bluuebunny/crossref_metadata_2025 huggingface dataset:
A new polar magnetic index of geomagnetic activity
Authors: Lyatsky Wladislaw , Khazanov George V.
Published: June 2008

We developed a new polar magnetic (PM) index of geomagnetic activity which, similarly to the existing polar cap index, was computed from magnetic field data from near‐pole geomagnetic observatories. However, we used a different method for its calculation, which provided the high correlation of this index with both solar wind data and many events in geospace environment. This improves significantly the reliability of forecasting geomagnetic disturbances and such key parameters as cross‐polar‐cap voltage and Joule heating in high‐latitude ionosphere, which play an important role in the development of global geomagnetic, ionospheric, and thermospheric disturbances. In this paper, we examined PM index in the Northern Hemisphere only. We tested the PM index for 10‐year period. The correlation between PM index and upstream solar wind data for all these years is very high (the squared correlation coefficient R2 ≈ 0.74 which corresponds to the linear correlation coefficients R ≈ 0.86). The PM index also shows the high correlation with the cross‐polar‐cap voltage and hemispheric Joule heating (the squared correlation coefficient R2 between the actual and predicted values of these parameters reaches ∼0.81 which corresponds to the linear correlation coefficients R ≈ 0.9), which results in significant increasing the prediction reliability of these parameters. Thus, the polar magnetic (PM) index of geomagnetic activity provides a significant increase in the forecasting reliability of geomagnetic disturbances and related events in geospace environment, and it may be used as an important input parameter in modeling ionospheric, magnetospheric, and thermospheric processes.
Non‐Fickian dispersion in porous media: 1. Multiscale measurements using single‐well injection withdrawal tracer tests
Authors: Gouze P. , Le Borgne T. , Leprovost R. , Lods G. , Poidras T. , Pezard P.
Published: June 2008

We present a set of single‐well injection withdrawal tracer tests in a paleoreef porous reservoir displaying important small‐scale heterogeneity. An improved dual‐packer probe was designed to perform dirac‐like tracer injection and accurate downhole automatic measurements of the tracer concentration during the recovery phase. By flushing the tracer, at constant flow rate, for increasing time duration, we can probe distinctly different reservoir volumes and test the multiscale predictability of the (non‐Fickian) dispersion models. First we describe the characteristics, from microscale to meter scale, of the reservoir rock. Second, the specificity of the tracer test setup and the results obtained using two different tracers and measurement methods (salinity‐conductivity and fluorescent dye–optical measurement, respectively) are presented. All the tracer tests display strongly tailed breakthrough curves (BTC) consistent with diffusion in immobile regions. Conductivity results, measured over 3 orders of magnitude only, could have been easily interpreted by the conventional mobile‐immobile (MIM) diffusive mass transfer model of asymptotic log‐log slope of −2. However, the fluorescent dye sensor, which allows exploring much lower concentration values, shows that a change in the log‐log slope occurs at larger time with an asymptotic value of −1.5, corresponding to the double‐porosity model. These results suggest that the conventional, one‐slope MIM transfer rate model is too simplistic to account for the real multiscale heterogeneity of the diffusion‐dominant fraction of the reservoir.
Non‐Fickian dispersion in porous media: 2. Model validation from measurements at different scales
Authors: Le Borgne T. , Gouze P.
Published: June 2008

We aim at testing and validating a mobile‐immobile mass transfer model from a set of single‐well injection withdrawal tracer tests in a heterogeneous porous aquifer. By varying the duration of the injection phase, different volumes of aquifer are investigated by the tracer. Hence, we focus the transport model validation not only on reproducing a single breakthrough curve (BTC) but also on the model's capacity to predict the amount of mixing as a function of the volume visited by the tracer. All the BTCs are strongly asymmetric, as expected when dispersion is controlled by diffusive mass transfers between the mobile water and the immobile water part of the porosity. However, the BTC cannot be modeled by a conventional mobile‐immobile mass transfer model with a simple power law memory function. To account for that, we implement a continuous time random walk model in which the transition time distribution ψ (t), which is related to the excursion time probability of the tracer in the immobile domain, is a dual‐slope power law distribution. The model best fits the BTC data set with a transitional regime controlled by ψ(t) ∼ t−2 and an asymptotic regime characteristic of the conventional double‐porosity model with ψ(t) ∼ t−1.5 . This work emphasizes that high‐resolution concentration measurement and multiple‐scale tracer tests are required for assessing solute dispersion models in heterogeneous reservoirs and for subsequently obtaining reliable predictions.
Methane, manganese, and helium in hydrothermal plumes following volcanic eruptions on the East Pacific Rise near 9°50′N
Authors: Love Brooke A. , Resing Joseph A. , Cowen James P. , Lupton John E. , Fornari Daniel J. , Shank Timothy M. , Biller Dondra
Published: June 2008

As part of a rapid response cruise in May 2006, we surveyed water column hydrothermal plumes and bottom conditions on the East Pacific Rise between 9°46.0′N and 9°57.6′N, where recent seafloor volcanic activity was suspected. Real‐time measurements included temperature, light transmission, and salinity. Samples of the plume waters were analyzed for methane, manganese, helium concentrations, and the δ13C of methane. These data allow us to examine the effects of the 2005–2006 volcanic eruption(s) on plume chemistry. Methane and manganese are sensitive tracers of hydrothermal plumes, and both were present in high concentrations. Methane reached 347 nM in upper plume samples (250 m above seafloor) and exceeded 1085 nM in a near‐bottom sample. Mn reached 54 nM in the upper plume and 98 nM in near‐bottom samples. The concentrations of methane and Mn were higher than measurements made after a volcanic eruption in the same area in 1991, but the ratio of CH4/Mn, at 6.7, is slightly lower, though still well above the ratios measured in chronic plumes. High concentrations of methane in near‐bottom samples were associated with areas of microbial mats and diffuse venting documented in seafloor imagery. The isotopic composition of the methane carbon shows evidence of active microbial oxidation; however, neither the fractionation factor nor the source of the eruption‐associated methane can be determined with any certainty. Considerable scatter in the isotopic data is due to diverse sources for the methane as well as fractionation as methane is consumed. One sample at +21‰ versus Peedee belemnite standard is among the most enriched methane carbon values reported in a hydrothermal plume to date.
Changes in West Antarctic ice stream dynamics observed with ALOS PALSAR data
Authors: Rignot Eric
Published: June 2008

The Advanced Land Observation System (ALOS) Phased‐Array Synthetic‐Aperture Radar (PALSAR) is an L‐band frequency (1.27 GHz) radar capable of continental‐scale interferometric observations of ice sheet motion. Here, we show that PALSAR data yield excellent measurements of ice motion compared to C‐band (5.6 GHz) radar data because of greater temporal coherence over snow and firn. We compare PALSAR velocities from year 2006 in Pine Island Bay, West Antarctica with those spanning years 1974 to 2007. Between 1996 and 2007, Pine Island Glacier sped up 42% and ungrounded over most of its ice plain. Smith Glacier accelerated 83% and ungrounded as well. Their largest speed up are recorded in 2007. Thwaites Glacier is not accelerating but widening with time and its eastern ice shelf doubled its speed. Total ice discharge from these glaciers increased 30% in 12 yr and the net mass loss increased 170% from 39 ± 15 Gt/yr to 105 ± 27 Gt/yr. Longer‐term velocity changes suggest only a moderate loss in the 1970s. As the glaciers unground into the deeper, smoother beds inland, the mass loss from this region will grow considerably larger in years to come.
Experimental study on the rate dependent strength of ice‐silica mixture with silica volume fractions up to 0.63
Authors: Yasui Minami , Arakawa Masahiko
Published: June 2008

We conducted deformation experiments of ice‐1 μm silica beads mixture to clarify the effects of silica beads volume fraction and temperature on the strength. The silica beads volume fraction was changed from 0 to 0.63 to simulate the surfaces of icy bodies. Unconfined uniaxial compression tests were made in a cold room at the temperatures from −10°C to −25°C and the constant strain rates ranged from 2.9 × 10−3 to 8.5 × 10−7 s−1. We determined the rate dependent strength of the mixture written by = A · σmaxn from the relationship between the maximum stress, σmax, on the stress‐strain curve and the applied strain rate, . At −10°C, the mixtures with silica volume fractions of 0.004–0.04 had almost the same strength with pure ice and the stress exponent, n, is about 3. On the other hands, at the silica volume fractions more than 0.15, the mixture became harder as the beads were more included, and it had the same stress exponent, about 6. This high stress exponent might be caused by crack generation. Also, we found that the A for silica volume fractions more than 0.15 was written by an exponential equation related to the silica volume fraction, ϕ, A = 6.86 × 10−8exp(−6.35ϕ). Furthermore, we found that the n of ϕ = 0.15 was independent of the temperature, and the brittle‐ductile boundary of ϕ = 0.29 and 0.63 was more than 30°C higher than that of pure ice.
Shear strain localization in elastodynamic rupture simulations
Authors: Daub Eric G. , Manning M. Lisa , Carlson Jean M.
Published: June 2008

We study strain localization as an enhanced velocity weakening mechanism on earthquake faults. Fault friction is modeled using Shear Transformation Zone (STZ) Theory, a microscopic physical model for non‐affine rearrangements in granular fault gouge. STZ Theory is implemented in spring slider and dynamic rupture models of faults. We compare dynamic shear localization to deformation that is uniform throughout the gouge layer, and find that localized slip enhances the velocity weakening of the gouge. Localized elastodynamic ruptures have larger stress drops and higher peak slip rates than ruptures with homogeneous strain.
Titan’s influence on Saturnian substorm occurrence
Authors: Russell C. T. , Jackman C. M. , Wei H. Y. , Bertucci C. , Dougherty M. K.
Published: June 2008

Substorms play an important role in the energization and transport of plasmas in planetary magnetospheres, including the shedding of the mass added by moons in the case of Jupiter and Saturn. Mass shedding occurs through rapid reconnection in the near tail resulting in dipolarization on the magnetospheric side of the reconnection point and plasmoid formation down tail. Observations of these sudden reconnection events in Saturn’s near‐tail region provide additional insight into this process. Saturnian substorms, at least on occasion, have a plasmoid formation phase leading to a traveling compression region. Changes in the field strength across reconnection events suggest that open flux has been removed from the tail. The timing of tail reconnection events appears to be controlled by both the orbital phase of Titan, and the variable stretching of the near‐tail field as Saturn rotates.
The nature and character of the transition state for the ADP‐ribosyltransferase reaction
Authors: Jørgensen René , Wang Yolanda , Visschedyk Danielle , Merrill A Rod
Published: June 2008

Exotoxin A (ExoA) from Pseudomonas aeruginosa is an important virulence factor that belongs to a class of exotoxins that are secreted by pathogenic bacteria which cause human diseases such as cholera, diphtheria, pneumonia and whooping cough. We present the first crystal structures, to our knowledge, of ExoA in complex with elongation factor 2 (eEF2) and intact NAD+, which indicate a direct role of two active‐site loops in ExoA during the catalytic cycle. One loop moves to form a solvent cover for the active site of the enzyme and reaches towards the target residue (diphthamide) in eEF2 forming an important hydrogen bond. The NAD+ substrate adopts a conformation remarkably different from that of the NAD+ analogue, βTAD, observed in previous structures, and fails to trigger any loop movements. Mutational studies of the two loops in the toxin identify several residues important for catalytic activity, in particular Glu 546 and Arg 551, clearly supporting the new complex structures. On the basis of these data, we propose a transition‐state model for the toxin‐catalysed reaction.
VLDL exits from the endoplasmic reticulum in a specialized vesicle, the VLDL transport vesicle, in rat primary hepatocytes
Authors: Siddiqi Shadab A.
Published: June 2008

The movement of VLDL [very-LDL (low-density lipoprotein)] from the ER (endoplasmic reticulum) to the Golgi is required for its eventual secretion from hepatocytes and represents a potential target in controlling elevated concentrations of its metabolite LDL, the major determinant of atherosclerosis. To study this process, an in vitro ER-budding assay was developed to examine the generation of the VTV (VLDL transport vesicle) and PTV (protein transport vesicles) using ER isolated from [14C]TAG (triacylglycerol) and [3H]protein-labelled primary rat hepatocytes. VTVs do not contain albumin, as determined by immunoblots. VTVs were distributed in light-density fractions, whereas PTVs were mainly in the mid-portion of the sucrose gradient. Electron microscopy revealed that VTVs were larger (∼100–120 nm) in size than PTVs (∼55–70 nm). ER from 0.4 mM OA (oleic acid)-treated hepatocytes budded VTVs of a lighter density as compared with VTVs budded from ER of 0.1 mM or 0.004 mM OA-treated hepatocytes. The generation of VTVs from rat hepatic ER required cytosol, ATP, Sar1 (a GTPase) and incubation at 37 °C. Proteinase K treatment did not degrade the VTV cargo protein, apoB100 (apolipoprotein 100), indicating that VTVs were sealed. Immunoblots showed that VTV concentrated apoB100, Sar1 and rSec22b, and excluded albumin and calnexin. VTVs were shown to fuse with cis-Golgi and delivered their cargo to the Golgi lumen, as determined by in vitro fusion, and acquired endoglycosidase H resistance. These results suggest that a new ER-derived transport vesicle (VTV) has been identified and characterized which transports nascent VLDL from the hepatic ER to the Golgi.
Ankyrin repeats-containing cofactors interact with ADA3 and modulate its co-activator function
Authors: Li Chia-Wei , Dinh Gia Khanh , Zhang Aihua , Chen J. Don
Published: June 2008

ANCO (ankyrin repeats-containing cofactor)-1 and ANCO-2 are a family of unique transcriptional co-regulators with dual properties: they interact with both the co-activators and the co-repressors [Zhang, Yeung, Li, Tsai, Dinh, Wu, Li and Chen (2004) J. Biol. Chem. 279, 33799–33805]. Specifically, ANCO-1 is thought to recruit HDACs (histone deacetylases) to the p160 co-activator to repress transcriptional activation by nuclear receptors. In the present study, we provide new evidence to suggest further that ANCO-1 and ANCO-2 also interact with the co-activator ADA3 (alteration/deficiency in activation 3). The interaction occurs between the conserved C-terminal domain of ANCO-1 and the N-terminal transactivation domain of ADA3. Several subunits of the P/CAF {p300/CBP [CREB (cAMP-response-element-binding protein)-binding protein]-associated factor} complex, including ADA3, ADA2α/β and P/CAF, showed co-localization with ANCO-1 nuclear dots, indicating an in vivo association of ANCO-1 with the P/CAF complex. Furthermore, a transient reporter assay revealed that both ANCO-1 and ANCO-2 repress ADA3-mediated transcriptional co-activation on nuclear receptors, whereas ANCO-1 stimulated p53-mediated transactivation. These data suggest that ADA3 is a newly identified target of the ANCO proteins, which may modulate co-activator function in a transcription-factor-specific manner.
Translational regulation of lipoprotein lipase in adipocytes: depletion of cellular protein kinase Cα activates binding of the C subunit of protein kinase A to the 3′-untranslated region of the lipoprotein lipase mRNA
Authors: Unal Resat , Pokrovskaya Irina , Tripathi Preeti , Monia Brett P. , Kern Philip A. , Ranganathan Gouri
Published: June 2008

Adipose LPL (lipoprotein lipase) plays an important role in regulating plasma triacylglycerols and lipid metabolism. We have previously demonstrated that PKCα (protein kinase Cα) depletion inhibits LPL translation in 3T3-F442A adipocytes. Using in vitro translation experiments, the minimum essential region on the 3′UTR (3′-untranslated region) of LPL mRNA required for the inhibition of translation was identified as the proximal 39 nt. These results were confirmed by RNase protection analysis using cytoplasmic proteins isolated from the adipocytes treated with PKCα antisense oligomers and the LPL 3′UTR transcript (LPL 3′UTR nt: 1512–1640). The protein components involved in this RNA-binding interaction from PKCα depletion were passed through an affinity column containing a sequence of the LPL 3′UTR and, after Western blotting, the RNA-binding proteins were identified as the catalytic and the regulatory subunits of PKA (protein kinase A), Cα and RIIβ, and AKAP (A-kinase-anchoring protein) 121. This RNA inhibitory complex consisted of the same RNA-binding proteins that have been identified previously as mediators of LPL translational inhibition by PKA activation, suggesting that PKCα depletion inhibits LPL translation through PKA activation. In additional experiments, PKC depletion by prolonged PMA treatment or PKCα antisense oligomers resulted in an increase in PKA activity in 3T3-F442A adipocytes, comparable with PKA activation with adrenaline (epinephrine) treatment. These results demonstrate that LPL translational inhibition occurs through an RNA-binding complex involving PKA subunits and AKAP121, and this complex can be activated either through traditional PKA activation methods or through the depletion of PKCα.
Accumulation of free complex-type N-glycans in MKN7 and MKN45 stomach cancer cells
Authors: Ishizuka Aya , Hashimto Yuki , Naka Ryosuke , Kinoshita Mitsuhiro , Kakehi Kazuaki , Seino Junichi , Funakoshi Yoko , Suzuki Tadashi , Kameyama Akihiko , Narimatsu Hisashi
Published: June 2008

During the N-glycosylation reaction, it has been shown that ‘free’ N-glycans are generated either from lipid-linked oligosaccharides or from misfolded glycoproteins. In both cases, occurrence of high mannose-type free glycans is well-documented, and the molecular mechanism for their catabolism in the cytosol has been studied. On the other hand, little, if anything, is known with regard to the accumulation of more processed, complex-type free oligosaccharides in the cytosol of mammalian cells. During the course of comprehensive analysis of N-glycans in cancer cell membrane fractions [Naka et al. (2006) J. Proteome Res. 5, 88–97], we found that a significant amount of unusual, complex-type free N-glycans were accumulated in the stomach cancer-derived cell lines, MKN7 and MKN45. The most abundant and characteristic glycan found in these cells was determined to be NeuAcα2-6Galβ1-4GlcNAcβ1-2Manα1-3Manβ1-4GlcNAc. Biochemical analyses indicated that those glycans found were cytosolic glycans derived from lysosomes due to low integrity of the lysosomal membrane. Since the accumulation of these free N-glycans was specific to only two cell lines among the various cancer cell lines examined, these cytosolic N-glycans may serve as a specific biomarker for diagnosis of specific tumours. A cytosolic sialidase, Neu2, was shown to be involved in the degradation of these sialoglycans, indicating that the cytosol of mammalian cells might be equipped for metabolism of complex-type glycans.
Physiological heart activation by adrenaline involves parallel activation of ATP usage and supply
Authors: Korzeniewski Bernard , Deschodt-Arsac Véronique , Calmettes Guillaume , Franconi Jean-Michel , Diolez Philippe
Published: June 2008

During low-to-high work transition in adult mammalian heart in vivo the concentrations of free ADP, ATP, PCr (phosphocreatine), Pi and NADH are essentially constant, in striking contrast with skeletal muscle. The direct activation by calcium ions of ATP usage and feedback activation of ATP production by ADP (and Pi) alone cannot explain this perfect homoeostasis. A comparison of the response to adrenaline (increase in rate-pressure product and [PCr]) of the intact beating perfused rat heart with the elasticities of the PCr producer and consumer to PCr concentration demonstrated that both the ATP/PCr-producing block and ATP/PCr-consuming block are directly activated to a similar extent during physiological heart activation. Our finding constitutes a direct evidence for the parallel-activation mechanism of the regulation of oxidative phosphorylation in heart postulated previously in a theoretical way.
Catecholaminergic polymorphic ventricular tachycardia-related mutations R33Q and L167H alter calcium sensitivity of human cardiac calsequestrin
Authors: Valle Giorgia , Galla Daniela , Nori Alessandra , Priori Silvia G. , Gyorke Sandor , de Filippis Vincenzo , Volpe Pompeo
Published: June 2008

Two missense mutations, R33Q and L167H, of hCASQ2 (human cardiac calsequestrin), a protein segregated to the lumen of the sarcoplasmic reticulum, are linked to the autosomal recessive form of CPVT (catecholaminergic polymorphic ventricular tachycardia). The effects of these mutations on the conformational, stability and Ca2+ sensitivity properties of hCASQ2, were investigated. Recombinant WT (wild-type) and mutant CASQ2s were purified to homogeneity and characterized by spectroscopic (CD and fluorescence) and biochemical (size-exclusion chromatography and limited proteolysis) methods at 500 and 100 mM KCl, with or without Ca2+ at a physiological intraluminal concentration of 1 mM; Ca2+-induced polymerization properties were studied by turbidimetry. In the absence of Ca2+, mutations did not alter the conformation of monomeric CASQ2. For L167H only, at 100 mM KCl, emission fluorescence changes suggested tertiary structure alterations. Limited proteolysis showed that amino acid substitutions enhanced the conformational flexibility of CASQ2 mutants, which became more susceptible to tryptic cleavage, in the order L167H>R33Q>WT. Ca2+ at a concentration of 1 mM amplified such differences: Ca2+ stabilized WT CASQ2 against urea denaturation and tryptic cleavage, whereas this effect was reduced in R33Q and absent in L167H. Increasing [Ca2+] induced polymerization and precipitation of R33Q, but not that of L167H, which was insensitive to Ca2+. Based on CASQ2 models, we propose that the Arg33→Gln exchange made the Ca2+-dependent formation of front-to-front dimers more difficult, whereas the Leu167→His replacement almost completely inhibited back-to-back dimer interactions. Initial molecular events of CPVT pathogenesis begin to unveil and appear to be different depending upon the specific CASQ2 mutation.
Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes
Authors: Colcombet Jean , Hirt Heribert
Published: June 2008

Many changes in environmental conditions and hormones are mediated by MAPK (mitogen-activated protein kinase) cascades in all eukaryotes, including plants. Studies of MAPK pathways in genetic model organisms are especially informative in revealing the molecular mechanisms by means of which MAPK cascades are controlled and modulate cellular processes. The present review highlights recent insights into MAPK-based signalling in Arabidopsis thaliana (thale cress), revealing the complexity and future challenges to understanding signal-transduction networks on a global scale.
Insulin action on glucose transporters through molecular switches, tracks and tethers
Authors: Zaid Hilal , Antonescu Costin N. , Randhawa Varinder K. , Klip Amira
Published: June 2008

Glucose entry into muscle cells is precisely regulated by insulin, through recruitment of GLUT4 (glucose transporter-4) to the membrane of muscle and fat cells. Work done over more than two decades has contributed to mapping the insulin signalling and GLUT4 vesicle trafficking events underpinning this response. In spite of this intensive scientific research, there are outstanding questions that continue to challenge us today. The present review summarizes the knowledge in the field, with emphasis on the latest breakthroughs in insulin signalling at the level of AS160 (Akt substrate of 160 kDa), TBC1D1 (tre-2/USP6, BUB2, cdc16 domain family member 1) and their target Rab proteins; in vesicle trafficking at the level of vesicle mobilization, tethering, docking and fusion with the membrane; and in the participation of the cytoskeleton to achieve optimal temporal and spatial location of insulin-derived signals and GLUT4 vesicles.
Three-dimensional spiral waves in an excitable reaction system: Initiation and dynamics of scroll rings and scroll ring pairs
Authors: Bánsági Tamás , Steinbock Oliver
Published: June 2008

We report experimental results on spiral and scroll waves in the 1,4-cyclohexanedione Belousov–Zhabotinsky reaction. The propagating concentration waves are detected by two-dimensional photometry and optical tomography. Wave pulses can disappear in front-to-front and front-to-back collisions. This anomaly causes the nucleation of vortices from collisions of three nonrotating waves. In three-dimensional systems, these vortices are scroll rings that rotate around initially circular filaments. Depending on reactant concentrations, the filaments shrink or expand indicating positive and negative filament tensions, respectively. Shrinkage results in vortex annihilation. Expansion is accompanied by filament buckling and bending, which is interpreted as developing Winfree turbulence. We also describe the initiation of scroll ring pairs in four-wave collisions. The two filaments are stacked on top of each other and their motion suggests filament repulsion.
Testing for intracycle determinism in pseudoperiodic time series
Authors: Coelho Mara C. S. , Mendes Eduardo M. A. M. , Aguirre Luis A.
Published: June 2008

A determinism test is proposed based on the well-known method of the surrogate data. Assuming predictability to be a signature of determinism, the proposed method checks for intracycle (e.g., short-term) determinism in the pseudoperiodic time series for which standard methods of surrogate analysis do not apply. The approach presented is composed of two steps. First, the data are preprocessed to reduce the effects of seasonal and trend components. Second, standard tests of surrogate analysis can then be used. The determinism test is applied to simulated and experimental pseudoperiodic time series and the results show the applicability of the proposed test.
Synchronization engineering: Theoretical framework and application to dynamical clustering
Authors: Kori Hiroshi , Rusin Craig G. , Kiss István Z. , Hudson John L.
Published: June 2008

A method for engineering the global behavior of populations of rhythmic elements is presented. The framework, which is based on phase models, allows a nonlinear time-delayed global feedback signal to be constructed which produces an interaction function corresponding to the desired behavior of the system. It is shown theoretically and confirmed in numerical simulations that a polynomial, delayed feedback is a versatile tool to tune synchronization patterns. Dynamical states consisting of one to four clusters were engineered to demonstrate the application of synchronization engineering in an experimental electrochemical system.
Complex dynamics in the Oregonator model with linear delayed feedback
Authors: Sriram K. , Bernard S.
Published: June 2008

The Belousov–Zhabotinsky (BZ) reaction can display a rich dynamics when a delayed feedback is applied. We used the Oregonator model of the oscillating BZ reaction to explore the dynamics brought about by a linear delayed feedback. The time-delayed feedback can generate a succession of complex dynamics: period-doubling bifurcation route to chaos; amplitude death; fat, wrinkled, fractal, and broken tori; and mixed-mode oscillations. We observed that this dynamics arises due to a delay-driven transition, or toggling of the system between large and small amplitude oscillations, through a canard bifurcation. We used a combination of numerical bifurcation continuation techniques and other numerical methods to explore the dynamics in the strength of feedback-delay space. We observed that the period-doubling and quasiperiodic route to chaos span a low-dimensional subspace, perhaps due to the trapping of the trajectories in the small amplitude regime near the canard; and the trapped chaotic trajectories get ejected from the small amplitude regime due to a crowding effect to generate chaotic-excitable spikes. We also qualitatively explained the observed dynamics by projecting a three-dimensional phase portrait of the delayed dynamics on the two-dimensional nullclines. This is the first instance in which it is shown that the interaction of delay and canard can bring about complex dynamics.
A lot of strange attractors: Chaotic or not?
Authors: Badard R.
Published: June 2008

Iterations on R given by quasiperiodic displacement are closely linked with the quasiperiodic forcing of an oscillator. We begin by recalling how these problems are related. It enables us to predict the possibility of appearance of strange nonchaotic attractors (SNAs) for simple increasing maps of the real line with quasiperiodic displacement. Chaos is not possible in this case (Lyapounov exponents cannot be positive). Studying this model of iterations on R for larger variations, beyond critical values where it is no longer invertible, we can get chaotic motions. In this situation we can get a lot of strange attractors because we are able to smoothly adjust the value of the Lyapounov exponent. The SNAs obtained can be viewed as the result of pasting pieces of trajectories, some of which having positive local Lyapounov exponents and others having negative ones. This leads us to think that the distinction between these SNAs and chaotic attractors is rather weak.
Discretization error-free estimate of low temperature statistical dissociation rates in gas phase: Applications to Lennard-Jones clusters X13−nYn (n=–3)
Authors: Mella Massimo
Published: June 2008

In this work, an improved approach for computing cluster dissociation rates using Monte Carlo (MC) simulations is proposed and a discussion is provided on its applicability as a function of environmental variables (e.g., temperature). With an analytical transformation of the integrals required to compute variational transition state theory (vTST) dissociation rates, MC estimates of the expectation value for the Dirac delta δ(qrc−qc) have been made free of the discretization error that is present when a prelimit form for δ is used. As a by-product of this transformation, the statistical error associated with ⟨δ(qrc−qc)⟩ is reduced making this step in the calculation of vTST rates substantially more efficient (by a factor of 4–2500, roughly). The improved MC procedure is subsequently employed to compute the dissociation rate for Lennard-Jones clusters X13−nYn (n=0–3) as a function of temperature (T), composition, and X-Y interaction strength. The X13−nYn family has been previously studied as prototypical set of systems for which it may be possible to select and stabilize structures different from the icosahedral global minimum of X13. It was found that both the dissociation rate and the dissociation mechanism, as suggested by the statistical simulations, present a marked dependence on n, T, and the nature of Y. In particular, it was found that a vacancy is preferentially formed close to a surface impurity when the X-Y interaction is weaker than the X-X one whatever the temperature. Differently, the mechanism was found to depend on T for stronger X-Y interactions, with vacancies being formed opposite to surface impurities at higher temperature. These behaviors are a reflex of the important role played by the surface fluctuations in defining the properties of clusters.
Influence of the ambipolar-to-free diffusion transition on dust particle charge in a complex plasma afterglow
Authors: Couëdel L. , Samarian A. A. , Mikikian M. , Boufendi L.
Published: June 2008

The influence of diffusive losses on residual dust charge in a complex plasma afterglow has been investigated. The residual charge distribution was measured and exhibits a mean value Qdres∼(−3e−5e) with a tail in the positive region. The experimental results have been compared with simulated charge distributions. The dust residual charges were simulated based on a model developed to describe complex plasma decay. The experimental and simulated data show that the transition from ambipolar to free diffusion in the decaying plasma plays a significant role in determining the residual dust particle charges. The presence of positively charged dust particles is explained by a broadening of the charge distribution function in the afterglow plasma.
Phase effects on synchronization by dynamical relaying in delay-coupled systems
Authors: N. Chitra R. , Kuriakose V. C.
Published: June 2008

Synchronization in an array of mutually coupled systems with a finite time delay in coupling is studied using the Josephson junction as a model system. The sum of the transverse Lyapunov exponents is evaluated as a function of the parameters by linearizing the equation about the synchronization manifold. The dependence of synchronization on damping parameter, coupling constant, and time delay is studied numerically. The change in the dynamics of the system due to time delay and phase difference between the applied fields is studied. The case where a small frequency detuning between the applied fields is also discussed.
Time evolution of the rule 150 cellular automaton activity from a Fibonacci iteration
Authors: Claussen Jens Christian
Published: June 2008

The rule 150 cellular automaton is a remarkable discrete dynamical system, as it shows 1∕fα spectra if started from a single seed [J. Nagler and J. C. Claussen, Phys. Rev. E 71, 067103 (2005)]. Despite its simplicity, a feasible solution for its time behavior is not obvious. Its self-similarity does not follow a one-step iteration like other elementary cellular automata. Here it is shown how its time behavior can be solved as a two-step vectorial, or string, iteration, which can be viewed as a generalization of Fibonacci iteration generating the time series from a sequence of vectors of increasing length. This allows us to compute the total activity time series more efficiently than by simulating the whole spatiotemporal process or even by using the closed expression. The results are further extended to the generalization of rule 150 to the two-dimensional case and to Bethe lattices and the relation to corresponding integer sequences is discussed.
Balancing the ambipolar conduction for pentacene thin film transistors through bifunctional electrodes
Authors: Yang Chuan-Yi , Dhananjay  , Cheng Shiau-Shin , Ou Chun-Wei , Chuang You-Che , Wu Meng-Chyi , Chu Chih-Wei
Published: June 2008

We report an effective way to equilibrate hole and electron transport in ambipolar pentacene thin film transistors (TFTs). It was achieved by inserting an ultra thin lithium fluoride (LiF) layer at the electrode/organic interface to form a bifunctional source/drain electrode. It can be observed that the presence of ultrathin LiF layer will facilitate the injection of electrons from source/drain electrodes to organic semiconductor, resulting in a significant enhancement of the n-channel conduction, without sacrificing p-channel conduction for ambipolar pentacene TFTs. These factors make them potential candidates for the organic complementary circuits and inverter circuits of these ambipolar TFTs are also demonstrated.
Simple coupled-cluster singles and doubles method with perturbative inclusion of triples and explicitly correlated geminals: The CCSD(T)R12¯ model
Authors: Valeev Edward F. , Daniel Crawford T.
Published: June 2008

To approach the complete basis set limit of the “gold-standard” coupled-cluster singles and doubles plus perturbative triples [CCSD(T)] method, we extend the recently proposed perturbative explicitly correlated coupled-cluster singles and doubles method, CCSD(2)R12¯ [E. F. Valeev, Phys. Chem. Chem. Phys. 8, 106 (2008)], to account for the effect of connected three-electron correlations. The natural choice of the zeroth-order Hamiltonian produces a perturbation expansion with rigorously separable second-order energy corrections due to the explicitly correlated geminals and conventional triple and higher excitations. The resulting CCSD(T)R12¯ energy is defined as a sum of the standard CCSD(T) energy and an amplitude-dependent geminal correction. The method is technically very simple: Its implementation requires no modification of the standard CCSD(T) program and the formal cost of the geminal correction is small. We investigate the performance of the open-shell version of the CCSD(T)R12¯ method as a possible replacement of the standard complete-basis-set CCSD(T) energies in the high accuracy extrapolated ab initio thermochemistry model of Stanton et al. [J. Chem. Phys. 121, 11599 (2004)]. Correlation contributions to the heat of formation computed with the new method in an aug-cc-pCVXZ basis set have mean absolute basis set errors of 2.8 and 1.0kJ∕mol when X is T and Q, respectively. The corresponding errors of the standard CCSD(T) method are 9.1, 4.0, and 2.1kJ∕mol when X=T, Q, and 5. Simple two-point basis set extrapolations of standard CCSD(T) energies perform better than the explicitly correlated method for absolute correlation energies and atomization energies, but no such advantage found when computing heats of formation. A simple Schwenke-type two-point extrapolation of the CCSD(T)R12¯∕aug-cc-pCVXZ energies with X=T,Q yields the most accurate heats of formation found in this work, in error on average by 0.5kJ∕mol and at most by 1.7kJ∕mol.
Insight into the Raman shifts and optical absorption changes upon annealing polymer/fullerene solar cells
Authors: Yun Je-Jung , Peet Jeffrey , Cho Nam-Sung , Bazan Guillermo C. , Lee Seung Joon , Moskovits Martin
Published: June 2008

Raman shifts and optical absorption spectra of bulk heterojunction films were measured to elucidate the origin of the optimum annealing parameters. A series of device optimization studies revealed 413K to be the optimum annealing temperature, leading to a power conversion efficiency of 2.95%. The highest power conversion efficiency coincides with the highest peak in the UV-visible absorption and the lowest full width at half maximum of the CC symmetric stretching signal in the Raman spectra. The changes observed in the vibronic shifts could be useful in obtaining information about the optimal performance and processing conditions for polymer optoelectronic devices.
Twisted vortex filaments in the three-dimensional complex Ginzburg–Landau equation
Authors: Rousseau Guillaume , Chaté Hugues , Kapral Raymond
Published: June 2008

The structure and dynamics of vortex filaments that form the cores of scroll waves in three-dimensional oscillatory media described by the complex Ginzburg–Landau equation are investigated. The study focuses on the role that twist plays in determining the bifurcation structure in various regions of the (α,β) parameter space of this equation. As the degree of twist increases, initially straight filaments first undergo a Hopf bifurcation to helical filaments; further increase in the twist leads to a secondary Hopf bifurcation that results in supercoiled helices. In addition, localized states composed of superhelical segments interspersed with helical segments are found. If the twist is zero, zigzag filaments are found in certain regions of the parameter space. In very large systems disordered states comprising zigzag and helical segments with positive and negative senses exist. The behavior of vortex filaments in different regions of the parameter space is explored in some detail. In particular, an instability for nonzero twist near the α=β line suggests the existence of a nonsaturating state that reduces the stability domain of straight filaments. The results are obtained through extensive simulations of the complex Ginzburg–Landau equation on large domains for long times, in conjunction with simulations on equivalent two-dimensional reductions of this equation and analytical considerations based on topological concepts.
Effects of local gas-flow field on synthesis of oxide nanowires during thermal oxidation
Authors: Xu ChunHua , Yang XiangLong , Shi San-Qiang , Liu Yang , Surya Charles , Woo ChungHo
Published: June 2008

Ω -shaped copper specimens are oxidized in wet air. The results show that totally no-wire structure, CuO whiskers, and the high density of well-aligned CuO nanowires can be formed simultaneously on the different positions of the specimen. A three-dimensional flow simulation results indicate that the direction of velocity vectors of local gas flow affects the alignment of nanowires during oxidation while the shear stress of flowing gas near the surface of a Ω-shaped specimen controls the density of nanowires.
Optimal surface functionalization of silicon quantum dots
Authors: Li Q. S. , Zhang R. Q. , Lee S. T. , Niehaus T. A. , Frauenheim Th.
Published: June 2008

Surface functionalization is a critical step for Si nanocrystals being used as biological probes and sensors. Using density-functional tight-binding calculations, we systematically investigate the optical properties of silicon quantum dots (SiQDs) with various termination groups, including H, CH3, NH2, SH, and OH. Our calculations reveal that capping SiQDs with alkyl group (–Si–C–) induces minimal changes in the optical spectra, while covering the surface with NH2, SH, and OH results in evident changes compared to hydrogenated SiQDs. The structural deformations and electronic property changes due to surface passivation were shown to be responsible for the above-described features. Interestingly, we find that the optical properties of SiQDs can be controlled by varying the S coverage on the surface. This tuning effect may have important implications in device fabrications.
Hartree–Fock orbitals significantly improve the reaction barrier heights predicted by semilocal density functionals
Authors: Janesko Benjamin G. , Scuseria Gustavo E.
Published: June 2008

Semilocal density functional theory predictions for the barrier heights of representative hydrogen transfer, heavy-atom transfer, and nucleophilic substitution reactions are significantly improved in non-self-consistent calculations using Hartree–Fock orbitals. Orbitals from hybrid calculations yield related improvements. These results provide insight into compensating for one-electron self-interaction error in semilocal density functional theory.
Growth and pyroelectric properties of high Curie temperature relaxor-based ferroelectric Pb(In1∕2Nb1∕2)O3–Pb(Mg1∕3Nb2∕3)O3–PbTiO3 ternary single crystal
Authors: Yu Ping , Wang Feifei , Zhou Dan , Ge Wenwei , Zhao Xiangyong , Luo Haosu , Sun Jinglan , Meng Xiangjian , Chu Junhao
Published: June 2008

To enhance the service temperature of relaxor-PbTiO3 pyroelectric single crystals, high quality ternary perovskite single crystal was grown by a modified Bridgman technique. Analyzed by x-ray fluorescence, the as-grown crystal is 0.41Pb(In1∕2Nb1∕2)O3–0.17Pb(Mg1∕3Nb2∕3)O3–0.42PbTiO3 [PIMNT(41/17/42)], which appears to be a tetragonal ferroelectric phase with relatively high Curie temperature of 253°C. It exhibits the relative permittivity of 487 and low dielectric loss of 0.3% at 50Hz and room temperature. The pyroelectric properties with a pyroelectric coefficient of 5.7×10−4C∕m2K and a detectivity of 6.34×10−5Pa−1∕2 would satisfy the needs of operation as a high Curie temperature material. The results show that PIMNT crystal with better temperature stability, compared with the pure PMNT single crystals, is a good candidate as an infrared detector material.
Pyrochlore-based oxides with small temperature coefficient of dielectric constant
Authors: Prabhakar Rao P. , Ravindran Nair K. , Sibi K. S. , Koshy Peter
Published: June 2008

Pyrochlore based oxides with small temperature coefficient of dielectric constant (TCK) in Ca–RE–Ti–M–O (RE=Sm or Dy and M=Nb or Ta) system are reported. The 1MHz dielectric constants of these oxides vary from 26 to 102. The TCK in the vicinity of room temperature (20°C) dramatically decreases, from more than −200 for CaRETiMO7 to less than −3ppm∕°C in the solid solutions of CaRETiNbO7–CaRETiTaO7 phases. Rietveld analysis of the x-ray diffraction data establishes a cubic pyrochlore-type phase in the space group Fd3m (No. 227).
Interaction of SiC thermal oxidation by-products with SiO2
Authors: Radtke C. , Stedile F. C. , Soares G. V. , Krug C. , da Rosa E. B. O. , Driemeier C. , Baumvol I. J. R. , Pezzi R. P.
Published: June 2008

We investigated oxygen incorporation and exchange during thermal growth of silicon oxide films on silicon carbide. This investigation was carried out in parallel with the thermal growth of silicon oxide films on silicon for comparison. We provide experimental evidence that oxidation by-products of silicon carbide out-diffuse and interact with the silicon oxide overlayer, incorporating C and O. This and other results are in sharp contrast to those obtained for silicon samples, constituting a key issue in the stability of any dielectric material used on silicon carbide.
Observation of ν1+νn combination bands of the HOOO and DOOO radicals using infrared action spectroscopy
Authors: Derro Erika L. , Sechler Timothy D. , Murray Craig , Lester Marsha I.
Published: June 2008

Hydrogen trioxy (HOOO) and its deuterated analog (DOOO) have been generated in a supersonic free-jet expansion through association of photolytically generated OH or OD and molecular oxygen. The radicals were detected using infrared action spectroscopy, a highly sensitive double resonance technique. Rotationally resolved spectra of combination bands of HOOO and DOOO comprising one quantum of OH or OD stretch (ν1) and one quantum of a lower frequency mode (ν1+νn where n=3–6), including H∕DOO bend (ν3), OOO bend (ν4), central OO stretch (ν5), and H∕DOOO torsion (ν6), have been observed and assigned to the trans conformer. All but one of these bands are accompanied by unstructured features which are tentatively assigned to the corresponding vibration of the cis conformer. In total, five additional bands of HOOO and four of DOOO have been recorded and assigned. These data represent the first gas-phase observation of the low-frequency modes of HOOO and DOOO and they are found to differ significantly from previous matrix studies and theoretical predictions. Accurate knowledge of the vibrational frequencies is crucial in assessing thermochemical properties of HOOO and present possible means of detection in the atmosphere.