bluuebunny/crossref_metadata_2025 huggingface dataset:
Remarks on effective action and entanglement entropy of Maxwell field in generic gauge
Authors: Solodukhin Sergey N.
Published: December 2012

Abstract

We analyze the dependence of the effective action and the entanglement entropy in the Maxwell theory on the gauge fixing parameter a in d dimensions. For a generic value of a the corresponding vector operator is nonminimal. The operator can be diagonalized in terms of the transverse and longitudinal modes. Using this factorization we obtain an expression for the heat kernel coefficients of the nonminimal operator in terms of the coefficients of two minimal Beltrami-Laplace operators acting on 0- and 1-forms. This expression agrees with an earlier result by Gilkey et al. Working in a regularization scheme with the dimensionful UV regulators we introduce three different regulators: for transverse, longitudinal and ghost modes, respectively. We then show that the effective action and the entanglement entropy do not depend on the gauge fixing parameter a provided the certain (a-dependent) relations are imposed on the regulators. Comparing the entanglement entropy with the black hole entropy expressed in terms of the induced Newton’s constant we conclude that their difference, the so-called Kabat’s contact term, does not depend on the gauge fixing parameter a. We consider this as an indication of gauge invariance of the contact term.
Perceptions of prenatal and obstetric care in Sub‐Saharan Africa
Authors: Brighton Aimee , D'Arcy Rhiannon , Kirtley Shona , Kennedy Stephen
Published: December 2012

Background

The maternal mortality ratio in Sub‐Saharan Africa remains high, despite progress in reducing maternal mortality in other parts of the world.

Objective

To explore the perceptions of women and communities to identify barriers to the uptake of obstetric services.

Search strategy

A systematic review of qualitative studies exploring perceptions of pregnancy and obstetric services, with thematic synthesis of the included studies.

Selection criteria

Qualitative studies reporting findings from focus group discussions and in‐depth interviews between 1996 and 2009 were included.

Data collection and analysis

Thematic synthesis involved collating and reviewing quotations taken directly from included studies. Themes were generated and clustered for analysis.

Main results

Twenty‐seven studies were included and 6 major themes identified: perceptions of healthcare workers; perceptions of the hospital environment; cultural perceptions of women; cultural perceptions of pregnancy; perceptions of traditional birth attendants and traditional healers; and role of the community in pregnancy and birth.

Conclusion

Community attitudes regarding cultural beliefs and interactions with healthcare providers were identified as barriers to the utilization of healthcare services during pregnancy in Sub‐Saharan Africa. These prevent engagement with prenatal care and timely use of medical services. Addressing the barriers will be seminal to the success of any healthcare intervention.
Motivations and preferences of rural Nigerian women undergoing cervical cancer screening via visual inspection with acetic acid
Authors: Chigbu Chibuike O. , Onyebuchi Azubuike K. , Ajah Leonard O. , Onwudiwe Elijah N.
Published: December 2012

Objective

To determine the motivations and preferences of women participating in visual inspection with acetic acid (VIA) mass cervical cancer screening programs in southeastern Nigeria.

Methods

By means of interviewer‐based questionnaires, data were collected from women participating in mass cervical cancer screenings with VIA in 3 randomly selected communities in each of 2 southeastern Nigerian states between March 1, 2011, and March 31, 2012.

Results

A total of 2312 women were interviewed. Support from husband and community opinion leaders were the most frequently reported factors that motivated the women to participate in the screening. Most participants expected an immediate result for the screening test and immediate treatment for any abnormalities detected.

Conclusion

Community‐based advocacy for cervical cancer screening is a very effective method of creating awareness for cervical cancer screening. Support from spouses and community leaders are important factors in a woman's decision to utilize cervical cancer screening services in southeastern Nigeria. Immediate results and treatments would make the most impact. Family and community participation should be integrated into cervical cancer prevention programs. This, together with a “see and treat” approach, may be central to overcoming the poor utilization of cervical cancer screening services in Nigeria and similar rural settings.
Brain size and the compensation of Alzheimer's disease symptoms: A longitudinal cohort study
Authors: Guo Liang‐Hao , Alexopoulos Panagiotis , Wagenpfeil Stefan , Kurz Alexander , Perneczky Robert ,   Alzheimer's Disease Neuroimaging Initiative
Published: December 2012

Background

Greater intracranial volume (ICV) has been associated with less severe Alzheimer's disease (AD) symptoms at a given level of cerebral pathology. In this study we examine whether ICV modulates the association between clinical disease progression on the one hand and brain atrophy or the apolipoprotein E genotype on the other.

Methods

Six hundred seventy‐four subjects were studied from the AD Neuroimaging Initiative (ADNI). Subjects included 204 controls, 144 patients with AD dementia, and 326 with amnestic mild cognitive impairment (aMCI). Longitudinal analyses were conducted applying generalized estimating equations to examine the influence of ICV on clinical deterioration and atrophy progression. Follow‐up data were available for up to 60 months after the baseline visit (mean 31.42 months, SD 13.12 months).

Results

ICV was not directly associated with clinical worsening or atrophy progression. However, ICV attenuated the impact of atrophy and the apolipoprotein E ε4 allele on clinical disease progression in aMCI.

Conclusion

Greater ICV, that is, premorbid brain size, seems to protect against clinical deterioration in the face of AD‐related brain atrophy in aMCI. The results support the theory of a compensatory role of brain reserve in contrast to a neuroprotective role. The protective effects of morphologic reserve seem to be limited to early clinical AD; once a certain threshold of neurodegenerative burden is passed, a larger premorbid brain no longer offers an advantage in this context.
The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine
Authors: Reiner Joseph E. , Balijepalli Arvind , Robertson Joseph W. F. , Drown Bryon S. , Burden Daniel L. , Kasianowicz John J.
Published: December 2012

Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe nucleotide transport. The available data and analytical results suggest that the proposed method will be limited to reading <80 bases, imposed, in part, by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides.
Atomistic calculation of the local structure in bulk and strained semiconductor alloys
Authors: Woicik J. C.
Published: December 2012

We report the results of an atomistic, random-cluster calculation of the local structure (near-neighbor bond lengths, bond angles, and higher-neighbor distances) in both bulk and strained Ga1−xInxAs alloys. Agreement is found with published experimental extended x-ray-absorption fine-structure studies in all cases.
Nanoscale spatial resolution probes for scanning thermal microscopy of solid state materials
Authors: Tovee P. , Pumarol M. , Zeze D. , Kjoller Kevin , Kolosov O.
Published: December 2012

Scanning thermal microscopy (SThM) uses micromachined thermal sensors integrated in a force sensing cantilever with a nanoscale tip that can be highly useful for exploration of thermal management of nanoscale semiconductor devices as well as mapping of surface and subsurface properties of related materials. Whereas SThM is capable to image externally generated heat with nanoscale resolution, its ability to map and measure thermal conductivity of materials has been mainly limited to polymers or similar materials possessing low thermal conductivity in the range from 0.1 to 1 W m−1 K−1, with lateral resolution on the order of 1 μm. In this paper, we use linked experimental and theoretical approaches to analyse thermal performance and sensitivity of the micromachined SThM probes in order to expand their applicability to a broader range of nanostructures from polymers to semiconductors and metals. We develop physical models of interlinked thermal and electrical phenomena in these probes and their interaction with the sample on the mesoscopic length scale of few tens of nm and then validate these models using experimental measurements of the real probes, which provided the basis for analysing SThM performance in exploration of nanostructures. Our study then highlights critical features of these probes, namely, the geometrical location of the thermal sensor with respect to the probe apex, thermal conductance of the probe to the support base, heat conduction to the surrounding gas, and the thermal conductivity of tip material adjacent to the apex. It furthermore allows us to propose a novel design of the SThM probe that incorporates a multiwall carbon nanotube or similar high thermal conductivity graphene sheet material with longitudinal dimensions on micrometre length scale positioned near the probe apex that can provide contact areas with the sample on the order of few tens of nm. The new sensor is predicted to provide greatly improved spatial resolution to thermal properties of nanostructures as well as to expand the sensitivity of the SThM probe to materials with heat conductivity values up to 100–1000 W m−1 K−1.
Abnormal substrate temperature dependent out-of-plane anisotropy in FeCoNbB amorphous films
Authors: Yu Youxing , Yang Youran , Shan Yijiao , Bi Xiaofang
Published: December 2012

Out-of-plane magnetic anisotropy (OMA) of FeCoNbB amorphous films has been studied. The OMA is abnormally enhanced by elevating the substrate temperature from room-temperature to 500 °C, being much different from most soft-magnetic amorphous films. Furthermore, the films show a slightly decay in the OMA when annealed at a temperature lower than the respective deposition temperature. But when annealed at a temperature 50 °C higher than the respective deposition temperature, the OMA suddenly disappears. Such results indicate a distinguishing mechanism of non-magnetoelastic-anisotropy dominated OMA. A model of co-effects of magnetoelastic anisotropy and microshape anisotropy is proposed.
Quantum state discrimination bounds for finite sample size
Authors: Audenaert Koenraad M. R. , Mosonyi Milán , Verstraete Frank
Published: December 2012

In the problem of quantum state discrimination, one has to determine by measurements the state of a quantum system, based on the a priori side information that the true state is one of the two given and completely known states, ρ or σ. In general, it is not possible to decide the identity of the true state with certainty, and the optimal measurement strategy depends on whether the two possible errors (mistaking ρ for σ, or the other way around) are treated as of equal importance or not. Results on the quantum Chernoff and Hoeffding bounds and the quantum Stein's lemma show that, if several copies of the system are available then the optimal error probabilities decay exponentially in the number of copies, and the decay rate is given by a certain statistical distance between ρ and σ (the Chernoff distance, the Hoeffding distances, and the relative entropy, respectively). While these results provide a complete solution to the asymptotic problem, they are not completely satisfying from a practical point of view. Indeed, in realistic scenarios one has access only to finitely many copies of a system, and therefore it is desirable to have bounds on the error probabilities for finite sample size. In this paper we provide finite-size bounds on the so-called Stein errors, the Chernoff errors, the Hoeffding errors, and the mixed error probabilities related to the Chernoff and the Hoeffding errors.
Interstitial Ti for intermediate band formation in Ti-supersaturated silicon
Authors: Pastor D. , Olea J. , Muñoz-Martín A. , Climent-Font A. , Mártil I. , González-Díaz G.
Published: December 2012

We have analyzed by means of Rutherford backscattering spectrometry (RBS) the Ti lattice location and the degree of crystalline lattice recovery in heavily Ti implanted silicon layers subsequently pulsed laser melted (PLM). Theoretical studies have predicted that Ti should occupy interstitial sites in silicon for a metallic-intermediate band (IB) formation. The analysis of Ti lattice location after PLM processes is a crucial point to evaluate the IB formation that can be clarifyied by means of RBS measurements. After PLM, time-of-flight secondary ion mass spectrometry measurements show that the Ti concentration in the layers is well above the theoretical limit for IB formation. RBS measurements have shown a significant improvement of the lattice quality at the highest PLM energy density studied. The RBS channeling spectra reveals clearly that after PLM processes Ti impurities are mostly occupying interstitial lattice sites.
Examining the heavy p-block with a pseudopotential-based composite method: Atomic and molecular applications of rp-ccCA
Authors: Laury Marie L. , Wilson Angela K.
Published: December 2012

The relativistic pseudopotential variant of the correlation consistent composite approach (rp-ccCA) has been extended to lower p-block-containing molecules. The lower p-block is defined here as elements indium through iodine (In-I) and thallium through astatine (Tl-At). The accuracy of rp-ccCA has previously been established in a study of energetic properties of molecules containing 4p elements and thermodynamic data of 4d-containing molecules. In the current study, the atomic ionization potentials (IPs) and electron affinities (EAs) of In-I and Tl-At, as well as dissociation energies and enthalpies of formation of lower p-block mono-hydrides, mono-oxides, and dimers were determined with rp-ccCA. The compiled data set is referred to as the LP80 data set. The mean absolute deviation of the IPs and the EAs from the experimental data were 2.50 and 3.06 kcal mol−1, respectively. Additionally, the total atomization energy for lead clusters (Pbn, n = 2–6) was determined. For the lead clusters, a decrease in the total atomization energy was observed with the inclusion of spin-orbit coupling. The spin-orbit coupling of the molecules was determined with multireference configuration interaction, while scalar relativistic effects were accounted for within the pseudopotentials. The results obtained by rp-ccCA for the lower p-block support the utilization of the method in future studies where accurate energetic, spectroscopic, and thermodynamic data are necessary.
Development of FeNiMoB thin film materials for microfabricated magnetoelastic sensors
Authors: Liang Cai , Gooneratne Chinthaka , Cha Dongkyu , Chen Long , Gianchandani Yogesh , Kosel Jurgen
Published: December 2012

MetglasTM 2826MB foils of 25–30 μm thickness with the composition of Fe40Ni38Mo4B18 have been used for magnetoelastic sensors in various applications over many years. This work is directed at the investigation of ∼3 μm thick iron-nickel-molybdenum-boron (FeNiMoB) thin films that are intended for integrated microsystems. The films are deposited on Si substrate by co-sputtering of iron-nickel (FeNi), molybdenum (Mo), and boron (B) targets. The results show that dopants of Mo and B can significantly change the microstructure and magnetic properties of FeNi materials. When FeNi is doped with only Mo its crystal structure changes from polycrystalline to amorphous with the increase of dopant concentration; the transition point is found at about 10 at. % of Mo content. A significant change in anisotropic magnetic properties of FeNi is also observed as the Mo dopant level increases. The coercivity of FeNi films doped with Mo decreases to a value less than one third of the value without dopant. Doping the FeNi with B together with Mo considerably decreases the value of coercivity and the out-of-plane magnetic anisotropy properties, and it also greatly changes the microstructure of the material. In addition, doping B to FeNiMo remarkably reduces the remanence of the material. The film material that is fabricated using an optimized process is magnetically as soft as amorphous MetglasTM 2826MB with a coercivity of less than 40 Am−1. The findings of this study provide us a better understanding of the effects of the compositions and microstructure of FeNiMoB thin film materials on their magnetic properties.
Surface composition of BaTiO3/SrTiO3(001) films grown by atomic oxygen plasma assisted molecular beam epitaxy
Authors: Barbier A. , Mocuta C. , Stanescu D. , Jegou P. , Jedrecy N. , Magnan H.
Published: December 2012

We have investigated the growth of BaTiO3 thin films deposited on pure and 1% Nb-doped SrTiO3(001) single crystals using atomic oxygen assisted molecular beam epitaxy and dedicated Ba and Ti Knudsen cells. Thicknesses up to 30 nm were investigated for various layer compositions. We demonstrate 2D growth and epitaxial single crystalline BaTiO3 layers up to 10 nm before additional 3D features appear; lattice parameter relaxation occurs during the first few nanometers and is completed at ∼10 nm. The presence of a Ba oxide rich top layer that probably favors 2D growth is evidenced for well crystallized layers. We show that the Ba oxide rich top layer can be removed by chemical etching. The present work stresses the importance of stoichiometry and surface composition of BaTiO3 layers, especially in view of their integration in devices.
Quadratic coupling treatment of the Jahn-Teller effect in the triply-degenerate electronic state of $\bf CH_4^+$CH4+: Can one account for floppiness?
Authors: Mondal T. , Varandas A. J. C.
Published: December 2012

The Jahn-Teller (JT) coupling effects in the triply degenerate ground electronic state of methane radical cation are investigated theoretically within a quadratic vibronic coupling approach. The underlying potential energy surfaces over the two-dimensional space of nuclear coordinates, subject to the T2 ⊗ (e + t2 + t2) Jahn-Teller effect, are established from extensive ab initio calculations using the multi-reference configuration interaction method and then employed to determine the various parameters of a diabatic Hamiltonian of this system. Our previous investigation [T. Mondal and A. J. C. Varandas, J. Chem. Phys. 135, 174304 (2011)10.1063/1.3658641], relying on the linear vibronic coupling approach augmented by only a diagonal second-order term of the totally symmetric mode, are extended here by including all possible quadratic coupling constants of JT active e and t2 modes. Inclusion of these quadratic couplings is found to be important to reproduce correctly the broad vibrational structure and for a better description of dynamical JT effect in the first vibronic band of this radical cation. The impact of large amplitude motions (which are responsible for floppiness of the molecule) on the vibronic structure and dynamics of the first photoelectron band have been examined via readjustment of their linear coupling parameters up to ±10%.
Z-microscopy for parallel axial imaging with micro mirror array
Authors: Yang Chuan , Shi Kebin , Zhou Mingda , Zheng Siyang , Yin Shizhuo , Liu Zhiwen
Published: December 2012

We propose and demonstrate a method of “z-microscopy” by utilizing an array of 45°-tilted micro mirrors arranged along the axial direction. Image signals emitted from different axial positions can be orthogonally reflected by the corresponding micro mirrors and spatially separated for parallel detection, essentially converting the more challenging axial imaging to a lateral imaging problem. Each micro mirror also provides optical sectioning capability due to its finite dimension. Numerical analysis shows that nearly diffraction limited axial resolution can be achieved. Experimental demonstration of z-imaging of fluorescent microspheres is also presented.
Focused ion beam milling and deposition techniques in validation of mass change value and position determination method for micro and nanomechanical sensors
Authors: Nieradka K. , Stegmann H. , Gotszalk T.
Published: December 2012

In this paper, we apply the focused ion beam technique (FIB) to add and subtract material from a microcantilever sensor and use a non-uniform mass sensitivity model to determine the position and value of mass load. We add and remove a defined amount of mass from the cantilevers at specified positions by FIB assisted deposition and milling, thus we introduce non-uniform mass load. Utilizing intrinsic thermal noise of the cantilevers, we measure the frequencies of multiple modes of flexural vibrations in ambient air before and after FIB processing. By application of a theoretical mass sensitivity model, we are able to determine both, the amount of added or removed mass and its position along the cantilever length. The results obtained from the model are in good agreement with estimations based on scanning electron microscopy and FIB observations.
Rectifying and perfect spin filtering behavior realized by tailoring graphene nanoribbons
Authors: He Jun , Chen Ke-Qiu
Published: December 2012

An armchair graphene nanoribbon based electronic device with spin filtering and rectifying behavior is designed by means of molecular tailoring, and the electronic transport properties are calculated by using nonequilibrium Green's functions in combination with the density functional theory. The results show that the rectifying behavior can be observed in the junctions, and the rectifying ratio can be effectively tuned by edge doping. Furthermore, perfect spin polarization behavior can also be observed in the junctions.
Ferromagnetic behaviors in NiO-based nanofibers synthesized by electrospinning method
Authors: Luo Yi-Dong , Lin Yuan-Hua , Feng Yan-Nan , Zhang Yu-Jun , Song Yu , Shen Yang , Nan Ce-Wen
Published: December 2012

LixNi0.97-xFe0.03 nanofibers with different Li doping concentration have been synthesized by electrospinning method. The phase composition and microstructure analysis show that Fe and Li doping has no influence on the phase structure and morphology of NiO nanofibers, which reveal that the doped Fe and Li have been incorporated into the NiO host lattice. All the Li and Fe co-doped NiO nanofiber samples show obvious room-temperature ferromagnetic properties. The saturation magnetization can be enhanced with increase of the Li doping concentration. This phenomenon can be ascribed to the fact that the hole doping makes ferromagnetic coupling interactions between the holes and localized Fe 3d states more efficient.
Design and optimization of a light-emitting diode projection micro-stereolithography three-dimensional manufacturing system
Authors: Zheng Xiaoyu , Deotte Joshua , Alonso Matthew P. , Farquar George R. , Weisgraber Todd H. , Gemberling Steven , Lee Howon , Fang Nicholas , Spadaccini Christopher M.
Published: December 2012

The rapid manufacture of complex three-dimensional micro-scale components has eluded researchers for decades. Several additive manufacturing options have been limited by either speed or the ability to fabricate true three-dimensional structures. Projection micro-stereolithography (PμSL) is a low cost, high throughput additive fabrication technique capable of generating three-dimensional microstructures in a bottom-up, layer by layer fashion. The PμSL system is reliable and capable of manufacturing a variety of highly complex, three-dimensional structures from micro- to meso-scales with micro-scale architecture and submicron precision. Our PμSL system utilizes a reconfigurable digital mask and a 395 nm light-emitting diode (LED) array to polymerize a liquid monomer in a layer-by-layer manufacturing process. This paper discusses the critical process parameters that influence polymerization depth and structure quality. Experimental characterization and performance of the LED-based PμSL system for fabricating highly complex three-dimensional structures for a large range of applications is presented.
An alternating direction algorithm for two-phase flow visualization using gamma computed tomography
Authors: Xue Qian , Wang Huaxiang , Cui Ziqiang , Yang Chengyi
Published: December 2012

In order to build high-speed imaging systems with low cost and low radiation leakage, the number of radioactive sources and detectors in the multiphase flow computed tomography (CT) system has to be limited. Moreover, systematic and random errors are inevitable in practical applications. The limited and corrupted measurement data have made the tomographic inversion process the most critical part in multiphase flow CT. Although various iterative reconstruction algorithms have been developed based on least squares minimization, the imaging quality is still inadequate for the reconstruction of relatively complicated bubble flow. This paper extends an alternating direction method (ADM), which is originally proposed in compressed sensing, to image two-phase flow using a low-energy γ-CT system. An l1 norm-based regularization technique is utilized to treat the ill-posedness of the inverse problem, and the image reconstruction model is reformulated into one having partially separable objective functions, thereafter a dual-based ADM is adopted to solve the resulting problem. The feasibility is demonstrated in prototype experiments. Comparisons between the ADM and the conventional iterative algorithms show that the former has obviously improved the space resolution in reasonable time.
Multidimensional data reconstruction for two color fluorescence microscopy
Authors: Dilipkumar Shilpa , Mondal Partha Pratim
Published: December 2012

We propose an iterative data reconstruction technique specifically designed for multi-dimensional multi-color fluorescence imaging. Markov random field is employed (for modeling the multi-color image field) in conjunction with the classical maximum likelihood method. It is noted that, ill-posed nature of the inverse problem associated with multi-color fluorescence imaging forces iterative data reconstruction. Reconstruction of three-dimensional (3D) two-color images (obtained from nanobeads and cultured cell samples) show significant reduction in the background noise (improved signal-to-noise ratio) with an impressive overall improvement in the spatial resolution (≈250 nm) of the imaging system. Proposed data reconstruction technique may find immediate application in 3D in vivo and in vitro multi-color fluorescence imaging of biological specimens.
Ferrofluid pipe flow under the influence of the magnetic field of a cylindrical coil
Authors: Papadopoulos P. K. , Vafeas P. , Hatzikonstantinou P. M.
Published: December 2012

Ferrofluid pipe flow under the effect of a co-linear, finite length cylindrical coil is examined numerically. The specific flow configuration is chosen as it is encountered in engineering and bioengineering applications such as magnetic drug targeting systems. The objective of the paper is twofold: first, to investigate the accuracy of an analytical solution for the magnetization equation and assess its validity when used for non-uniform magnetic fields. It is found that it can be very helpful as a means of estimating the magnetization, especially for strong magnetic fields with low gradients; second, to examine the effects of the magnetic field on the flow and study the relevant importance of the magnetic terms of the momentum equation. The parameters that we examine are the strength of the magnetic field and of its gradients, the volumetric concentration of the magnetic particles, and the dimensions (length and diameter) of the coil. It is revealed that the axial pressure drop depends linearly on the volumetric concentration and that the magnetoviscosity effect is negligible in cases of non-uniform magnetic fields.
Magnetic turbulence suppression by a helical mode in a cylindrical geometry
Authors: Kim J.-H. , Terry P. W.
Published: December 2012

To study processes involved in a helical structure formation in reversed field pinch devices, the scaling of a turbulent boundary layer width associated with a vortex structure having large shears of magnetic field and flow is obtained for reduced magnetohydrodynamics. The coherent vortex, with its flow and magnetic shears, interacts with Alfvén turbulence, forming a turbulent boundary layer at the edge of the vortex. The layer arises from the balance between turbulence diffusion rates and shearing rates and suppresses the turbulence in the structure. The suppression of turbulence impedes relaxation of the coherent vortex profiles, leading to long coherence times. The scaling of the boundary layer width reveals that both magnetic shear and flow shear can effectively suppress magnetic turbulence.
Modeling of LbL multilayers with controlled thickness, roughness, and specific surface area
Authors: Batys Piotr , Weroński Paweł
Published: December 2012

We present computer simulation results of the layer by layer self-assembling process of colloidal particles. We have generated five multilayer structures of monodisperse spherical particles according to a generalized model of random sequential adsorption of hard spheres. The multilayers, each created at a different single-layer surface coverage, are of similar thickness. We have compared the transparency of the five multilayers and the structure of their outer layers in terms of the two-dimensional pair-correlation function. We have analyzed the variation of multilayer thickness with the number of adsorbed layers. We have also calculated the root-mean-square roughness of the multilayers as a function of the number of adsorption cycles. Finally, we have determined the specific surface area of the porous films as a function of the distance from the solid substrate. Our results suggest that in the limit of low porosity the multilayer transparency decreases exponentially with its porosity. The multilayer thickness is directly proportional to the number of adsorption cycles. The average single-layer thickness grows asymptotically with the single-layer coverage. We have also found that with the number of adsorbed layers the multilayer roughness increases to an asymptotic value. We have observed oscillatory variations of the multilayer specific surface area, decaying exponentially with the distance from the substrate. The decay length of the oscillation increases exponentially with the surface coverage. We have also determined the particle layer interpenetration for each multilayer and we have found that it decreases exponentially with the increase of the coverage. Our results suggest that all the film characteristics strongly depend on the method of its preparation and can be controlled by manipulating the single-layer surface coverage or deposition time. The results can be useful for efficient designing multilayers with desired properties.
High thermoelectric figure of merit in silicon-germanium superlattice structured nanowires
Authors: Shi Lihong , Jiang Jinwu , Zhang Gang , Li Baowen
Published: December 2012

By using a combination of the first-principles density functional theory and nonequilibrium Green's function for electron and phonon transport, we investigate the thermoelectric properties of silicon-germanium superlattice nanowires (NWs). Our results show that introducing superlattice structures always increases thermoelectric figure of merit, ZT, which depends on the periodic length of the superlattice NWs. For n-type superlattice NWs, the achievable maximum ZT is 4.7, which is 5-fold increase as compared to the equivalent pristine silicon NWs. For p-type wires, the achieved maximum ZT is 2.74, which is 4.6-fold increase as compared to the pristine silicon NWs.
Low-frequency noise in gallium nitride nanowire mechanical resonators
Authors: Gray Jason M. , Bertness Kris A. , Sanford Norman A. , Rogers Charles T.
Published: December 2012

We report on the low-frequency 1/f (flicker) parameter noise displayed by the resonance frequency of doubly clamped c-axis gallium nitride nanowire (NW) mechanical resonators. The resonators are electrostatically driven and their mechanical response is electronically detected via NW piezoresistance. With an applied dc voltage bias, a NW driven near its mechanical resonance generates a dc and Lorentzian rf current that both display 1/f noise. The rf current noise is proportional to the square of the derivative of the Lorentzian lineshape with a magnitude highly dependent on NW dc bias voltage conditions, consistent with a model wherein noise in the NW's electrical impedance leads to temperature noise from local Joule heating, which in turn generates resonance frequency noise via thermal expansion and the temperature-dependent Young's modulus. An example device with a 27.8 MHz resonance frequency experiences an approximate resonance frequency shift of −1.4 Hz/nW. The resonance frequency noise increases as the square of the bias voltage, indicating specific operating conditions that optimize the signal-to-noise ratio in proposed NW sensors.
Rotational and vibrational temperatures in a hydrogen discharge with a magnetic X-point
Authors: Tsankov Tsanko V. , Toko Kaoru , Czarnetzki Uwe
Published: December 2012

A novel plasma source with a magnetic X-point has been developed to probe an alternative for cesium-free negative hydrogen ion production. This study presents first results for the gas and vibrational temperatures in the source at 1 Pa and various RF powers. The temperatures are obtained from analysis of the intensity distribution of the molecular Fulcher-α bands. The gas temperature increases with the RF power, while the vibrational temperature remains constant in the studied range of RF powers. Both quantities show no appreciable spatial dependence. The obtained high values of the vibrational temperatures indicate a high population of the vibrational levels, favourable for the volume negative ion production. A theoretical concept indicates the presence of an optimum value for the vibrational temperature at which the negative hydrogen ion yield by volume processes has a maximum. Coincidently, the measured value is close to this optimum. This indicates that the novel concept can provide certain advantages compared to other sources based on volume production.
Growth analysis of (Ag,Cu)InSe2 thin films via real time spectroscopic ellipsometry
Authors: Little S. A. , Ranjan V. , Collins R. W. , Marsillac S.
Published: December 2012

In situ and ex situ characterization methods have been applied to investigate the properties of (Ag,Cu)InSe2 (ACIS) thin films. Data acquired from real time spectroscopic ellipsometry (RTSE) experiments were analyzed to extract the evolution of the nucleating, bulk, and surface roughness layer thicknesses. The evolution of these layer thicknesses suggests a transition from Volmer-Weber to Stranski-Krastanov type behavior when Cu is replaced by Ag. The complex dielectric functions of ACIS at both deposition and room temperature as a function of film composition were also extracted from the RTSE data, enabling parameterization of the alloy optical properties.
Analyzing threshold pressure limitations in microfluidic transistors for self-regulated microfluidic circuits
Authors: Kim Sung-Jin , Yokokawa Ryuji , Takayama Shuichi
Published: December 2012

This paper reveals a critical limitation in the electro-hydraulic analogy between a microfluidic membrane-valve (μMV) and an electronic transistor. Unlike typical transistors that have similar on and off threshold voltages, in hydraulic μMVs, the threshold pressures for opening and closing are significantly different and can change, even for the same μMVs depending on overall circuit design and operation conditions. We explain, in particular, how the negative values of the closing threshold pressures significantly constrain operation of even simple hydraulic μMV circuits such as autonomously switching two-valve microfluidic oscillators. These understandings have significant implications in designing self-regulated microfluidic devices.
Charge loss mechanism of non-volatile V3Si nano-particles memory device
Authors: Kim Dongwook , Uk Lee Dong , Kyu Kim Eun , Cho Won-Ju
Published: December 2012

We studied the charge loss mechanism of a non-volatile memory device with vanadium silicide (V3Si) nano-particles (NPs) embedded in a silicon dioxide dielectric layer. To fabricate the memory device, V3Si NPs with an average size of 4–6 nm were formed between the tunnel and control oxide layers by a thin film deposition and a post-annealing process at 800  °C for 5 s. Using the gate structure containing the V3Si NPs, a flash memory structure was fabricated with a channel length and width of 5 μm. This device maintained the memory window at about 1 V after 104 s when program/erase voltages of ±9 V were applied for 1 s. The activation energies of the V3Si NP memory devices with charge loss rates of 10%, 15%, 20%, and 25% were approximately 0.16, 0.24, 0.35, and 0.50 eV, respectively. The charge loss mechanism can be attributed to direct tunneling as a result of the NPs associating with the interface trap in the tunneling oxide, the Pool-Frenkel current, and the oxide defect.
Atomic layer deposition of Sc2O3 for passivating AlGaN/GaN high electron mobility transistor devices
Authors: Wang Xinwei , Saadat Omair I. , Xi Bin , Lou Xiabing , Molnar Richard J. , Palacios Tomás , Gordon Roy G.
Published: December 2012

Polycrystalline, partially epitaxial Sc2O3 films were grown on AlGaN/GaN substrates by atomic layer deposition (ALD). With this ALD Sc2O3 film as the insulator layer, the Sc2O3/AlGaN/GaN metal-insulator-semiconductor high electron mobility transistors showed excellent electrical performance with a high Ion/Ioff ratio of over 108 and a low subthreshold slope of 75 mV/dec. The UV/NH4OH surface treatment on AlGaN/GaN prior to ALD was found to be critical for achieving these excellent figures. In addition, the Sc2O3 dielectric is found to be negatively charged, which facilitates the enhancement-mode operation. While bare Sc2O3 suffers from moisture degradation, depositing a moisture blocking layer of ALD Al2O3 can effectively eliminate this effect.
Electric field measurement in microwave discharge ion thruster with electro-optic probe
Authors: Ise Toshiyuki , Tsukizaki Ryudo , Togo Hiroyoshi , Koizumi Hiroyuki , Kuninaka Hitoshi
Published: December 2012

In order to understand the internal phenomena in a microwave discharge ion thruster, it is important to measure the distribution of the microwave electric field inside the discharge chamber, which is directly related to the plasma production. In this study, we proposed a novel method of measuring a microwave electric field with an electro-optic (EO) probe based on the Pockels effect. The probe, including a cooling system, contains no metal and can be accessed in the discharge chamber with less disruption to the microwave distribution. This method enables measurement of the electric field profile under ion beam acceleration. We first verified the measurement with the EO probe by a comparison with a finite-difference time domain numerical simulation of the microwave electric field in atmosphere. Second, we showed that the deviations of the reflected microwave power and the beam current were less than 8% due to inserting the EO probe into the ion thruster under ion beam acceleration. Finally, we successfully demonstrated the measurement of the electric-field profile in the ion thruster under ion beam acceleration. These measurements show that the electric field distribution in the thruster dramatically changes in the ion thruster under ion beam acceleration as the propellant mass flow rate increases. These results indicate that this new method using an EO probe can provide a useful guide for improving the propulsion of microwave discharge ion thrusters.
Incommensurate phases of a supported nanoparticle film subjected to uniaxial compression
Authors: Chua Yenchao , Leahy Brian , Zhang Minke , You Siheng , Lee Ka Yee C. , Coppersmith Susan N. , Lin Binhua
Published: December 2012

We investigate experimentally and theoretically the sequence of phases that occurs when a self-assembled monolayer of gold nanoparticles supported on a fluid is compressed uniaxially in a Langmuir trough. Uniaxial compression of the monolayer results in the appearance of lines that have been shown to be regions of trilayer. These lines exhibit complex patterns that depend on the extent of compression. We show that these patterns can be understood in terms of an equilibrium statistical mechanical theory, originally developed in the context of commensurate–incommensurate transitions in krypton monolayers adsorbed on graphite, in which there is an energy cost to line deformations and to line intersections. Even though line intersections are energetically costly, they lower the free energy because they cause the entropy of the system to increase when the density of lines is low enough. Our analytic and Monte Carlo analyses of the model demonstrate that the model exhibits two-phase coexistence. Our experimental observations are qualitatively consistent with the predictions of the model.
Influences of Cyclic, High Temperatures on Juvenile Channel Catfish Growth and Feeding
Authors: Arnold Michael B , Torrans Eugene L , Allen Peter J
Published: December 2012

Effects of high summer temperatures on Channel Catfish Ictalurus punctatus are poorly understood, particularly for thermal regimes that mimic pond aquaculture conditions. Therefore, this study examined the effects of three cycling upper-range temperature regimes (23–27°C, 27–31°C, and 31–35°C) characteristic of aquaculture environments in the Mississippi Delta. Feed conversion ratio, feed consumption, specific growth rate, activity levels, survival, and overall growth in terms of wet weight and TL were measured in fingerling channel catfish over an 8-week period in a flow-through, multiple-tank system. Specific growth rate, feed consumption, TL, and wet weight of fish increased significantly in the 27–31°C treatment in contrast to the 23–27°C and 31–35°C treatments. Feed conversion ratio was lowest in the 27–31°C treatment, whereas activity levels were highest in the 31–35°C treatment. Survival significantly decreased for catfish in the warmest treatment compared with catfish in the coolest treatment. These results indicate that high temperatures decrease growth in Channel Catfish, largely due to reduced food consumption and feed conversion and increased levels of activity. Therefore, increases in temperatures, such as from climate change, present challenges to the culture and management of Channel Catfish.
ChromoZoom: a flexible, fluid, web-based genome browser
Authors: Pak Theodore R. , Roth Frederick P.
Published: December 2012

Summary: Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data. ChromoZoom thereby enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets.

Availability: Human and yeast genome researchers may browse recent assemblies within ChromoZoom at http://chromozoom.org/. Source code is available at http://github.com/rothlab/chromozoom/.

Contact:  fritz.roth@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
nestly—a framework for running software with nested parameter choices and aggregating results
Authors: McCoy Connor O. , Gallagher Aaron , Hoffman Noah G. , Matsen Frederick A.
Published: December 2012

Summary: The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

Availability: Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).

Contact:  cmccoy@fhcrc.org or matsen@fhcrc.org
A knowledge-based orientation potential for transcription factor-DNA docking
Authors: Takeda Takako , Corona Rosario I. , Guo Jun-tao
Published: December 2012

Motivation: Computational modeling of protein–DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein–DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.

Results: We demonstrated the performance of this new potential in TF–DNA binding affinity prediction, discrimination of native protein–DNA complex from decoy structures, and most importantly in rigid TF–DNA docking. The rigid TF–DNA docking with the new orientation potential, on a benchmark of 38 complexes, successfully predicts 42% of the cases with root mean square deviations lower than 1 Å and 55% of the cases with root mean square deviations lower than 3 Å. The results suggest that docking with this new orientation-dependent, coarse-grained statistical potential can achieve high-docking accuracy and can serve as a crucial first step in multi-stage flexible protein–DNA docking.

Availability and implementation: The new potential is available at http://bioinfozen.uncc.edu/Protein_DNA_orientation_potential.tar.

Contact:  jguo4@uncc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.