bluuebunny/crossref_metadata_2025 huggingface dataset:
The polymerization of acetylene on supported metal clusters
Authors: Gilb S. , Arenz M. , Heiz U.
Published: December 2006

The polymerization of acetylene was studied by thermal programmed reaction on model catalysts consisting of size-selected Ag, Rh, and Pd atoms and Pdn (1⩽n⩽30) clusters on well-characterized MgO(111) thin films. In a single-pass heating cycle experiment, benzene, butadiene, and butane were catalyzed with different selectivities as function of cluster size: palladium and rhodium atoms selectively produce benzene, and the highest selectivity for butadiene is observed for Pd6, whereas Pd20 reveals the highest selectivity for butane. Ag atoms are inert. These results provide an atom-by-atom observation of the selectivity of small cluster catalysts.
Exciton condensation in quantum wells
Authors: Sugakov V. I.
Published: December 2006

The theory of exciton condensation is given in two-dimensional systems under the suggestion that condensation occurs in real space and condensed phase arises as a result of an attractive interaction between excitons. Due to the finite value of exciton lifetime, the sizes of exciton condensed phase regions are restricted and the condensed phase appears in a form of system of islands amid exciton gas. The joint solution of kinetic equations for island size and exciton diffusion equation in the space between islands has been obtained. The theory is applied to explanation of experimental manifestation of condensed phase in quantum wells and also to explanation of the periodical fragmentation, which was observed in luminescence spectrum from a ring around a laser spot in a crystal with double quantum wells. For such explanations, the theory does not require the exciton Bose–Einstein condensation.
Super-resolution with a nonlinear thin film: Beam reshaping via internal multi-interference
Authors: Wei Jingsong , Xiao Mufei , Zhang Feng
Published: December 2006

In laser applications, the size of the focus spot can be reduced beyond the diffraction limit with a thin film of strong nonlinear optical Kerr effect. We present a concise theoretical simulation of the device. The origin of the super-resolution is found to be mainly from the reshaping effect due to the strongly nonlinear refraction mediated multi-interference inside the thin film. In addition, both diffraction and self-focusing effects have been explored and found negligible for highly refractive and ultrathin films in comparison with the reshaping effect. Finally, the theoretic model has been verified in experiments with single Ge2Sb2Te5 film and SiN∕Si∕SiN∕Ge2Sb2Te2 multilayer structures.
Momentum transfer to rotating magnetized plasma from gun plasma injection
Authors: Shamim Imran , Hassam A. B. , Ellis R. F. , Witherspoon F. D. , Phillips M. W.
Published: December 2006

Numerical simulations are carried out to investigate the penetration and momentum coupling of a gun-injected plasma slug into a rotating magnetized plasma. An experiment along these lines is envisioned for the Maryland Centrifugal Experiment (MCX) [R. F. Ellis et al., Phys. Plasmas 8, 2057 (2001)] using a coaxial plasma accelerator gun developed by HyperV Technologies Corp. [F. D. Witherspoon et al., Bull. Am. Phys. Soc. 50, LP1–87 (2005)]. The plasma gun would be located in the axial midplane and fired off-axis into the rotating MCX plasma annulus. The numerical simulation is set up so that the initial momentum in the injected plasma slug is of the order of the initial momentum of the target plasma. Several numerical firings are done into the cylindrical rotating plasma. Axial symmetry is assumed. The slug is seen to penetrate readily and deform into a mushroom, characteristic of interchange deformations. It is found that up to 25% of the momentum in the slug can be transferred to the background plasma in one pass across a cylindrical chord. For the same initial momentum, a high-speed low density slug gives more momentum transfer than a low-speed high density slug. Details of the numerical simulations and a scaling study are presented.
Evolution of the fastest-growing relativistic mixed mode instability driven by a tenuous plasma beam in one and two dimensions
Authors: Dieckmann M. E. , Frederiksen J. T. , Bret A. , Shukla P. K.
Published: December 2006

Particle-in-cell simulations confirm here that a mixed plasma mode is the fastest growing when a highly relativistic tenuous electron-proton beam interacts with an unmagnetized plasma. The mixed modes grow faster than the filamentation and two-stream modes in simulations with beam Lorentz factors Γ of 4, 16, and 256, and are responsible for thermalizing the electrons. The mixed modes are followed to their saturation for the case of Γ=4 and electron phase space holes are shown to form in the bulk plasma, while the electron beam becomes filamentary. The initial saturation is electrostatic in nature in the considered one- and two-dimensional geometries. Simulations performed with two different particle-in-cell simulation codes evidence that a finite grid instability couples energy into high-frequency electromagnetic waves, imposing simulation constraints.
Nonlinear wave interactions in quantum magnetoplasmas
Authors: Shukla P. K. , Ali S. , Stenflo L. , Marklund M.
Published: December 2006

Nonlinear interactions involving electrostatic upper-hybrid (UH), ion-cyclotron (IC), lower-hybrid (LH), and Alfvén waves in quantum magnetoplasmas are considered. For this purpose, the quantum hydrodynamical equations are used to derive the governing equations for nonlinearly coupled UH, IC, LH, and Alfvén waves. The equations are then Fourier analyzed to obtain nonlinear dispersion relations, which admit both decay and modulational instabilities of the UH waves at quantum scales. The growth rates of the instabilities are presented. They can be useful in applications of our work to diagnostics in laboratory and astrophysical settings.
Diffusion in alumina
Authors: Doremus Robert H.
Published: December 2006

Experimental results on diffusion in alumina are summarized and critically discussed. The most reliable results are those on volume diffusion in single crystals (sapphire), and are available for a wide variety of substances, including the structural elements oxygen and alumina, water, monovalent cations, and trivalent cations. Experimental results on volume diffusion in polycrystalline alumina have also been reported for hydrogen, water, some actinides, and rare earths. Diffusion coefficients have been deduced from deep penetration tails on diffusion profiles, and have been interpreted to result from fast diffusion along dislocations or grain boundaries. However, there are questions about these interpretations that are discussed. Mechanisms of diffusion in alumina are uncertain; a variety of charged defects has been suggested to control diffusion in alumina, but no interpretation is widely accepted because of discrepancies with experimental results. The possibility of an AlO defect is put forward to stimulate exploration and discussions; together with a diffusion-reaction mechanism, it can explain many puzzling features of diffusion in alumina. The electrical conductivity of alumina results from the transport of H+(H3O+) ions if the OH concentration in the alumina is greater than about 3×10−7 OH groups per Al atom. At lower OH concentrations electronic conductivity becomes dominant.
New experimental device for infrared spectral directional emissivity measurements in a controlled environment
Authors: del Campo Leire , Pérez-Sáez Raúl B. , Esquisabel Xabier , Fernández Ignacio , Tello Manuel J.
Published: December 2006

A new experimental device for infrared spectral directional emissivity measurements in a controlled atmosphere is presented. The sample holder, which permits to measure spectral directional emissivity up to 1050K, is placed inside a stainless steel sample chamber that can be evacuated or filled with different gases. The signal detection is carried out by means of a Fourier transform infrared spectrometer. The experimental results focus on the capability of the device to perform emissivity measurements as a function of temperature, emission angle, and in situ surface state evolution. A careful study of the sample temperature homogeneity and the measurement method has been done, including the background radiation, the apparatus response function, and temperature differences between the sample and the blackbody radiator. As a consequence, a compact expression for the sample emissivity that generalizes those previously obtained for the direct radiometric measurement method is found. The error assessment shows that the main contribution to the emissivity uncertainty is related to the sample temperature. The overall uncertainty at intermediate temperature is estimated to be around 3% at short wavelengths. Emissivity measurements of Armco iron were used in order to check the accuracy of the experimental device. The experimental results show an excellent fit with direct emissivity data accessible in the literature, as well as with the theoretical emissivity obtained from the Hagen-Rubens relation.
Nonambipolar electron source
Authors: Longmier B. , Baalrud S. , Hershkowitz N.
Published: December 2006

A radio frequency (rf) plasma-based electron source that does not rely on electron emission at a cathode surface has been constructed. All of the random electron flux incident on an exit aperture is extracted through an electron sheath resulting in total nonambipolar flow within the device when the ratio of the ion loss area to the electron loss area is approximately equal to the square root of the ratio of the ion mass to the electron mass, and the ion sheath potential drop at the chamber walls is much larger than Te∕e. The nonambipolar electron source (NES) has an axisymmetric magnetic field of 100G at the extraction aperture that results in a uniform plasma potential across the aperture, allowing the extraction of all the incident electron flux without the use of grids. A prototype NES has produced 15A of continuous electron current, using 15SCCM (SCCM denotes cubic centimeter per minute at STP) Ar, 1200W rf power at 13.56MHz, and 6 times gas utilization. Alternatively 8A of electron current can be produced, using 3SCCM Ar at 1200W rf and 20 times gas utilization. NES could replace hollow cathode electron sources in a wide variety of applications.
Koopmans’ theorem in the ROHF method: Canonical form for the Hartree-Fock Hamiltonian
Authors: Plakhutin B. N. , Gorelik E. V. , Breslavskaya N. N.
Published: December 2006

Since the classic work of Roothaan [Rev. Mod. Phys. 32, 179 (1960)], the one-electron energies of a ROHF method are known as ambiguous quantities having no physical meaning. Together with this, it is often assumed in present-day computational studies that Koopmans’ theorem is valid in a ROHF method. In this work we analyze the specific dependence of orbital energies on the choice of the basic equations in a ROHF method which are the Euler equations and different forms of the generalized Hartree-Fock equation. We first prove that the one-electron open-shell energies εm derived by the Euler equations can be related to the respective ionization potentials Im via the modified Koopmans’ formula Im=−εm∕fm where fm is an occupation number. As compared to this, neither the closed-shell orbital energies nor the virtual ones derived by the Euler equations can be related to the respective ionization potentials and electron affinities via Koopmans’ theorem. Based on this analysis, we derive the new (canonical) form for the Hamiltonian of the Hartree-Fock equation, the eigenvalues of which obey Koopmans’ theorem for the whole energy spectrum. A discussion of new orbital energies is presented on the examples of a free N atom and an endohedral N@C60 (Ih). The vertical ionization potentials and electron affinities estimated via Koopmans’ theorem are compared with the respective observed data and, for completeness, with the respective estimates derived via a ΔSCF method. The agreement between observed data and their estimates via Koopmans’ theorem is qualitative and, in general, appears to possess the same accuracy level as in the closed-shell SCF.
Magnetohydrodynamic activity inside a sphere
Authors: Mininni Pablo D. , Montgomery David C.
Published: December 2006

We present a computational method to solve the magnetohydrodynamic equations in spherical geometry. The technique is fully nonlinear and wholly spectral, and uses an expansion basis that is adapted to the geometry: Chandrasekhar-Kendall vector eigenfunctions of the curl. The resulting lower spatial resolution is somewhat offset by being able to build all the boundary conditions into each of the orthogonal expansion functions and by the disappearance of any difficulties caused by singularities at the center of the sphere. The results reported here are for mechanically and magnetically isolated spheres, although different boundary conditions could be studied by adapting the same method. The intent is to be able to study the nonlinear dynamical evolution of those aspects that are peculiar to the spherical geometry at only moderate Reynolds numbers. The code is parallelized, and will preserve to high accuracy the ideal magnetohydrodynamic invariants of the system (global energy, magnetic helicity, cross helicity). Examples of results for selective decay and mechanically driven dynamo simulations are discussed. In the dynamo cases, spontaneous flips of the dipole orientation are observed.
30
nm
resolution x-ray imaging at 8keV using third order diffraction of a zone plate lens objective in a transmission microscope
Authors: Yin Gung-Chian , Song Yen-Fang , Tang Mau-Tsu , Chen Fu-Rong , Liang Keng S. , Duewer Frederick W. , Feser Michael , Yun Wenbing , Shieh Han-Ping D.
Published: December 2006

A hard x-ray transmission microscope with 30nm spatial resolution has been developed employing the third diffraction order of a zone plate objective. The microscope utilizes a capillary type condenser with suitable surface figure to generate a hollow cone illumination which is matched in illumination range to the numerical aperture of the third order diffraction of a zone plate with an outmost zone width of 50nm. Using a test sample of a 150nm thick gold spoke pattern with finest half-pitch of 30nm, the authors obtained x-ray images with 30nm resolution at 8keV x-ray energy.
On turbulent kinetic energy production and dissipation in dilute polymer solutions
Authors: Liberzon A. , Guala M. , Kinzelbach W. , Tsinober A.
Published: December 2006

Drag reduction by dilute polymer solutions is the most recognized phenomenon in wall-bounded turbulent flows, which is associated with large scales (e.g., velocity scales) in spite of a consensus that polymers act mainly on much smaller scales of velocity derivatives. We demonstrate that drag reduction is only one sort of polymers’ effect on a turbulent flow and show how turbulent velocity and velocity derivatives are altered in the presence of dilute polymers, irrespective of drag reduction phenomena. This is an experimental study on the interaction of dilute polymers with a complex three-dimensional turbulent flow with small mean velocity gradients. Lagrangian data (e.g., velocities and velocity gradients) of flow tracers were obtained by using three-dimensional particle tracking velocimetry in an observational volume in the turbulent bulk region, far from the boundaries. The focus is on aspects related to the turbulent kinetic energy (TKE) production, −⟨uiuj⟩Sij (ui is the fluctuating velocity, ⟨uiuj⟩ is the Reynolds stress tensor, and Sij is the mean rate-of-strain tensor), such as an anisotropy of Reynolds stresses and the alignment of the velocity vector field with respect to the eigenframe of Sij, among others. We base our study on the comparison of turbulent quantities in flows of water and of dilute polymer solution, forced in two distinct ways: frictional forcing by smooth rotating disks and inertial forcing by disks with baffles. The comparison of the results from the water and from the dilute polymer solution flows allows a critical examination of the influence of polymers on the TKE production, viscous dissipation, and the related turbulent properties. We conclude with (i) quantification of the direct effect of polymers on the small scales of velocity derivatives, (ii) evidence of an additional dissipation mechanism by the polymers, which is the main reason for the strong inhibition of the viscous dissipation, 2νs2, in a turbulent bulk, (iii) verification that TKE production does not change if the energy input to the flow is at the scales that are not affected by polymers (e.g., inertial forcing or a very rough wall), and last, (iv) evidence for qualitative modification of the turbulent structure, which is not exhausted by the additional dissipation mechanism.
Relativistic quaternionic wave equation
Authors: Schwartz Charles
Published: December 2006

We study a one-component quaternionic wave equation which is relativistically covariant. Bilinear forms include a conserved four-vector current and an antisymmetric second rank tensor. Waves propagate within the light cone and there is a conserved quantity which looks like helicity. The principle of superposition is retained in a slightly altered manner. External potentials can be introduced in a way that allows for gauge invariance. There are some results for scattering theory and for two-particle wave functions as well as the beginnings of second quantization. However, we are unable to find a suitable Lagrangian or an energy-momentum tensor.
Nonlinear ponderomotive force by low frequency waves and nonresonant current drive
Authors: Gao Zhe , Fisch Nathaniel J. , Qin Hong
Published: December 2006

The collisionless nonresonant force by low frequency waves has been thought to be capable of driving the nonresonant current. However, for a single particle, the ponderomotive force is in the direction of the gradient of the wave field energy. For cold plasmas, the Reynolds stress acting on the Lagrangian fluid element fully counteracts the nonresonant force offered by the quasilinear electromagnetic force. For hot plasmas, the collisionless nonresonant force is also cancelled by the nonlinear kinetic stress force. Therefore, in collisionless plasmas, none of the ponderomotive forces by low frequency waves can drive the nonresonant current.
Benchmarking the performance of density functional theory based Green’s function formalism utilizing different self-energy models in calculating electronic transmission through molecular systems
Authors: Prociuk Alexander , Van Kuiken Ben , Dunietz Barry D.
Published: December 2006

Electronic transmission through a metal-molecule-metal system is calculated by employing a Green’s function formalism in the scattering based scheme. Self-energy models representing the bulk and the potential bias are used to describe electron transport through the molecular system. Different self-energies can be defined by varying the partition between device and bulk regions of the metal-molecule-metal model system. In addition, the self-energies are calculated with different representations of the bulk through its Green’s function. In this work, the dependence of the calculated transmission on varying the self-energy subspaces is benchmarked. The calculated transmission is monitored with respect to the different choices defining the self-energy model. In this report, we focus on one-dimensional model systems with electronic structures calculated at the density functional level of theory.
Liquid friction on charged surfaces: From hydrodynamic slippage to electrokinetics
Authors: Joly Laurent , Ybert Christophe , Trizac Emmanuel , Bocquet Lydéric
Published: December 2006

Hydrodynamic behavior at the vicinity of a confining wall is closely related to the friction properties of the liquid/solid interface. Here we consider, using molecular dynamics simulations, the electric contribution to friction for charged surfaces, and the induced modification of the hydrodynamic boundary condition at the confining boundary. The consequences of liquid slippage for electrokinetic phenomena, through the coupling between hydrodynamics and electrostatics within the electric double layer, are explored. Strong amplification of electro-osmotic effects is revealed, and the nontrivial effect of surface charge is discussed. This work allows us to reconsider existing experimental data, concerning ζ potentials of hydrophobic surfaces and suggests the possibility to generate “giant” electro-osmotic and electrophoretic effects, with direct applications in microfluidics.
Estimation of in vivo brain-to-skull conductivity ratio in humans
Authors: Zhang Yingchun , van Drongelen Wim , He Bin
Published: December 2006

The electrical conductivity value of the human skull is important for biophysics research of the brain. In the present study, the human brain-to-skull conductivity ratio was estimated through in vivo experiments utilizing intracranial electrical stimulation in two epilepsy patients. A realistic geometry inhomogeneous head model including the implanted silastic grids was constructed with the aid of the finite element method, and used to estimate the conductivity ratio. Averaging over 49 sets of measurements, the mean value and standard deviation of the brain-to-skull conductivity ratio were found to be 18.7 and 2.1, respectively.
Fabry-Perot type sensor with surface plasmon resonance
Authors: Lu Guowei , Cheng Bolin , Shen Hong , Zhou Yueliang , Chen Zhenghao , Yang Guozhen , Tillement Olivier , Roux Stéphane , Perriat Pascal
Published: December 2006

The main point of this letter concerns the fabrication of an optical sensor with improved sensitivity for detecting molecular adsorption onto a gold surface. The sensor consists of a Fabry-Perot interferometer whose one of two reflective layers is constituted by an island-type gold film having a pronounced local surface plasmon resonance. The results presented in the letter show that the binding of molecules on the device surface induces a differential interference pattern whose amplitude is increased by the plasmon resonance. The sensor sensitivity can be improved by further deposition of Au nanoparticles on the reflective layer. This kind of sensor has potential advantages since it is easy to fabricate and use and it possesses a submonolayer sensitivity.
Applying solid immersion near-field optics to Raman analysis of strained silicon thin films
Authors: Lerman Gilad M. , Israel Abraham , Lewis Aaron
Published: December 2006

A solid immersion lens (SIL) is applied with Raman spectroscopy to selectively analyze strained silicon thin films. The SIL was fabricated using a high index optical fiber, n=1.9. The fabrication allows for integration with an atomic force microscope (AFM) for repeated approach and feedback of the SIL to the surface. The evanescent field emanating from the SIL was investigated using near-field optical microscopy and the decay length was ∼150nm. This was then combined with a Raman spectrometer coupled to an online AFM having a completely free optical axis permitting optical investigations of opaque samples such as strained silicon.
Characterization of As-doped, p-type ZnO by x-ray absorption near-edge structure spectroscopy: Theory
Authors: Limpijumnong Sukit , Smith M. F. , Zhang S. B.
Published: December 2006

Vaithianathan et al. [Appl. Phys. Lett. 88, 112103 (2006)] measured x-ray absorption near-edge structure (XANES) of As-doped ZnO and analyzed it as evidence for AsO acceptors. However, upon carrying out first principles calculations, we found that the simulated XANES spectrum for AsO is very different from that observed. Instead, the simulated spectrum for AsZn–2VZn defect complex, which is predicted to be an acceptor [S. Limpijumnong et al., Phys. Rev. Lett. 92, 155504 (2004)], is far more consistent with the XANES data. The combination of our study, with the XANES of Vaithianathan et al. might be, until now, the strongest support for the AsZn–2VZn model.
Organic thin film transistor by using polymer electrolyte to modulate the conductivity of conjugated polymer
Authors: Lin Yu-Ju , Li Yu-Chang , Yeh Chih-Chieh , Chung Sheng-Feng , Huang Li-Ming , Wen Ten-Chin , Wang Yeong-Her
Published: December 2006

This work presents an organic thin film transistor using double polymer layers, polymer electrolyte/conjugated polymer, i.e., poly(diallyldimethylammonium chloride) (PDDA)/poly(diphenylamine) (PDPA) structure. The single mobile anions (Cl−) pending on the PDDA are stuffed into the conjugated polymer to dope the nitrogen atoms (imine) by applying the gate bias, resulting a higher drain current under the same source-drain voltage. The PDDA/PDPA polymer structure working in the enhancement mode which operates under atmospheric conditions as a typical p-channel transistor is demonstrated.
Internal electric field in organic-semiconductor-based photovoltaic devices
Authors: Lungenschmied C. , Dennler G. , Neugebauer H. , Sariciftci N. S. , Ehrenfreund E.
Published: December 2006

The authors performed transient photocurrent measurements under applied bias and electroabsorption spectroscopy on devices based on a pristine poly(phenylene vinylene) derivative as well as its mixture with 1% of a methanofullerene electron acceptor. Combining both techniques allows us to directly determine the internal electric field and to conclude on its implication on the photovoltaic performance of the devices. The electric field is identified as the driving force of the photocurrent, hence indicating the maximum obtainable photovoltage. Acceptor concentrations as low as 1% shift the energetic alignment of the top electrode to the reduction potential of the acceptor, reducing the internal electric field.
Simple approach to β-SiC nanowires: Synthesis, optical, and electrical properties
Authors: Zhou Weimin , Liu Xuan , Zhang Yafei
Published: December 2006

High-quality β-SiC nanowires were synthesized on activated carbon fiber via a thermal evaporation method without the use of metal catalyst. Their structure and chemical composition were studied by Raman spectroscopy and high-resolution electron microscopy. Field effect transistors were fabricated to investigate the β-SiC nanowire electrical behavior possessing n-channel characterization. The carrier mobility of the devices was 15.9cm2∕Vs when the Vds is 0.01V. This result contributes to the development of efficient nanodevices based on β-SiC nanowires, as well as nanocomposites.
Si-assisted growth of InAs nanowires
Authors: Park Hyun D. , Prokes S. M. , Twigg M. E. , Cammarata Robert C. , Gaillot Anne-Claire
Published: December 2006

The authors report on the growth of InAs nanowires using nanometer-sized Si clusters in a closed system without any metal catalyst. The growth was performed at 580°C for 30min using 1.3nm thickness of SiOx. It is suggested that the nanowire growth occurred due to highly reactive nanometer-sized Si clusters, which are formed by phase separation of SiOx. The authors have also examined the vapor-liquid-solid (VLS) mechanism under various oxidizing conditions, including different oxygen pressures (200 and 800mTorr) and oxidized Au–In tip. The results indicate the inhibiting effect of oxygen on the VLS mechanism.
Normal and inverse current-induced magnetization switching in a single nanopillar
Authors: Dassow H. , Lehndorff R. , Bürgler D. E. , Buchmeier M. , Grünberg P. A. , Schneider C. M. , van der Hart A.
Published: December 2006

The authors report on current-induced magnetization switching (CIMS) in single-crystalline nanopillars. Fe(14nm)∕Cr(0.9nm)∕Fe(10nm)∕Ag(6nm)∕Fe(2nm) multilayers are deposited by molecular-beam epitaxy. The central Fe layer is coupled to the thick one by interlayer exchange coupling over Cr, while the topmost Fe layer is decoupled. Nanopillars with 150nm diameter are prepared by optical and e-beam lithographies. The opposite spin scattering asymmetries of the Fe∕Cr and Fe∕Ag interfaces enabled the authors to observe normal and inverse CIMS for the two subsystems, which are combined in a single device. At high magnetic fields, steplike resistance changes are measured at positive currents and are attributed to current-driven magnetic excitations.
Self-assembly of epitaxial monolayers for vacuum wafer bonding
Authors: Altfeder Igor , Huang Biqin , Appelbaum Ian , Walker B. C.
Published: December 2006

Self-assembled epitaxial metal monolayers can be used for heterointegration of mismatched semiconductors, leading to simultaneously low interfacial resistance and high optical transparency. Lattice-mismatched wafers of Si(100) and Si(111) were bonded at room temperature in situ after vacuum deposition of a single atomic layer of Ag. The interfacial resistance was measured to be 3.9×10−4Ωcm2 and the optical transmission of the interface at 2500nm is approximately 98%. Electron confinement in ultrathin Ag layers as a possible contributor to the bonding energy.
Analytic expression for the temperature of the current-heated nanowire for the current-induced domain wall motion
Authors: You Chun-Yeol , Sung In Mo , Joe Byung-Kyu
Published: December 2006

The authors find a simple analytic expression for the temperature of Joule heated nanowire by current pulse, which is important in the study of the current induced domain wall motion. Since the effect of spin transfer torque depends on the thermal energy of the system, the temperature of the nanowire is a vital information. Even though the numerical solution of the heat conduction equation is well established, not only does it require a lot of numerical effort, but neither does it give any physical insight. With appropriate assumptions and Green’s function method, the author derive a simple expression for the temperature of the nanowire as a function of the current density, sample geometry, and thermal properties of the substrate. The authors confirm the validity of their analytic expression by the comparison between the results of a simple expression and a commercial finite element method.
How surface-enhanced chemiluminescence depends on the distance from a corrugated metal film
Authors: Lu Guowei , Shen Hong , Cheng Bolin , Chen Zhenghao , Marquette Christophe A. , Blum Loic J. , Tillement Olivier , Roux Stéphane , Ledoux Gilles , Ou Meigui , Perriat Pascal
Published: December 2006

Peroxidase labeled streptavidin was immobilized onto the surface of bulk and clusterlike metal films at a distance controlled by a peptide chain with a length between 1.3 and 7.8nm. Luminol chemiluminescence which occurred at peroxidase vicinity depends on the metal nanostructure. When peroxidase is attached on a bulklike film, chemiluminescence increases monotonously with the distance because of a decrease of the light emission quenching by metal. When peroxidase is attached on a clusterlike film, chemiluminescence undergoes a complex variation with the metal/catalyst distance evidencing a competition between the already mentioned quenching process and a nanostructure-induced catalysis enhancement.
First principles calculation on polytypes of ordered defect compound CuIn5Se8
Authors: Jiang Fangdan , Feng Jiayou
Published: December 2006

Polytypes of ordered defect compound CuIn5Se8 were constructed based on chalcopyrite and CuAu-like CuInSe2. First principles calculation was used to perform structural optimization and calculate the total energy. Total energy calculation shows that P4¯ symmetry polytype is slightly stable than P222 symmetry polytype. After structural optimization, P4¯ and P222 symmetry polytypes show small differences in lattice parameters and electronic properties. The calculated band gap of CuIn5Se8 polytypes is 0.30(+0.01)eV higher than that of CuInSe2. The neglect of P222 symmetry polytype is attributed to the imperceptible differences between P4¯ and P222 symmetry polytypes.
Defect induced formation of CoSi2 nanowires by focused ion beam synthesis
Authors: Akhmadaliev C. , Schmidt B. , Bischoff L.
Published: December 2006

Cobalt implantation with a focused ion beam (FIB) was applied to study ion beam synthesis of cobalt disilicide nanowires in silicon. Two mechanisms of CoSi2 nanowire formation were investigated: (a) conventional synthesis by Co++ FIB implantation at elevated temperatures into silicon along in-plane ⟨110⟩ Si crystal direction and subsequent annealing and (b) self-aligned CoSi2 nanowire growth in cobalt supersaturated silicon on FIB-induced defects at room temperature during subsequent annealing. The obtained CoSi2 nanowires are 20–100nm in diameter and several micrometers long.
Nanosilicon dot arrays with a bit pitch and a track pitch of 25nm formed by electron-beam drawing and reactive ion etching for 1Tbit∕in.2 storage
Authors: Hosaka Sumio , Sano Hirotaka , Shirai Masumi , Sone Hayato
Published: December 2006

The formation of very fine Si dots with a bit pitch and a track pitch of less than 25nm using electron-beam (EB) lithography on ZEP520 and calixarene EB resists and CF4 reactive ion etching has been demonstrated. The experimental results indicate that the calixarene resist is very suitable for forming an ultrahigh-packed bit array pattern of Si dots. This result promises to open the way toward 1Tbit∕in.2 storage using patterned media with a dot size of <15nm.
Temperature dependence of the exciton transition in semiconductor quantum dots
Authors: Liptay Thomas J. , Ram Rajeev J.
Published: December 2006

The authors measure the temperature dependence of the first absorption feature (dE∕dT) for different sizes of CdSe∕ZnS nanocrystals. In contrast to previous experiments, they find that dE∕dT is experimentally identical for all nanocrystal sizes considered and agrees well with the bulk CdSe value. They show that a first order model that only considers the exciton confinement energy can explain the existing experimental dE∕dT values for both epitaxial quantum dots (InAs, In0.6Ga0.4As, GaAs) and colloidal nanocrystals (CdSe, PbS, PbSe).
Improved electroluminescent performances of europium-complex based devices by doping into electron-transporting/hole-blocking host
Authors: Xin Q. , Li W. L. , Che G. B. , Su W. M. , Sun X. Y. , Chu B. , Li B.
Published: December 2006

High-efficiency, pure red organic light-emitting devices were fabricated by doping a europium-complex Eu(DBM)3pyzphen (DBM=dibenzoylmethane, pyzphen=pyrazino[2,3-f][1,10]phenanthroline) into 4,7-diphenyl-1,10-phenanthroline as emission layer. A maximum current efficiency of 5.1cd∕A at the current density of 1.2mA∕cm2 and a maximum luminance of 1400cd∕m2 were obtained from a 25wt% Eu(DBM)3pyzphen doped device. High efficiencies were maintained at high current densities and high luminance. For example, at the current density of 10mA∕cm2, the efficiency reached 3.8cd∕A. It means that the efficiency roll-off, a major obstacle to the development of Eu-complex ogranic light-emitting devices, was greatly alleviated. The mechanisms behind the improvement are discussed.
High-performance pentacene thin-film transistors with high dielectric constant gate insulators
Authors: Kitamura M. , Arakawa Y.
Published: December 2006

Pentacene thin-film transistors (TFTs) with titanium silicon oxide (Ti1−xSixO2) gate insulator have been fabricated to realize high field-effect mobility at practical voltages. The Ti1−xSixO2 films deposited by rf sputtering exhibited a flat surface and high dielectric constant. The pentacene TFT with the Ti1−xSixO2 gate insulator had high performance with a threshold voltage of −1.6V, an inverse subthreshold slope of 0.13V∕decade, and a current on/off ratio of 107 at a voltage of −10V. The field-effect mobilities of higher than 1cm2∕Vs were obtained in the whole voltage range of −2to−15V.
Viral structural transitions: An all-atom multiscale theory
Authors: Miao Yinglong , Ortoleva Peter J.
Published: December 2006

An all-atom theory of viral structural transitions (STs) is developed based on a multiscale analysis of the N-atom Liouville equation. The approach yields an understanding of viral STs from first principles and a calibrated interatomic force field. To carry out the multiscale analysis, we introduce slow variables characterizing the whole-virus dynamics. Use of the “nanocanonical ensemble” technique and the fundamental hypothesis of statistical mechanics (i.e., the equivalence of long-time and ensemble averages) is shown to imply a Fokker-Planck equation yielding the coarse-grained evolution of the slow variables. As viral STs occur on long time scales, transition state theory is used to estimate the energy barrier of transition between free energy wells implied by observed hysteresis in viral STs. Its application to Nudaurelia capensis ω virus provides an upper bound on the free energy barrier when a single dilatational order parameter is used. The long time scale of viral STs is shown to follow from the aggregate effect of inertia, energy barrier, and entropic effects. Our formulation can be generalized for multiple order parameter models to account for lower free energy barrier pathways for transition. The theory with its all-atom description can be applied to nonviral nanoparticles as well.
Statistical mechanical theory for steady state systems. VI. Variational principles
Authors: Attard Phil
Published: December 2006

Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard’s expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.
Effect of initial condition on the sound generation by flow past a rotary-oscillating circular cylinder
Authors: Inoue Osamu
Published: December 2006

Effects of forced rotary oscillation on the generation of the sound from a circular cylinder in a uniform flow are investigated by direct solution of the two-dimensional, unsteady, compressible Navier-Stokes equations. Results show that the effect on the sound generation of rotary oscillation with frequency f is equivalent to that of periodic blowing and suction with frequency 2f; the sound field is determined by the interaction between the monopole generated by rotary oscillation and the dipole generated by vortex shedding from the cylinder. Results also show that, depending on initial conditions, different sound fields as well as flow fields can be generated for same flow parameters.
Production of hydrogen peroxide in the atmosphere of a Snowball Earth and the origin of oxygenic photosynthesis
Authors: Liang Mao-Chang , Hartman Hyman , Kopp Robert E. , Kirschvink Joseph L. , Yung Yuk L.
Published: December 2006

During Proterozoic time, Earth experienced two intervals with one or more episodes of low-latitude glaciation, which are probable “Snowball Earth” events. Although the severity of the historical glaciations is debated, theoretical “hard Snowball” conditions are associated with the nearly complete shutdown of the hydrological cycle. We show here that, during such long and severe glacial intervals, a weak hydrological cycle coupled with photochemical reactions involving water vapor would give rise to the sustained production of hydrogen peroxide. The photochemical production of hydrogen peroxide has been proposed previously as the primary mechanism for oxidizing the surface of Mars. During a Snowball, hydrogen peroxide could be stored in the ice; it would then be released directly into the ocean and the atmosphere upon melting and could mediate global oxidation events in the aftermath of the Snowball, such as that recorded in the Fe and Mn oxides of the Kalahari Manganese Field, deposited after the Paleoproterozoic low-latitude Makganyene glaciation. Low levels of peroxides and molecular oxygen generated during Archean and earliest Proterozoic non-Snowball glacial intervals could have driven the evolution of oxygen-mediating and -using enzymes and thereby paved the way for the eventual appearance of oxygenic photosynthesis.
Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns
Authors: Lezon Timothy R. , Banavar Jayanth R. , Cieplak Marek , Maritan Amos , Fedoroff Nina V.
Published: December 2006

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in
Saccharomyces cerevisiae
chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems.
Crystallographic protein model-building on the web
Authors: Gopal Kreshna , McKee Erik , Romo Tod , Pai Reetal , Smith Jacob , Sacchettini James , Ioerger Thomas
Published: December 2006

Summary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation.

Availability: Web interface, downloadable binaries and documentation at

Contact:  textal@tamu.edu
Prophet, a web-based tool for class prediction using microarray data
Authors: Medina Ignacio , Montaner David , Tárraga Joaquín , Dopazo Joaquín
Published: December 2006

Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found.

Availability: Prophet can be found at the URL or within the GEPAS package at

Contact:  jdopazo@cipf.es

Supplementary information:
BioNetBuilder: automatic integration of biological networks
Authors: Avila-Campillo Iliana , Drew Kevin , Lin John , Reiss David J. , Bonneau Richard
Published: December 2006

BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for ∼1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases.

Availability:  

Contact:  iliana_avila-campillo@merck.com
K-Fold: a tool for the prediction of the protein folding kinetic order and rate
Authors: Capriotti E. , Casadio R.
Published: December 2006

Summary: K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature. The method predicts whether a protein of known atomic structure folds according to a two-state or a multi-state kinetics and correctly classifies 81% of the folding mechanisms when tested over the training set of the 63 proteins. It also predicts as a further option the logarithm of the folding rate. To the best of our knowledge, the tool discriminates for the first time whether a protein is characterized by a two state or a multiple state kinetics, during the folding process, and concomitantly estimates also the value of the constant rate of the process. When used to predict the logarithm of the folding rate, K-Fold scores with a correlation value to the experimental data of 0.74 (with a SE of 1.2).

Availability:  

Contact:  emidio@biocomp.unibo.it

Supplementary information:
Flexible empirical Bayes models for differential gene expression
Authors: Lo Kenneth , Gottardo Raphael
Published: December 2006

Motivation: Inference about differential expression is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular for this type of problem. The two most common hierarchical models are the hierarchical Gamma–Gamma (GG) and Lognormal–Normal (LNN) models. However, to facilitate inference, some unrealistic assumptions have been made. One such assumption is that of a common coefficient of variation across genes, which can adversely affect the resulting inference.

Results: In this paper, we extend both the GG and LNN modeling frameworks to allow for gene-specific variances and propose EM based algorithms for parameter estimation. The proposed methodology is evaluated on three experimental datasets: one cDNA microarray experiment and two Affymetrix spike-in experiments. The two extended models significantly reduce the false positive rate while keeping a high sensitivity when compared to the originals. Finally, using a simulation study we show that the new frameworks are also more robust to model misspecification.

Availability: The R code for implementing the proposed methodology can be downloaded at

Contact:  c.lo@stat.ubc.ca

Supplementary information: The supplementary material is available at