bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid decrease in Martian crustal magnetization in the Noachian era: Implications for the dynamo and climate of early Mars
Authors: Lillis R. J. , Frey H. V. , Manga M.
Published: July 2008

The magnetic signatures and crater retention ages of the 19 largest (>1000 km diameter) impact basins on Mars are examined to constrain the history of the acquisition of crustal magnetization during the Noachian era. The 5 most clearly impact‐demagnetized basins are younger than the 14 basins within which lies substantially re‐magnetized crust. Poisson analysis shows that the most likely time of this magnetization cessation was 4.115–4.13 Ga (model age) and that it occurred quickly, taking less than 20 Ma. A global decrease in effective crustal magnetic susceptibility due, e.g., to a decrease in the rate of hydrothermal alteration, is one possible explanation. Alternatively, the cessation of post‐impact magnetization reflects the rapid death of the Martian dynamo.
Equatorial Kelvin wave influences may reach the Bering Sea during 2002 to 2005
Authors: Lyman John M. , Johnson Gregory C.
Published: July 2008

The time‐history of sea surface height (SSH) anomaly data from the TOPEX and Jason‐1 altimeters is examined along the equator and northward following the west coast of the Americas. Along‐track TOPEX and Jason‐1 altimeter data are put into an alongshore–offshore coordinate system and then smoothed. This procedure increases the degrees of freedom in individual estimates of long‐wavelength coastally trapped waves (CTWs) during times when both satellites are available (2002–2005). Equatorially trapped Kelvin waves are detected during the 2002–2003 El Niño. These Kelvin waves excite CTWs that travel northward along the west coast of the Americas. While CTWs associated with the 2002–2003 equatorial Kelvin waves are not always discernible along the entire coast, correlations of the coastal and equatorial SSH over the entire period of TOPEX and Jason‐1 overlap show a clear phase progression. This phase progression implies remote influence of equatorial Kelvin waves that may reach as far north as the Bering Sea during the weak to moderate El Niño events that occurred from 2002 to 2005.
Statistical analysis of injection/dispersion events in Saturn's inner magnetosphere
Authors: Chen Y. , Hill T. W.
Published: July 2008

In the inner magnetosphere of a rapidly rotating planet such as Jupiter and Saturn, radial transport of plasma mainly comprises hot, tenuous plasma moving inward and cold, denser plasma moving outward. A distinctive phenomenon resulting from the drift dispersion of injecting hot plasma provides direct evidence for this convective motion. Particle instruments aboard the Cassini spacecraft, including the Magnetospheric Imaging Instrument (MIMI) and the Cassini Plasma Spectrometer (CAPS), have made numerous observations of such signatures. The statistics of the properties of such events are studied in this paper by analyzing CAPS data from 26 Cassini orbits. A statistical picture of their major characteristics is developed, including the distributions of ages, longitudinal widths, radial distances, and longitudes and local times of injection. An unexpected longitude modulation of these events appears in the old SLS longitude system, which is based on the Saturn kilometric radiation (SKR) observations by Voyager around 1980, while no such modulation seems to exist in the new SKR longitude system of the Cassini era. A Lomb periodogram analysis, however, reveals no significant periodic modulation of these events. The injection structures are found to occupy a small fraction (∼5–10) of the available longitude space.
Morphology and dynamics of Venus oxygen airglow from Venus Express/Visible and Infrared Thermal Imaging Spectrometer observations
Authors: Hueso R. , Sánchez‐Lavega A. , Piccioni G. , Drossart P. , Gérard J. C. , Khatuntsev I. , Zasova L. , Migliorini A.
Published: July 2008

Images obtained by the Visible and Infrared Thermal Imaging Spectrometer (VIRTIS)‐M channel instrument onboard Venus Express have been used to retrieve maps and apparent motions of the O2 (1Δ) infrared nightglow on Venus at 1.27 μm. The nightglow distribution is highly inhomogeneous with the regions of brightest emission generally located at low latitudes near the midnight meridian. Unexpectedly some orbits show also intense airglow activity over the south polar region. The spatially resolved airglow is spectacularly variable not only in its morphology and intensity but also in the apparent motions of the airglow small‐ and large‐scale structures. Visual tracking of the bright features allowed to obtain mean zonal and meridional motions related to the subsolar to antisolar circulation. The zonal velocity is dominated by an intense prograde jet (contrary to the retrograde planetary rotation) from dawn to midnight extending up to 22 hours in local time with lower velocities and reversed sign from dusk. Typical zonal velocities range between +60 (prograde) to −50 (retrograde) m/s, whereas most meridional velocities range from −20 (poleward) to +100 m/s (equatorward) with an average meridional circulation of +20 m/s toward low latitudes. The brightest small‐scale (∼100 km) features appear correlated with locations of apparent convergence which may be a signature of compression and downwelling, whereas this is not evident for the large‐scale structures suggesting slow subsidence over large areas mixed with horizontal motions. We argue that part of the tracked motions are representative of real motions at the mesosphere over an altitude range of 95–107 km.
A new ubiquitin ligase involved in p57KIP2 proteolysis regulates osteoblast cell differentiation
Authors: Kim Minsoo , Nakamoto Takashi , Nishimori Shigeki , Tanaka Keiji , Chiba Tomoki
Published: July 2008

Transforming growth factor‐β1 (TGF‐β1) has many physiological functions and inhibits the differentiation of osteoblasts. Previously, we reported that TGF‐β1 stimulation induces the degradation of p57KIP2 in osteoblasts. p57KIP2 proteolysis depends on the ubiquitin–proteasome pathway and SMAD‐mediated transcription; however, the molecular mechanism underlying p57KIP2 degradation has been largely unknown. Here, we show that FBL12, a new F‐box protein expressed in the limb bud of developing embryos, is involved in TGF‐β1‐induced degradation of p57KIP2. FBL12 formed an SCFFBL12 complex and directly ubiquitinated p57KIP2 in a phosphorylation‐dependent manner. Inhibition of FBL12 by RNA interference suppressed the degradation of p57KIP2 and a dominant‐negative mutant of FBL12 (FBL12ΔF) increased the steady‐state level of p57KIP2. Furthermore, wild‐type FBL12 inhibited and FBL12ΔF promoted the differentiation of primary osteoblasts. As overexpression of p57KIP2 promoted osteoblast differentiation, these results indicate the importance of FBL12 and the degradation of p57KIP2 in the regulation of osteoblast cell differentiation.
Involvement of RhoA, ROCK I and myosin II in inverted orientation of epithelial polarity
Authors: Yu Wei , Shewan Annette M , Brakeman Paul , Eastburn Dennis J , Datta Anirban , Bryant David M , Fan Qi‐Wen , Weiss William A , Zegers Mirjam M P , Mostov Keith E
Published: July 2008

In multicellular epithelial tissues, the orientation of polarity of each cell must be coordinated. Previously, we reported that for Madin–Darby canine kidney cells in three‐dimensional collagen gel culture, blockade of β1‐integrin by the AIIB2 antibody or expression of dominant‐negative Rac1N17 led to an inversion of polarity, such that the apical surfaces of the cells were misorientated towards the extracellular matrix. Here, we show that this process results from the activation of RhoA. Knockdown of RhoA by short hairpin RNA reverses the inverted orientation of polarity, resulting in normal cysts. Inhibition of RhoA downstream effectors, Rho kinase (ROCK I) and myosin II, has similar effects. We conclude that the RhoA–ROCK I–myosin II pathway controls the inversion of orientation of epithelial polarity caused by AIIB2 or Rac1N17. These results might be relevant to the hyperactivation of RhoA and disruption of normal polarity frequently observed in human epithelial cancers.
Expression and immunogenicity of recombinant polypeptide VP1 of human hepatitis A virus in stably transformed fruitfly (Drosophila melanogaster) Schneider 2 cells
Authors: Lee Jong Min , Lee Hyun Ho , Hwang‐Bo Jeon , Shon Dong Hwa , Kim Wonyong , Chung In Sik
Published: July 2008

We describe the secretory expression and immunogenicity of the recombinant HAV (hepatitis A virus) structural polypeptide VP1 from stably transformed Drosophila melanogaster S2 (Schneider 2) cells. Southern‐blot analysis indicated that transformed S2 cells contained multiple copies of the HAV VP1 gene in the genome. Recombinant VP1 was secreted into a culture medium with a molecular mass of 42–49 kDa. A maximum production level of 6.24 mg of recombinant VP1/litre was obtained in a T‐flask culture of Drosophila S2 cells 5 days after induction with 0.5 mM CuSO4. The recombinant HAV VP1 protein elicited the production of specific IgA in the small intestine by oral immunization and production of specific IgG in the serum by intraperitoneal immunization. Our findings show that secretory recombinant VP1 from transformed Drosophila S2 cells can be used as an effective experimental immunogen for research in vaccine development.
Tryptophan residues are targets in hypothiocyanous acid-mediated protein oxidation
Authors: Hawkins Clare L. , Pattison David I. , Stanley Naomi R. , Davies Michael J.
Published: July 2008

Myeloperoxidase, released by activated phagocytes, forms reactive oxidants by catalysing the reaction of halide and pseudo-halide ions with H2O2. These oxidants have been linked to tissue damage in a range of inflammatory diseases. With physiological levels of halide and pseudo-halide ions, similar amounts of HOCl (hypochlorous acid) and HOSCN (hypothiocyanous acid) are produced by myeloperoxidase. Although the importance of HOSCN in initiating cellular damage via thiol oxidation is becoming increasingly recognized, there are limited data on the reactions of HOSCN with other targets. In the present study, the products of the reaction of HOSCN with proteins has been studied. With albumin, thiols are oxidized preferentially forming unstable sulfenyl thiocyanate derivatives, as evidenced by the reversible incorporation of 14C from HOS14CN. On consumption of the HSA (human serum albumin) free thiol group, the formation of stable 14C-containing products and oxidation of tryptophan residues are observed. Oxidation of tryptophan residues is observed on reaction of HOSCN with other proteins (including myoglobin, lysozyme and trypsin inhibitor), but not free tryptophan, or tryptophan-containing peptides. Peptide mass mapping studies with HOSCN-treated myoglobin, showed the addition of two oxygen atoms on either Trp7 or Trp14 with equimolar or less oxidant, and the addition of a further two oxygen atoms to the other tryptophan with higher oxidant concentrations (≥2-fold). Tryptophan oxidation was observed on treating myoglobin with HOSCN in the presence of glutathione and ascorbate. Thus tryptophan residues are likely to be favourable targets for the reaction in biological systems, and the oxidation products formed may be useful biomarkers of HOSCN-mediated protein oxidation.
Differential regulation of threonine and tyrosine phosphorylations on protein kinase Cδ by G-protein-mediated pathways in platelets
Authors: Murugappan Swaminathan , Chari Ramya , Palli Vasu M. , Jin Jianguo , Kunapuli Satya P.
Published: July 2008

Phosphorylation of activation loop threonine (Thr505) and regulatory domain tyrosine (Tyr311) residues are key regulators of PKC (protein kinase C) δ function in platelets. In the present study, we show that Gq and G12/13 pathways regulate the Thr505 and Tyr311 phosphorylation on PKCδ in an interdependent manner. DiC8 (1,2-dioctanoylglycerol), a synthetic analogue of DAG (diacylglycerol), caused Thr505, but not Tyr311, phosphorylation on PKCδ, whereas selective activation of G12/13 pathways by the YFLLRNP peptide failed to cause phosphorylation of either residue. However, simultaneous activation by DiC8 and YFLLRNP resulted in Thr505 and Tyr311 phosphorylation on PKCδ. In addition, we found that the activation of SFKs (Src family tyrosine kinases) is essential for G12/13-mediated Tyr311 phosphorylation of PKCδ. These results were confirmed using Gq-deficient mouse platelets. Finally, we investigated whether Thr505 phosphorylation is required for Tyr311 phosphorylation. A T505A PKCδ mutant failed to be phosphorylated at Tyr311, even upon stimulation of both Gq and G12/13 pathways. We conclude that (i) PKCδ binding to DAG, downstream of Gq pathways, and its translocation results in Thr505 phosphorylation, (ii) G12/13 pathways activate SFKs required for the phosphorylation of Tyr311 on Thr505-phosphorylated PKCδ, and (iii) Thr505 phosphorylation is a prerequisite for Tyr311 phosphorylation on PKCδ.
Protein glycationin vivo: functional and structural effects on yeast enolase
Authors: Gomes Ricardo A. , Oliveira Luís M. A. , Silva Mariana , Ascenso Carla , Quintas Alexandre , Costa Gonçalo , Coelho Ana V. , Sousa Silva Marta , Ferreira António E. N. , Ponces Freire Ana , Cordeiro Carlos
Published: July 2008

Protein glycation is involved in structure and stability changes that impair protein functionality, which is associated with several human diseases, such as diabetes and amyloidotic neuropathies (Alzheimer's disease, Parkinson's disease and Andrade's syndrome). To understand the relationship of protein glycation with protein dysfunction, unfolding and β-fibre formation, numerous studies have been carried out in vitro. All of these previous experiments were conducted in non-physiological or pseudo-physiological conditions that bear little to no resemblance to what may happen in a living cell. In vivo, glycation occurs in a crowded and organized environment, where proteins are exposed to a steady-state of glycation agents, namely methylglyoxal, whereas in vitro, a bolus of a suitable glycation agent is added to diluted protein samples. In the present study, yeast was shown to be an ideal model to investigate glycation in vivo since it shows different glycation phenotypes and presents specific protein glycation targets. A comparison between in vivo glycated enolase and purified enolase glycated in vitro revealed marked differences. All effects regarding structure and stability changes were enhanced when the protein was glycated in vitro. The same applies to enzyme activity loss, dimer dissociation and unfolding. However, the major difference lies in the nature and location of specific advanced glycation end-products. In vivo, glycation appears to be a specific process, where the same residues are consistently modified in the same way, whereas in vitro several residues are modified with different advanced glycation end-products.
Transcriptional regulation of theTGF-β1promoter by androgen receptor
Authors: Qi Wei , Gao Shen , Wang Zhengxin
Published: July 2008

TGF (transforming growth factor)-β1 is a multifunctional cytokine that influences homoeostatic processes of various tissues. TGF-β1 expression is inhibited by androgens in the prostate gland, whereas its expression is enhanced by androgens in highly metastatic prostate cancer cells. Here, we examined regulation of human TGF-β1 promoter activity by androgen in prostate cancer cells. The full-length (−3363 to +110) promoter showed a high level of activity in response to androgen in PC3mm2 cells expressing AR (androgen receptor). Further deletion analysis revealed three distal and three proximal AREs (androgen-response elements) in the promoter. Gel-shift and footprint assays show that these AREs physically interact with the DNA-binding domain of AR. Chromatin immunoprecipitation assays revealed the androgen-dependent recruitment of AR to the ARE-containing regions of the TGF-β1 gene. More importantly, a negative ARE was detected in the TGF-β1 promoter. Both positive and negative AREs are functional in the androgen-regulated transcription of the TGF-β1 promoter. These findings imply that androgen signalling may positively or negatively regulate TGF-β1 expression in response to various signals or under different environmental conditions.
SMILE, a new orphan nuclear receptor SHP-interacting protein, regulates SHP-repressed estrogen receptor transactivation
Authors: Xie Yuan-Bin , Lee Ok-Hee , Nedumaran Balachandar , Seong Hyun-A , Lee Kyeong-Min , Ha Hyunjung , Lee In-Kyu , Yun Yungdae , Choi Hueng-Sik
Published: July 2008

SHP (small heterodimer partner) is a well-known NR (nuclear receptor) co-regulator. In the present study, we have identified a new SHP-interacting protein, termed SMILE (SHP-interacting leucine zipper protein), which was previously designated as ZF (Zhangfei) via a yeast two-hybrid system. We have determined that the SMILE gene generates two isoforms [SMILE-L (long isoform of SMILE) and SMILE-S (short isoform of SMILE)]. Mutational analysis has demonstrated that the SMILE isoforms arise from the alternative usage of initiation codons. We have confirmed the in vivo interaction and co-localization of the SMILE isoforms and SHP. Domain-mapping analysis indicates that the entire N-terminus of SHP and the middle region of SMILE-L are involved in this interaction. Interestingly, the SMILE isoforms counteract the SHP repressive effect on the transactivation of ERs (estrogen receptors) in HEK-293T cells (human embryonic kidney cells expressing the large T-antigen of simian virus 40), but enhance the SHP-repressive effect in MCF-7, T47D and MDA-MB-435 cells. Knockdown of SMILE gene expression using siRNA (small interfering RNA) in MCF-7 cells increases ER-mediated transcriptional activity. Moreover, adenovirus-mediated overexpression of SMILE and SHP down-regulates estrogen-induced mRNA expression of the critical cell-cycle regulator E2F1. Collectively, these results indicate that SMILE isoforms regulate the inhibition of ER transactivation by SHP in a cell-type-specific manner and act as a novel transcriptional co-regulator in ER signalling.
An IR study of (CO2)n+ (n=3–8) cluster ions in the 1000–3800 cm–1 region
Authors: Inokuchi Yoshiya , Muraoka Azusa , Nagata Takashi , Ebata Takayuki
Published: July 2008

Infrared photodissociation (IRPD) spectra of carbon dioxide cluster ions, (CO2)n+ with n=3–8, are measured in the 1000–3800 cm–1 region. IR bands assignable to solvent CO2 molecules are observed at positions close to the vibrational frequencies of neutral CO2 [1290 and 1400 cm–1 (ν1 and 2ν2), 2350 cm–1 (ν3), and 3610 and 3713 cm–1 (ν1+ν3 and 2ν2+ν3)]. The ion core in (CO2)n+ shows several IR bands in the 1200–1350, 2100–2200, and 3250–3500 cm–1 regions. On the basis of previous IR studies in solid Ne and quantum chemical calculations, these bands are ascribed to the C2O4+ ion, which has a semicovalent bond between the CO2 components. The number of the bands and the bandwidth of the IRPD spectra drastically change with an increase in the cluster size up to n=6, which is ascribed to the symmetry change of (CO2)n+ by the solvation of CO2 molecules and a full occupation of the first solvation shell at n=6.
Time-dependent V-representability on lattice systems
Authors: Li Yonghui , Ullrich C. A.
Published: July 2008

We study the mapping between time-dependent densities and potentials for noninteracting electronic systems on lattices. As discovered recently by Baer [J. Chem. Phys. 128, 044103 (2008)], there exist well-behaved time-dependent density functions on lattices which cannot be associated with any real time-dependent potential. This breakdown of time-dependent V-representability can be tracked down to problems with the continuity equation which arise from discretization of the kinetic-energy operator. Examples are given for lattices with two points and with N points, and implications for practical numerical applications of time-dependent density-functional theory are discussed. In the continuum limit, time-dependent noninteracting V-representability is restored.
Vibrational energies of PH3 calculated variationally at the complete basis set limit
Authors: Ovsyannikov Roman I. , Thiel Walter , Yurchenko Sergei N. , Carvajal Miguel , Jensen Per
Published: July 2008

The potential energy surface for the electronic ground state of PH3 was calculated at the CCSD(T) level using aug-cc-pV(Q+d)Z and aug-cc-pVQZ basis sets for P and H, respectively, with scalar relativistic corrections included. A parametrized function was fitted through these ab initio points, and one parameter of this function was empirically adjusted. This analytical PES was employed in variational calculations of vibrational energies with the newly developed program TROVE. The convergence of the calculated vibrational energies with increasing vibrational basis set size was improved by means of an extrapolation scheme analogous to the complete basis set limit schemes used in ab initio electronic structure calculations. The resulting theoretical energy values are in excellent agreement with the available experimentally derived values.
Electronic and geometrical structure of Mn13 anions, cations, and neutrals
Authors: Gutsev G. L. , Mochena M. D. , Bauschlicher Charles W. , Zheng W.-J. , Thomas O. C. , Bowen Kit H.
Published: July 2008

We have computed the electronic and geometrical structures of thirteen atom manganese clusters in all three charge states, Mn13−, Mn13+, and Mn13 by using density functional theory with the generalized gradient approximation. Our results for Mn13− are compared with our anion photoelectron spectrum of Mn13−, published in this paper. Our results for Mn13+ are compared with the previously published photoionization results of Knickelbein [J. Chem. Phys. 106, 9810 (1997)]. There is a good agreement between theoretical and experimental values of ionization and electron attachment energies.
Modified Jeans instability criteria for magnetized systems
Authors: Lundin J. , Marklund M. , Brodin G.
Published: July 2008

The Jeans instability is analyzed for dense magnetohydrodynamic plasmas with intrinsic magnetization, the latter due to collective electron spin effects. Furthermore, the effects of electron tunneling as well as the Fermi pressure are included. It is found that the intrinsic magnetization of the plasma will enhance the Jeans instability, and can significantly modify the structure of the instability spectra. Implications and limitations of our results are discussed, as well as possible generalizations.
Dynamic effects in nonlinearly coupled elastic deformation and diffusion fields in solids
Authors: Spicer J. B. , Dikmelik Y.
Published: July 2008

The linear coupling of elastic deformations and solute diffusion in solids produces effects such as strain-induced diffusion and solute-induced dilatation. While this coupling also affects changes in certain material properties, many important physical effects must be described within a framework that includes the nonlinear coupling of the diffusion and deformation fields. The nonlinear coupling of these fields is developed using a continuum approach based in thermodynamics that considers the possible effects that might arise in elastic solids containing a mobile solute species. Among others, this coupling produces effects including point defect-related modulus variations, harmonic generation in acoustic waves, and diffusion in the presence of transient, equivoluminal strain fields.
Nanoscale capacitance microscopy of thin dielectric films
Authors: Gomila G. , Toset J. , Fumagalli L.
Published: July 2008

We present an analytical model to interpret nanoscale capacitance microscopy measurements on thin dielectric films. The model displays a logarithmic dependence on the tip-sample distance and on the film thickness-dielectric constant ratio and shows an excellent agreement with finite-element numerical simulations and experimental results on a broad range of values. Based on these results, we discuss the capabilities of nanoscale capacitance microscopy for the quantitative extraction of the dielectric constant and the thickness of thin dielectric films at the nanoscale.
Ion beam synthesis and charge storage behavior of Au nanocrystals in thin SiO2 layers
Authors: Beyer V. , Eichhorn F. , von Borany J. , Mücklich A. , Müller T.
Published: July 2008

Au nanocrystals (NCs) were synthesized in a thin SiO2 layer by ion implantation and annealing in a tight distribution close to the Si/SiO2 interface. Between the NCs and the Si substrate a thin tunneling oxide forms self-organized during annealing totally depleted from Au NCs. Memory behavior is demonstrated by electron charging and discharging on metal–oxide–semiconductor capacitors. Lenticular liquid Au:Si droplets nucleate at the Si/SiO2 interface from silicon regions supersaturated by Au close to the oxide. Au NCs embedded in SiO2 above these droplets are stabilized during annealing due to a modified detailed balance of Au atom detachment and attachment. Capacitance-voltage and spreading resistance measurements reveal the impact of the Au contamination in the Si substrate. Structure and distribution of Au droplets and NCs are characterized by x-ray diffraction and transmission electron microscopy.
Heavy (or large) ions in a fluid in an electric field: The diffusion equation exactly following from the Fokker–Planck equation
Authors: Ferrari Leonardo
Published: July 2008

The problem of the derivation of the diffusion equation exactly following from the Fokker–Planck (or Klein–Kramers) equation for heavy (or large) particles in a fluid in an external force field is solved in the case in which the particles are ions subject to a uniform (but in general time-varying) electric field. It is found that such a diffusion equation maintains memory of the initial ion velocity distribution, unless sufficiently large values of time are considered. In such temporal asymptotic limit, the diffusion equation exactly becomes (i) the Smoluchowski equation when the electric field is constant in time, and (ii) a new equation generalizing the Smoluchowski equation, when the electric field is arbitrarily time varying. Finally, it is shown that the obtained exact (or asymptotic) results make questionable the procedures and the results of approximate theories developed in the past to get a “corrected” Smoluchowski equation when the external force can also be, in general, position dependent.
Friction of rodlike particles adsorbed to a planar surface in shear flow
Authors: Ekiel-Jeżewska Maria L. , Sadlej Krzysztof , Wajnryb Eligiusz
Published: July 2008

A planar hard surface covered with elongated stiff rodlike particles in shear flow is considered in the low-Reynolds-number regime assuming low particle surface coverage. The particles are modeled as straight chains of spherical beads. Multipole expansion of the Stokes equations (the accurate HYDROMULTIPOLE algorithm) is applied to evaluate the hydrodynamic force exerted by the fluid on the rodlike particles, depending on their shape, i.e., on the number of beads and their orientation with respect to the wall and to the ambient shear flow.
Role of nonadiabatic untrapped electrons in global electrostatic ion temperature gradient driven modes in a tokamak
Authors: Chowdhury J. , Ganesh R. , Angelino P. , Vaclavik J. , Villard L. , Brunner S.
Published: July 2008

In this work, role of nonadiabatic untrapped electrons in the context of a global ion temperature gradient driven mode has been investigated. In past studies, untrapped electrons have been assumed to be able to respond “instantaneously” to a disturbance. It is proposed that such adiabatic electron models should be reexamined for two important reasons: (i) It is known that global modes with n in the range of 3⩽n⩽15 (n is the toroidal mode number) have eigenmode widths spanning several mode-rational surfaces. It is being argued that close to these mode-rational surfaces, adiabatic electron models fail and a consistent treatment of nonadiabatic electrons is crucial for global modes. (ii) Electromagnetic effects depend on passing nonadiabatic electron dynamics. A minimal nontrivial model for the benchmarking of global linear and nonlinear gyrokinetic codes in the future becomes necessary, which can treat both passing ions and electrons on the same physics footing. As a first step, a study of the effect of nonadiabatic passing electrons in global electrostatic ion temperature gradients is presented. Interesting results include a demonstration of multiscale structure, downshift in critical ηi with increasing ηe, and a reduction in mixing-length based transport.
Dynamic model and phase transitions for liquid helium
Authors: Ma Tian , Wang Shouhong
Published: July 2008

This article presents a phenomenological dynamic phase transition theory—modeling and analysis—for liquid helium-4. First we derive a time-dependent Ginzburg–Landau model for helium-4 by (1) separating the superfluid and the normal fluid densities with the superfluid density given in terms of a wave function and (2) using a unified dynamical Ginzburg–Landau model. One the one hand, the analysis of this model leads to phase diagrams consistent with the classical ones for liquid helium-4. On the other hand, it leads to predictions of (1) the existence of a metastable region H, where both solid and liquid He II states are metastable and appear randomly depending on fluctuations and (2) the existence of a switch point M on the λ curve, where the transitions changes types. It is hoped that these predictions will be useful for designing better physical experiments and lead to better understanding of the physical mechanism of superfluidity.
Nonlinear electron motion in a coherent whistler wave packet
Authors: Khazanov George , Tel’nikhin Alexander , Kronberg Tatiana
Published: July 2008

Map equations are derived, with which nonlinear electron motion in a coherent whistler wave packet is investigated. All solutions of these equations belong to a certain strange attractor and describe chaotic motion with the stable means. The class of solutions determined the intermittent dynamics as the control parameter of the wave-particle system increases above the appropriate critical value is found. An application of the results to the problem of the stability of Earth’s radiation belts is considered. It is shown that the efficient acceleration processes take place for relativistic electrons of a few MeV.
Particle transfer in edge transport barrier with stochastic magnetic field
Authors: Tokar M. Z. , Evans T. E. , Singh R. , Unterberg B.
Published: July 2008

Charged particle losses at the plasma edge affected by resonant magnetic perturbations (RMP) are considered by taking into account the electron and ion flows both parallel and perpendicular to perturbed field lines. Calculations are done for H-mode plasmas of low collisionality, i.e., under conditions where significant pump out of particles has been observed in experiments on the DIII-D tokamak [J. Luxon, Nucl. Fusion 42, 614 (2002)] with RMP from the I-coils. It is demonstrated that the perpendicular ion flux, arising by magnetic field stochastization due to the deviation of poloidal rotation from the neoclassical one, is of more importance than the parallel ion flow. With both loss contributions included, computations provide a pump out level in agreement with observations if the screening of RMP by the plasma rotation is taken into account. The impact of possible enhancement in the perpendicular electron transport due to fluctuations observed with RMP in the edge transport barrier is assessed.
An analytical demonstration of coupling schemes between magnetohydrodynamic codes and eddy current codes
Authors: Liu Yueqiang , Albanese R. , Portone A. , Rubinacci G. , Villone F.
Published: July 2008

In order to model a magnetohydrodynamic (MHD) instability that strongly couples to external conducting structures (walls and/or coils) in a fusion device, it is often necessary to combine a MHD code solving for the plasma response, with an eddy current code computing the fields and currents of conductors. We present a rigorous proof of the coupling schemes between these two types of codes. One of the coupling schemes has been introduced and implemented in the CARMA code [R. Albanese, Y. Q. Liu, A. Portone, G. Rubinacci, and F. Villone, IEEE Trans. Magn. 44, 1654 (2008); A. Portone, F. Villone, Y. Q. Liu, R. Albanese, and G. Rubinacci, Plasma Phys. Controlled Fusion 50, 085004 (2008)] that couples the MHD code MARS-F [Y. Q. Liu, A. Bondeson, C. M. Fransson, B. Lennartson, and C. Breitholtz, Phys. Plasmas 7, 3681 (2000)] and the eddy current code CARIDDI [R. Albanese and G. Rubinacci, Adv. Imaging Electron Phys. 102, 1 (1998)]. While the coupling schemes are described for a general toroidal geometry, we give the analytical proof for a cylindrical plasma.
Perpendicular anisotropy dependence of oscillatory interlayer coupling behavior in [Pt/Co]5/Ru/[Co/Pt]5 multilayers
Authors: Zhao J. , Wang Y. J. , Liu Y. Z. , Han X. F. , Zhang Z.
Published: July 2008

The experiments on the [t1Pt/0.4Co]5/(0.2–5.0)Ru/[0.4Co/t2Pt]5 (thickness unit is nm) multilayers with perpendicular anisotropy (PA) indicate that the interlayer coupling shows an antiferromagnetic (AF) and a ferromagnetic oscillatory behavior with the thickness of Ru spacer layers from 0 to 5.0 nm, and that the AF oscillations display a superposition of two different periods, which are 0.8 and 1.1 nm, respectively. Moreover, we found that the magnitude of AF coupling strength J is closely related to the magnitude of PA caused by varied thickness of nonmagnetic Pt layer. Our experimental results can be explained by Bruno’s electron-optics model.
Measurement of the redistribution of arsenic at nickel silicide/silicon interface by secondary ion mass spectrometry: artifact and optimized analysis conditions
Authors: Hoummada K. , Mangelinck D. , Perrin C. , Carron V. , Holliger P.
Published: July 2008

The arsenic redistribution after NiSi formation has been measured by secondary ion mass spectrometry (SIMS). The NiSi film has been obtained by solid state reaction of a Ni thin film with a silicon substrate doped with As. An increase in the As SIMS signal at the NiSi/Si interface was observed for some experimental conditions. By varying the SIMS experimental parameters (incidence angle and the impact energy), the As signal at NiSi/Si interface was found to change. The SIMS experimental parameters have been optimized and were found to be an impact energy of 1 keV and an incidence angle superior to 50°. This allows us to minimize differences in sputtering rate and ion yield between NiSi and Si and to obtain a good depth resolution and dynamic range. Under these conditions the bump in the As signal does not appear: this illustrates the difficulty to measure concentration at interface by SIMS.
Correlation of photoluminescent quantum efficiency and device characteristics for the soluble electrophosphorescent light emitter with interfacial layers
Authors: Kang Nam Su , Ju Byeong-Kwon , Kim Ji Whan , Kim Jang-Joo , Yu Jae-Woong , Chin Byung Doo
Published: July 2008

We have investigated the effects of interfacial layers on the properties of soluble phosphorescent organic light emitting devices. Two kinds of polyfluorene-based interfacial layer materials have been studied; both were spin coated on top of PEDOT:PSS to form the insoluble layers by thermal annealing. The molecular-doped, phosphorescent light emitting layer comprising a polymeric host, small molecular host, and guest molecule was fabricated onto the thin interfacial layer. The photoluminescence quantum yield (PLQY) of these layers was measured with an integrating sphere. We have calculated the PLQY values of the single phosphorescent light emitting layer and various organic multilayers incorporating the interfacial layers, showing that a reduction in PLQY due to the interfacial quenching is more significant in the thicker interfacial layer structures. In spite of the decrease in PLQY induced by the triplet energy mismatch, polyfluorene-based interfacial layers improved the charge injection from PEDOT:PSS to the emitting layer, which results in the enhanced brightness and current. The triplet quenching by the interfacial layer could explain the reduction in luminous efficiency of the devices compared to the reference. This was also investigated by studying the charge carrier trapping, change in the spectral characteristics induced by the shift in the emission zone, and the analysis on the carrier balance of devices.
A hyperthermal energy ion beamline for probing hot electron chemistry at surfaces
Authors: Ray M. P. , Lake R. E. , Moody S. A. , Magadala V. , Sosolik C. E.
Published: July 2008

An ultrahigh vacuum ion beamline and chamber have been assembled to produce hyperthermal (<400eV) energy ions for studying hot electron chemistry at surfaces. The specific design requirements for this modified instrument were chosen to enable the exposure of a metal-oxide-semiconductor (MOS) device to monoenergtic, well-collimated beams of alkali ions while monitoring both the scattered beam flux and the device characteristics. Our goal is to explore the role that hot electrons injected toward the MOS device surface play in the neutralization of scattered ions. To illustrate the functionality of our system, we present energy-resolved spectra for Na+, K+, and Cs+ ions scattered from the surface of a Ag(001) single crystal for a range of incident energies. In addition, we show MOS device current-voltage characteristics measured in situ in a new rapid-turnaround load lock and sample translation stage.
Whole-cell response of the pennate diatom
Phaeodactylum tricornutum
to iron starvation
Authors: Allen Andrew E. , LaRoche Julie , Maheswari Uma , Lommer Markus , Schauer Nicolas , Lopez Pascal J. , Finazzi Giovanni , Fernie Alisdair R. , Bowler Chris
Published: July 2008

Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by
Phaeo dactylum tricornutum
at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the
Thalassiosira pseudonana
genome that encode for components of iron capture and uptake mechanisms.
A positive-feedback mechanism promotes reovirus particle conversion to the intermediate associated with membrane penetration
Authors: Agosto Melina A. , Myers Kimberly S. , Ivanovic Tijana , Nibert Max L.
Published: July 2008

Membrane penetration by reovirus is associated with conversion of a metastable intermediate, the ISVP, to a further-disassembled particle, the ISVP*. Factors that promote this conversion in cells are poorly understood. Here, we report the
in vitro
characterization of a positive-feedback mechanism for promoting ISVP* conversion. At high particle concentration, conversion approximated second-order kinetics, and products of the reaction operated
in trans
to promote the conversion of target ISVPs. Pore-forming peptide μ1N, which is released from particles during conversion, was sufficient for promoting activity. A mutant that does not undergo μ1N release failed to exhibit second-order conversion kinetics and also failed to promote conversion of wild-type target ISVPs. Susceptibility of target ISVPs to promotion
in trans
was temperature dependent and correlated with target stability, suggesting that capsid dynamics are required to expose the interacting epitope. A positive-feedback mechanism of promoting escape from the metastable intermediate has not been reported for other viruses but represents a generalizable device for sensing a confined volume, such as that encountered during cell entry.
SNMP is a signaling component required for pheromone sensitivity in
Drosophila
Authors: Jin Xin , Ha Tal Soo , Smith Dean P.
Published: July 2008

The only known volatile pheromone in
Drosophila
, 11-
cis
-vaccenyl acetate (cVA), mediates a variety of behaviors including aggregation, mate recognition, and sexual behavior. cVA is detected by a small set of olfactory neurons located in T1 trichoid sensilla on the antennae of males and females. Two components known to be required for cVA reception are the odorant receptor Or67d and the extracellular pheromone-binding protein LUSH. Using a genetic screen for cVA-insensitive mutants, we have identified a third component required for cVA reception: sensory neuron membrane protein (SNMP). SNMP is a homolog of CD36, a scavenger receptor important for lipoprotein binding and uptake of cholesterol and lipids in vertebrates. In humans, loss of CD36 is linked to a wide range of disorders including insulin resistance, dyslipidemia, and atherosclerosis, but how CD36 functions in lipid transport and signal transduction is poorly understood. We show that SNMP is required in pheromone-sensitive neurons for cVA sensitivity but is not required for sensitivity to general odorants. Using antiserum to SNMP infused directly into the sensillum lymph, we show that SNMP function is required on the dendrites of cVA-sensitive neurons; this finding is consistent with a direct role in cVA signal transduction. Therefore, pheromone perception in
Drosophila
should serve as an excellent model to elucidate the role of CD36 members in transmembrane signaling.
Application of a polarizable force field to calculations of relative protein–ligand binding affinities
Authors: Khoruzhii Oleg , Donchev Alexander G. , Galkin Nikolay , Illarionov Alexei , Olevanov Mikhail , Ozrin Vladimir , Queen Cary , Tarasov Vladimir
Published: July 2008

An explicitly polarizable force field based exclusively on quantum data is applied to calculations of relative binding affinities of ligands to proteins. Five ligands, differing by replacement of an atom or functional group, in complexes with three serine proteases—trypsin, thrombin, and urokinase-type plasminogen activator—with available experimental binding data are used as test systems. A special protocol of thermodynamic integration was developed and used to provide sufficiently low levels of systematic error along with high numerical efficiency and statistical stability. The calculated results are in excellent quantitative (rmsd = 1.0 kcal/mol) and qualitative (R2= 0.90) agreement with experimental data. The potential of the methodology to explain the observed differences in the ligand affinities is also demonstrated.
Classification and Evolutionary Trends of Icosahedral Viral Capsids
Authors: Kerner Richard
Published: July 2008

A classification of icosahedral viral capsids is proposed. We show how the self‐organization of capsids during their formation implies a definite composition of their elementary building blocks. The exact number of hexamers with three different admissible symmetries is related to capsids′ sizes, labelled by their T‐numbers. Simple rules determining these numbers for each value of T are deduced and certain consequences concerning the probabilities of mutations and evolution of viruses are discussed.
HIV‐1 Integrase–DNA Interactions Investigated by Molecular Modelling
Authors: Fenollar-Ferrer C. , Carnevale V. , Raugei S. , Carloni P.
Published: July 2008

HIV‐1 integrase is the viral enzyme responsible for the insertion of the viral DNA into the host cell chromosome. This process occurs through two distinct biochemical reactions: the 3′‐processing of the viral DNA and the transesterification reaction. Because experimental structural information on the reaction intermediate is not available, several molecular models have been developed. Unfortunately, none of the models of the enzyme–substrate complex is fully consistent with the available molecular biological data. We have constructed a new theoretical model based on mutagenesis experiments and cross‐linking data, using a relatively accurate computational setup. The structural features of the model along with its limitations are discussed here.
Biologic Constraints on Modelling Virus Assembly
Authors: Garcea Robert L.
Published: July 2008

The mathematic modelling of icosahedral virus assembly has drawn increasing interest because of the symmetric geometry of the outer shell structures. Many models involve equilibrium expressions of subunit binding, with reversible subunit additions forming various intermediate structures. The underlying assumption is that a final lowest energy state drives the equilibrium toward assembly. In their simplest forms, these models have explained why high subunit protein concentrations and strong subunit association constants can result in kinetic traps forming off pathway partial and aberrant structures. However, the cell biology of virus assembly is exceedingly complex. The biochemistry and biology of polyoma and papillomavirus assembly described here illustrates many of these specific issues. Variables include the use of cellular ‘chaperone’ proteins as mediators of assembly fidelity, the coupling of assembly to encapsidation of a specific nucleic acid genome, the use of cellular structures as ‘workbenches’ upon which assembly occurs, and the underlying problem of making a capsid structure that is metastable and capable of rapid disassembly upon infection. Although formidable to model, incorporating these considerations could advance the relevance of mathematical models of virus assembly to the real world.
Irregular and Semi‐Regular Polyhedral Models for Rous Sarcoma Virus Cores
Authors: Heymann J. Bernard , Butan Carmen , Winkler Dennis C. , Craven Rebecca C. , Steven Alasdair C.
Published: July 2008

Whereas many viruses have capsids of uniquely defined sizes that observe icosahedral symmetry, retrovirus capsids are highly polymorphic. Nevertheless, they may also be described as polyhedral foldings of a fullerene lattice on which the capsid protein (CA) is arrayed. Lacking the high order of symmetry that facilitates the reconstruction of icosahedral capsids from cryo‐electron micrographs, the 3D structures of individual retrovirus capsids may be determined by cryo‐electron tomography, albeit at lower resolution. Here, we describe computational and graphical methods used to construct polyhedral models that match in size and shape, capsids of Rous sarcoma virus (RSV) observed within intact virions. The capsids fall into several shape classes, including tubes, ‘lozenges’ and ‘coffins’. The extent to which a capsid departs from icosahedral symmetry reflects the irregularity of the distribution of pentamers, which are always 12 in number for a closed polyhedral capsid. The number of geometrically distinct polyhedra grows rapidly with increasing quotas of hexamers, and ranks in the millions for particles in the size range of RSV capsids, which typically have 150–300 hexamers. Unlike the CAs of icosahedral viruses that assume a minimal number of quasi‐equivalent conformations equal to the triangulation number (T), retroviral CAs exhibit a near‐continuum of quasi‐equivalent conformations – a property that may be attributed to the flexible hinge linking the N‐ and C‐terminal domains.