bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-focusing of a Gaussian electromagnetic beam in a complex plasma
Authors: Mishra S. K. , Misra Shikha , Sodha M. S.
Published: April 2011

This paper analyzes the propagation of a Gaussian electromagnetic beam in a complex plasma; the paraxial approach has been invoked for the study of the propagation characteristics. The analytical model emphasizes the open nature of complex plasmas and incorporates the charge, number density, and energy balance of the plasma constituents along with the plasma neutrality. Diffusion due to the density and temperature gradients, thermal conduction, Ohmic heating, and energy exchange in collisions/accretion have also been taken into account. For a numerical appreciation of the results, the critical curves for the propagation of the beam in dark plasmas have been discussed. The dependence of the beam width parameter on distance of propagation has been evaluated for three typical cases viz., of steady divergence, oscillatory divergence, and self-focusing. The equality of electron and ion density, an assumption inherent in the earlier analysis, has been discarded on account of the presence of charged dust particles.
The automorphism group of separable states in quantum information theory
Authors: Friedland Shmuel , Li Chi-Kwong , Poon Yiu-Tung , Sze Nung-Sing
Published: April 2011

We show that the linear group of automorphism of Hermitian matrices which preserves the set of separable states is generated by natural automorphisms: change of an orthonormal basis in each tensor factor, partial transpose in each tensor factor, and interchanging two tensor factors of the same dimension. We apply our results to the preservers of the product numerical range.
Induced migration of non-magnetic particles and fabrication of metallic-based graded materials by applying a strong magnetic field
Authors: Sun Z. , Guo M. , Vleugels J. , Blanpain B. , Van der Biest O.
Published: April 2011

Strong magnetic fields e.g., 10 T are now frequently used during materials preparation. In the present paper, a method of metal-ceramics graded materials preparation is proposed by applying a strong magnetic field with a high gradient. Experimental and theoretical analyses are performed to investigate the effect of the strong magnetic field on the migration and interaction behavior of diamagnetic oxide particles in a liquid metal. The migration of micrometer or sub-micrometer sized particles is clearly enhanced by the magnetic field gradient. After being treated by the strong magnetic field, a self-assembly structure of the particles is achieved. Various factors such as the magnetic dipole-dipole interaction and chain-chain interaction, are governing the particles assembly. The present results provide direct evidence that nonmetallic particles of micrometer size or less can be manipulated in a conductive melt by applying a strong magnetic field and as a consequence graded materials can be prepared.
In situ studies of strain dependent transport properties of conducting polymers on elastomeric substrates
Authors: Vijay Venugopalan , Rao Arun D. , Narayan K. S.
Published: April 2011

We report the changes in the surface electrical resistance, R, of conducting polymer, Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) films coated on appropriate flexible substrates in stretched conditions. These studies are important in the context of flexible organic electronic applications. In situ conductivity measurements on pristine PEDOT:PSS thin films on elastomeric substrates upon stretching reveal a minima in R as a function of strain, x, prior to the expected increase at higher strain levels. The studies emphasize (i) role of substrates, (ii) stress-induced anisotropic features, and temperature dependence of R (iii) in comparison of R(x) in polymer films to that of conventional metal films. The stress induced changes is modeled in terms of effective medium approximation.
Perturbation between two traps in dual-trap optical tweezers
Authors: Ling Lin , Zhou Fei , Huang Lu , Guo Honglian , Li Zhaolin , Li Zhi-Yuan
Published: April 2011

Dual-trap optical tweezers are widely used in biological sciences and many other areas. The two traps are generally considered to be independent of each other in most situations. But when they are close and even touch side by side, the influence may not be negligible. We calculate the optical force of dielectric spherical particles trapped in dual-trap optical tweezers by means of the discrete dipole approximation method and analyze the perturbation effect between the two traps. We find that the electric field does not change much when it is scattered by the trapped particles. As a result, the scattering light from one sphere has a little perturbation effect on the trapping force upon the other sphere. The perturbation mainly comes from the other trap and is thus affected by the distance between the two traps. In the experiment, the displacement of the sphere trapped in an immovable trap is observed when another trap is moving close. The experiment data of relative displacement match qualitatively with the calculation data.
Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser
Authors: Pedersoli Emanuele , Capotondi Flavio , Cocco Daniele , Zangrando Marco , Kaulich Burkhard , Menk Ralf H. , Locatelli Andrea , Mentes Tevfik O. , Spezzani Carlo , Sandrin Gilio , Bacescu Daniel M. , Kiskinova Maya , Bajt Saša , Barthelmess Miriam , Barty Anton , Schulz Joachim , Gumprecht Lars , Chapman Henry N. , Nelson A. J. , Frank Matthias , Pivovaroff Michael J. , Woods Bruce W. , Bogan Michael J. , Hajdu Janos
Published: April 2011

We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.
Large optical gain AlGaN-delta-GaN quantum wells laser active regions in mid- and deep-ultraviolet spectral regimes
Authors: Zhang Jing , Zhao Hongping , Tansu Nelson
Published: April 2011

The gain characteristics of high Al-content AlGaN-delta-GaN quantum wells (QWs) are investigated for mid- and deep-ultraviolet (UV) lasers. The insertion of an ultrathin GaN layer in high Al-content AlGaN QWs leads to valence subbands rearrangement, which in turn results in large optical gain for mid- and deep-UV lasers.
Metallic characteristics in superlattices composed of insulators, NdMnO3/SrMnO3/LaMnO3
Authors: Seo J. W. , Phan B. T. , Lee J. , Kim H.-D. , Panagopoulos C.
Published: April 2011

We report on the electronic properties of superlattices composed of three different antiferromagnetic insulators, NdMnO3/SrMnO3/LaMnO3 grown on SrTiO3 substrates. Photoemission spectra obtained by tuning the x-ray energy at the Mn 2p→3d edge show a Fermi cut-off, indicating metallic behavior mainly originating from Mn eg electrons. Furthermore, the density of states near the Fermi energy and the magnetization obey a similar temperature dependence, suggesting a correlation between the spin and charge degrees of freedom at the interfaces of these oxides.
Observation of surface-guided waves in holey hypersonic phononic crystal
Authors: Benchabane Sarah , Gaiffe Olivier , Ulliac Gwenn , Salut Roland , Achaoui Younes , Laude Vincent
Published: April 2011

We observe experimentally the propagation of surface-guided waves in a hypersonic phononic crystal, both in the radiative and nonradiative regions of the spectrum. Combining electrical measurements in reflection and transmission as well as optical maps of the surface displacement, a band gap extending from 0.6 to 0.95 GHz is identified in a square lattice array of 1 μm radius air holes milled in lithium niobate. The optical measurements reveal the transmission of surface-guided waves above the band gap, well inside the sound cone.
Formation of graphene sheets through laser exfoliation of highly ordered pyrolytic graphite
Authors: Qian Min , Zhou Yun Shen , Gao Yang , Park Jong Bok , Feng Tao , Huang Su Mei , Sun Zhuo , Jiang Lan , Lu Yong Feng
Published: April 2011

Freestanding two-dimensional (2D) few-layer graphene was formed through laser exfoliation of highly ordered pyrolytic graphite, using a pulsed neodymium-doped yttrium aluminum garnet (Nd:YAG) laser. Graphene sheets of several nanometers in thickness and micrometers in size were obtained. The laser exfoliation process was investigated at different laser fluences and distances between target and substrate. Three different phases, amorphous carbon, few-layer graphene sheets, and thin graphite films, were obtained as the laser fluence increased. This study reveals an existing route of forming freestanding 2D nanostructures through laser exfoliation.
Quantum magnetoresistance of the PrFeAsO oxypnictide
Authors: Bhoi D. , Mandal P. , Choudhury P. , Pandya S. , Ganesan V.
Published: April 2011

We report the observation of an unusual B dependence of transverse magnetoresistance (MR) in the PrFeAsO, one of the parent compound of pnictide superconductors. Below the spin density wave transition, MR is large, positive and increases with decreasing temperature. At low temperatures, MR increases linearly with B up to 14 T. For T≥40 K, MR versus B curve develops a weak curvature in the low-field region which indicates a crossover from B linear to B2 dependence as B→0. The B linear MR originates from the Dirac cone states and has been explained by the quantum mechanical model proposed by Abrikosov.
Two-screen single-shot electron spectrometer for laser wakefield accelerated electron beams
Authors: Soloviev A. A. , Starodubtsev M. V. , Burdonov K. F. , Kostyukov I. Yu. , Nerush E. N. , Shaykin A. A. , Khazanov E. A.
Published: April 2011

The laser wakefield acceleration electron beams can essentially deviate from the axis of the system, which distinguishes them greatly from beams of conventional accelerators. In case of energy measurements by means of a permanent-magnet electron spectrometer, the deviation angle can affect accuracy, especially for high energies. A two-screen single-shot electron spectrometer that correctly allows for variations of the angle of entry is considered. The spectrometer design enables enhancing accuracy of measuring narrow electron beams significantly as compared to a one-screen spectrometer with analogous magnetic field, size, and angular acceptance.
The contribution of heterotrophic nanoflagellate grazing towards bacterial mortality in tropical waters: comparing estuaries and coastal ecosystems
Authors: Bong Chui Wei , Lee Choon Weng
Published: April 2011

Heterotrophic nanoflagellate (HNF) grazing depends on both temperature and trophic status of an ecosystem. As most microbes already function at their temperature optimum in tropical waters, we hypothesised that HNF grazing rates would be higher in more productive sites such as estuaries than in less productive areas such as coastal waters. We sampled two estuaries and three coastal sites along the Straits of Malacca and the South China Sea near the Malaysia Peninsula. Bacterial abundance ranged 0.9–6.3 × 106 cells mL–1, whereas HNF abundance ranged 1.8–10.1 ×103 cells mL–1. Bacterial production ranged 1.1–12.7 × 105 cells mL–1 h–1, whereas HNF grazing rates were an order of magnitude lower at 1.0–78.5 × 104 cells mL–1 h–1. Bacterial abundance, net bacterial production and HNF grazing rates were higher in estuaries than coastal waters but HNF abundance did not differ between the two areas. Across all stations, HNF grazing rates increased with bacterial production, and accounted for ~33% of bacterial production. Our results suggest that in the tropical waters studied, there was a bacterial production–grazing imbalance. Other loss factors such as viral lysis, sedimentation or the presence of benthic filter feeders could account for this imbalance.
Disproportionate importance of nearshore habitat for the food web of a deep oligotrophic lake
Authors: Hampton Stephanie E. , Fradkin Steven C. , Leavitt Peter R. , Rosenberger Elizabeth E.
Published: April 2011

In large deep oligotrophic lakes, multiple lines of evidence suggest that the shallow nearshore water provides disproportionately important feeding and breeding habitat for the whole-lake food web. We examined the trophic importance of the nearshore environment, human impacts nearshore, and several approaches to disturbance detection in a deep (190 m) oligotrophic lake with relatively modest residential development. In Lake Crescent, on the Olympic Peninsula of Washington (USA), stable isotope analysis demonstrated that apex salmonid predators derived more than 50% of their carbon from nearshore waters, even though this nearshore water accounted for only 2.5% of total lake volume. Unfortunately, it is this land–water interface that is initially degraded as shorelines are developed. We hypothesised that under these conditions of relatively modest disturbance, the effects of residential development would be strongly localised near to shore. Indeed, we found striking differences between developed and undeveloped sites in periphyton and associated organic matter, though there were no offshore signals of human impact in water nutrient analysis or paleolimnological investigations. Together, these results suggest that nearshore biological monitoring should be integrated in lake management plans to provide ‘early warning’ of potential food-web repercussions before pollution problems are evident in open water and comparatively intractable.
Sessile biofouling on tags from recaptured raggedtooth sharks (Carcharias taurus) and their effects on tagging studies
Authors: Dicken M. L. , Nance S. Parker , Smale M. J.
Published: April 2011

Biofouling of external tags can damage both the animal and the tag. It is an inherent problem to many fish-tagging studies; however, it has received little attention. Between 2005 and 2007, we investigated the taxonomic group and wet weight of sessile multicellular eukaryonts growing on 33 B-type dart tags recaptured from raggedtooth sharks (Carcharias taurus Rafinesque, 1810) along the eastern coast of South Africa. All tags, except one from a shark that had been at liberty only for 13 days, contained some degree of macro-fouling that ranged from 0.031 to 7.687 g wet weight. Barnacles and hydroids were the first colonisers and were recorded on tags after only 47 days. Bivalves, polychaetes and algae succeeded within 60 days. The last two taxa to be recorded were ascidians and sponges. There was no significant relationship between either the biomass of sessile organisms (P = 0.17) or the number of taxa (P = 0.59) found growing on tags and their time at liberty. Calcium carbonate plugs, ranging in weight from 0.16 to 9.18 g, were found at the site of the tag insertion wound on 27.3% of recaptures. The present study highlights the extent of biofouling growth on tags and its potential to bias results from tagging studies.
Zoosporic true fungi in marine ecosystems: a review
Authors: Gleason Frank H. , Küpper Frithjof C. , Amon James P. , Picard Kathryn , Gachon Claire M. M. , Marano Agostina V. , Sime-Ngando Télesphore , Lilje Osu
Published: April 2011

Although many species of zoosporic true fungi have been frequently observed and studied in freshwater and soil ecosystems, only three species have been properly identified and partially characterised from brackish and marine ecosystems, namely Rhizophydium littoreum Amon, Thalassochytrium gracilariopsis Nyvall, Pedersén et Longcore and Chytridium polysiphoniae Cohn. These species are either facultative or obligate parasites of marine macroalgae and invertebrates. Also, some species of Olpidium and Rhizophydium are parasites of small marine green algae and diatoms. Although the physiological effects of these pathogens on the growth and metabolism of their hosts are poorly understood, parasitism by C. polysiphoniae possibly affects the rates of photosynthesis and patterns of growth in infected communities of brown algae. Saprobic ecotypes of R. littoreum can also colonise dead-plant and animal substrates. Zoospores from zoosporic true fungi and other groups of microbes possibly provide important food resources for grazing and filter-feeding zooplankton and metazoans in marine ecosystems where the prevalence of disease is high or where accumulated detritus enhances biodiversity in food webs. However, quantitative studies have not yet been attempted. Recently, environmental sampling with molecular techniques has revealed unknown clades of zoosporic true fungi in extreme marine ecosystems. These fungi have been grossly under-sampled and under-studied in marine environments.
Response of stream invertebrate communities to vegetation damage from overgrazing by exotic rabbits on subantarctic Macquarie Island
Authors: Marchant R. , Kefford B. J. , Wasley J. , King C. K. , Doube J. , Nugegoda D.
Published: April 2011

Widespread damage to vegetation on an isolated oceanic island (Macquarie Island), due to overgrazing (since 2002) by an expanding exotic rabbit population, could affect the nature of catchment runoff and result in changes to stream habitats and the composition of their invertebrate communities. To test this hypothesis, stream invertebrate communities that had been sampled originally in 1992 (at 15 sites when rabbit numbers were historically low), were re-sampled in 2008 (17 sites) and in 2010 (12 sites). The number of taxa recorded at each site was 25–36% lower in 2008 (7.4 taxa per site) and in 2010 (8.7 taxa) than in 1992 (11.6 taxa) and an abundance index showed a substantial decline across most taxa. Ordination indicated that composition at all sites changed markedly between years. The greatest compositional changes occurred at sites exposed to moderate or severe levels of vegetation damage, suggesting that stream invertebrates responded to habitat changes associated with increased grazing. An altered input of organic material into the streams as a result of vegetation damage may have been responsible. If communities of stream invertebrates on isolated islands are degraded, then composition may be altered permanently, unless refuges are available.
Nitrososphaera viennensis
, an ammonia oxidizing archaeon from soil
Authors: Tourna Maria , Stieglmeier Michaela , Spang Anja , Könneke Martin , Schintlmeister Arno , Urich Tim , Engel Marion , Schloter Michael , Wagner Michael , Richter Andreas , Schleper Christa
Published: April 2011

Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate,
Nitrosopumilus maritimus
. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.
Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors
Authors: Li Wenlin , Sun Woong , Zhang Yu , Wei Wanguo , Ambasudhan Rajesh , Xia Peng , Talantova Maria , Lin Tongxiang , Kim Janghwan , Wang Xiaolei , Kim Woon Ryoung , Lipton Stuart A. , Zhang Kang , Ding Sheng
Published: April 2011

Human embryonic stem cells (hESCs) hold enormous promise for regenerative medicine. Typically, hESC-based applications would require their in vitro differentiation into a desirable homogenous cell population. A major challenge of the current hESC differentiation paradigm is the inability to effectively capture and, in the long-term, stably expand primitive lineage-specific stem/precursor cells that retain broad differentiation potential and, more importantly, developmental stage-specific differentiation propensity. Here, we report synergistic inhibition of glycogen synthase kinase 3 (GSK3), transforming growth factor β (TGF-β), and Notch signaling pathways by small molecules can efficiently convert monolayer cultured hESCs into homogenous primitive neuroepithelium within 1 wk under chemically defined condition. These primitive neuroepithelia can stably self-renew in the presence of leukemia inhibitory factor, GSK3 inhibitor (CHIR99021), and TGF-β receptor inhibitor (SB431542); retain high neurogenic potential and responsiveness to instructive neural patterning cues toward midbrain and hindbrain neuronal subtypes; and exhibit in vivo integration. Our work uniformly captures and maintains primitive neural stem cells from hESCs.
Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird
Authors: Bonneaud Camille , Balenger Susan L. , Russell Andrew F. , Zhang Jiangwen , Hill Geoffrey E. , Edwards Scott V.
Published: April 2011

Wild organisms are under increasing pressure to adapt rapidly to environmental changes. Predicting the impact of these changes on natural populations requires an understanding of the speed with which adaptive phenotypes can arise and spread, as well as of the underlying mechanisms. However, our understanding of these parameters is poor in natural populations. Here we use experimental and molecular approaches to investigate the recent emergence of resistance in eastern populations of North American house finches (
Carpodacus mexicanus
) to
Mycoplasma galliseptum
(MG), a severe conjunctivitis-causing bacterium. Two weeks following an experimental infection that took place in 2007, finches from eastern US populations with a 12-y history of exposure to MG harbored 33% lower MG loads in their conjunctivae than finches from western US populations with no prior exposure to MG. Using a cDNA microarray, we show that this phenotypic difference in resistance was associated with differences in splenic gene expression, with finches from the exposed populations up-regulating immune genes postinfection and those from the unexposed populations generally down-regulating them. The expression response of western US birds to experimental infection in 2007 was more similar to that of the eastern US birds studied in 2000, 7 y earlier in the epizootic, than to that of eastern birds in 2007. These results support the hypothesis that resistance has evolved by natural selection in the exposed populations over the 12 y of the epizootic. We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation.
Electron delocalization in the
S
1
and
T
1
metal-to-ligand charge transfer states of
trans
-substituted metal quadruply bonded complexes
Authors: Alberding Brian G. , Chisholm Malcolm H. , Gallucci Judith C. , Ghosh Yagnaseni , Gustafson Terry L.
Published: April 2011

The singlet
S
1
and triplet
T
1
photoexcited states of the compounds containing MM quadruple bonds
trans
-M
2
(T

i

PB)
2
(O
2
CC
6
H
4
-4-CN)
2
, where T

i

PB = 2,4,6-triisopropylbenzoate and M = Mo (
I
) or M = W (
I
′
), and
trans
-M
2
(O
2
CMe)
2
((N[

i

 Pr ])
2
CC ≡ CC
6
H
5
)
2
, where M = Mo (
II
) and M = W (
II
′
), have been investigated by a variety of spectroscopic techniques including femtosecond time-resolved infrared spectroscopy. The singlet states are shown to be delocalized metal-to-ligand charge transfer (MLCT) states for
I
and
I
′
but localized for
II
and
II
′
involving the cyanobenzoate or amidinate ligands, respectively. The triplet states are MoMo
δδ
* for both
I
and
II
but delocalized
3
MLCT for
I
′
and localized
3
MLCT for
II
′
. These differences arise from consideration of the relative orbital energies of the M
2
δ
or M
2
δ
* and the ligand
π
∗
as well as the magnitudes of orbital overlap.
Heat shock protein 90 from
Escherichia coli
collaborates with the DnaK chaperone system in client protein remodeling
Authors: Genest Olivier , Hoskins Joel R. , Camberg Jodi L. , Doyle Shannon M. , Wickner Sue
Published: April 2011

Molecular chaperones are proteins that assist the folding, unfolding, and remodeling of other proteins. In eukaryotes, heat shock protein 90 (Hsp90) proteins are essential ATP-dependent molecular chaperones that remodel and activate hundreds of client proteins with the assistance of cochaperones. In
Escherichia coli
, the activity of the Hsp90 homolog, HtpG, has remained elusive. To explore the mechanism of action of
E. coli
Hsp90, we used in vitro protein reactivation assays. We found that
E. coli
Hsp90 promotes reactivation of heat-inactivated luciferase in a reaction that requires the prokaryotic Hsp70 chaperone system, known as the DnaK system. An Hsp90 ATPase inhibitor, geldanamycin, inhibits luciferase reactivation demonstrating the importance of the ATP-dependent chaperone activity of
E. coli
Hsp90 during client protein remodeling. Reactivation also depends upon the ATP-dependent chaperone activity of the DnaK system. Our results suggest that the DnaK system acts first on the client protein, and then
E. coli
Hsp90 and the DnaK system collaborate synergistically to complete remodeling of the client protein. Results indicate that
E. coli
Hsp90 and DnaK interact in vivo and in vitro, providing additional evidence to suggest that
E. coli
Hsp90 and the DnaK system function together.
Acetylation of lysine 120 of p53 endows DNA-binding specificity at effective physiological salt concentration
Authors: Arbely Eyal , Natan Eviatar , Brandt Tobias , Allen Mark D. , Veprintsev Dmitry B. , Robinson Carol V. , Chin Jason W. , Joerger Andreas C. , Fersht Alan R.
Published: April 2011

Lys120 in the DNA-binding domain (DBD) of p53 becomes acetylated in response to DNA damage. But, the role and effects of acetylation are obscure. We prepared p53 specifically acetylated at Lys120, AcK120p53, by in vivo incorporation of acetylated lysine to study biophysical and structural consequences of acetylation that may shed light on its biological role. Acetylation had no affect on the overall crystal structure of the DBD at 1.9-Å resolution, but significantly altered the effects of salt concentration on specificity of DNA binding. p53 binds DNA randomly in vitro at effective physiological salt concentration and does not bind specifically to DNA or distinguish among its different response elements until higher salt concentrations. But, on acetylation, AcK120p53 exhibited specific DNA binding and discriminated among response elements at effective physiological salt concentration. AcK120p53 and p53 had the highest affinity to the same DNA sequence, although acetylation reduced the importance of the consensus C and G at positions 4 and 7, respectively. Mass spectrometry of p53 and AcK120p53 DBDs bound to DNA showed they preferentially segregated into complexes that were either DNA(p53DBD)
4
or DNA(AcK120DBD)
4
, indicating that the different DBDs prefer different quaternary structures. These results are consistent with electron microscopy observations that p53 binds to nonspecific DNA in different, relaxed, quaternary states from those bound to specific sequences. Evidence is accumulating that p53 can be sequestered by random DNA, and target search requires acetylation of Lys120 and/or interaction with other factors to impose specificity of binding via modulating changes in quaternary structure.
Better Elementary Number Processing in Higher Skill Arithmetic Problem Solvers: Evidence from the Encoding Step
Authors: Thevenot Catherine , Barrouillet Pierre , Castel Caroline , Jimenez Sonia
Published: April 2011

This paper addresses the relationship between basic numerical processes and higher level numerical abilities in normal achieving adults. In the first experiment we inferred the elementary numerical abilities of university students from the time they needed to encode numerical information involved in complex additions and subtractions. We interpreted the shorter encoding times in good arithmetic problem solvers as revealing clearer or more accessible representations of numbers. The second experiment shows that these results cannot be due to the fact that lower skilled individuals experience more maths anxiety or put more cognitive efforts into calculations than do higher skilled individuals. Moreover, the third experiment involving non-numerical information supports the hypothesis that these interindividual differences are specific to number processing. The possible causal relationships between basic and higher level numerical abilities are discussed.
Towards a reduced chemistry module of a He–Ar–Cu hollow cathode discharge
Authors: Mihailova D , van Dijk J , Grozeva M , Degrez G , van der Mullen J J A M
Published: April 2011

This study is aimed at finding a reduced chemistry module for a hollow cathode discharge (HCD) excited in a He–Ar–Cu mixture. This enables us to construct lean and reliable models that can be used as a part of the design tool of HCDs. To this end estimative calculations and numerical simulations are performed under optimal conditions for lasing. An analysis of the species behaviour and reactions is made and as a result the model is simplified by means of reducing the number of species and reactions. The consequences of these reductions are justified by comparing the results of the simplified models with those of a more complete one. This study delivers a model that is chemically lean and thus, much less time consuming. It can be used in optimization studies to find the optimum in the plasma control parameter set of HCDs. The technique developed in this study for HCDs can be applied to glow discharges in general.
Modelling and simulation of unsteady dc electric arcs and their interactions with electrodes
Authors: Chemartin L , Lalande P , Delalondre C , Cheron B , Lago F
Published: April 2011

This paper is devoted to the study of unsteady electric arcs and the effects of electrodes on their dynamics. One of the objectives is to simulate and understand the three-dimensional behaviour of arcs in complex geometries, which create important fluctuations of the column and reattachments on the electrodes. The usual methods to solve the problem of arc–electrodes coupling are not suitable to simulate three-dimensional unsteady arcs. We propose a numerical development to simulate both steady-state and unsteady arcs without additional assumptions. The method is based on the incorporation of electrodes into the computational domain. It is validated with measurements from the literature, in the case of a point–plane steady-state argon arc. The model is used to study the lightning certification test device, which simulates in laboratory the effects of lightning arcs on fuselage panels. The results bring to light, in agreement with the observations in laboratory, the fundamental role of the electrodes on the three-dimensional behaviour of the arc column. The model is also used to simulate the development of the free jet of a plasma on an aluminium planar anode. The objective is to characterize the interaction region and the thermal constraint of the arc.
Comparison of coupling techniques in a high-order discontinuous Galerkin-based particle-in-cell solver
Authors: Stindl T , Neudorfer J , Stock A , Auweter-Kurtz M , Munz C-D , Roller S , Schneider R
Published: April 2011

Highly rarefied plasma flows in technical devices are physically modelled by the Maxwell–Lorentz equations. They combine the solution of the Maxwell equations, where the electric field E and magnetic induction B are determined, with the Lorentz system, accounting for the movement of charged particles due to the electromagnetic forces. To solve these equations for complex-shaped domains, a fully electromagnetic particle-in-cell (PIC) code has been developed using high-order discontinuous Galerkin methods for the Maxwell equations on a computational mesh, coupled with a Lorentz solver on the basis of a second-order leapfrog scheme, acting on the particles at their current positions. Since the particles move freely in space, the mesh-based and the mesh-free values have to be coupled. This coupling includes the deposition of the charge and current densities from the current particle positions onto the mesh as well as the interpolation of the electromagnetic fields from the mesh to the actual particle positions. Both steps have to be computed with appropriate accuracy. Different approaches to particle-grid coupling within the PIC solver have been investigated. In this paper, these concepts are described and corresponding simulation results with respect to accuracy and computational demand are presented.
Comparative study of plasma-deposited fluorocarbon coatings on different substrates
Authors: Farsari E , Kostopoulou M , Amanatides E , Mataras D , Rapakoulias D E
Published: April 2011

The deposition of hydrophobic fluorocarbon coatings from C2F6 and C2F6–H2 rf discharges on different substrates was examined. Polyester textile, glass and two different ceramic compounds were used as substrates. The effect of the total gas pressure, the rf power dissipation and the deposition time on the hydrophobic character of the samples was investigated. Films deposited on polyester textiles at low pressure (0.03 mbar) and power consumption (16 mW cm−2) using pure C2F6 presented the highest water contact angles (∼150°). On the other hand, the addition of hydrogen was necessary in order to deposit stable hydrophobic coatings on glass and ceramic substrates. Coatings deposited on glass at intermediate deposition rates (∼100 Å min−1) and pressures presented the highest angles (∼105°). Concerning the heavy clay ceramics, samples treated in low-pressure (0.05 mbar) and low-power (16 mW cm−2) discharges showed the highest contact angles. The deposition time was found to play an important role in the hydrophobicity and long-term behaviour of porous and rough substrates.
A self-consistent three-dimensional model of the arc, electrode and weld pool in gas–metal arc welding
Authors: Murphy Anthony B
Published: April 2011

The development of a three-dimensional computational model of gas–metal arc welding is described. The wire electrode, arc plasma and weld pool are included in the computational domain self-consistently. The model takes into account the motion of the electrode, flow in the weld pool, deformation of the weld-pool surface and the influence of metal droplet transfer. Results are presented for welding of an aluminium alloy. The current density distribution at the interface between the arc and the weld pool is strongly dependent on the surface profile of the weld pool. This in turn affects the temperature distribution in the weld pool. The momentum transferred by the droplet affects the direction of flow in the weld pool, and together with the energy transfer, increases the weld-pool depth. The results demonstrate the importance of including the arc plasma in the computational domain. Fair agreement is found between a measured weld profile and the predictions of the model. Inclusion of the influence of metal vapour in the model is expected to improve the agreement.
Plasma diagnostics using the He I 447.1 nm line at high and low densities
Authors: González Manuel Á , Ivković Milivoje , Gigosos Marco A , Jovićević Sonja , Lara Natividad , Konjević Nikola
Published: April 2011

The broadening of the He I 447.1 nm line and its forbidden components in plasmas is studied using computer simulation techniques and the results are compared with our and other experiments. In these calculations wide ranges of electron densities and temperatures are considered. Experimental measurements are performed with a high electron density pulsed discharge and with a low electron density microwave torch at atmospheric pressure. Both calculations and experimental measurements are extended from previous works towards low electron densities in order to study the accuracy of plasma diagnostics using this line in ranges of interest in different practical applications. The calculation results are compared with experimental profiles registered in plasmas diagnosed using independent techniques. The obtained agreement justifies the use of these line parameters for plasma diagnostics. The influence of self-absorption on line parameters is also analysed. It is shown that the separation between the peaks of the allowed and forbidden components exhibits a clear dependence upon plasma electron density free of self-absorption influence. This allows the peak separation to be used as a good parameter for plasma diagnostics. From the simulation results, a simple fitting formula is applied that permits obtaining the electron number density plasma diagnostics in the range 5 × 1022–7 × 1023 m−3. At lower densities the fitting of simulated to experimental full profiles is a reliable method for N
e determination.
STARDUST experimental campaign and numerical simulations: influence of obstacles and temperature on dust resuspension in a vacuum vessel under LOVA
Authors: Bellecci C. , Gaudio P. , Lupelli I. , Malizia A. , Porfiri M.T. , Quaranta R. , Richetta M.
Published: April 2011

Activated dust mobilization during a Loss of Vacuum Accident (LOVA) is one of the safety concerns for the International Thermonuclear Experimental Reactor (ITER). Intense thermal loads in fusion devices occur during plasma disruptions, edge localized modes and vertical displacement events. They will result in macroscopic erosion of the plasma facing materials and consequent accumulation of activated dust into the ITER vacuum vessel (VV). These kinds of events can cause dust leakage outside the VV that represents a high radiological risk for the workers and the population. A small facility, Small Tank for Aerosol Removal and Dust (STARDUST), was set up at the ENEA Frascati laboratories to perform experiments concerning the dust mobilization in a volume with the initial conditions similar to those existing in ITER VV. The aim of this work was to reproduce a low pressurization rate (300 Pa s−1) LOVA event in a VV due to a small air leakage for two different positions of the leak, at the equatorial port level and at the divertor port level, in order to evaluate the influence of obstacles and walls temperature on dust resuspension during both maintenance (MC) and accident conditions (AC) (T
walls = 25 °C MC, 110 °C AC). The dusts used were tungsten (W), stainless steel 316 (SS316) and carbon (C), similar to those produced inside the vacuum chamber in a fusion reactor when the plasma facing materials vaporize due to the high energy deposition. The experimental campaign has been carried out by introducing inside STARDUST facility an obstacle to simulate the presence of objects, such as divertor. In the obstacle a slit was cut to simulate the limiter–divertor gap inside ITER VV. In this paper experimental campaign results are shown in order to investigate how the divertor and limiter–divertor gap influence dust mobilization into a VV. A two-dimensional (2D) modelling of STARDUST was made using the CFD commercial code FLUENT, in order to get a preliminary overview of the fluid dynamics behaviour during a LOVA event and to justify the mobilization data. In addition, a numerical model was developed to compare numerical results with experimental ones.
The role of spatial and temporal radiation deposition in inertial fusion chambers: the case of HiPER
Authors: Alvarez J. , Garoz D. , Gonzalez-Arrabal R. , Rivera A. , Perlado M.
Published: April 2011

The first wall armour for the reactor chamber of HiPER will have to face short energy pulses of 5 to 20 MJ mostly in the form of x-rays and charged particles at a repetition rate of 5–10 Hz. Armour material and chamber dimensions have to be chosen to avoid/minimize damage to the chamber, ensuring the proper functioning of the facility during its planned lifetime. The maximum energy fluence that the armour can withstand without risk of failure, is determined by temporal and spatial deposition of the radiation energy inside the material. In this paper, simulations on the thermal effect of the radiation–armour interaction are carried out with an increasing definition of the temporal and spatial deposition of energy to prove their influence on the final results. These calculations will lead us to present the first values of the thermo-mechanical behaviour of the tungsten armour designed for the HiPER project under a shock ignition target of 48 MJ. The results will show that only the crossing of the plasticity limit in the first few micrometres might be a threat after thousands of shots for the survivability of the armour.
Multi-scale MHD analysis incorporating pressure transport equation for beta-increasing LHD plasma
Authors: Ichiguchi Katsuji , Carreras Benjamin A.
Published: April 2011

A multi-scale MHD numerical scheme is developed for analysis of nonlinear evolution of a beta-increasing plasma. The scheme is based on iterative calculations of nonlinear dynamics based on the reduced MHD (RMHD) equations and three-dimensional static equilibrium. The equation for average pressure in the RMHD equations plays the role of a transport equation that involves a heat source term and background pressure diffusion terms. The heat source term is controlled so that the beta value should be increased at a constant rate. The scheme is applied to a Large Helical Device (LHD) plasma up to average beta of 1.05%, which is unstable against linear ideal interchange modes while beta values much higher than the stability limit are obtained in the experiments. The result with the multi-scale scheme indicates that many local flat regions are generated in the background pressure profile in the nonlinear evolution of the interchange modes. This structure of the pressure profile suppresses disruptive phenomena because it reduces the driving force of the modes at higher beta value. Such self-organization in the pressure profile is considered to be the stabilizing mechanism in the plasma.
On empty lattice simplices in dimension 4
Authors: Barile Margherita , Bernardi Dominique , Borisov Alexander , Kantor Jean-Michel
Published: April 2011

We give an almost complete classification of empty lattice simplices in dimension 4 using the conjectural results of Mori-Morrison-Morrison, which were later proved by Sankaran and Bober. In particular, all of these simplices correspond to cyclic quotient singularities, and all but finitely many of them have width bounded by 2.
Derived equivalence induced by infinitely generated 𝑛-tilting modules
Authors: Bazzoni Silvana , Mantese Francesca , Tonolo Alberto
Published: April 2011

Let

T
R

T_R

be a right

n
n

-tilting module over an arbitrary associative ring

R
R

. In this paper we prove that there exists an

n
n

-tilting module

T
R
′

T’_R

equivalent to

T
R

T_R

which induces a derived equivalence between the unbounded derived category

D

(
R
)

\mathcal {D}(R)

and a triangulated subcategory

E

⊥

\mathcal E_{\perp }

of

D

(
End
⁡
(

T
′

)
)

\mathcal {D}(\operatorname {End}(T’))

equivalent to the quotient category of

D

(
End
⁡
(

T
′

)
)

\mathcal {D}(\operatorname {End}(T’))

modulo the kernel of the total left derived functor

−

⊗

S
′

L

T
′

-\otimes ^{\mathbb L}_{S’}T’

. If

T
R

T_R

is a classical

n
n

-tilting module, we have that

T
=

T
′

T=T’

and the subcategory

E

⊥

\mathcal E_{\perp }

coincides with

D

(
End
⁡

|

(
T
)
)

\mathcal {D}(\operatorname {End}|(T))

, recovering the classical case.
C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking
Authors: Scrivens P. James , Noueihed Baraa , Shahrzad Nassim , Hul Sokunthear , Brunet Stephanie , Sacher Michael
Published: April 2011

TRAPP is a multisubunit tethering complex implicated in multiple vesicle trafficking steps in Saccharomyces cerevisiae and conserved throughout eukarya, including humans. Here we confirm the role of TRAPPC2L as a stable component of mammalian TRAPP and report the identification of four novel components of the complex: C4orf41, TTC-15, KIAA1012, and Bet3L. Two of the components, KIAA1012 and Bet3L, are mammalian homologues of Trs85p and Bet3p, respectively. The remaining two novel TRAPP components, C4orf41 and TTC-15, have no homologues in S. cerevisiae. With this work, human homologues of all the S. cerevisiae TRAPP proteins, with the exception of the Saccharomycotina-specific subunit Trs65p, have now been reported. Through a multidisciplinary approach, we demonstrate that the novel proteins are bona fide components of human TRAPP and implicate C4orf41 and TTC-15 (which we call TRAPPC11 and TRAPPC12, respectively) in ER-to-Golgi trafficking at a very early stage. We further present a binary interaction map for all known mammalian TRAPP components and evidence that TRAPP oligomerizes. Our data are consistent with the absence of a TRAPP I–equivalent complex in mammalian cells, suggesting that the fundamental unit of mammalian TRAPP is distinct from that characterized in S. cerevisiae.
The LC3 recruitment mechanism is separate from Atg9L1-dependent membrane formation in the autophagic response againstSalmonella
Authors: Kageyama Shun , Omori Hiroko , Saitoh Tatsuya , Sone Takefumi , Guan Jun-Lin , Akira Shizuo , Imamoto Fumio , Noda Takeshi , Yoshimori Tamotsu
Published: April 2011

Salmonella develops into resident bacteria in epithelial cells, and the autophagic machinery (Atg) is thought to play an important role in this process. In this paper, we show that an autophagosome-like double-membrane structure surrounds the Salmonella still residing within the Salmonella-containing vacuole (SCV). This double membrane is defective in Atg9L1- and FAK family-interacting protein of 200 kDa (FIP200)-deficient cells. Atg9L1 and FIP200 are important for autophagy-specific recruitment of the phosphatidylinositol 3-kinase (PI3K) complex. However, in the absence of Atg9L1, FIP200, and the PI3K complex, LC3 and its E3-like enzyme, the Atg16L complex, are still recruited to Salmonella. We propose that the LC3 system is recruited through a mechanism that is independent of isolation membrane generation.
Mitochondrial protein turnover: role of the precursor intermediate peptidase Oct1 in protein stabilization
Authors: Vögtle F.-Nora , Prinz Claudia , Kellermann Josef , Lottspeich Friedrich , Pfanner Nikolaus , Meisinger Chris
Published: April 2011

Most mitochondrial proteins are encoded in the nucleus as precursor proteins and carry N-terminal presequences for import into the organelle. The vast majority of presequences are proteolytically removed by the mitochondrial processing peptidase (MPP) localized in the matrix. A subset of precursors with a characteristic amino acid motif is additionally processed by the mitochondrial intermediate peptidase (MIP) octapeptidyl aminopeptidase 1 (Oct1), which removes an octapeptide from the N-terminus of the precursor intermediate. However, the function of this second cleavage step is elusive. In this paper, we report the identification of a novel Oct1 substrate protein with an unusual cleavage motif. Inspection of the Oct1 substrates revealed that the N-termini of the intermediates typically carry a destabilizing amino acid residue according to the N-end rule of protein degradation, whereas mature proteins carry stabilizing N-terminal residues. We compared the stability of intermediate and mature forms of Oct1 substrate proteins in organello and in vivo and found that Oct1 cleavage increases the half-life of its substrate proteins, most likely by removing destabilizing amino acids at the intermediate's N-terminus. Thus Oct1 converts unstable precursor intermediates generated by MPP into stable mature proteins.