coupling between the eight-fold indirect L-valleys and the zone-center Γ-valley due to intervalley phonon scattering at room temperature in the absence of built-in strain. Pulse modulation of EL at 10-MHz is consistent with the relevance of the direct-gap transition.
Site-preference and valency for rare-earth sites in (R-Ce)2Fe14B magnets
Authors: Alam Aftab , Khan Mahmud , McCallum R. W. , Johnson D. D.
Published: January 2013

Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two R-sites (Wyckoff 4f and 4g, with four-fold multiplicity) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1−xCex) 2Fe14B [R = La,Nd] using density functional theory (DFT) methods—including a DFT + U scheme to treat localized 4f-electrons. Fe moments compare well with neutron data—almost unaffected by Hubbard U, and weakly affected by spin-orbit coupling. In La2Fe14B, Ce alloys for 0≤x≤1 and prefers smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas, in Nd2Fe14B, Ce is predicted to have limited alloying (x≤0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. The Curie temperatures versus x for (Nd,Ce) were predicted for a typical sample processing and verified experimentally.
Size-dependent transition of deformation mechanism, and nonlinear elasticity in Ni3Al nanowires
Authors: Wang Yun-Jiang , Gao Guo-Jie J. , Ogata Shigenobu
Published: January 2013

A size-dependent transition of deformation mechanism is revealed in Ni3Al nanowire under atomistic uniaxial tension. Deformation twinning is replaced by phase transformation when the diameter of Ni3Al nanowire reduces to a critical value near 4 nm. Enhanced size-dependent nonlinear elasticity is observed in the nanowires, in comparison to their bulk counterpart which is benchmarked by combined density functional and atomistic study. This study provide fundamental understanding on the size-dependent deformation mechanisms of nanostructured alloys.
Chiroptical hot spots in twisted nanowire plasmonic oscillators
Authors: Tang Yiqiao , Sun Li , Cohen Adam E.
Published: January 2013

We image the chiroptical response of crossed nanowire junctions as a function of the vertical offset between the nanowires and the incident wavelength. These samples show chiroptical “hot spots” with strongly localized circular differential scattering at the nanowire crossing points. These chiroptical hot spots are not apparent in the spatially averaged spectra. The sign and magnitude of the chiroptical enhancement show a complex dependence on sample geometry, which we reproduce with a fully retarded analytical scattering model. These results suggest strategies for engineering devices with enhanced chiral light-matter interactions.
Dynamic stabilization of Rayleigh-Taylor instability: Experiments with Newtonian fluids as surrogates for ablation fronts
Authors: Rodriguez Prieto G. , Piriz A. R. , Lopez Cela J. J. , Tahir N. A.
Published: January 2013

A previous theory on dynamic stabilization of Rayleigh-Taylor instability at interfaces between Newtonian fluids is reformulated in order to make evident the analogy of this problem with the related one on dynamic stabilization of ablation fronts in the framework of inertial confinement fusion. Explicit analytical expressions are obtained for the boundaries of the dynamically stable region which turns out to be completely analogue to the stability charts obtained for the case of ablation fronts. These results allow proposing experiments with Newtonian fluids as surrogates for studying the case of ablation fronts. Experiments with Newtonian fluids are presented which demonstrate the validity of the theoretical approach and encourage to pursue experimental research on ablation fronts to settle the feasibility of dynamic stabilization in the inertial confinement fusion scenario.
Dielectric, ferroelectric and magnetic properties of Mn-doped LuFeO3 ceramics
Authors: Qin Ying , Qiang Liu Xiao , Ming Chen Xiang
Published: January 2013

LuFe1−xMnxO3 (x = 0, 0.05) ceramics with the orthorhombic distorted perovskite structure in space group Pbnm were synthesized using a solid-state reaction process. The dielectric, ferroelectric, and magnetic properties were investigated systematically. With Mn-substitution, the low temperature dielectric relaxation was suppressed and only one dielectric anomaly around 360–530 K was observed. Obvious ferroelectric hysteresis loops were detected at room temperature in LuFe0.95Mn0.05O3, the smaller polarization compared with LuFeO3 suggested the important role of the electron hopping between Fe2+ and Fe3+ ions in ferroelectricity. The results of thermal analysis indicated that the Néel temperature decreased with Mn-substitution, which could be ascribed to the weaker Fe3+-Mn3+ and Mn3+-Mn3+ exchange interactions compared with Fe3+-Fe3+ interaction. Due to the strong anisotropy of Mn3+ ions, a spin reorientation transition could be induced in LuFe0.95Mn0.05O3. Moreover, weak ferromagnetic characteristic was also detected at room temperature in LuFe0.95Mn0.05O3 ceramics.