bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolomics and fluxomics approaches
Authors: Cascante Marta , Marin Silvia
Published: September 2008

Systems biology is based on the understanding that the behaviour of the whole is greater than would be expected from the sum of its parts. Thus the ultimate goal of systems biology is to predict the behaviour of the whole system on the basis of the list of components involved. Recent advances in ‘-omics’ technologies and the development of new computational techniques and algorithms have greatly contributed to progress in this field of biology. Among the main ‘-omics’ technologies, metabolomics is expected to play a significant role in bridging the phenotype–genotype gap, since it amplifies changes in the proteome and provides a better representation of the phenotype of an organism than other methods. However, knowledge of the complete set of metabolites is not enough to predict the phenotype, especially for higher cells in which the distinct metabolic processes involved in their production and degradation are finely regulated and interconnected. In these cases, quantitative knowledge of intracellular fluxes is required for a comprehensive characterization of metabolic networks and their functional operation. These intracellular fluxes cannot be detected directly, but can be estimated through interpretation of stable isotope patterns in metabolites. Moreover, analysis of these fluxes by means of metabolic control theories offers a potentially unifying, holistic paradigm to explain the regulation of cell metabolism. In this chapter, we provide an overview of metabolomics and fluxomics, highlighting stable isotope strategies for fluxome characterization. We also discuss some of the tools used to quantitatively analyse the control exerted by components of the network over both the metabolome and the fluxome. Finally, we outline the role and future of metabolomics and fluxomics in drug discovery.
Case study in systematic modelling: thiamine uptake in the yeast Saccharomyces cerevisiae
Authors: Ericsson Abraham , Mojzita Dominik , Schmidt Henning , Hohmann Stefan
Published: September 2008

In recent years, with important advances in molecular biology, experimental and measurement technologies, it has become possible to generate the quantitative data that are needed for building mathematical models of complex biochemical processes. Cartoon-like diagrams of biological pathways can be turned into dynamical models, allowing simulation and analysis to gain an insight into the underlying control mechanisms and the behaviour of the overall system. This kind of system-level understanding has not been reachable from the study of the components of pathways in isolation. However, mathematical modelling does not only integrate the available knowledge about a certain system with newly generated experimental results. During the process of modelling, questions need to be addressed that lead to an increased quantitative understanding of the system. Models can be used to optimize experimental approaches and protocols and to test different hypotheses about the underlying biological mechanisms. Finally, a validated mathematical model can be used to perform in silico experiments that might be hard or impossible to do in the laboratory. In this chapter we present a case study of a systematic modelling approach applied to the thiamine uptake system of the yeast Saccharomyces cerevisiae. This example is part of our broader effort to model the whole of thiamine metabolism in yeast, which involves several additional processes such as thiamine utilization, biosynthesis and gene regulation. Our main goal is to describe how systematic modelling has improved the knowledge about the system under study.
Network reconstruction based on steady-state data
Authors: Sontag Eduardo D.
Published: September 2008

This paper discusses a theoretical method for the “reverse engineering” of networks based solely on steady-state (and quasi-steady-state) data.
Sensitivity analysis: from model parameters to system behaviour
Authors: Ingalls Brian
Published: September 2008

Sensitivity analysis addresses the manner in which model behaviour depends on model parametrization. Global sensitivity analysis makes use of statistical tools to address system behaviour over a wide range of operating conditions, whereas local sensitivity analysis focuses attention on a specific set of nominal parameter values. This narrow focus allows a complete analytical treatment and straightforward interpretation in the local case. Sensitivity analysis is a valuable tool for model construction and interpretation, and can be applied in medicine and biotechnology to predict the effect of interventions.
Standards and ontologies in computational systems biology
Authors: Sauro Herbert M. , Bergmann Frank T.
Published: September 2008

With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.
Promoter CpG methylation of oestrogen receptors in leukaemia
Authors: Yao Jie , Huang Qing , Zhang Xiao-Bing , Fu Wei-Ling
Published: September 2008

Previous studies have suggested an important role of ERs (oestrogen receptors) in the pathogenesis of leukaemias. However, there is no information so far about the epigenetic characteristics of ERα isoforms and ERβ in leukaemias. In the present study, the mRNA expression and promoter CpG methylation of ERα isoforms (i.e. ERα-A, -B and -C) and ERβ in leukaemia cell lines were evaluated using RT–PCR (reverse transcription–PCR) and MSP (methylation-specific PCR) respectively. The methylation of ERs was further analysed in acute leukaemia patients by MSP and direct DNA sequencing. Although all ERα isoforms and ERβ were methylated in all leukaemia cell lines, except for ERα-C, which was unmethylated in HL-60 and K562 cell lines, only the expression of ERα-A was deficient in all cell lines and its expression could be reactivated by DNA demethylation reagents. With regard to the methylation characteristics in acute leukaemia patients, only ERα-A was inactivated and specifically methylated (95%; 38/40) in almost all patients and unmethylated in all healthy controls, whereas ERα-B, -C and ERβ were methylated in both patients and healthy controls. This result suggested that the methylated status of ERα-A might serve as an epigenetic biomarker of leukaemias. The present study is the first report that demonstrates selective inactivation of ERα isoforms through the promoter CpG methylation pathway in leukaemias.
Autoactivation of human ADAM8: a novel pre-processing step is required for catalytic activity
Authors: Hall Troii , Leone Joseph W. , Wiese Joseph F. , Griggs David W. , Pegg Lyle E. , Pauley Adele M. , Tomasselli Alfredo G. , Zack Marc D.
Published: September 2008

Members of the ADAM (a disintegrin and metalloproteinase) family of proteins possess a multidomain architecture which permits functionalities as adhesion molecules, signalling intermediates and proteolytic enzymes. ADAM8 is found on immune cells and is induced by multiple pro-inflammatory stimuli suggesting a role in inflammation. Here we describe an activation mechanism for recombinant human ADAM8 that is independent from classical PC (pro-protein convertase)-mediated activation. N-terminal sequencing revealed that, unlike other ADAMs, ADAM8 undergoes pre-processing at Glu158, which fractures the Pro (pro-segment)-domain before terminal activation takes place to remove the putative cysteine switch (Cys167). ADAM8 lacking the DIS (disintegrin) and/or CR (cysteine-rich) and EGF (epidermal growth factor) domains displayed impaired ability to complete this event. Thus pre-processing of the Pro-domain is co-ordinated by DIS and CR/EGF domains. Furthermore, by placing an EK (enterokinase) recognition motif between the Pro- and catalytic domains of multiple constructs, we were able to artificially remove the pro-segment prior to pre-processing. In the absence of pre-processing of the Pro-domain a marked decrease in specific activity was observed with the autoactivated enzyme, suggesting that the Pro-domain continued to associate and inhibit active enzyme. Thus, pre-processing of the Pro-domain of human ADAM8 is important for enzyme maturation by preventing re-association of the pro-segment with the catalytic domain. Given the observed necessity of DIS and CR/EGF for pre-processing, we conclude that these domains are crucial for the proper activation and maturation of human ADAM8.
Predictive value of the decrease in circulating dendritic cell precursors in stable coronary artery disease
Authors: Yilmaz Atilla , Schaller Tina , Cicha Iwona , Altendorf Regina , Stumpf Christian , Klinghammer Lutz , Ludwig Josef , Daniel Werner G. , Garlichs Christoph D.
Published: September 2008

DCs (dendritic cells) are present in atherosclerotic lesions leading to vascular inflammation, and the number of vascular DCs increases during atherosclerosis. Previously, we have shown that the levels of circulating DCPs (DC precursors) are reduced in acute coronary syndromes through vascular recruitment. In the present study, we have investigated whether DCP levels are also reduced in stable CAD (coronary artery disease). The levels of circulating mDCPs (myeloid DCPs), pDCPs (plasmacytoid DCPs) and tDCP (total DCPs) were investigated using flow cytometry in 290 patients with suspected stable CAD. A coronary angiogram was used to evaluate a CAD score for each patient as follows: (i) CAD excluded (n=57); (ii) early CAD (n=63); (iii) moderate CAD (n=85); and (iv) advanced CAD (n=85). Compared with controls, patients with advanced stable CAD had lower HDL (high-density lipoprotein)-cholesterol (P=0.03) and higher creatinine (P=0.003). In advanced CAD, a significant decrease in circulating mDCPs, pDCPs and tDCPs was observed (each P<0.001). A significant inverse correlation was observed between the CAD score and mDCPs, pDCPs or tDCPs (each P<0.001). Patients who required percutaneous coronary intervention or coronary artery bypass grafting had less circulating mDCPs, pDCPs and tDCPs than controls (each P<0.001). Multiple stepwise logistic regression analysis suggested mDCPs, pDCPs and tDCPs as independent predictors of CAD. In conclusion, we have shown that patients with stable CAD have significantly lower levels of circulating DCPs than healthy individuals. Their decrease appears to be an independent predictor of the presence of, and subsequent therapeutic procedure in, stable CAD.
Towards a Theory of Organizational Information Services
Authors: Mathiassen Lars , Soreness Carsten
Published: September 2008

The use of information technology (IT) in organizations has undergone dramatic changes during the past 30 years. As a result, it has become increasingly common to adopt services rather than traditional systems perspective to more accurately capture contemporary practices. There is, however, a lack of theories that can help us understand, assess, and design information services in organizational contexts. On this backdrop, we combine general notions of information processing options and requirements to outline a contingency theory of organizational use of information services. The theory suggests that information services are configurations of heterogeneous information processing capabilities; these services are evoked by organizational actors to help execute tasks, and evoking different configurations may lead to equally satisfactory outcomes. The theory distinguishes between four types of services computational, adaptive, networking, and collaborative services, and it suggests that organizational actors need portfolios of information services that are suited to the equivocality and uncertainty profile of the information processing they face. The paper defines four types of services and how they relate to information processing requirements; it applies the theory to a study of information services in response to vehicle policing; and it outlines how the theory relates to standardization and unintended consequences of information services. We conclude by discussing the theory and its implications for research and practice.
Multiple film cracking in film/substrate systems with mismatch strain and applied strain
Authors: Zhang X. C. , Xuan F. Z. , Zhang Y. K. , Tu S. T.
Published: September 2008

Multiple cracking of brittle films deposited on the relatively soft substrate was commonly used in different applications. In the present paper, multiple film cracking in the film/substrate systems was analyzed. The system was subjected to the combination of the residual stresses due to the mismatch strain between the film and substrate and the applied stress due to the unidirectional strain on the substrate. First, a simply analytical model was developed to derive the closed-form solutions for the residual stress distribution and redistribution due to the edge effects in the film segment. Second, the energy and strength criteria were adopted to perform the analysis on the multiple film cracking on the basis of the knowledge on the residual stress distributions. Third, the case of SiOx film/polyethylene terephthalate substrate system was used to illustrate the implementation of this model. The relationship between the fracture energy as well as the film strength and the film thickness was obtained. The predicted crack density against the applied strain was compared with the existing experimental measurements. The effect of the mismatch strain on the crack density of the film was also discussed.
The modification of self-assembled monolayer on indium tin oxide as cathode in inverted bottom-emitting organic light-emitting diodes
Authors: Xiong Tao , Ma Dongge
Published: September 2008

Self-assembled monolayers (SAMs) of a series of p-substituted benzoyl chlorides were formed on indium tin oxide as the cathode for the fabrication of inverted bottom-emitting organic light-emitting diodes (IBOLEDs). The studies on the efficiency of electron injection and device performances showed that the direct tunneling of electron and the formation of dipole associated with the monolayer-forming molecule lead to significant enhancement in electron injection. Consequently, the device efficiency is greatly improved. The maximum current efficiency and power efficiency, respectively, reach 4.60 cd/A and 2.40 lm/W, which are over 1.2 times that of the conventional IBOLED without SAM modification.
Diffraction of dust acoustic waves by a circular cylinder
Authors: Kim S.-H. , Heinrich J. R. , Merlino R. L.
Published: September 2008

The diffraction of dust acoustic (DA) waves around a long dielectric rod is observed using video imaging methods. The DA waves are spontaneously excited in a dusty plasma produced in a direct current glow discharge plasma. The rod acquires a negative charge that produces a coaxial dust void around it. The diameter of the void is the effective size of the “obstacle” encountered by the waves. The wavelength of the DA waves is approximately the size of the void. The observations are considered in relation to the classical problem of the diffraction of sound waves from a circular cylinder, a problem first analyzed by Lord Rayleigh [Theory of Sound, 2nd ed. (MacMillan, London, 1896)].
Statistically optimal analysis of samples from multiple equilibrium states
Authors: Shirts Michael R. , Chodera John D.
Published: September 2008

We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we call the multistate Bennett acceptance ratio estimator (MBAR) because it reduces to the Bennett acceptance ratio estimator (BAR) when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.
Superconducting calorimetric alpha particle sensors for nuclear nonproliferation applications
Authors: Horansky Robert D. , Ullom Joel N. , Beall James A. , Hilton Gene C. , Irwin Kent D. , Dry Donald E. , Hastings Elizabeth P. , Lamont Stephen P. , Rudy Clifford R. , Rabin Michael W.
Published: September 2008

Identification of trace nuclear materials is usually accomplished by alpha spectrometry. Current detectors cannot distinguish critical elements and isotopes. We have developed a detector called a microcalorimeter, which achieves a resolution of 1.06 keV for 5.3 MeV alphas, the highest resolving power of any energy dispersive measurement. With this exquisite resolution, we can unambiguously identify the P240u/P239u ratio in Pu, a critical measurement for ascertaining the intended use of nuclear material. Furthermore, we have made a direct measurement of the P209o ground state decay.
Surface traps in vapor-phase-grown bulk ZnO studied by deep level transient spectroscopy
Authors: Fang Z.-Q. , Claflin B. , Look D. C. , Dong Y. F. , Mosbacker H. L. , Brillson L. J.
Published: September 2008

Deep level transient spectroscopy, current-voltage, and capacitance-voltage measurements are used to study interface traps in metal-on-bulk-ZnO Schottky barrier diodes (SBDs). c-axis-oriented ZnO samples were cut from two different vapor-phase-grown crystals, and Au- and Pd-SBDs were formed on their (0001) surfaces after remote oxygen-plasma treatment. As compared to Au-SBDs, the Pd-SBDs demonstrated higher reverse-bias leakage current and forward-bias current evidently due to higher carrier concentrations, which might have been caused by hydrogen in-diffusion through the thin Pd metal. The dominant traps included the well-known bulk traps E3 (0.27 eV) and E4 (0.49 eV). In addition, a surface-related trap, Es (0.49 eV), is observed but only in the Pd-SBDs, not in the Au-SBDs. Trap Es is located at depths less than about 95 nm and shows an electron capture behavior indicative of extended defects. A possible correspondence between trap Es and the well-known 2.45 eV green band is suggested by depth-resolved cathodoluminescence spectroscopy on the same samples, which reveals an increase in the intensity of this band within ∼100 nm of the Pd/ZnO interface.
Determining quasidiabatic coupled electronic state Hamiltonians using derivative couplings: A normal equations based method
Authors: Papas Brian N. , Schuurman Michael S. , Yarkony David R.
Published: September 2008

A self-consistent procedure for constructing a quasidiabatic Hamiltonian representing Nstate coupled electronic states in the vicinity of an arbitrary point in nuclear coordinate space is described. The matrix elements of the Hamiltonian are polynomials of arbitrary order. Employing a crude adiabatic basis, the coefficients of the linear terms are determined exactly using analytic gradient techniques. The remaining polynomial coefficients are determined from the normal form of a system of pseudolinear equations, which uses energy gradient and derivative coupling information obtained from reliable multireference configuration interaction wave functions. In a previous implementation energy gradient and derivative coupling information were employed to limit the number of nuclear configurations at which ab initio data were required to determine the unknown coefficients. Conversely, the key aspect of the current approach is the use of ab initio data over an extended range of nuclear configurations. The normal form of the system of pseudolinear equations is introduced here to obtain a least-squares fit to what would have been an (intractable) overcomplete set of data in the previous approach. This method provides a quasidiabatic representation that minimizes the residual derivative coupling in a least-squares sense, a means to extend the domain of accuracy of the diabatic Hamiltonian or refine its accuracy within a given domain, and a way to impose point group symmetry and hermiticity. These attributes are illustrated using the 1A12 and 1E2 states of the 1-propynyl radical, CH3CC.
Josephson vortices as flexible waveguides for terahertz waves
Authors: Gulevich D. R. , Savel’ev Sergey , Yampol’skii V. A. , Kusmartsev F. V. , Nori Franco
Published: September 2008

We propose using the Josephson vortices (fluxons) as adjustable and malleable waveguides of electromagnetic radiation. Our theoretical and numerical calculations show that electromagnetic waves can propagate along the Josephson vortices and always follow the vortex lines. By changing external parameters, such as electric currents or magnetic fields, the shape and configuration of the guiding vortex lines can be controlled. We describe the design of a multifunctional three-terminal device that controls the transmission (redirecting or splitting) of a beam of electromagnetic waves.
Electronic transport and spin-polarization effects of relativisticlike particles in mesoscopic graphene structures
Authors: Nam Do V. , Nguyen V. Hung , Dollfus P. , Bournel A.
Published: September 2008

Motivated by recent studies on the use of graphene for new concepts of electronic/spintronic devices, the authors develop an efficient calculation method based on the nonequilibrium Green’s function to solve the quantum relativisticlike Dirac’s equation that governs the low-energy excited states in graphene. The approach is then applied to investigate the electronic transport and the spin polarization in a single-graphene barrier structure. The obtained results are presented and analyzed in detail aiming to highlight typical properties of the considered graphene structure as well as the efficiency of the developed approach that both may be helpful for further development in electronic devices and in spintronics.
The dissipated power in atomic force microscopy due to interactions with a capillary fluid layer
Authors: Hashemi N. , Paul M. R. , Dankowicz H. , Lee M. , Jhe W.
Published: September 2008

We study the power dissipated by the tip of an oscillating micron-scale cantilever as it interacts with a sample using a nonlinear model of the tip-surface force interactions that includes attractive, adhesive, repulsive, and capillary contributions. The force interactions of the model are entirely conservative and the dissipated power is due to the hysteretic nature of the interaction with the capillary fluid layer. Using numerical techniques tailored for nonlinear and discontinuous dynamical systems we compute the exact dissipated power over a range of experimentally relevant conditions. This is accomplished by computing precisely the fraction of oscillations that break the fluid meniscus. We find that the dissipated power as a function of the equilibrium cantilever-surface separation has a characteristic shape that we directly relate to the cantilever dynamics. Even for regions where the cantilever dynamics are highly irregular the fraction of oscillations breaking the fluid meniscus exhibits a simple trend. Using our results we also explore the accuracy of the often used harmonic approximation in determining dissipated power.
Structural, magnetic, and electric properties of La0.7Sr0.3MnO3/PbZrxTi1−xO3 heterostructures
Authors: Ziese M. , Setzer A. , Vrejoiu I. , Birajdar B. I. , Rodriguez B. J. , Hesse D.
Published: September 2008

Epitaxial La0.7Sr0.3MnO3/PbZrxTi1−xO3 multilayers were fabricated by pulsed-laser deposition and studied by structural, magnetic, and electric characterization techniques. Transmission electron microscopy and x-ray diffractometry proved the excellent structural quality of the samples. A high ferroelectric polarization and stable piezoelectric switching were found for the lead zirconate titanate layers, whereas the manganite layers showed bulklike resistivity and magnetoresistance, both attesting to the high quality of the layers. In a detailed study of the magnetic response of the multilayers multiple magnetization switching was observed that was related to the complex strain state.
Analysis of nonuniform transmission gratings recorded in photopolymerizable silica glass materials
Authors: Murciano A. , Blaya S. , Carretero L. , Acebal P. , Pérez-Molina M. , Madrigal R. F. , Fimia A.
Published: September 2008

We theoretically and experimentally analyze the angular selectivity curves of nonuniform gratings recorded in a photopolymerizable silica glass. Due to the rigidity of this material, shrinkage would not cause fringe bending, so we propose that the coupling of the beams at the recording stage (two-wave mixing) produces the resulting nonuniformities. Nonuniform transmission holographic gratings can be analyzed in rigid media using the coupled-wave theory but introducing the results obtained from the two-wave mixing treatment and taking into account the absorption and the nonlinear effects produced by the mechanism of photopolymerization and diffusion. Good agreement between theory and experience is obtained.
UV photon-induced defect and its control in plasma etching processes
Authors: Ishikawa Yasushi , Ichihashi Yoshinari , Yamasaki Satoshi , Samukawa Seiji
Published: September 2008

We found that the use of pulse-time-modulated (TM) plasma reduces ultraviolet (UV) photon-induced defects in SiO2 films formed during plasma etching. The pulse timing of the radio-frequency power in the TM plasma was modulated at a few tens of microseconds. During the pulse-off period, UV photon radiation significantly decreased because of reduced electron energy in the plasma. As a result, the density of UV photon-induced defects, such as E′ centers, in SiO2 films was reduced when the TM plasma was used compared with that when a continuous wave (CW) plasma was used. In addition, we found that the energy level of excitation states of the E′ centers generated in the TM plasma was less than that generated when the CW plasma was used. Low-temperature annealing was needed to reduce the number of E′ centers when the TM plasma was used; whereas higher-temperature annealing was needed when the CW plasma was used. These results showed that the energy level of excitation states of UV photon-induced defects in SiO2 films was reduced by using the TM plasma.
Field solution of nonlinear magnetic surface wave for a planar superconductor-antiferromagnet transmission line
Authors: Wu Chien-Jang
Published: September 2008

A sinusoidal field solution for a nonlinear transverse magnetic surface wave in a symmetric planar transmission line made of a superconducting film and two antiferromagnets is derived. This solution enables us to investigate the propagation characteristics in the infrared frequency region. Propagation characteristics such as the attenuation constant and the phase constant are numerically analyzed as a function of the frequency, the temperature, and the thickness of a superconductor as well. In the temperature-dependent attenuation constant, it is found that there exists a characteristic temperature at which the attenuation constant attains a maximum. This characteristic temperature decreases with increasing frequency. In addition, it is seen that both the attenuation constant and the phase constant decrease with increasing thickness of a superconducting film. Finally, numerical result in the total power flow reveals that there exists a cutoff propagation constant. Electromagnetic wave can propagate through the line when the propagation constant is greater than this cutoff value.
Direct numerical simulation and Lagrangian modeling of joint scalar statistics in ternary mixing
Authors: Sawford Brian L. , de Bruyn Kops Stephen M.
Published: September 2008

Direct numerical simulation (DNS) results are presented for the joint statistics of two inhomogeneous scalar fields, one due to a mixing layer source and the other due to a contiguous top-hat source. These two sources form the basis for all scalar mixing across three streams. The results are used to assess the performance of a Lagrangian stochastic modeling system incorporating the interaction with the conditional mean mixing model at two different times: A near-field time when there is little spatial overlap between the two scalar fields, and a far-field time when there is strong overlap. In the near field we find that for both the model and the DNS, the joint probability density function is essentially confined to two lines in concentration phase space; the diagonal ψ1+ψ2=1 and the axis ψ1=0, where ψ1 and ψ2 are the phase space concentrations for the mixing layer and top-hat scalars, respectively. The model and DNS results along these sections are in excellent quantitative agreement for a range of statistics. In the far field the DNS results show significant levels of probability density throughout the concentration domain ψ1+ψ2⩽1, but the model results have a much more limited range in the top-hat scalar, with less unmixed fluid reflecting excessive mixing. This inevitably results in quantitative differences in other statistics, but the conditional mean diffusion for the model shows semiquantitative agreement with the DNS. The most striking difference between model and DNS results in the far field is shown in the conditional mean velocity for which the model shows oscillations in sign not present in the DNS.
A formula for the profile of voltammogram spikes in the quasistatic regime
Authors: Medved’ I.
Published: September 2008

A phase transition occurring at electrode-electrolyte interfaces is reflected in voltammograms (the current versus voltage plots) as a sharp spike. We derive a general formula fitting the profile of the spikes due to the first-order phase transitions that can be microscopically modeled by classical two-dimensional lattice gases. The quasistatic (near equilibrium) regime is required. The profile is especially essential when interpreting generic voltammograms, where two or more close or overlapping spikes usually appear. Simple direct links between the microscopics of a phase transition and the macroscopic properties of the associated spike are explicitly given. We demonstrate our results on the voltammograms for the underpotential deposition of copper on platinum (111) and (100) and on gold (111) and achieve very good agreement with experiment.
Structural and optoelectronic properties of silicon germanium alloy thin films deposited by pulsed radio frequency plasma enhanced chemical vapor deposition
Authors: Bhaduri A. , Chaudhuri P. , Williamson D. L. , Vignoli S. , Ray P. P. , Longeaud C.
Published: September 2008

Hydrogenated amorphous silicon germanium (a-SiGe:H) alloy films are still under study to improve their incorporation into tandem solar cells. In this paper we have investigated the quality of films deposited in a radio frequency powered plasma enhanced chemical vapor deposition unit. Two series of samples were prepared either from a mixture of silane and germane diluted into hydrogen or from the same mixture to which a small amount of argon was added. The applied rf power at 13.56 MHz was either continuous or modulated by a square wave pulse at a frequency of 1356 kHz. Different films were deposited in the two series controlling the time the plasma was “on.” The ratio of the on time to the total period of the modulation, the duty cycle, was varied between 100% (continuous mode) and 50%. The plasma during deposition as well as structural and optoelectronic properties of the resulting films was studied with several techniques. We found an optimum in the transport properties for a duty cycle of 75%: an ambipolar diffusion length of the order of 100 nm for a material presenting a bandgap of 1.44 eV. To explain this promising result, we present a discussion on the growth mechanisms of such layers linking the structural results to the transport data.
Oxides of small Rhodium clusters: Theoretical investigation of experimental reactivities
Authors: Harding D. J. , Davies R. D. L. , Mackenzie S. R. , Walsh T. R.
Published: September 2008

Density functional theory is used to investigate the structures of cationic rhodium cluster oxides, Rh6Om+ (m=1,4). On the monoxide and dioxide, the oxygen atoms occupy bridge sites, while on trioxide and tetroxide clusters, high-coordination sites are favored. A range of spin multiplicities are investigated for each cluster, with high spin multiplicities found to be less favored for the oxides compared with the naked metal clusters. The dissociation of nitric oxide on low-energy isomers of Rh6O4+ is investigated and found to be unfavorable compared to molecular adsorption due to a combination of thermodynamic and kinetic factors. These calculations are consistent with, and help to account for, the experimentally observed reactivity of rhodium and rhodium oxide clusters with nitric oxide [M. S. Ford et al., Phys. Chem. Chem. Phys. 7, 975 (2005)].
Natural convection in enclosures with partially thermally active side walls containing internal heat sources
Authors: Kandaswamy P. , Nithyadevi N. , Ng C. O.
Published: September 2008

Unsteady laminar natural convection in an enclosure with partially thermally active side walls and internal heat generation is studied numerically. Thermally inactive parts of the side walls and horizontal walls are thermally insulated. The governing equations are solved using the control volume method with a power law scheme. Nine different combinations of the hot and cold thermally active zones are considered. The effects of heat generations, aspect ratios, different Prandtl numbers, and locations of the thermally active part of the side walls on the flow pattern (streamlines), heat distribution (isotherms), midheight velocity, and rate of heat transfer from the walls of the enclosure are presented. It is observed that the heat transfer rate increases with increasing the Grashof number due to an increase in buoyancy force and decreases with an increase in heat generation. The heat transfer is found to be the maximum when the hot and cold thermally active locations are placed at the middle of the side walls.
Classification and time evolution of density matrices for a N-state system
Authors: Mendaš Istok P.
Published: September 2008

A possible method of classifying all density matrices for a N-state quantum system into different types, using the sameness of the characteristic polynomial of density matrices belonging to a given type, is discussed. The method employs the SU(N) generator expansion of density matrices. It is demonstrated that density matrices belonging to a given type, although different, share many common properties including the same eigenvalues, the same shape of the region in the parametric space in which lie the allowed parameter values, and the same global averages of the pertinent observables. Furthermore, we discuss the time evolution of a given type of density matrices and show that, in the appropriately defined time-dependent comoving matrix basis, a density matrix of a given type belongs, during entire unitary evolution, to the same type. In this way one is able to group and organize the multitude of different density matrices with certain analogous properties, into a smaller number of types, thus systematizing and cataloguing different mixed and pure states of a N-state system. The general discussion is illustrated throughout with the special case of a N=4-state quantum system. Two- and three-dimensional cross sections of the space of generalized Bloch vectors are determined by the Monte Carlo sampling method for several types of density matrices, providing some insight into the intricate and complex geometric structure of the space of density matrices.
Seed induced growth of binary Ag/Au nanostructures on a graphite surface
Authors: Lidgi-Guigui N. , Mulheran P. , Palmer R. E.
Published: September 2008

The growth of Ag on a graphite surface decorated by size selected Au “seed” nanoclusters is investigated. Compared with the behavior on bare graphite, the deposition of the Au clusters decreases the lateral diffusion of Ag atoms and enables the growth of Ag/Au nanostructures on/around the top of the initial Au clusters. Depending on the Au cluster shape, which can be tuned by the cluster deposition energy, Ag deposition either leads to 2 ML high platelets or three-dimensional nanoclusters. This cluster seeding technique shows potential for the rapid production of binary model catalysts, biochips, and optical films.
Plasmonic nanocavity arrays for enhanced efficiency in organic photovoltaic cells
Authors: Lindquist Nathan C. , Luhman Wade A. , Oh Sang-Hyun , Holmes Russell J.
Published: September 2008

We demonstrate enhanced power conversion efficiency in organic photovoltaic (OPV) cells incorporated into a plasmonic nanocavity array. The nanocavity array is formed between a patterned Ag anode and an unpatterned Al cathode. This structure leads to the confinement of optical energy and enhanced absorption in the OPV. Devices characterized under simulated solar illumination show a 3.2-fold increase in power conversion efficiency compared to OPVs with unpatterned Ag anodes. The observed enhancement is also reflected in the external quantum efficiency, and the spectral response is consistent with optical finite-difference time-domain simulations of the structure.
Comment on “A direct approach to study radiative emission from triplet excitations in molecular semiconductors and conjugated polymers” [J. Chem. Phys. 129, 041103 (2008)]
Authors: Lim Edward C.
Published: September 2008

Comparison of the experimental radiative lifetimes of the lowest triplet (T1) state of aromatic hydrocarbons with the lifetimes calculated using spin-orbit interaction and time-dependent spin-orbit-photon interaction operators indicates that the traditional approach, based on spin-orbit interaction, yields much better agreement with experiment.
Polymer thin film deposited on liquid for varifocal encapsulated liquid lenses
Authors: Binh-Khiem Nguyen , Matsumoto Kiyoshi , Shimoyama Isao
Published: September 2008

We developed a process for making liquid lenses that have a tunable focal distance. In our process, polymer thin films are directly deposited on liquid droplets in vacuum. Conducting the deposition in vacuum helps preserve the delicate spherical droplet shape so that they can be used as lenses. The polymer film is mechanically stable, which protects the droplets from the ambient, but it is also extremely thin and flexible, which allows the droplets to deform. The droplets are deformed using electrostatic force to change their focal distance. Our lens is structurally simple and can be operated by an electrical input.
A 500 MHz carbon nanotube transistor oscillator
Authors: Pesetski A. A. , Baumgardner J. E. , Krishnaswamy S. V. , Zhang H. , Adam J. D. , Kocabas C. , Banks T. , Rogers J. A.
Published: September 2008

Operation of a carbon nanotube field effect transistor (FET) oscillator at a record frequency of 500 MHz is described. The FET was fabricated using a large parallel array of single-walled nanotubes grown by chemical vapor deposition on ST-quartz substrates. Matching of the gate capacitance with a series inductor enabled greater than unity net oscillator loop gain to be achieved at 500 MHz.
A single-pixel terahertz imaging system based on compressed sensing
Authors: Chan Wai Lam , Charan Kriti , Takhar Dharmpal , Kelly Kevin F. , Baraniuk Richard G. , Mittleman Daniel M.
Published: September 2008

We describe a terahertz imaging system that uses a single pixel detector in combination with a series of random masks to enable high-speed image acquisition. The image formation is based on the theory of compressed sensing, which permits the reconstruction of a N-by-N pixel image using much fewer than N2 measurements. This approach eliminates the need for raster scanning of the object or the terahertz beam, while maintaining the high sensitivity of a single-element detector. We demonstrate the concept using a pulsed terahertz time-domain system and show the reconstruction of both amplitude and phase-contrast images. The idea of compressed sensing is quite general and could also be implemented with a continuous-wave terahertz source.
Photoluminescence enhancement in thin films of PbSe nanocrystals
Authors: Christova C. G. , Stouwdam J. W. , Eijkemans T. J. , Silov A. Yu. , van der Heijden R. W. , Kemerink M. , Janssen R. A. J. , Salemink H. W. M.
Published: September 2008

Remarkable photoluminescence enhancement (PLE) in submonolayer films of PbSe nanocrystals (NCs) upon continuous illumination was observed. The intensity increase from films on InP substrates was highest in vacuum, while for films on Si/SiO2 substrates the PLE was stronger in air. The magnitude of the PLE was found to depend on the excitation intensity, being higher for a weaker irradiation power. The possible mechanisms behind the phenomenon of the PLE are discussed and it is suggested to originate mainly from charge trapping outside the NCs core.
Improved electron injection in polymer light-emitting diodes using anionic conjugated polyelectrolyte
Authors: Jin Youngeup , Bazan Guillermo C. , Heeger Alan J. , Kim Jin Young , Lee Kwanghee
Published: September 2008

We report improved performance in polymer light-emitting diodes incorporating conjugated polyelectrolytes as an electron injection layer (EIL). When we introduce water soluble conjugated polymers, poly[9,9′-bis(4-sulfonatobutyl)fluorene-co-alt-1,4-phenylene] (anionic PFP), between the aluminum (Al) cathode and emissive layer, the devices show an increased electroluminescence efficiency with a lowered turn-on voltage. We believe the mobile Na+ ions in the EIL layer directly influences the device efficiency by forming a low work function layer at the interface between the EIL and Al cathode, thereby facilitating the electron injection into the emissive layer.
Chirality control and switching of vortices formed in hexagonal shaped ferromagnetic elements
Authors: Lua S. Y. H. , Kushvaha S. S. , Wu Y. H. , Teo K. L. , Chong T. C.
Published: September 2008

We report on magnetic imaging study of hexagonal shaped ferromagnetic elements arranged in a ring network. Magnetic force microscopy images revealed the existence of vortex states in the hexagons, which agrees well with the micromagnetic modeling results. By making use of the stray field of moderate strength and well-defined symmetry, which is lacking in vortices formed in circular elements, we show that it is possible to realize vortex chains with well-defined alternative arrangement of chirality in a ring network. The chirality can be switched forth and back using a magnetic field applied along selected edges of the hexagons.
GaInSb/AlInSb multi-quantum-wells for mid-infrared lasers
Authors: Yin M. , Nash G. R. , Coomber S. D. , Buckle L. , Carrington P. J. , Krier A. , Andreev A. , Przeslak S. J. B. , de Valicourt G. , Smith S. J. , Emeny M. T. , Ashley T.
Published: September 2008

Photoluminescence (PL) from GaInSb/AlInSb type I multi-quantum-wells, grown on GaAs, has been investigated as a function of strain in the quantum wells. Luminescence, between 3 and 4 μm, was observed for all samples, with good agreement between the measured and calculated peak emission energies. Analysis of the temperature dependence of the luminescence suggests that population of excited quantum well hole subbands occurs at high temperature, leading to a reduction in the PL signal. Room temperature luminescence was obtained from a sample with ∼0.8% strain in the quantum wells. Preliminary results from laser diodes fabricated from companion wafers indicate lasing up to 220 K.
Regulating the Release of GMOs: Contrasts between the European Union and Norway
Authors: Kvakkestad Valborg , Vatn Arild
Published: September 2008

The European Union (EU) and Norway have assessed the release of genetically modified organisms as commercial products quite differently. Of twenty-four notifications approved by the EU, Norway has approved four, rejected ten, and has ten pending. We analyse whether these differences could be explained by different value judgments. Three aspects of the formulation and implementation of the regulations are discussed: the effects to be prevented and encouraged, response to uncertainty and ignorance, and the burden of proof necessary. Norwegian rejections are found to be explicable by the combination of no real benefit to society, lack of scientific knowledge, and involved risks. EU approvals are based upon seeing no reason to believe that there will be any adverse effects on health and the environment. We conclude that problems arise when value conflicts are understood and treated solely as technical issues, as normal in the EU.
Scenario Planning for the Edinburgh City Region
Authors: Docherty Iain , McKiernan Peter
Published: September 2008

We examine the application of scenario-planning techniques to the detailed and daunting challenge of city repositioning when policy makers are faced with a heavy history and a complex future context. We review a process of scenario planning undertaken in the Edinburgh city region, exploring the scenario process and its contribution to strategies and policies for city repositioning. Strongly rooted in the recent literature on urban and regional economic development, the text outlines how key individuals and organisations involved in the process participated in far-reaching analyses of the possible future worlds in which the Edinburgh city region might find itself.
Knowledge Flows, Spatial Strategy Making, and the Roles of Academics
Authors: Healey Patsy
Published: September 2008

I explore the contribution of academics to the activity of spatial strategy making for urban areas. I focus on how academics have been involved in such policy formation work, their contribution to the framing of key strategic concepts, the extent to which academic contributions have affected the understanding of urban and regional dynamics embodied in such frames, and the role of academics in legitimating the strategies produced. I use examples from cases from Italy, the Netherlands, and the UK to highlight the significance of the institutional contexts in which academics have been drawn into spatial strategy-making activity, and the different kinds of relationships which have developed. I conclude that more attention is needed to this issue, in the context of improving the knowledge ability of spatial strategy-making practices, encouraging more reflexivity among academics involved in such activity about the institutional dynamics and ethical challenges of such involvement, and promoting more attention among policy makers to how they use experts in different kinds of institutional context when undertaking spatial strategy-making work.