bluuebunny/crossref_metadata_2025 huggingface dataset:
Using mitochondria-targeted molecules to study mitochondrial radical production and its consequences
Authors: Smith R.A.J. , Kelso G.F. , Blaikie F.H. , Porteous C.M. , Ledgerwood E.C. , Hughes G. , James A.M. , Ross M.F. , Asin-Cayuela J. , Cochemé H.M. , Filipovska A. , Murphy M.P.
Published: December 2008

The production of ROS (reactive oxygen species) by the mitochondrial respiratory chain contributes to a range of pathologies, including neurodegenerative diseases, ischaemia/reperfusion injury and aging. There are also indications that mitochondrial ROS production plays a role in damage response and signal transduction pathways. To unravel the role of mitochondrial ROS production in these processes, we have developed a range of mitochondria-targeted probe molecules. Covalent attachment of a lipophilic cation leads to their accumulation into mitochondria, driven by the membrane potential. Molecules developed so far include antioxidants designed to intercept mitochondrial ROS and reagents that specifically label mitochondrial thiol proteins. Here we outline how mitochondrial ROS formation and its consequences can be investigated using these probes.
Glyoxalase I – structure, function and a critical role in the enzymatic defence against glycation
Authors: Thornalley P.J.
Published: December 2008

Glyoxalase I is part of the glyoxalase system present in the cytosol of cells. The glyoxalase system catalyses the conversion of reactive, acyclic α-oxoaldehydes into the corresponding α-hydroxyacids. Glyoxalase I catalyses the isomerization of the hemithioacetal, formed spontaneously from α-oxoaldehyde and GSH, to S-2-hydroxyacylglutathione derivatives [RCOCH(OH)-SG→RCH(OH)CO-SG], and in so doing decreases the steady-state concentrations of physiological α-oxoaldehydes and associated glycation reactions. Physiological substrates of glyoxalase I are methylglyoxal, glyoxal and other acyclic α-oxoaldehydes. Human glyoxalase I is a dimeric Zn2+ metalloenzyme of molecular mass 42 kDa. Glyoxalase I from Escherichia coli is a Ni2+ metalloenzyme. The crystal structures of human and E. coli glyoxalase I have been determined to 1.7 and 1.5 Å resolution. The Zn2+ site comprises two structurally equivalent residues from each domain – Gln-33A, Glu-99A, His-126B, Glu-172B and two water molecules. The Ni2+ binding site comprises His-5A, Glu-56A, His-74B, Glu-122B and two water molecules. The catalytic reaction involves base-catalysed shielded-proton transfer from C-1 to C-2 of the hemithioacetal to form an ene-diol intermediate and rapid ketonization to the thioester product. R- and S-enantiomers of the hemithioacetal are bound in the active site, displacing the water molecules in the metal ion primary co-ordination shell. It has been proposed that Glu-172 is the catalytic base for the S-substrate enantiomer and Glu-99 the catalytic base for the R-substrate enantiomer; Glu-172 then reprotonates the ene-diol stereospecifically to form the R-2-hydroxyacylglutathione product. By analogy with the human enzyme, Glu-56 and Glu-122 may be the bases involved in the catalytic mechanism of E. coli glyoxalase I. The suppression of α-oxoaldehyde-mediated glycation by glyoxalase I is particularly important in diabetes and uraemia, where α-oxoaldehyde concentrations are increased. Decreased glyoxalase I activity in situ due to the aging process and oxidative stress results in increased glycation and tissue damage. Inhibition of glyoxalase I pharmacologically with specific inhibitors leads to the accumulation of α-oxoaldehydes to cytotoxic levels; cell-permeable glyoxalase I inhibitors are antitumour and antimalarial agents. Glyoxalase I has a critical role in the prevention of glycation reactions mediated by methylglyoxal, glyoxal and other α-oxoaldehydes in vivo.
Enzymatic deglycation with amadoriase enzymes from Aspergillus sp. as a potential strategy against the complications of diabetes and aging
Authors: Monnier V.M. , Wu X.
Published: December 2008

The Amadori compound is the major single modification of the extracellular matrix by the Maillard reaction in vivo. It is also a source of biologically active glycoxidation products and the formation of glucosepane, the major protein cross-link found in biological tissues so far. For this reason, introduction of deglycating enzymes as anti-aging strategy would be desirable. This article provides an update on amadoriase enzymes from fungi which, one day, will hopefully help prevent the in vivo consequences of glycation.
Aldose reductase and the importance of experimental design
Authors: Crabbe M.J.C.
Published: December 2008

Kinetic studies on the AR (aldose reductase) protein have shown that it does not behave as a classical enzyme in relation to ring aldose sugars. As with non-enzymatic glycation reactions, there is probably a free-radical element involved derived from monosaccharide autoxidation. In the case of AR, there is free radical oxidation of NADPH by autoxidizing monosaccharides, which is enhanced in the presence of the NADPH-binding protein. Thus any assay for AR based on the oxidation of NADPH in the presence of autoxidizing monosaccharides is invalid, and tissue AR measurements based on this method are also invalid, and should be reassessed. AR exhibits broad specificity for both hydrophilic and hydrophobic aldehydes that suggests that the protein may be involved in detoxification. The last thing we would want to do is to inhibit it. ARIs (AR inhibitors) have a number of actions in the cell which are not specific, and which do not involve them binding to AR. These include peroxy-radical scavenging and effects of metal ion chelation. The AR/ARI story emphasizes the importance of correct experimental design in all biocatalytic experiments. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has led to the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of Km and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimizes the error in the parameters estimated, and is suitable for simple or complex steady-state models.
Bacterial production of methylglyoxal: a survival strategy or death by misadventure?
Authors: Booth I.R. , Ferguson G.P. , Miller S. , Li C. , Gunasekera B. , Kinghorn S.
Published: December 2008

The production of MG (methylglyoxal) in bacterial cells must be maintained in balance with the capacity for detoxification and protection against this electrophile. Excessive production of MG leads to cell death. Survival of exposure to MG is best understood in the Gram-negative bacteria. The major mechanism of protection is the spontaneous reaction of MG with GSH to form hemithiolacetal, followed by detoxification by the glyoxalase system leading to the production of d-lactate. The KefB and KefC glutathione-gated K+ efflux systems are integrated with the activity of the glyoxalase system to regulate the cytoplasmic pH in response to exposure to electrophiles. Bacteria only produce MG when an imbalance occurs in metabolism. Operation of the MG bypass enables cells to adapt, such that balance is restored to metabolism. Excessive production of MG is an adaptive ploy, which, if it fails, has fatal consequences. On this basis one might define MG-induced loss of life as ‘death by misadventure’ rather than suicide!
Mass spectrometric analysis of glucose-modified ribonuclease
Authors: Cotham W.E. , Hinton D.J.S. , Metz T.O. , Brock J.W.C. , Thorpe S.R. , Baynes J.W. , Ames J.M.
Published: December 2008

RNase A (1 mM) was incubated with glucose (0.4 M) at 37°C for up to 14 days in phosphate buffer (0.2 M, pH 7.4), digested with trypsin and analysed by LC-MS. The major sites of fructoselysine formation were Lys1, Lys7, Lys37 and Lys41. Three of these sites (Lys7, Lys37 and Lys41) were also the major sites of N∊-(carboxymethyl)lysine formation.
Vascular endothelial dysfunction in aging: loss of Akt-dependent endothelial nitric oxide synthase phosphorylation and partial restoration by (R)-α-lipoic acid
Authors: Smith A.R. , Hagen T.M.
Published: December 2008

Aging is the single largest risk factor for cardiovascular diseases, which in turn are the leading cause of death of individuals over the age of 65 years. In part, this risk is due to a profound loss of vasomotor function of the major conduit arteries, primarily because of lower levels of endothelial-derived nitric oxide. The mechanisms involved in vascular dysfunction are not entirely understood, but age-related alterations in eNOS (endothelial nitric oxide synthase) activity appear to be a likely source of the aging lesion. However, age-related changes in cell signalling that ultimately affect eNOS phosphorylation and its activity have not been explored. Results in our laboratory indicate that levels of eNOS phosphorylation in aortas from aged F344×BN rats (28–30 months old) are almost 50% lower than in aortas from young animals (3 months old). Lower eNOS phosphorylation is directly attributable to loss of constitutive Akt/protein kinase B activity. The decline in eNOS phosphorylation can be partially restored by treating old rats with (R)-α-lipoic acid. These results thus suggest that age-related changes in eNOS phosphorylation may be a significant factor in the overall loss of vasomotor function in the elderly.
Co-localization of cell surface receptors at high spatial resolution by single-particle fluorescence imaging
Authors: Karakikes I. , Barber R.E. , Morrison I.E.G. , Fernández N. , Cherry R.J.
Published: December 2008

Dual-wavelength single-particle fluorescence imaging has been used to quantify the co-localization of receptors and/or ligands on cells by widefield microscopy. Methods for correction of chromatic aberration and identification of submicroscopic artefacts are presented, with data for the lipopolysaccharide/CD14 and MHC class II/CD74 systems.
Unravelling Nature's networks
Authors: Monk N.A.M.
Published: December 2008

Dramatic progress has been made recently in determining the genetic and molecular composition of cells. This has prompted the development of new approaches to the challenge of understanding how basic cellular mechanisms are coordinated to produce the dazzling complexity of living systems. To face this challenge fully, it is critical not only to know what genes and proteins are expressed in cells, but also to understand the spatiotemporal dynamics of their networks of interactions. The sheer scale and complexity of cellular interaction networks necessitates a multi-disciplinary effort in which sophisticated experimental techniques are employed in combination with computational analysis and mathematical modelling. Such approaches are beginning to provide insight into basic structures and mechanisms, and promise to become critical to the post-genomic mission of understanding the cell as a complex dynamical system.
Signalling networks, inflammation and innate immunity
Authors: Dower S.K. , Qwarnstrom E.E.
Published: December 2008

We have been analysing the signalling systems that couple to receptors of the TIR (Toll/interleukin-1 receptor) family, which signal through a common cytoplasm region; the TIR domain. These systems are of both practical and fundamental biological significance, being central to the pathogenesis of chronic inflammatory diseases such as atherosclerosis, to host defence throughout the biological world, and are ancient in the context of life on earth, having originated more than 1 billion years ago: prior to the divergence of plants and animals. TIR domain receptors couple to at least two sets of well-characterized pathways: those leading to the activation of inhibitory κB kinase complexes/nuclear factor κB, and those leading to the activation of mitogen-activated protein kinase/AP-1/ATF-2 etc. We have been investigating these systems using a combination of expression screening methods to identify new components, and real-time green fluorescent protein-based techniques to observe execution of signalling programmes in real time. Our data reveal that there is a very large level of cell-to-cell variation in signal programme execution even in clonal populations and that at least one mechanism for dealing with this heterogeneity is the assembly of signal transduction components into large multiprotein complexes.
Systems biology markup language: Level 2 and beyond
Authors: Finney A. , Hucka M.
Published: December 2008

The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.
Deriving statistical models for predicting peptide tandem MS product ion intensities
Authors: Schütz F. , Kapp E.A. , Simpson R.J. , Speed T.P.
Published: December 2008

Improved search algorithms and scoring functions are required before the identification of peptide tandem MS data can be considered to be fully reliable and automatable. The development of models that can accurately predict product ion spectra from a peptide sequence would certainly help achieve this goal, but this firstly requires a better understanding of the process of fragmentation of peptides in the gas-phase. We summarize recent developments in this area and show that the prediction of product ion spectra is feasible and should improve the identification of peptide tandem MS data, especially for peptides that currently give low or insignificant scores with current search algorithms.
Identification of surrogate markers for determining drug activity using proteomics
Authors: McClelland C.M. , Gullick W.J.
Published: December 2008

In a high proportion of human carcinomas overexpression of the EGFR (epidermal growth factor receptor), a receptor tyrosine kinase, represents a potential target for cancer treatment. EGFR is induced to dimerize through ligand binding which activates the tyrosine kinase activity of the receptor. This catalyses the transfer of ATP's γ-phosphate to hydroxyl groups of tyrosine residues on the receptor, creating binding sites that recruit downstream signalling proteins. New drugs, SMTKIs (small-molecule tyrosine kinase inhibitors), have been designed to inhibit the tyrosine kinase activity of the receptor, producing an anti-tumour effect. The development of surrogate markers to determine the drug activity of these new inhibitors would be of great benefit in drug evaluation and in the subsequent management of patient disease. This review describes current treatments of cancer using tyrosine kinase inhibitors and the use of proteomic analysis to identify possible markers of activity of these new drugs.
Analysis and modelling of signal transduction pathways in systems biology
Authors: Cho K.-H. , Wolkenhauer O.
Published: December 2008

There is general agreement that a systems approach is needed for a better understanding of causal and functional relationships that generate the dynamics of biological networks and pathways. These observations have been the basis for efforts to get the engineering and physical sciences involved in life sciences. The emergence of systems biology as a new area of research is evidence for these developments. Dynamic modelling and simulation of signal transduction pathways is an important theme in systems biology and is getting growing attention from researchers with an interest in the analysis of dynamic systems. This paper introduces systems biology in terms of the analysis and modelling of signal transduction pathways. Focusing on mathematical representations of cellular dynamics, a number of emerging challenges and perspectives are discussed.
A probabilistic model for the extraction of expression levels from oligonucleotide arrays
Authors: Milo M. , Fazeli A. , Niranjan M. , Lawrence N.D.
Published: December 2008

In this work we present a probabilistic model to estimate summaries of Affymetrix GeneChip probe level data. Comparisons with two different models were made both on a publicly available dataset and on a study performed in our laboratory, showing that our model performs better for consistency of fold change.
Reverse engineering of genetic networks with Bayesian networks
Authors: Husmeier D.
Published: December 2008

This paper provides a brief introduction to learning Bayesian networks from gene-expression data. The method is contrasted with other approaches to the reverse engineering of biochemical networks, and the Bayesian learning paradigm is briefly described. The article demonstrates an application to a simple synthetic toy problem and evaluates the inference performance in terms of ROC (receiver operator characteristic) curves.
Reconstructing gene networks: what are the limits?
Authors: Stark J. , Brewer D. , Barenco M. , Tomescu D. , Callard R. , Hubank M.
Published: December 2008

To fully realize the benefits of high-throughput post-genomic technologies it is necessary to reconstruct and analyse the complicated network of interactions through which most genes operate. We briefly summarize the mathematical frameworks that can be used to model such networks, and the types of algorithms available for their reconstruction. We then focus on dynamic models, typically described using differential equations, and explain the two main reconstruction approaches in current use. We discuss the data requirements of these algorithms and ask how well they correspond to current microarray data.
Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery
Authors: WALLACE B.A. , JANES ROBERT W.
Published: December 2008

On the title page of the article (p. 631), the first author's name was shown incorrectly as “Bonnie A. Wallace”; this should have been “B.A. Wallace”. This has been corrected for the online journal.
Study of ion flow dynamics in an inertial electrostatic confinement device through sequential grid construction
Authors: Murali S. Krupakar , Kulcinski G. L. , Santarius J. F.
Published: December 2008

Experiments were performed to understand the dynamics of the ion flow in an inertial electrostatic confinement (IEC) device. This was done by monitoring the fusion rate as the symmetry of the grid was increased starting with a single loop all the way until the entire grid is constructed. The fusion rate was observed to increase with grid symmetry and eventually saturate. A single loop grid was observed to generate a cylindrical (∼line) fusion source. The ion flow distribution was measured by introducing fine wires across a single loop of the grid in the form of a chord of a circle (chord wires). This study revealed that with increased symmetry of the cathode grid wires the convergence of the ions improves. The chord wires provided electrons for ionization even at low pressures (∼6.67mPa) and helped sustain the plasma. The impinging ions heat these wires locally and the temperature of the wires was measured using an infrared thermometer that was used to understand the ion flow distribution across the cathode grid. The presence of the grid wires seems to affect the fusion rate more drastically than previously thought (was assumed to be uniform around the central grid). Most of the fusion reactions were observed to occur in the ion microchannels that form in gaps between the cathode wires. This work helps understand the fusion source regimes and calibrate the IEC device.
Criteria for ductility in Cr alloys based on electronic structures
Authors: Ma Ning , Cooper Bernard R. , Lewis James P. , Kang Bruce S.
Published: December 2008

We proposed several hypotheses based on Rice’s [Mech. & Phys. of Sol. 40, 239 (1992)] brittle-dutile criterion to explain materials’ mechanical properties from their electronic structures. These criteria were used in the study of mechanisms behind the ductility enhancement in Cr alloys by MgO dispersions through first principles methods and molecular dynamics simulations. The understanding of the mechanisms may help provide systematic strategy to further improve this and other related material’s mechanical properties.
P 3 M algorithm for dipolar interactions
Authors: Cerdà Juan J. , Ballenegger V. , Lenz O. , Holm C.
Published: December 2008

An extension to the P3M algorithm for electrostatic interactions is presented that allows to efficiently compute dipolar interactions in periodic boundary conditions. Theoretical estimates for the root-mean-square error of the forces, torques, and the energy are derived. The applicability of the estimates is tested and confirmed in several numerical examples. A comparison of the computational performance of the new algorithm to a standard dipolar-Ewald summation methods shows a performance crossover from the Ewald method to the dipolar P3M method for as few as 300 dipolar particles. In larger systems, the new algorithm represents a substantial improvement in performance with respect to the dipolar standard Ewald method. Finally, a test comparing point-dipole-based and charged-pair based models shows that point-dipole-based models exhibit a better performance than charged-pair based models.
Activated instability of homogeneous droplet nucleation and growth
Authors: Uline Mark J. , Corti David S.
Published: December 2008

For the pure-component supercooled Lennard-Jones vapor, the free energy of forming a droplet with a given particle number and volume is calculated using density-functional theory. In contrast to what was noted in previous studies, the free energy surface beyond the pseudosaddle point no longer exhibits a valley but rather channels the nuclei toward a locus of instabilities, initiating an unstable growth phase. Similar to a previous study of bubble formation in superheated liquids [M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007)], a new picture of homogeneous droplet nucleation and growth emerges.
Obtaining a nonsingular two-dimensional cloak of complex shape from a perfect three-dimensional cloak
Authors: Zhang Pu , Jin Yi , He Sailing
Published: December 2008

A general method is proposed to construct an approximate nonsingular two-dimensional (2D) cloak by taking constitutive parameter tensors (CPTs) of a three-dimensional perfect cloak on a mirror-symmetric cross section in order to avoid any singularity at the inner boundary of a perfect 2D cloak. As two examples, reduced 2D models for an elliptic cloak and a bow-tie cloak are derived. The reduced 2D models are characterized explicitly with CPT of finite values and good cloaking effects are verified numerically.
On the origin of the electrostatic potential difference at a liquid-vacuum interface
Authors: Harder Edward , Roux Benoît
Published: December 2008

The microscopic origin of the interface potential calculated from computer simulations is elucidated by considering a simple model of molecules near an interface. The model posits that molecules are isotropically oriented and their charge density is Gaussian distributed. Molecules that have a charge density that is more negative toward their interior tend to give rise to a negative interface potential relative to the gaseous phase, while charge densities more positive toward their interior give rise to a positive interface potential. The interface potential for the model is compared to the interface potential computed from molecular dynamics simulations of the nonpolar vacuum-methane system and the polar vacuum-water interface system. The computed vacuum-methane interface potential from a molecular dynamics simulation (−220 mV) is captured with quantitative precision by the model. For the vacuum-water interface system, the model predicts a potential of −400 mV compared to −510 mV, calculated from a molecular dynamics simulation. The physical implications of this isotropic contribution to the interface potential is examined using the example of ion solvation in liquid methane.
A comparative study of plasma-enhanced chemical vapor gate dielectrics for solution-processed polymer thin-film transistor circuit integration
Authors: Li Flora M. , Nathan Arokia , Wu Yiliang , Ong Beng S.
Published: December 2008

This paper considers plasma-enhanced chemical vapor deposited (PECVD) silicon nitride (SiNx) and silicon oxide (SiOx) as gate dielectrics for organic thin-film transistors (OTFTs), with solution-processed poly[5,5′-bis(3-dodecyl-2-thienyl)-2,2′-bithiophene] (PQT-12) as the active semiconductor layer. We examine transistors with SiNx films of varying composition deposited at 300 °C as well as 150 °C for plastic compatibility. The transistors show over 100% (two times) improvement in field-effect mobility as the silicon content in SiNx increases, with mobility (μFE) up to 0.14 cm2/V s and on/off current ratio (ION/IOFF) of 108. With PECVD SiOx gate dielectric, preliminary devices exhibit a μFE of 0.4 cm2/V s and ION/IOFF of 108. PQT-12 OTFTs with PECVD SiNx and SiOx gate dielectrics on flexible plastic substrates are also presented. These results demonstrate the viability of using PECVD SiNx and SiOx as gate dielectrics for OTFT circuit integration, where the low temperature and large area deposition capabilities of PECVD films are highly amenable to integration of OTFT circuits targeted for flexible and lightweight applications.
Midinfrared luminescence properties and laser potentials of Pr3+ doped KPb2Cl5 and CsCdBr3
Authors: Ferrier A. , Velázquez M. , Doualan J.-L. , Moncorgé R.
Published: December 2008

The paper presents the spectroscopic and the fluorescence properties of the Pr3+ doped low-energy phonon and nonhygroscopic chloride and bromide single crystals KPb2Cl5 and CsCdBr3. Room temperature absorption spectra have been registered and analyzed, by using standard as well as modified versions of the Judd–Ofelt formalism, to derive the values for the radiative lifetimes and the branching ratios of the various emission transitions in both compounds. Low temperature absorption and emission spectra have been registered and exploited to derive the detailed positions of the Pr3+ energy levels in KPb2Cl5. These experimental values have been confronted to and completed by calculated ones obtained by using a standard crystal-field procedure. These data, combined with results of fluorescence decays and emission spectra measurements, then have been used to determine the emission and gain cross sections of the main midinfrared (mid-IR) emission transitions of interest in these materials. Finally, the different mid-IR transitions have been discussed for the two crystals in order to determine their laser potentials.
Equilibrium critical thickness for misfit dislocations in III-nitrides
Authors: Holec David , Zhang Yucheng , Rao D. V. Sridhara , Kappers Menno J. , McAleese Clifford , Humphreys Colin J.
Published: December 2008

The critical thickness gives the transition point between fully strained and relaxed heteroepitaxial films and determines the onset of defect generation, including misfit dislocations, cracks, and V-pits. An important variable in critical thickness calculations concerning misfit dislocations is the dislocation energy. It consists of two contributions: the elastic energy of the bulk material around a dislocation and the energy of the dislocation core. The latter part is often neglected. Recent atomistic calculations have estimated this quantity together with the radius of dislocation cores in wurtzite III-nitrides. The effect of the dislocation core energy on equilibrium critical thickness values for III-nitrides is investigated theoretically and is shown to be significant. The calculated values of the critical thickness are compared with experimentally determined values of the critical thickness for misfit dislocations in the InGaN/GaN system using transmission electron microscopy and x-ray diffraction techniques. A comparison of the present model with experimental observations, together with a wide range of data from the literature for both AlGaN/GaN and InGaN/GaN systems, shows reasonable agreement. Finally, we speculate on a possible reason for differences between theory and experiment.
Absorption enhancement in solar cells by localized plasmon polaritons
Authors: Rockstuhl Carsten , Fahr Stephan , Lederer Falk
Published: December 2008

By means of a rigorous diffraction theory, we investigate the possibility to enhance the absorption in solar cells by employing localized plasmon polaritons excited in metallic nanowires. The solar cells are assumed to be made of amorphous silicon. We identify two reasons for increased absorption; namely, the giant near-field enhancement and the enhanced scattering cross section upon exciting localized plasmon polaritons. It will be shown that by a careful and rational adjustment of the system parameters an enhancement in the number of absorbed photons from the solar spectrum up to a factor of 1.6 is feasible.
Gas-liquid nucleation in a two dimensional system
Authors: Santra Mantu , Chakrabarty Suman , Bagchi Biman
Published: December 2008

We study the nucleation of liquid phase from a supersaturated vapor in two dimensions, where the particles interact through Lennard-Jones (LJ) pairwise potential. Using different Monte Carlo simulation methods, we calculate the free energy barrier for nucleation, the line tension, and bulk densities of equilibrium liquid and vapor phases, and also investigate the size and shape of the critical nucleus. The study is carried out at an intermediate level of supersaturation (away from the spinodal limit). In two dimensions, a surprisingly large cutoff (rc≥7.0σ, σ is the diameter of LJ particles) in the truncation of the LJ potential is required to obtain converged results. A lower cutoff [typically 2.5σ which is generally sufficient in three dimensional (3D) studies] leads to a substantial error in the values of the line tension, nucleation barrier, and characteristics of the critical cluster. It is found that in two dimensions, the classical nucleation theory (CNT) fails to provide a reliable estimate of the free energy barrier. It underestimates the barrier by as much as 50% at the saturation ratio S=1.1 (defined as S=P/PC, where PC is the coexistence pressure) and at the reduced temperature T∗=0.427 (defined as T∗=kBT/ε, where ε is the depth of the potential well). Interestingly, CNT has been found to overestimate the nucleation free energy barrier in 3D systems near the triple point. In fact, the agreement of the calculated nucleation rate with CNT is much worse in two dimensions than in three dimensions. The reason for the inadequacy of the CNT can be attributed to the noncircular nature of the critical clusters. Although the shape becomes increasingly circular and the clusters become more compact with increase in cutoff radius, an appreciable noncircular nature remains even without any cutoff to make the simple CNT inaccurate.
Polarization lowering of charge injection barriers at a ribonucleic acid/Au interface
Authors: Magulick J. , Beerbom M. M. , Schlaf R.
Published: December 2008

The orbital line-up at a ribonucleic acid (RNA)/Au interface was investigated using photoemission spectroscopy. The particular interface, polyuridine (polyrU) homopolymer/Au, was prepared by injecting polyrU in aqueous solution into vacuum through an electrospray deposition system. This enabled buildup of the interface in multiple growth steps with intermediate characterization by x-ray and ultraviolet photoemission spectroscopy measurements. The results suggest significant polarization effects in the RNA layer close to the interface as indicated by observed final state screening shifts in the photoemission spectra. The polarization at the interface causes a reduction in the electron and hole charge injection barriers, easing charge transfer between Au and polyrU.
Band gap bowing parameter of In1−xAlxN
Authors: Jones R. E. , Broesler R. , Yu K. M. , Ager J. W. , Haller E. E. , Walukiewicz W. , Chen X. , Schaff W. J.
Published: December 2008

We report a band gap bowing parameter for In1−xAlxN of 4.7 eV from a study of high quality and homogenous samples with x=0.017–0.60. Optical absorption data were modeled to extract the band gaps in order to consider the complications of the band structure of In-rich InAlN, including the Burstein–Moss shift, nonparabolic conduction band, and broadening of the absorption edge. The alloy compositions were accurately determined using Rutherford backscattering spectrometry and the sample quality was evaluated using x-ray diffraction and channeling-RBS.
Demixing in binary mixtures of apolar and dipolar hard spheres
Authors: Almarza N. G. , Lomba E. , Martín C. , Gallardo A.
Published: December 2008

We study the demixing transition of mixtures of equal size hard spheres and dipolar hard spheres using computer simulation and integral equation theories. Calculations are carried out at constant pressure, and it is found that there is a strong correlation between the total density and the composition. The critical temperature and the critical total density are found to increase with pressure. The critical mole fraction of the dipolar component on the contrary decreases as pressure is augmented. These qualitative trends are reproduced by the theoretical approaches that on the other hand overestimate by far the value of the critical temperature. Interestingly, the critical parameters for the liquid-vapor equilibrium extrapolated from the mixture results in the limit of vanishing neutral hard sphere concentration agree rather well with recent estimates based on the extrapolation of charged hard dumbbell phase equilibria when dumbbell elongation shrinks to zero [G. Ganzenmüller and P. J. Camp, J. Chem. Phys. 126, 191104 (2007)].
Dust ion-acoustic surface waves and Landau damping in a semi-bounded Lorentzian plasma
Authors: Kim Taejoon , Lee Myoung-Jae
Published: December 2008

Dust ion-acoustic surface waves propagating on the interface between a vacuum and a semi-bounded Lorentzian (kappa) plasma are kinetically investigated. For a collisionless and unmagnetized Lorentzian plasma, the dispersion relation shows that dust ion-acoustic surface modes are stable against small linear perturbation. The damping rates of the Lorentzian waves are generally increased as the superthermal particles are increased. The ion-to-electron density ratio also greatly enhances the damping rate. As the wave number becomes large, the damping of the wave is quickly decreased. The effects of superthermal particles and dust particles on the phase and the group velocities are discussed in this work as well.
Comparison of magnetotransport properties of nano- and microcrystalline La0.7Ca0.3MnO3 manganites in high magnetic field
Authors: Pękała Marek , Kozlova Nadezda , Drozd Vadym
Published: December 2008

The nanocrystalline (mean grain size 20 nm) and microcrystalline magnetoresistive manganites with composition La0.7Ca0.3MnO3 were studied using a four probe electrical resistivity measurement in a strong magnetic field. The room temperature values of electrical resistivity are found to be 20 times larger for the nanocrystalline than for the microcrystalline sample, and therefore show a remarkable influence of fine grain microstructure. Such a difference reveals a more intense electron scattering inside the structurally and magnetically disordered grain boundaries in the nanocrystalline material than in the microcrystalline material. A pulsed magnetic field of 47 T reduces electrical resistivity three and eight times for the nano- and microcrystalline samples, respectively, and causes a monotonic shift of the transition temperature from TP=150 to 180 K in nanocrystalline manganite. In the microcrystalline sample TP shifts only from 250 to 270 K. The temperature dependencies of electrical resistivity above TP confirm that the polaronic model is applicable up to 47 T. The activation energy of the microcrystalline manganite decreases from about 2000 K down to 300 K between the 0 and 47 T. The high field activation energy of the nanocrystalline manganite is twice as large as that of the microcrystalline manganite. The strong negative magnetoresistance effect in both nano- and microcrystalline manganites reaches about 90% at 47 T in different temperature ranges. Most abrupt changes of magnetoresistance occurring at the lowest temperatures in magnetic fields up to 2 T are followed by a relatively slower approach to saturation at stronger fields for both microstructures. The magnetoresistance hysteresis found in the nanocrystalline manganite at low temperatures is related to the magnetization hysteresis appearing at relatively weak magnetic fields. The saturation magnetization in the grain bulk and grain boundaries is determined. The influence of magnetic viscosity effects on electrical resistivity of the nanocrystalline manganite is also analyzed.
Generation of negative ions in the gas phase from a 12CaO⋅7Al2O3 membrane-coated ceramic heater under atmospheric pressure
Authors: Yamamoto Mitsuo , Shima Akio , Nishioka Masateru , Sadakata Masayoshi
Published: December 2008

12 CaO ⋅ 7 Al 2 O 3 (C12A7) crystal is able to generate strong and high purity oxygen anion (O−) beam under reduced pressure. However, the emission of O− or related species under atmospheric pressure has not been evaluated. In this study, the characteristics of negative ion species emissions from the C12A7 membrane-coated ceramic heater under atmospheric pressure were investigated by quadrupole mass spectrometer. Negative ion species were confirmed to be emitted even under atmospheric pressure. It was supposed that the detected negative ion clusters, such as O−(H2O)n, O2−(H2O)n, and CO4−(H2O)n, were generated by the reaction of negative ions emitted from the heater with impurities in He gas.
Electrically injected InGaAs/GaAs photonic crystal membrane light emitting microcavity with spatially localized gain
Authors: Kim Yong K. , Elarde Victor C. , Long Christopher M. , Coleman James J. , Choquette Kent D.
Published: December 2008

Electrically injected photonic crystal membrane light emitting microcavities with spatially localized optical gain are reported. The localization of the InGaAs quantum well inside the defect cavity of the photonic crystal allows for efficient coupling of the optical mode to the gain medium and reduces nonradiative carrier recombination. The use of a buried oxide layer under the semiconductor membrane enables optical and electrical confinement and a submicron diameter oxide aperture provides a current path. Enhancement of the electroluminescence intensity is observed as a result of the spatial localization of the quantum well, and the spectral characteristics at room temperature indicate the photonic crystal microcavity confinement.
Competing geometric and inertial effects on local flow structure in thick gravity-driven fluid films
Authors: Scholle M. , Haas A. , Aksel N. , Wilson M. C. T. , Thompson H. M. , Gaskell P. H.
Published: December 2008

The formation and presence of eddies within thick gravity-driven free-surface film flow over a corrugated substrate are considered, with the governing equations solved semianalytically using a complex variable method for Stokes flow and numerically via a full finite element formulation for the more general problem when inertia is significant. The effect of varying geometry (involving changes in the film thickness or the amplitude and wavelength of the substrate) and inertia is explored separately. For Stokes-like flow and varying geometry, excellent agreement is found between prediction and existing flow visualizations and measured eddy center locations associated with the switch from attached to locally detached flow. It is argued that an appropriate measure of the influence of inertia at the substrate is in terms of a local Reynolds number based on the characteristic corrugation length scale. Since, for small local Reynolds numbers, the local flow structure there becomes effectively decoupled from the inertia-dominated overlying film and immune from instabilities at the free-surface; the influence of inertia manifests itself as a skewing of the dividing streamline (separatrix). It is shown that the formation and presence of eddies can be manipulated in one of two ways. While an decrease/increase in the corrugation steepness leads to the disappearance/appearance of kinematically induced eddies, an increase/decrease in the inertia present in the system leads to the appearance/disappearance of inertially induced eddies. A critical corrugation steepness for a given film thickness is defined, demarking the transition from a kinematically to an inertially induced local eddy flow structure and vice versa.
A comprehensive investigation on the phase transformation behavior and electrical properties of (Pb1−xBax)ZrO3 (≤x≤0.5) thin films
Authors: Hao Xihong , Zhai Jiwei , Yao Xi
Published: December 2008

( Pb 1 − x Ba x ) ZrO 3 (PBZ) (0≤x≤0.5) thin films were successfully fabricated on Pt(111)/TiO2/SiO2/Si substrates by the sol-gel technique, and the influence of the Ba2+ content on the microstructure, electrical properties, and phase transformation behavior of PBZ films was investigated in detail. With the increase in Ba2+ concentration, the orientation of the PBZ films was changed from (111) to (110) gradually. Simultaneously the grain size of the films decreased, and the surface became more and more homogeneous and uniform. The room-temperature state of PBZ thin films experienced a transformation from an antiferroelectric to a ferroelectric phase and then to a paraelectric phase with the increase in Ba2+ content. The typical ferroelectric relaxor behavior was observed due to the Ba2+ substitution, and the degree of the relaxor behavior was enhanced with the increase in Ba2+ content.
Tunable lateral shift and polarization beam splitting of the transmitted light beam through electro-optic crystals
Authors: Chen Xi , Shen Ming , Zhang Zhen-Fu , Li Chun-Fang
Published: December 2008

We have investigated the tunable lateral shift and polarization beam splitting of the transmitted light beam through electro-optic crystals, based on the Pockels effect. The positive and negative lateral shifts could be easily controlled by adjusting the permittivity tensor, which is modulated by the external applied electric field. An alternative way to realize the polarization beam splitter was also proposed by the polarization-dependent lateral shifts. Numerical simulations for Gaussian-shaped incident beam have demonstrated the above theoretical results obtained by stationary phase method. All these phenomena have potential applications in optical devices.
Role of boundary roughness in the electronic transport of Bi nanowires
Authors: Huber T. E. , Nikolaeva A. , Gitsu D. , Konopko L. , Graf M. J.
Published: December 2008

We present a study of electronic transport in 200 nm diameter bismuth nanowire arrays embedded in an alumina matrix where the nanowires are oriented preferentially with the trigonal crystalline axis parallel to the wire length. The study is based on measurements of the resistance and thermopower over a wide range of temperatures (4–300 K) as well as of magnetoresistance for fields of up to 9 T. The Fermi energies are obtained from the Landau level spectrum; results show that the wires have the intrinsic electron and hole concentrations. At high temperatures, the mobilities are temperature dependent and the electron mobility is several orders of magnitude larger than that of holes. This nanowire mobility behavior, which is also observed in the bulk, is attributed to carrier-phonon scattering. At low temperatures, the mobilities are temperature independent and roughly the same for electrons and holes. An interpretation in terms of boundary roughness scattering is proposed.
Ohmic contacts to SnS films: Selection and estimation of thermal stability
Authors: Devika M. , Reddy N. Koteeswara , Patolsky F. , Gunasekhar K. R.
Published: December 2008

Selection of Ohmic contacts to SnS films is one of the crucial tasks for the fabrication of efficient SnS devices. Thus, we examined different nonalloyed metallization schemes, namely, Ag, Al, In, and Sn to SnS films since their Fermi level pins exactly in between the conduction and valance bands of SnS. To explore the Ohmic behavior of M/SnS (M=Ag,Al,In,Sn) structures, the electrical properties of as-grown structures have been studied at different temperatures. From these studies it is noticed that at room temperature all M/SnS structures, except Ag/SnS, have an excellent Ohmic behavior over the voltage range from −10 to 10 V. However, Ag/SnS structures showed Ohmic trend only in the voltage range of ±6 V. The stability of the M/SnS structures was also examined by annealing them at different temperatures (300–500 °C) and the obtained peculiar results are reported.
Influence of hydrogen incorporation on the optical properties and crystallization of GeTe2 thin films
Authors: Cao Ke , Ferizovic Dino , Muñoz Martin
Published: December 2008

Thin films of GeTe2 were deposited on glass substrates using radio-frequency magnetron sputtering with various hydrogen flow rates in the growth chamber. Transmission data of deposited films were taken and used to determine optical constants [refractive index (n), extinction coefficient (κ), and absorption coefficient (α)] and the energies corresponding to absorption coefficients of 104 and 103 cm−1 (E04,E03), Tauc band gap ETauc, and Urbach energy EU. An increase in these energies was observed as a function of the hydrogen flow rate. An increase in the disorder in the hydrogenated GeTe2 thin films was determined from Tauc’s slope B1/2 parameter, Urbach energy, and full width at half maximum of Raman vibrational modes. Crystallization of GeTe2 occurs via a phase separation into Te and GeTe crystalline phases. The crystallization temperature increases with the addition of hydrogen. A large change (∼60% decrease) in the optical transmission occurs after the phase change from amorphous to crystalline.
Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions
Authors: Kast Stefan M. , Kloss Thomas
Published: December 2008

A general, path-independent expression is derived for the excess chemical potential of integral equation closure approximations that contain a bridge function which depends on a renormalized indirect correlation function. Closed-form results are obtained for various cases, among them a partial series expansion of the hypernetted chain closure.
Instabilities, pattern formation, and mixing in active suspensions
Authors: Saintillan David , Shelley Michael J.
Published: December 2008

Suspensions of self-propelled particles, such as swimming micro-organisms, are known to undergo complex dynamics as a result of hydrodynamic interactions. To elucidate these dynamics, a kinetic theory is developed and applied to study the linear stability and the nonlinear pattern formation in these systems. The evolution of a suspension of self-propelled particles is modeled using a conservation equation for the particle configurations, coupled to a mean-field description of the flow arising from the stress exerted by the particles on the fluid. Based on this model, we first investigate the stability of both aligned and isotropic suspensions. In aligned suspensions, an instability is shown to always occur at finite wavelengths, a result that extends previous predictions by Simha and Ramaswamy [“Hydrodynamic fluctuations and instabilities in ordered suspensions of self-propelled particles,” Phys. Rev. Lett. 89, 058101 (2002)]. In isotropic suspensions, we demonstrate the existence of an instability for the active particle stress, in which shear stresses are eigenmodes and grow exponentially at long scales. Nonlinear effects are also investigated using numerical simulations in two dimensions. These simulations confirm the results of the stability analysis, and the long-time nonlinear behavior is shown to be characterized by the formation of strong density fluctuations, which merge and breakup in time in a quasiperiodic fashion. These complex motions result in very efficient fluid mixing, which we quantify by means of a multiscale mixing norm.