bluuebunny/crossref_metadata_2025 huggingface dataset:
10Be measured in a GRIP snow pit and modeled using the ECHAM5‐HAM general circulation model
Authors: Heikkilä U. , Beer J. , Jouzel J. , Feichter J. , Kubik P.
Published: March 2008

10Be measured in a Greenland Ice Core Project (GRIP) snow pit (1986–1990) with a seasonal resolution is compared with the ECHAM5–HAM GCM run. The mean modeled 10Be concentration in ice (1.0·104 atoms/g) agrees well with the measured value (1.2·104 atoms/g). The measured 10Be deposition flux (88 atoms/m2/s) also agrees well with the modeled flux (69 atoms/m2/s) and the measured precipitation rate (0.67 mm/day) agrees with the modeled rate (0.61 mm/day). The mean surface temperature of −31°C estimated from δ18O is lower than the temperature measured at a near‐by weather station (−29°C) and the modeled temperature (−26°C). During the 5‐year period the concentrations and deposition fluxes, both measured and modeled, show a decreasing trend consistent with the increase in the solar activity. The variability of the measured and modeled concentrations and deposition fluxes is very similar suggesting that the variability is linked to a variability in production rather than the local meteorology.
Comparison of hyporheic exchange under covered and uncovered channels based on linked surface and groundwater flow simulations
Authors: Cardenas M. Bayani , Gooseff Michael N.
Published: March 2008

Hyporheic exchange is an important process upon which stream biogeochemical cycling is dependent. The potential for hyporheic exchange in covered channels (i.e., ice‐covered channels, karst conduits, fractures) with permeable sediments has not yet been assessed. We characterize the potential for hyporheic exchange in covered channels using linked turbulent channel flow/groundwater flow simulations. Simulations show that hyporheic exchange occurs in covered channels which have shallower hyporheic zones and larger hyporheic fluxes than equivalent‐depth equivalent‐discharge uncovered channels. We also analyzed hyporheic exchange for the case of freely floating covers with rough undersides and found that hyporheic exchange decreases with increasing cover roughness which in turn is driven by subdued bed topography, a response to additional resistance due to covers. The results suggest that hyporheic exchange occurs in covered channels and may be just as or perhaps more important to the ecology and biogeochemistry of these channels than to open channel streams.
Lipoic acid supplementation and endothelial function
Authors: Tardif J‐C , Rhéaume E
Published: March 2008

Endothelial dysfunction is caused by all the recognized cardiovascular risk factors and has been implicated in the complex processes leading to the initiation and progression of atherosclerosis. Short‐term treatment with lipoic acid is shown in the current issue of the British Journal of Pharmacology to improve endothelial function of aortic rings of old rats. The age‐related decrease in phosphorylation of nitric oxide synthase and Akt was improved by lipoic acid supplementation. The improved phosphorylation status may have been due to reduced activity of the phosphatase PPA2, associated with decreased levels of endothelial ceramide induced by lipoic acid. Neutral sphingomyelinase activity was also reduced by lipoic acid, which was due, at least in part, to increased glutathione levels in endothelial cells. The favourable antioxidant, anti‐inflammatory, metabolic and endothelial effects of lipoic acid shown in rodents, in this and other recently published studies, warrant further assessment of its potential role for prevention and treatment of cardiovascular diseases.

British Journal of Pharmacology (2008) 153, 1587–1588; doi:10.1038/bjp.2008.74; published online 17 March 2008
Lentivector‐mediated rescue from cerebellar ataxia in a mouse model of spinocerebellar ataxia
Authors: Torashima Takashi , Koyama Chiho , Iizuka Akira , Mitsumura Kazuhiro , Takayama Kiyohiko , Yanagi Shigeru , Oue Miho , Yamaguchi Haruyasu , Hirai Hirokazu
Published: March 2008

Polyglutamine disorders are inherited neurodegenerative diseases caused by the accumulation of expanded polyglutamine protein (polyQ). Previously, we identified a new guanosine triphosphatase, CRAG, which facilitates the degradation of polyQ aggregates through the ubiquitin–proteasome pathway in cultured cells. Because expression of CRAG decreases in the adult brain, a reduced level of CRAG could underlie the onset of polyglutamine diseases. To examine the potential of CRAG expression for treating polyglutamine diseases, we generated model mice expressing polyQ predominantly in Purkinje cells. The model mice showed poor dendritic arborization of Purkinje cells, a markedly atrophied cerebellum and severe ataxia. Lentivector‐mediated expression of CRAG in Purkinje cells of model mice extensively cleared polyQ aggregates and re‐activated dendritic differentiation, resulting in a striking rescue from ataxia. Our in vivo data substantiate previous cell‐culture‐based results and extend further the usefulness of targeted delivery of CRAG as a gene therapy for polyglutamine diseases.
Gene induction following wounding of wild‐type versus macrophage‐deficient Drosophila embryos
Authors: Stramer Brian , Winfield Mark , Shaw Tanya , Millard Thomas H , Woolner Sarah , Martin Paul
Published: March 2008

By using a microarray screen to compare gene responses after sterile laser wounding of wild‐type and ‘macrophageless’ serpent mutant Drosophila embryos, we show the wound‐induced programmes that are independent of a pathogenic response and distinguish which of the genes are macrophage dependent. The evolutionarily conserved nature of this response is highlighted by our finding that one such new inflammation‐associated gene, growth arrest and DNA damage‐inducible gene 45 (GADD45), is upregulated in both Drosophila and murine repair models. Comparison of unwounded wild‐type and serpent mutant embryos also shows a portfolio of ‘macrophage‐specific’ genes, which suggest analogous functions with vertebrate inflammatory cells. Besides identifying the various classes of wound‐ and macrophage‐related genes, our data indicate that sterile injury per se, in the absence of pathogens, triggers induction of a ‘pathogen response’, which might prime the organism for what is likely to be an increased risk of infection.
Renal cells activate the platelet receptor CLEC-2 through podoplanin
Authors: Christou Charita M. , Pearce Andrew C. , Watson Aleksandra A. , Mistry Anita R. , Pollitt Alice Y. , Fenton-May Angharad E. , Johnson Louise A. , Jackson David G. , Watson Steve P. , O'callaghan Chris A.
Published: March 2008

We have recently shown that the C-type lectin-like receptor, CLEC-2, is expressed on platelets and that it mediates powerful platelet aggregation by the snake venom toxin rhodocytin. In addition, we have provided indirect evidence for an endogenous ligand for CLEC-2 in renal cells expressing HIV-1. This putative ligand facilitates transmission of HIV through its incorporation into the viral envelope and binding to CLEC-2 on platelets. The aim of the present study was to identify the ligand on these cells which binds to CLEC-2 on platelets. Recombinant CLEC-2 exhibits specific binding to HEK-293T (human embryonic kidney) cells in which the HIV can be grown. Furthermore, HEK-293T cells activate both platelets and CLEC-2-transfected DT-40 B-cells. The transmembrane protein podoplanin was identified on HEK-293T cells and was demonstrated to mediate both binding of HEK-293T cells to CLEC-2 and HEK-293T cell activation of CLEC-2-transfected DT-40 B-cells. Podoplanin is expressed on renal cells (podocytes). Furthermore, a direct interaction between CLEC-2 and podoplanin was confirmed using surface plasmon resonance and was shown to be independent of glycosylation of CLEC-2. The interaction has an affinity of 24.5±3.7 μM. The present study identifies podoplanin as a ligand for CLEC-2 on renal cells.
Rab10 in insulin-stimulated GLUT4 translocation
Authors: Sano Hiroyuki , Roach William G. , Peck Grantley R. , Fukuda Mitsunori , Lienhard Gustav E.
Published: March 2008

In fat and muscle cells, insulin stimulates the movement to and fusion of intracellular vesicles containing GLUT4 with the plasma membrane, a process referred to as GLUT4 translocation. Previous studies have indicated that Akt [also known as PKB (protein kinase B)] phosphorylation of AS160, a GAP (GTPase-activating protein) for Rabs, is required for GLUT4 translocation. The results suggest that this phosphorylation suppresses the GAP activity and leads to the elevation of the GTP form of one or more Rabs required for GLUT4 translocation. Based on their presence in GLUT4 vesicles and activity as AS160 GAP substrates, Rabs 8A, 8B, 10 and 14 are candidate Rabs. Here, we provide further evidence that Rab10 participates in GLUT4 translocation in 3T3-L1 adipocytes. Among Rabs 8A, 8B, 10 and 14, only the knockdown of Rab10 inhibited GLUT4 translocation. In addition, we describe the subcellular distribution of Rab10 and estimate the fraction of Rab10 in the active GTP form in vivo. Approx. 5% of the total Rab10 was present in GLUT4 vesicles isolated from the low-density microsomes. In both the basal and the insulin state, 90% of the total Rab10 was in the inactive GDP state. Thus, if insulin increases the GTP form of Rab10, the increase is limited to a small portion of the total Rab10. Finally, we report that the Rab10 mutant considered to be constitutively active (Rab10 Q68L) is a substrate for the AS160 GAP domain and, hence, cannot be used to deduce rigorously the function of Rab10 in its GTP form.
Plk3 phosphorylates topoisomerase IIα at Thr1342, a site that is not recognized by Plk1
Authors: Iida Masato , Matsuda Masao , Komatani Hideya
Published: March 2008

The Plk (polo-like kinase) family is involved in cell-cycle machinery. Despite the possible overlapping involvement of Plk1 and Plk3 in cell-cycle distribution, the precise role of each Plk might be different. To investigate mechanisms that may differentiate their physiological roles, we compared the substrate specificities of Plk1 and Plk3 using synthetic peptides. Among these substrate peptides, topoisomerase IIα EKT1342DDE-containing synthetic peptide was strongly phosphorylated by Plk3 but not by Plk1. By modulating the topoisomerase IIα peptide, we identified residues at positions +1, +2 and +4 as determinants of differential substrate recognition between Plk1 and Plk3. Acidic residues at positions +2 and +4 appear to be a positive determinant for Plk3 but not Plk1. Variation at position +1 appears to be tolerated by Plk3, while a hydrophobic residue at +1 is critical for Plk1 activity. The direct phosphorylation of Thr1342 of topoisomerase IIα by Plk3 was demonstrated with an in vitro kinase assay, and overexpression of Plk3 induced the phosphorylation of Thr1342 in cellular topoisomerase IIα. Furthermore, the physical interaction between Plk3 and topoisomerase IIα was also demonstrated in cells in addition to phosphorylation. These data suggest that topoisomerase IIα is a novel physiological substrate for Plk3 and that Plk1 and Plk3 play different roles in cell-cycle regulation.
Peroxiredoxin IV is an endoplasmic reticulum-localized enzyme forming oligomeric complexes in human cells
Authors: Tavender Timothy J. , Sheppard Alyson M. , Bulleid Neil J.
Published: March 2008

The peroxiredoxins are a ubiquitous family of proteins involved in protection against oxidative stress through the detoxification of cellular peroxides. In addition, the typical 2-Cys peroxiredoxins function in signalling of peroxide stress and as molecular chaperones, functions that are influenced by their oligomeric state. Of the human peroxiredoxins, Prx IV (peroxiredoxin IV) is unique in possessing an N-terminal signal peptide believed to allow secretion from the cell. Here, we present a characterization of Prx IV in human cells demonstrating that it is actually retained within the ER (endoplasmic reticulum). Stable knockdown of Prx IV expression led to detrimental effects on the viability of human HT1080 cells following treatment with exogenous H2O2. However, these effects were not consistent with a dose-dependent correlation between Prx IV expression and peroxide tolerance. Moreover, modulation of Prx IV expression showed no obvious effect on ER-associated stress, redox conditions or H2O2 turnover. Subsequent investigation demonstrated that Prx IV forms complex structures within the ER, consistent with the formation of homodecamers. Furthermore, Prx IV oligomeric interactions are stabilized by additional non-catalytic disulfide bonds, indicative of a primary role other than peroxide elimination.
Sequential regulation of ferroportin expression after erythrophagocytosis in murine macrophages: early mRNA induction by haem, followed by iron-dependent protein expression
Authors: Delaby Constance , Pilard Nathalie , Puy Hervé , Canonne-Hergaux François
Published: March 2008

Tissue macrophages play an essential role in iron recycling through the phagocytosis of senescent RBCs (red blood cells). Following haem catabolism by HO1 (haem oxygenase 1), they recycle iron back into the plasma through the iron exporter Fpn (ferroportin). We previously described a cellular model of EP (erythrophagocytosis), based on primary cultures of mouse BMDMs (bone-marrow-derived macrophages) and aged murine RBCs, and showed that EP induces changes in the expression profiles of Fpn and HO1. In the present paper, we demonstrate that haem derived from human or murine RBCs or from an exogenous source of haem led to marked transcriptional activation of the Fpn and HO1 genes. Iron released from haem catabolism subsequently stimulated the Fpn mRNA and protein expression associated with localization of the transporter at the cell surface, which probably promotes the export of iron into the plasma. These findings highlight a dual mechanism of Fpn regulation in BMDMs, characterized by early induction of the gene transcription predominantly mediated by haem, followed by iron-mediated post-transcriptional regulation of the exporter.
Oxidative folding competes with mitochondrial import of the small Tim proteins
Authors: Morgan Bruce , Lu Hui
Published: March 2008

All small Tim proteins of the mitochondrial intermembrane space contain two conserved CX3C motifs, which form two intramolecular disulfide bonds essential for function, but only the cysteine-reduced, but not oxidized, proteins can be imported into mitochondria. We have shown that Tim10 can be oxidized by glutathione under cytosolic concentrations. However, it was unknown whether oxidative folding of other small Tims can occur under similar conditions and whether oxidative folding competes kinetically with mitochondrial import. In the present study, the effect of glutathione on the cysteine-redox state of Tim9 was investigated, and the standard redox potential of Tim9 was determined to be approx. −0.31 V at pH 7.4 and 25 °C with both the wild-type and Tim9F43W mutant proteins, using reverse-phase HPLC and fluorescence approaches. The results show that reduced Tim9 can be oxidized by glutathione under cytosolic concentrations. Next, we studied the rate of mitochondrial import and oxidative folding of Tim9 under identical conditions. The rate of import was approx. 3-fold slower than that of oxidative folding of Tim9, resulting in approx. 20% of the precursor protein being imported into an excess amount of mitochondria. A similar correlation between import and oxidative folding was obtained for Tim10. Therefore we conclude that oxidative folding and mitochondrial import are kinetically competitive processes. The efficiency of mitochondrial import of the small Tim proteins is controlled, at least partially in vitro, by the rate of oxidative folding, suggesting that a cofactor is required to stabilize the cysteine residues of the precursors from oxidation in vivo.
Elevated intracellular calcium increases ferritin H expression through an NFAT-independent post-transcriptional mechanism involving mRNA stabilization
Authors: Mackenzie Elizabeth L. , Tsuji Yoshiaki
Published: March 2008

An increase in intracellular Ca2+ is one of the initiating events in T-cell activation. A calcium-mediated signalling cascade in T-cells involves activation of calcineurin and the dephosphorylation and translocation of NFAT (nuclear factor of activated T-cells), resulting in the transcriptional activation of target genes such as IL-2 (interleukin-2). In the present study, we found that increased intracellular calcium leads to induction of the antioxidant protein ferritin H. We previously reported that the ferritin H gene is transcriptionally activated under oxidative stress conditions through an ARE (antioxidant-responsive element). The facts that the ferritin H ARE contains a composite AP-1 (activator protein 1) site and that NFAT collaborates with AP-1 transcription factors led us to test whether calcium-activated NFAT is involved in the ferritin H induction through the ARE. Treatment of Jurkat T-cells with the calcium ionophore, ionomycin, increased ferritin H mRNA and protein expression. Although NFAT translocated to the nucleus and bound a consensus NFAT sequence located in the IL-2 promoter after ionomycin treatment, it did not activate ferritin H transcription despite the presence of a putative NFAT-binding sequence in the ferritin H ARE. In addition, the calcineurin inhibitor cyclosporin A treatment blocked ionomycin-mediated NFAT nuclear translocation but failed to abrogate the increase in ferritin H mRNA. Analysis of mRNA stability after actinomycin D treatment revealed that ionomycin prolongs ferritin H mRNA half-life. Taken together, these results suggest that ionomycin-mediated induction of ferritin H may occur in an NFAT-independent manner but through post-transcriptional stabilization of the ferritin H mRNA.
Liver fibrosis
Authors: Wallace Karen , Burt Alastair D. , Wright Matthew C.
Published: March 2008

Liver damage leads to an inflammatory response and to the activation and proliferation of mesenchymal cell populations within the liver which remodel the extracellular matrix as part of an orchestrated wound-healing response. Chronic damage results in a progressive accumulation of scarring proteins (fibrosis) that, with increasing severity, alters tissue structure and function, leading to cirrhosis and liver failure. Efforts to modulate the fibrogenesis process have focused on understanding the biology of the heterogeneous liver fibroblast populations. The fibroblasts are derived from sources within and outwith the liver. Fibroblasts expressing α-smooth muscle actin (myofibroblasts) may be derived from the transdifferentiation of quiescent hepatic stellate cells. Other fibroblasts emerge from the portal tracts within the liver. At least a proportion of these cells in diseased liver originate from the bone marrow. In addition, fibrogenic fibroblasts may also be generated through liver epithelial (hepatocyte and biliary epithelial cell)–mesenchymal transition. Whatever their origin, it is clear that fibrogenic fibroblast activity is sensitive to (and may be active in) the cytokine and chemokine profiles of liver-resident leucocytes such as macrophages. They may also be a component driving the regeneration of tissue. Understanding the complex intercellular interactions regulating liver fibrogenesis is of increasing importance in view of predicted increases in chronic liver disease and the current paucity of effective therapies.
Ca2+ signalling: a new route to NAADP
Authors: Rutter Guy A. , Bellomo Elisa A.
Published: March 2008

NAADP (nicotinic acid–adenine dinucleotide phosphate) is a derivative of NADP (nicotinamide–adenine dinucleotide phosphate), which differs by the presence of a nicotinic acid instead of a nicotinamide moiety. This small structural difference makes NAADP one of the most powerful second messengers known, able to mobilize intracellular Ca2+ in a wide range of cellular models, ranging from invertebrates to mammals. Despite this, our understanding of NAADP homoeostasis, metabolism and physiological action is still limited. A new report by Vasudevan and colleagues in this issue of the Biochemical Journal provides important new data by describing a new synthetic activity in sperm cells which may turn out to represent the most physiologically relevant route to this second messenger.
Biomolecular simulation: historical picture and future perspectives
Authors: van Gunsteren Wilfred F. , Dolenc Jožica
Published: March 2008

Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.
Calculating enzyme kinetic parameters from protein structures
Authors: Stein Matthias , Gabdoulline Razif R. , Wade Rebecca C.
Published: March 2008

Enzyme kinetic parameters can differ between different species and isoenzymes for the same catalysed reaction. Computational approaches to calculate enzymatic kinetic parameters from the three-dimensional structures of proteins will be reviewed briefly here. Enzyme kinetic parameters may be derived by modelling and simulating the rate-determining process. An alternative, approximate, but more computationally efficient approach is the comparison of molecular interaction fields for experimentally characterized enzymes and those for which parameters should be determined. A correlation between differences in interaction fields and experimentally determined kinetic parameters can be used to determine parameters for orthologous enzymes from other species. The estimation of enzymatic kinetic parameters is an important step in setting up mathematical models of biochemical pathways in systems biology.
Low-grade inflammation and arterial wave reflection in patients with chronic fatigue syndrome
Authors: Spence Vance A. , Kennedy Gwen , Belch Jill J. F. , Hill Alexander , Khan Faisel
Published: March 2008

Some of the symptoms reported by people with CFS (chronic fatigue syndrome) are associated with various cardiovascular phenomena. Markers of cardiovascular risk, including inflammation and oxidative stress, have been demonstrated in some patients with CFS, but little is known about the relationship between these and prognostic indicators of cardiovascular risk in this patient group. In the present study, we investigated the relationship between inflammation and oxidative stress and augmentation index, a measure of arterial stiffness, in 41 well-characterized patients with CFS and in 30 healthy subjects. AIx@75 (augmentation index normalized for a heart rate of 75 beats/min) was significantly greater in patients with CFS than in control subjects (22.5±1.7 compared with 13.3±2.3% respectively; P=0.002). Patients with CFS also had significantly increased levels of CRP (C-reactive protein) (2.58±2.91 compared with 1.07±2.16 μg/ml respectively; P<0.01) and 8-iso-prostaglandin F2α isoprostanes (470.7±250.9 compared with 331.1±97.6 pg/ml respectively; P<0.005). In patients with CFS, AIx@75 correlated significantly with logCRP (r=0.507, P=0.001), isoprostanes (r=0.366, P=0.026), oxidized LDL (low-density lipoprotein) (r=0.333, P=0.039) and systolic blood pressure (r=0.371, P=0.017). In a stepwise multiple regression model, including systolic and diastolic blood pressure, body mass index, CRP, tumour necrosis factor-α, interleukin-1, oxidized LDL, high-density lipoprotein-cholesterol levels, isoprostanes, age and gender, AIx@75 was independently associated with logCRP (β=0.385, P=0.006), age (β=0.363, P=0.022) and female gender (β=0.302, P=0.03) in patients with CFS. The combination of increased arterial wave reflection, inflammation and oxidative stress may result in an increased risk of future cardiovascular events. Assessment of arterial wave reflection might be useful for determining cardiovascular risk in this patient group.
Adaptive minimum action method for the study of rare events
Authors: Zhou Xiang , Ren Weiqing , E Weinan
Published: March 2008

An adaptive minimum action method is proposed for computing the most probable transition paths between stable equilibria in metastable systems that do not necessarily have an underlying energy function, by minimizing the action functional associated with such transition paths. This new algorithm uses the moving mesh strategy to adaptively adjust the grid points over the time interval of transition. Numerical examples are presented to demonstrate the efficiency of the adaptive minimum action method.
The dissociation and equation of state of dense fluid oxygen at high pressures and high temperatures
Authors: Chen Q. F. , Cai L. C. , Zhang Y. , Gu Y. J.
Published: March 2008

The dissociation, pressure, and internal energy of dense fluid oxygen at high temperatures and densities have been calculated from the free-energy functions using the self-consistent fluid variational theory. In this paper, we focused on a mixture of oxygen atoms and molecules, and investigated the phenomenon of pressure dissociation at finite temperature. The single-shock Hugoniot derived from this equation of state agrees well with gas-gun experiments for pressure versus density. The equation of state and dissociation degree are predicted in the ranges of temperature of 5000–16000K and density of 0.1–4.5g∕cm3. These data are formulated in the analytical forms of dissociation degree-density-temperature and pressure-density-temperature equation of state.
Synthesis of monosized magnetic-optical AuFe alloy nanoparticles
Authors: Liu Hong Ling , Wu Jun Hua , Min Ji Hyun , Kim Young Keun
Published: March 2008

We report the preparation and characterization of multifunctional AuFe alloy nanoparticles of three compositions, Au0.25Fe0.75, Au0.5Fe0.5, and Au0.75Fe0.25, by a polyol process. It is found that the fusion of the two elements into one nanostructure entity retains the optical and magnetic properties of the individual components. The x-ray diffraction and transmission electron microscopy analyses confirm the formation of the alloy nanostructure with a narrow distribution of particle sizes and provides the detailed structural arrangements. The magnetic investigation shows the superparamagnetic or soft ferromagnetic behavior of the nanoparticles at room temperature, whereas the UV-visible measurements display the variation of the absorption bands at ∼560nm. The AuFe nanoparticles are rendered water soluble after thiolation.
Barrierless reactions between two closed-shell molecules. I. Dynamics of F2+CH3SCH3 reaction
Authors: Lu Yu-Ju , Lee Lance , Pan Jun-Wei , Xie Tingxian , Witek Henryk A. , Lin Jim J.
Published: March 2008

A detailed experimental and theoretical investigation of the first-reported barrierless reaction between two closed-shell molecules [J. Chem. Phys. 127, 101101 (2007)] is presented. The translational energy and angular distributions of two product channels, HF+CH2SFCH3 and F+CH3SFCH3, determined at several collision energies, have been analyzed to reveal the dynamics of the studied reaction. Detailed analysis of the experimental and computational results supports the proposed reaction mechanism involving a short-lived F−F−S(CH3)2 intermediate, which can be formed without any activation energy. Other possible reaction mechanisms have been discriminated. The decay of the intermediate and competition between the two product channels have been discussed.
Molecular dynamics of immiscible fluids in chemically patterned nanochannels
Authors: Cieplak Marek , Banavar Jayanth R.
Published: March 2008

Molecular dynamics simulations of chain molecules are used to elucidate physical phenomena involved in flows of dense immiscible fluids in nanochannels. We first consider a force driven flow in which the channel walls are homogeneous and wetting to one fluid and nonwetting to the other fluid. The coating of the walls by the wetting fluid provides a fluctuating surface that confines the flow of the nonwetting fluid. The resulting dissipation yields stationary Poiseuille-like flows in contrast to the accelerating nature of flow in the absence of the coating. We then consider walls consisting of patches whose wetting preferences to a fluid alternate along the walls. In the resulting flow, the immiscible components exhibit periodic structures in their velocity fields such that the crests are located at the wettability steps in contrast to the behavior of a single fluid for which the crest occurs in the wetting region. We demonstrate that for a single fluid, the modulated velocity field scales with the size of the chain molecules.
Ruderman–Kittel–Kasuyama–Yoshida and Néel contributions to the interlayer coupling of MnIr-based spin valves: Influence of deposition rate, roughness and spacer thickness
Authors: Teixeira J. M. , Ventura J. , Fermento R. , Araújo J. P. , Sousa J. B. , Cardoso S. , Freitas P. P.
Published: March 2008

We study the interlayer coupling field (Hcoupl) as a function of temperature (T) for two spin valve (SV) series of NiFe∕CoFe∕Cu(t)∕CoFe∕MnIr, with different deposition rates (DRs) of the layers and Cu thickness t ranging from 16to26Å. In series 1, the DRs were 0.49Å∕s for Cu and 0.29Å∕s for CoFe. In series 2, the DRs were lower: 0.28Å∕s for Cu and 0.23Å∕s for CoFe. The Hcoupl(T) dependence was obtained from magnetoresistance measurements (20–300K) at low magnetic fields. By considering the T dependence of both Ruderman–Kittel–Kasuyama–Yoshida (RKKY)-like [(T∕T0)∕sinh(T∕T0), where T0 is characteristic temperature] and Néel interactions, we were able to analyze the contribution of each to Hcoupl and study the influence of DR, roughness, and Cu t on T0, RKKY-like, and Néel coupling energies. We found that the Néel contribution to Hcoupl is more significative in the SVs with the higher DR, an effect that we relate to the corresponding higher γ observed experimentally by atomic force microscopy. On the other hand, the RKKY-like contribution is approximately constant with t for the higher DR-SVs but varies significatively for the SVs with the lower DR, showing an antiferromagnetic coupling at t=21Å.
Micromagnetic modeling of ferromagnetic resonance assisted switching
Authors: Scholz Werner , Batra Sharat
Published: March 2008

We studied the steady state behavior and magnetization switching process of single domain particles subject to ac and dc magnetic fields using analytical and numerical models based on the Landau–Lifshitz–Gilbert equation. We compared the analytical solutions for circularly polarized fields with a numerical single spin model and circularly and linearly polarized ac magnetic fields. It has been found, that the initial conditions and the dynamics of the external fields (field ramps and amplitude changes) strongly determine which precession orbit the magnetization converges to, if the magnetization precession is stable, and if the magnetization switches. We also studied the effects of field amplitudes, field angles, and damping on the switching behavior. The presented results can be applied to high power ferromagnetic resonance experiments and ferromagnetic resonance assisted magnetic recording schemes.
Initial studies on microelectromechanical system flux concentrators
Authors: Burnette James E. , Edelstein Alan S. , Fischer G. A. , Nowak E. , Bernard W. , Cheng Shu Fan , Nordman Cathy , Egelhoff W. F.
Published: March 2008

To take advantage of the potential offered by the recent increase in the magnetoresistance of magnetic tunnel junctions, it is necessary to address the problem of 1∕f noise. ARL has been working on a device, the microelectromechanical system (MEMS) flux concentrator, that mitigates this problem by modulating the sensed magnetic field so that the sensor operates at a higher frequency region where the 1∕f noise is smaller. Initial results of testing the device are reported. Though the final step in the fabrication of the device appears to have adversely affected the MEMS motion, two important results were obtained. They are (1) applying the large amplitude voltage at kilohertz frequencies necessary to drive the MEMS structure does not increase the background noise and (2) even though the width of the drive voltage is several hertz, one can demodulate the signal using a lock-in amplifier in order to extract 1Hz modulation signals. This last result shows that the sensor can be used to detect slow moving or varying magnetic anomalies.
An investigation of the sodium patterning in NaxCoO2 (0.5⩽x⩽1) by density functional theory methods
Authors: Meng Ying S. , Hinuma Yoyo , Ceder Gerbrand
Published: March 2008

Extensive experimental work has been carried out to characterize the stable Na-vacancy ordering patterns at various compositions of layered NaxCoO2. However, contradictions and debates prevail in the literature, particularly at high Na concentrations x>0.5. Understanding of the exotic electronic properties in this system requires a thorough understanding of the Na-vacancy structural orderings. Using density functional theory in the generalized gradient approximation (GGA), combined with a cluster expansion structure prediction algorithm we have found an intricate set of Na-vacancy ordered ground states in NaxCoO2 (0.5⩽x⩽1). We demonstrate a newly predicted ordering pattern between 0.67⩽x⩽0.71. By comparing the first principles electronic structure methods within the GGA and GGA+U (Hubbard U correction) approximations, we demonstrate that at certain Na concentration the stable ordering is affected by charge localization on the Co layer through coupling between the Na and Co lattices.
Photofragment translational spectroscopy of propargyl radicals at 248nm
Authors: Goncher Scott J. , Moore David T. , Sveum Niels E. , Neumark Daniel M.
Published: March 2008

The photodissociation of propargyl radical, C3H3, and its perdeuterated isotopolog was investigated using photofragment translational spectroscopy. Propargyl radicals were produced by 193nm photolysis of allene entrained in a molecular beam expansion and then photodissociated at 248nm. Photofragment time-of-flight spectra were measured at a series of laboratory angles using electron impact ionization coupled to a mass spectrometer. Data for ion masses corresponding to C3H2+, C3H+, C3+, and the analogous deuterated species show that both H and H2 loss occur. The translational energy distributions for these processes have average values ⟨ET⟩=5.7 and 15.3kcal∕mol, respectively, and are consistent with dissociation on the ground state following internal conversion, with no exit barrier for H loss but a tight transition state for H2 loss. Our translational energy distribution for H atom loss is similar to that in a previous work on propargyl in which the H atom, rather than the heavy fragment, was detected. The branching ratio for H loss/H2 loss was determined to be 97.6∕2.4±1.2, in good agreement with previous calculations.
Electron energy dependence of defect generation in high-k gate stacks
Authors: O’Connor Robert , Pantisano Luigi , Degraeve Robin , Kauerauf Thomas , Kaczer Ben , Roussel Phillipe , Groeseneken Guido
Published: March 2008

In this work, we employ the substrate hot electron injection technique as a characterization tool to examine the defect creation mechanisms in high-k HfSiON gate stacks, taking advantage of the independent control over oxide field, electron fluence, and injected electron energy which the technique allows. We show that defect creation and oxide breakdown are dependent on the energy of the injected electrons and not on the oxide field. Furthermore, we show that the energy of the injected electrons governs whether the majority of the defects are created at the Si∕SiO2 interface or in the bulk of the material. Results show that at operating conditions, the primary threat to device reliability from hot carrier damage is the introduction of a permanent 3D positive bias temperature instability component introduced by increased interface trap generation, even for carriers with energy slightly above that of field accelerated electrons. We also discuss the feasibility of using substrate hot electron injection as a means to accelerate time dependent dielectric breakdown measurements, thereby allowing degradation at lower oxide fields to be probed.
Magnetization reversal in patterned (Co∕Pd)n multilayers
Authors: E Chunsheng , Parekh Vishal , Ruchhoeft Paul , Khizroev Sakhrat , Litvinov Dmitri
Published: March 2008

In this work, the physics of magnetization reversal in patterned high anisotropy (Co∕Pd)n magnetic multilayer arrays is investigated where the magnetic island size, pitch, recording layer thickness, and the underlying multilayer magnetic properties are varied. Magnetization reversal was studied using magneto-optical Kerr effect magnetometry and magnetic force microscopy and supported by micromagnetic modeling. It is found that magnetic island dimension and/or pitch cannot alone explain the variations in the switching behavior of the patterned arrays and the observed values of switching field distribution (SFD). It is found that the ratio of switched magnetic islands to the total number of islands for a giving reversing field depends strongly on the magnetic island geometry. Stray fields from neighboring magnetic islands result in relatively minor influence on the switching characteristics. Micromagnetic modeling was used to further understand the magnetization reversal in patterned arrays. It is found that the bit-edge imperfections such as tapering contribute significantly to the SFD.
Breakdown of electrostatic predictions for the nonlinear dispersion relation of a stimulated Raman scattering driven plasma wave
Authors: Bénisti Didier , Strozzi David J. , Gremillet Laurent
Published: March 2008

The kinetic nonlinear dispersion relation, and frequency shift δωsrs, of a plasma wave driven by stimulated Raman scattering are presented. Our theoretical calculations are fully electromagnetic, and use an adiabatic expression for the electron susceptibility which accounts for the change in phase velocity as the wave grows. When kλD≳0.35 (k being the plasma wave number and λD the Debye length), δωsrs is significantly larger than could be inferred by assuming that the wave is freely propagating. Our theory is in excellent agreement with 1D Eulerian Vlasov–Maxwell simulations when 0.3≤kλD≤0.58, and allows discussion of previously proposed mechanisms for Raman saturation. In particular, we find that no “loss of resonance” of the plasma wave would limit the Raman growth rate, and that saturation through a phase detuning between the plasma wave and the laser drive is mitigated by wave number shifts.
Heating mechanisms and particle flow balancing of capacitively coupled plasmas driven by combined dc/rf sources
Authors: Jiang Wei , Xu Xiang , Dai Zhong-Ling , Wang You-Nian
Published: March 2008

Heating mechanisms and particle flow balancing of capacitively coupled plasmas driven by combined dc/rf sources have been investigated by particle-in-cell/Monte Carlo simulations. At low pressure, Ohmic heating will be suppressed and stochastic heating will be enhanced while increasing dc voltage. But the overall heating power will decrease. No heating mode transitions are observed. At high pressure, bulk plasma density decreases at low dc and rf voltage, and the one-side α-γ transition will occur while increasing dc voltage. After the transition, the plasma density abruptly increases and average electron energy drops. As the result of that, the plasma is sustained by secondary electrons instead of the Ohmic heating of the bulk electrons. The dc source will reduce, or even eliminate at high voltage, the electron charge flowing into the dc powered electrode. Therefore the ratio of electron-to-ion charge flowing into the rf powered electrode over one period increases from −1.0 to −2.0–−2.3 for low pressure and −2.2–−5.0 for high pressure.
Phase behavior of density-dependent pair potentials
Authors: Zhou Shiqi
Published: March 2008

Phase diagram is calculated by a recently proposed third-order thermodynamic perturbation theory (TPT) for fluid phase and a recently proposed first-order TPT for solid phases; the underlying interparticle potential consists of a hard sphere repulsion and a perturbation tail of an attractive inverse power law type or Yukawa type whose range varies with bulk densities. It is found that besides usual phase transitions associated with density-independent potentials, the density dependence of the perturbation tail evokes some additional novel phase transitions including isostructural solid-solid transition and liquid-liquid transition. Novel triple points are also exhibited which includes stable fluid (vapor or liquid)-face-centered cubic(fcc)-fcc and liquid-liquid-fcc, metastable liquid-body-centered cubic(bcc)-bcc. It also is found that the phase diagram sensitively depends on the density dependence and the concrete mathematical form of the underlying potentials. Some of the disclosed novel transitions has been observed experimentally in complex fluids and molecular liquids, while others still remain to be experimentally verified.
Nuclear spin conversion of methane in solid parahydrogen
Authors: Miyamoto Yuki , Fushitani Mizuho , Ando Daisuke , Momose Takamasa
Published: March 2008

The nuclear spin conversion of CH4 and CD4 isolated in solid parahydrogen was investigated by high resolution Fourier transform infrared spectroscopy. From the analysis of the temporal changes of rovibrational absorption spectra, the nuclear spin conversion rates associated with the rotational relaxation from the J=1 state to the J=0 state for both species were determined at temperatures between 1 and 6K. The conversion rate of CD4 was found to be 2–100 times faster than that of CH4 in this temperature range. The faster conversion in CD4 is attributed to the quadrupole interaction of D atoms in CD4, while the conversion in CH4 takes place mainly through the nuclear spin–nuclear spin interaction. The conversion rates depend on crystal temperature strongly above 3.5K for CH4 and above 2K for CD4, while the rates were almost constant below these temperatures. The temperature dependence indicates that the one-phonon process is dominant at low temperatures, while two-phonon processes become important at higher temperatures as a cause of the nuclear spin conversion.
Transport of perpendicular edge momentum by drift-interchange turbulence and blobs
Authors: Myra J. R. , Russell D. A. , D’Ippolito D. A.
Published: March 2008

Turbulence in the vicinity of the last closed surface transports plasma momentum away from the core region toward the wall, and hence provides a momentum “source” that can induce net core plasma rotation as well as sheared flows in the edge. Here, numerical simulations of this process for the binormal (approximately poloidal) component of momentum are described that use a minimal two-dimensional model, in the plane perpendicular to the magnetic field, incorporating directionality (drift-waves), radial transport (Reynolds stress and blobs), and dissipation (sheath loss terms). A zonally averaged momentum conservation law is used to advance the zonal flows. The net momentum transferred to the core is shown to be influenced by a number of physical effects: dissipation, the competition between momentum transport by Reynolds stress and passive convection by particles, intermittency (the role of blobs carrying momentum), and velocity shear regulation of turbulence. It is shown that the edge momentum source adjusts to match the rate of momentum transfer into the core, keeping the edge velocity shear nearly constant. The simulation results are also compared with the predictions of quasilinear theory.
Rotating dipolar gyres on a γ-plane
Authors: Derzho Oleg G. , Afanasyev Yakov D.
Published: March 2008

Nonlinear dipolar vortices/gyres on a γ-plane are investigated both experimentally and theoretically. The solutions describe a fundamental dipolar mode of large scale barotropic motion of the polar ocean or atmosphere on the rotating planet. The entire dipolar gyre is predicted to rotate anticyclonically with a specific angular velocity. The existence and stability of the theoretically predicted flow are confirmed in a laboratory experiment on a rotating platform. The laboratory flows are induced by an electromagnetic method and are observed using the nonintrusive optical method of altimetric imaging velocimetry. The rotation rate of the experimental flow is in good agreement with that predicted theoretically. Detailed measurements of the velocity field and surface elevation demonstrate that an assumption of linearity of the relation between the relative vorticity and the stream function is valid.
Fast electron generation in cones with ultraintense laser pulses
Authors: Van Woerkom L. , Akli K. U. , Bartal T. , Beg F. N. , Chawla S. , Chen C. D. , Chowdhury E. , Freeman R. R. , Hey D. , Key M. H. , King J. A. , Link A. , Ma T. , MacKinnon A. J. , MacPhee A. G. , Offermann D. , Ovchinnikov V. , Patel P. K. , Schumacher D. W. , Stephens R. B. , Tsui Y. Y.
Published: March 2008

Experimental results from copper cones irradiated with ultraintense laser light are presented. Spatial images and total yields of CuKα fluorescence were measured as a function of the laser focusing properties. The fluorescence emission extends into the cone approximately 300μm from the cone tip and cannot be explained by ray tracing including cone wall absorption. In addition, the total fluorescence yield from cones is an order of magnitude higher than for equivalent mass foil targets. Indications are that the physics of the laser-cone interaction is dominated by preplasma created from the long duration, low-energy prepulse from the laser.
Excitation of the l=2 diocotron mode with a resistive load
Authors: Bettega G. , Cavaliere F. , Paroli B. , Pozzoli R. , Romé M. , Cavenago M.
Published: March 2008

The resistive wall instability of the l=2 diocotron mode in a pure electron plasma has been investigated with a systematic variation of the parameters of the external impedance connected to a pair of sectored electrodes. The measured growth rate is well described by a linear perturbation theory of the two-dimensional drift-Poisson system.
Electron-phonon coupling in ion implanted cobalt silicide below 1K
Authors: Tuboltsev V. , Savin A. , Räisänen J.
Published: March 2008

Cobalt silicide is a popular compound in semiconductor technology for fabricating resistive microcomponents and metallization. In advanced silicon-based cryogenic devices, such as radiation detectors and coolers, the electronic energy distribution is fundamentally determined by the thermal state of the mesoscopic system. In this work, electron-phonon heat transport at cryogenic temperatures was studied in a silicide formed by high fluence ion implantation of Co into Si. A heat flow between electrons and phonons was found to be proportional to (Telp−Tphp) with p=3.3. The electron-phonon coupling constant that characterizes the thermal resistance between electrons and phonons was derived from the power dependence of the electron temperature measured well bellow 1K. The constant was found to be temperature dependent in the implanted cobalt silicide.