bluuebunny/crossref_metadata_2025 huggingface dataset:
Operation Request Gatekeeper: A software system for remote access control of diagnostic instruments in fusion experiments
Authors: Abla G. , Fredian T. W. , Schissel D. P. , Stillerman J. A. , Greenwald M. J. , Stepanov D. N. , Ciarlette D. J.
Published: October 2010

Tokamak diagnostic settings are repeatedly modified to meet the changing needs of each experiment. Enabling the remote diagnostic control has significant challenges due to security and efficiency requirements. The Operation Request Gatekeeper (ORG) is a software system that addresses the challenges of remotely but securely submitting modification requests. The ORG provides a framework for screening all the requests before they enter the secure machine zone and are executed by performing user authentication and authorization, grammar validation, and validity checks. A prototype ORG was developed for the ITER CODAC that satisfies their initial requirements for remote request submission and has been tested with remote control of the KSTAR Plasma Control System. This paper describes the software design principles and implementation of ORG as well as worldwide test results.
Prediction of a structural transition in the hard disk fluid
Authors: Piasecki Jarosław , Szymczak Piotr , Kozak John J.
Published: October 2010

Starting from the second equilibrium equation in the BBGKY hierarchy under the Kirkwood superposition closure, we implement a new method for studying the asymptotic decay of correlations in the hard disk fluid in the high density regime. From our analysis and complementary numerical studies, we find that exponentially damped oscillations can occur only up to a packing fraction η∗∼0.718, a value that is in substantial agreement with the packing fraction, η∼0.723, believed to characterize the transition from the ordered solid phase to a dense fluid phase, as inferred from Mak’s Monte Carlo simulations [Phys. Rev. E 73, 065104 (2006)]. Next, we show that the same method of analysis predicts that the exponential damping of oscillations in the hard sphere fluid becomes impossible when λ=4nπσ3[1+H(1)]≥34.81, where H(1) is the contact value of the correlation function, n is the number density, and σ is the sphere diameter in exact agreement with the condition, λ≥34.8, which is first reported in a numerical study of the Kirkwood equation by Kirkwood et al. [J. Chem. Phys. 18, 1040 (1950)]. Finally, we show that our method confirms the absence of any structural transition in hard rods for the entire range of densities below close packing.
High speed digital holography for density and fluctuation measurements (invited)
Authors: Thomas C. E. , Baylor L. R. , Combs S. K. , Meitner S. J. , Rasmussen D. A. , Granstedt E. M. , Majeski R. P. , Kaita R.
Published: October 2010

The state of the art in electro-optics has advanced to the point where digital holographic acquisition of wavefronts is now possible. Holographic wavefront acquisition provides the phase of the wavefront at every measurement point. This can be done with accuracy on the order of a thousandth of a wavelength, given that there is sufficient care in the design of the system. At wave frequencies which are much greater than the plasma frequency, the plasma index of refraction is linearly proportional to the electron density and wavelength, and the measurement of the phase of a wavefront passing through the plasma gives the chord-integrated density directly for all points measured on the wavefront. High-speed infrared cameras (up to ∼40 000 fps at ∼64×4 pixels) with resolutions up to 640×512 pixels suitable for use with a CO2 laser are readily available, if expensive.
Reinforcing multiwall carbon nanotubes by electron beam irradiation
Authors: Duchamp Martial , Meunier Richard , Smajda Rita , Mionic Marijana , Magrez Arnaud , Seo Jin Won , Forró László , Song Bo , Tománek David
Published: October 2010

We study the effect of electron beam irradiation on the bending modulus of multiwall carbon nanotubes grown by chemical vapor deposition. Atomic force microscopy observations of the nanotube deflection in the suspended-beam geometry suggest an internal, reversible stick-slip motion prior to irradiation, indicating presence of extended defects. Upon electron beam irradiation, nanotubes with an initial bending modulus exceeding 10 GPa initially get stiffer, before softening at high doses. Highly defective nanotubes with smaller initial bending moduli do not exhibit the initial reinforcement. These data are explained by ab initio molecular dynamics calculations suggesting a spontaneous cross-linking of neighboring nanotube walls at extended vacancy defects created by the electron beam, in agreement with electron microscopy observations. At low defect concentration, depending on the edge morphology, the covalent bonds between neighboring nanotube walls cause reinforcement by resisting relative motion of neighboring walls. At high concentration of defects that are present initially or induced by high electron beam dose, the structural integrity of the entire system suffers from increasing electron beam damage.
Path integral based calculations of symmetrized time correlation functions. II
Authors: Bonella S. , Monteferrante M. , Pierleoni C. , Ciccotti G.
Published: October 2010

Schofield’s form of quantum time correlation functions is used as the starting point to derive a computable expression for these quantities. The time composition property of the propagators in complex time is exploited to approximate Schofield’s function in terms of a sequence of short time classical propagations interspersed with path integrals that, combined, represent the thermal density of the system. The approximation amounts to linearization of the real time propagators and it becomes exact with increasing number of propagation legs. Within this scheme, the correlation function is interpreted as an expectation value over a probability density defined on the thermal and real path space and calculated by a Monte Carlo algorithm. The performance of the algorithm is tested on a set of benchmark problems. Although the numerical effort required is considerable, we show that the algorithm converges systematically to the exact answer with increasing number of iterations and that it is stable for times longer than those accessible via a brute force, path integral based, calculation of the correlation function. Scaling of the algorithm with dimensionality is also examined and, when the method is combined with commonly used filtering schemes, found to be comparable to that of alternative semiclassical methods.
Optical cavity modes in semicurved Fabry–Pérot resonators
Authors: Mornet Stéphane , Teule-Gay Lionel , Talaga David , Ravaine Serge , Vallée Renaud A. L.
Published: October 2010

We present a nanofabrication method which combines bottom-up and top-down techniques to realize nanosized curved Fabry–Pérot cavities. These cavities are made of a hexagonal closed packed monolayer of silica particles enclosed between flat and curved metallic mirrors. They exhibit geometric cavity modes such as those found in gold shell colloids. These modes manifest as dips in the reflection spectra which shift as a function of the diameter of the used nanoparticles. An excellent agreement is found between experiment and theory which allows us to properly interpret our data. The work presented here constitutes a further step to the development of curved photonics.
Breakup control of a liquid jet by disturbance manipulation
Authors: Rohani Mina , Jabbari Faryar , Dunn-Rankin Derek
Published: October 2010

In this paper, we study the breakup of a circular jet subject to a manipulated disturbance applied by an actuator (here a piezoelectric) in order to control droplets sizes and patterns over a wide range. According to previous studies, breakup of a jet is strongly affected by the characteristics of the disturbance. When the breakup is not periodic and repeatable, it is described as an irregular or random breakup. On the other hand, over a frequency range for the disturbance, the breakup can be made repeatable, though not necessarily uniform, in which the droplets pinch off the stream at a constant rate. In this case, the breakup is called regular, although satellites or secondary droplets might form among the main droplets. In most applications, a very narrow frequency range (much narrower than the regular breakup frequency range) is used for operation, since it is the only range where uniform droplets form. This work demonstrates that by eliminating secondary droplets or satellites, the entire regular breakup regime becomes available for desirable operation, i.e., uniform droplet generation. The regular breakup regime is specified experimentally and an additional disturbance is added to the driving disturbance in order to eliminate the nonuniform droplets. This method provides us with droplets of the desired size when they cannot be produced with a single frequency disturbance alone. The results also demonstrate that different frequencies for the additional disturbance produce different patterns for the droplets sizes.
Thomson scattering diagnostic upgrade on DIII-D
Authors: Ponce-Marquez D. M. , Bray B. D. , Deterly T. M. , Liu C. , Eldon D.
Published: October 2010

The DIII-D Thomson scattering system has been upgraded. A new data acquisition hardware was installed, adding the capacity for additional spatial channels and longer acquisition times for temperature and density measurements. Detector modules were replaced with faster transimpedance circuitry, increasing the signal-to-noise ratio by a factor of 2. This allows for future expansion to the edge system. A second phase upgrade scheduled for 2010–2011 includes the installation of four 1 J/pulse Nd:YAG lasers at 50 Hz repetition rate. This paper presents the first completed phase of the upgrade and performance comparison between the original system and the upgraded system. The plan for the second phase is also presented.
Development and application of setup for ac magnetic field in neutron scattering experiments
Authors: Klimko Sergey , Zhernenkov Kirill , Toperverg Boris P. , Zabel Hartmut
Published: October 2010

We report on a new setup developed for neutron scattering experiments in periodically alternating magnetic fields at the sample position. The assembly consisting of rf generator, amplifier, wide band transformer, and resonance circuit. It allows to generate homogeneous ac magnetic fields over a volume of a few cm3 and variable within a wide range of amplitudes and frequencies. The applicability of the device is exemplified by ac polarized neutron reflectometry (PNR): a new method established to probe remagnetization kinetics in soft ferromagnetic films. Test experiments with iron films demonstrate that the ac field within the accessible range of frequencies and amplitudes produces a dramatic effect on the PNR signal. This shows that the relevant ac field parameters generated by the device match well with the scales involved in the remagnetization processes. Other possible applications of the rf unit are briefly discussed.
The response of a fast phosphor screen scintillator (ZnO:Ga) to low energy ions (0–60 keV)
Authors: Jiménez-Rey D. , Zurro B. , Rodríguez-Barquero L. , Baciero A. , Navarro M.
Published: October 2010

ZnO:Ga is a promising, high time resolution candidate for use as a fast-ion-loss detector in TJ-II. We compare its ionoluminescence with that of the standard fast-ion-loss detector material, SrGa2S4:Eu (also known as TG-Green), when irradiated by H+ ions with a range of energies E≤60 keV using a dedicated laboratory setup. It is found that ZnO:Ga is a reasonably good candidate for detecting low energy (E<60 keV) ions as it has excellent time resolution; however, its sensitivity is about 100 times lower than TG-Green, potentially limiting it to applications with high energy ion loss signals.
Standard design for National Ignition Facility x-ray streak and framing cameras
Authors: Kimbrough J. R. , Bell P. M. , Bradley D. K. , Holder J. P. , Kalantar D. K. , MacPhee A. G. , Telford S.
Published: October 2010

The x-ray streak camera and x-ray framing camera for the National Ignition Facility were redesigned to improve electromagnetic pulse hardening, protect high voltage circuits from pressure transients, and maximize the use of common parts and operational software. Both instruments use the same PC104 based controller, interface, power supply, charge coupled device camera, protective hermetically sealed housing, and mechanical interfaces. Communication is over fiber optics with identical facility hardware for both instruments. Each has three triggers that can be either fiber optic or coax. High voltage protection consists of a vacuum sensor to enable the high voltage and pulsed microchannel plate phosphor voltage. In the streak camera, the high voltage is removed after the sweep. Both rely on the hardened aluminum box and a custom power supply to reduce electromagnetic pulse/electromagnetic interference (EMP/EMI) getting into the electronics. In addition, the streak camera has an EMP/EMI shield enclosing the front of the streak tube.
Heat capacity, enthalpy fluctuations, and configurational entropy in broken ergodic systems
Authors: Mauro John C. , Loucks Roger J. , Sen Sabyasachi
Published: October 2010

A common assumption in the glass science community is that the entropy of a glass can be calculated by integration of measured heat capacity curves through the glass transition. Such integration assumes that glass is an equilibrium material and that the glass transition is a reversible process. However, as a nonequilibrium and nonergodic material, the equations from equilibrium thermodynamics are not directly applicable to the glassy state. Here we investigate the connection between heat capacity and configurational entropy in broken ergodic systems such as glass. We show that it is not possible, in general, to calculate the entropy of a glass from heat capacity curves alone, since additional information must be known related to the details of microscopic fluctuations. Our analysis demonstrates that a time-average formalism is essential to account correctly for the experimentally observed dependence of thermodynamic properties on observation time, e.g., in specific heat spectroscopy. This result serves as experimental and theoretical proof for the nonexistence of residual glass entropy at absolute zero temperature. Example measurements are shown for Corning code 7059 glass.
Mechanisms of magnetic and temperature hysteresis in ErFeO3 and TmFeO3 single crystals
Authors: Tsymbal L. T. , Bazaliy Ya. B. , Kakazei G. N. , Vasiliev S. V.
Published: October 2010

Magnetic hysteresis is studied in the orthoferrites ErFeO3 and TmFeO3 using the single crystal samples of millimeter dimensions. It is shown that in both materials one observes a temperature transition manifesting itself through the temperature hysteresis of the magnetic moment and a peculiar temperature evolution of the field hysteresis loop shapes near this transition. Experiments rule out the hypothesis that the ordering of the orthoferrite’s rare-earth magnetic moments plays an important role in these phenomena. The hysteresis curves can be explained by a few-domain magnetic state of the samples that results from the weak ferromagnetism of the orthoferrites. The phenomenon is generic for weak ferromagnets with temperature dependent magnetization. A large characteristic magnetic length makes the behavior of the relatively big samples analogous to that observed in the nanosize samples of strong ferromagnets.
One- and two-photon spectroscopy of highly excited states of alkali-metal atoms on helium nanodroplets
Authors: Pifrader Alexandra , Allard Olivier , Auböck Gerald , Callegari Carlo , Ernst Wolfgang E. , Huber Robert , Ancilotto Francesco
Published: October 2010

Alkali-metal atoms captured on the surface of superfluid helium droplets are excited to high energies (≈3 eV) by means of pulsed lasers, and their laser-induced-fluorescence spectra are recorded. We report on the one-photon excitation of the (n+1)p←ns transition of K, Rb, and Cs (n=4, 5, and 6, respectively) and on the two-photon one-color excitation of the 5d←5s transition of Rb. Gated-photon-counting measurements are consistent with the relaxation rates of the bare atoms, hence consistent with the reasonable expectation that atoms quickly desorb from the droplet and droplet-induced relaxation need not be invoked.
Interfacial reaction of Si islands on SiO2 during high-temperature annealing
Authors: Sudoh K. , Naito M.
Published: October 2010

We examine the interfacial reaction between submicron Si islands and SiO2 during high-temperature annealing under ultrahigh vacuum, using atomic force microscopy and transmission electron microscopy. We show that Si island/SiO2 interfaces are much more reactive than interfaces of wetting thin Si films on SiO2. This indicates that important processes responsible for the reaction occur at the Si island edges. During the reaction removal of O atoms from the SiO2 side of the interface occurs, resulting in depression of the Si island/SiO2 interface. Our observations indicate that the interfacial reaction advances via O out-diffusion from SiO2 into the Si island, O lateral diffusion along the interface, SiO formation at the edge of the Si island, and SiO desorption from the surface.
Iwasawa N=8 attractors
Authors: Cacciatori Sergio L. , Cerchiai Bianca L. , Marrani Alessio
Published: October 2010

Starting from the symplectic construction of the Lie algebra e7(7) due to Adams, we consider an Iwasawa parametrization of the coset E7(7)SU(8), which is the scalar manifold of N=8, d=4 supergravity. Our approach, and the manifest off-shell symmetry of the resulting symplectic frame, is determined by a noncompact Cartan subalgebra of the maximal subgroup SL(8,R) of E7(7). In the absence of gauging, we utilize the explicit expression of the Lie algebra to study the origin of E7(7)SU(8) as scalar configuration of a 18-BPS extremal black hole attractor. In such a framework, we highlight the action of a U(1) symmetry spanning the dyonic 18-BPS attractors. Within a suitable supersymmetry truncation allowing for the embedding of the Reissner–Nördstrom black hole, this U(1) action is interpreted as nothing but the global R-symmetry of pure N=2 supergravity. Moreover, we find that the above mentioned U(1) symmetry is broken down to a discrete subgroup Z4, implying that all 18-BPS Iwasawa attractors are nondyonic near the origin of the scalar manifold. We can trace this phenomenon back to the fact that the Cartan subalgebra of SL(8,R) used in our construction endows the symplectic frame with a manifest off-shell covariance which is smaller than SL(8,R) itself. Thus, the consistence of the Adams–Iwasawa symplectic basis with the action of the U(1) symmetry gives rise to the observed Z4 residual nondyonic symmetry.
Capillary condensation in cylindrical pores: Monte Carlo study of the interplay of surface and finite size effects
Authors: Winkler A. , Wilms D. , Virnau P. , Binder K.
Published: October 2010

When a fluid that undergoes a vapor to liquid transition in the bulk is confined to a long cylindrical pore, the phase transition is shifted (mostly due to surface effects at the walls of the pore) and rounded (due to finite size effects). The nature of the phase coexistence at the transition depends on the length of the pore: for very long pores, the system is axially homogeneous at low temperatures. At the chemical potential where the transition takes place, fluctuations occur between vapor- and liquidlike states of the cylinder as a whole. At somewhat higher temperatures (but still far below bulk criticality), the system at phase coexistence is in an axially inhomogeneous multidomain state, where long cylindrical liquid- and vaporlike domains alternate. Using Monte Carlo simulations for the Ising/lattice gas model and the Asakura–Oosawa model of colloid-polymer mixtures, the transition between these two different scenarios is characterized. It is shown that the density distribution changes gradually from a double-peak structure to a triple-peak shape, and the correlation length in the axial direction (measuring the equilibrium domain length) becomes much smaller than the cylinder length. The (rounded) transition to the disordered phase of the fluid occurs when the axial correlation length has decreased to a value comparable to the cylinder diameter. It is also suggested that adsorption hysteresis vanishes when the transition from the simple domain state to the multidomain state of the cylindrical pore occurs. We predict that the difference between the pore critical temperature and the hysteresis critical temperature should increase logarithmically with the length of the pore.
Three wave mixing of airy beams in a quadratic nonlinear photonic crystals
Authors: Dolev Ido , Arie Ady
Published: October 2010

We study three wave mixing processes of accelerating Airy beams in quadratic nonlinear crystals. In order to frequency convert these beams, the nonlinear process should be performed with the Fourier transform of the beam, rather than with the beam itself. This was confirmed experimentally by frequency doubling of one-dimensional and two-dimensional Airy beams in a periodically poled crystal. Sum-frequency or difference frequency process between two accelerating beam enable to set the acceleration rate and direction of the generated beam.
Self-biased planar millimeter wave notch filters based on magnetostatic wave excitation in barium hexagonal ferrite thin films
Authors: Song Young-Yeal , Sun Yiyan , Lu Lei , Bevivino Joshua , Wu Mingzhong
Published: October 2010

The use of M-type barium hexagonal ferrite (BaM) thin films for self-biased planar millimeter wave notch filters was demonstrated for the first time. The BaM film was grown by pulsed laser deposition and showed a remanent to saturation magnetization ratio of 0.99 and a 60 GHz ferromagnetic resonance linewidth of about 300 Oe. The filter consisted of a BaM film element positioned on the top of a coplanar waveguide and showed a band-stop response at 53 GHz for zero external fields. This filtering response resulted from power absorption due to magnetostatic wave excitation in the BaM film.
Geometric dependence of radio-frequency breakdown in normal conducting accelerating structures
Authors: Dolgashev Valery , Tantawi Sami , Higashi Yasuo , Spataro Bruno
Published: October 2010

We present the experimental results of a systematic study of rf breakdown phenomenon in high vacuum accelerator structures. In this study, the surface processing, geometry, and materials of the structures have been varied, one parameter at a time. The breakdown rate or alternatively, the probability of breakdown/pulse/meter has been recorded for different operating parameters. These statistical data reveal a strong dependence of breakdown probability on surface magnetic field, or alternatively on surface pulsed heating. This is in contrast to the classical view of electric field dependence. We will present our experimental methodology and results showing this remarkable correlation.
Temporal and spatial locking of nonlinear systems
Authors: Rittersdorf Ian M. , Lau Y. Y. , Zier Jacob C. , Gilgenbach Ronald M. , Cruz Edward J. , Luginsland John W.
Published: October 2010

Peer-to-peer locking of two magnetrons is analyzed including the effects of a frequency chirp and of low frequency noise. It is found that complete phase locking cannot be achieved in either case. However, as long as the locking condition is well satisfied instantaneously, a high degree of locking occurs. This analysis in the time domain is adapted to locking in the spatial domain, in particular to the interpretation of some recent experiments on the spatial correlation of two ablating current-carrying wires that are placed sufficiently close to each other.
Tilt angle control of nanocolumns grown by glancing angle sputtering at variable argon pressures
Authors: García-Martín J. M. , Alvarez R. , Romero-Gómez P. , Cebollada A. , Palmero A.
Published: October 2010

We show that the tilt angle of nanostructures obtained by glancing angle sputtering is finely tuned by selecting the adequate argon pressure. At low pressures, a ballistic deposition regime dominates, yielding high directional atoms that form tilted nanocolumns. High pressures lead to a diffusive regime which gives rise to vertical columnar growth. Monte Carlo simulations reproduce the experimental results indicating that the loss of directionality of the sputtered particles in the gas phase, together with the self-shadowing mechanism at the surface, are the main processes responsible for the development of the columns.
An endocardial pathway involving Tbx5, Gata4, and Nos3 required for atrial septum formation
Authors: Nadeau Mathieu , Georges Romain O. , Laforest Brigitte , Yamak Abir , Lefebvre Chantal , Beauregard Janie , Paradis Pierre , Bruneau Benoit G. , Andelfinger Gregor , Nemer Mona
Published: October 2010

In humans, septal defects are among the most prevalent congenital heart diseases, but their cellular and molecular origins are not fully understood. We report that transcription factor
Tbx5
is present in a subpopulation of endocardial cells and that its deletion therein results in fully penetrant, dose-dependent atrial septal defects in mice. Increased apoptosis of endocardial cells lacking
Tbx5
, as well as neighboring TBX5-positive myocardial cells of the atrial septum through activation of endocardial NOS (
Nos3
), is the underlying mechanism of disease. Compound
Tbx5
and
Nos3
haploinsufficiency in mice worsens the cardiac phenotype. The data identify a pathway for endocardial cell survival and unravel a cell-autonomous role for
Tbx5
therein. The finding that
Nos3
, a gene regulated by many congenital heart disease risk factors including stress and diabetes, interacts genetically with
Tbx5
provides a molecular framework to understand gene–environment interaction in the setting of human birth defects.
Glial cell line-derived neurotrophic factor defines the path of developing and regenerating axons in the lateral line system of zebrafish
Authors: Schuster Kevin , Dambly-Chaudière Christine , Ghysen Alain
Published: October 2010

How the peripheral axons of sensory neurons are guided to distant target organs is not well understood. Here we examine this question in the case of the posterior lateral line (PLL) system of zebrafish, where sensory organs are deposited by a migrating primordium. Sensory neurites accompany this primordium during its migration and are thereby guided to their prospective target organs. We show that the inactivation of glial cell line-derived neurotrophic factor (GDNF) signaling leads to defects of innervation and that these defects are due to the inability of sensory axons to track the migrating primordium. GDNF signaling is also used as a guidance cue during axonal regeneration following nerve cut. We conclude that GDNF is a major determinant of directed neuritic growth and of target finding in this system, and we propose that GDNF acts by promoting local neurite outgrowth.
Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize
Authors: Lu Yanli , Zhang Shihuang , Shah Trushar , Xie Chuanxiao , Hao Zhuanfang , Li Xinhai , Farkhari Mohammad , Ribaut Jean-Marcel , Cao Moju , Rong Tingzhao , Xu Yunbi
Published: October 2010

This paper describes two joint linkage–linkage disequilibrium (LD) mapping approaches: parallel mapping (independent linkage and LD analysis) and integrated mapping (datasets analyzed in combination). These approaches were achieved using 2,052 single nucleotide polymorphism (SNP) markers, including 659 SNPs developed from drought-response candidate genes, screened across three recombinant inbred line (RIL) populations and 305 diverse inbred lines, with anthesis-silking interval (ASI), an important trait for maize drought tolerance, as the target trait. Mapping efficiency was improved significantly due to increased population size and allele diversity and balanced allele frequencies. Integrated mapping identified 18 additional quantitative trait loci (QTL) not detected by parallel mapping. The use of haplotypes improved mapping efficiency, with the sum of phenotypic variation explained (PVE) increasing from 5.4% to 23.3% for single SNP-based analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency (<5%) in 305 lines were recovered in three RIL populations, three of which were significantly associated with ASI. The candidate genes identified by two significant haplotype loci included one for a SET domain protein involved in the control of flowering time and the other encoding aldo/keto reductase associated with detoxification pathways that contribute to cellular damage due to environmental stress. Joint linkage–LD mapping is a powerful approach for detecting QTL underlying complex traits, including drought tolerance.
Engineering a protein–protein interface using a computationally designed library
Authors: Guntas Gurkan , Purbeck Carrie , Kuhlman Brian
Published: October 2010

Computational algorithms for protein design can sample large regions of sequence space, but suffer from undersampling of conformational space and energy function inaccuracies. Experimental screening of combinatorial protein libraries avoids the need for accurate energy functions, but has limited access to vast amounts of sequence space. Here, we test if these two traditionally alternative, but potentially complementary approaches can be combined to design a variant of the ubiquitin-ligase E6AP that will bind to a nonnatural partner, the NEDD8-conjugating enzyme Ubc12. Three E6AP libraries were constructed: (
i
) a naive library in which all 20 amino acids were allowed at every position on the target-binding surface of E6AP (13 positions), (
ii
) a semidirected library that varied the same residue positions as in the naive library but disallowed mutations computationally predicted to destabilize E6AP, and (
iii
) a directed library that used docking and sequence optimization simulations to identify mutations predicted to be favorable for binding Ubc12. Both of the directed libraries showed > 30-fold enrichment over the naive library after the first round of screening with a split-dihydrofolate reductase complementation assay and produced multiple tight binders (
K

d

 < 100 nM) after four rounds of selection. Four rounds of selection with the naive library failed to produce any binders with
K

d

’s lower than 50 μM. These results indicate that protein design simulations can be used to create directed libraries that are enriched in tight binders and that in some cases it is sufficient to computationally screen for well-folded sequences without explicit binding calculations.
RETRACTED: Properdin homeostasis requires turnover of the alternative complement pathway
Authors: Wu Xiaobo , Xu Thomas Q. , Atkinson John P.
Published: October 2010

Properdin is a plasma protein and is also released from neutrophil granules following stimulation. At inflammatory sites it can bind bacteria and apoptotic bodies to trigger alternative pathway (AP) activation. Principles governing properdin homeostasis are unknown. We monitored properdin during AP activation and in complement-deficient mice. There was a >90% reduction of properdin in the Crry single-knockout mice (
Crry SKO
). These membrane complement regulatory protein-deficient mice feature accelerated AP turnover, leading to reduced C3 and fB. Injecting cobra venom factor into wild-type mice activated the AP and led to the consumption of C3, fB, and properdin. However, and unexpectedly, properdin was also deficient in

C3
−/−

,

fB
−/−

, and

fD
−/−

mice. It was present in

C1q
−/−

,

C4
−/−

, and

C5
−/−

mice. These findings implicate AP turnover in the maintenance of basal levels of properdin in the blood. To explore the mechanism, classical pathway-activating immune complexes were infused. Within 10 min, properdin was partially restored in

fB
−/−

but not in

C3
−/−

mice. Markedly reduced properdin in mice deficient in an AP component and its partial restoration by activating C3 suggest a requirement for continuous C3 activation via AP tickover to maintain properdin homeostasis. The mechanism underlying this C3-dependent process was not identified. Engagement of C3a and C5a receptors was ruled out. These findings represent an instructive example of how a positive regulator of an innate immune recognition and effector pathway is controlled. A rationale for such a means to supply properdin for immune reactions is proposed.
Chiral N-heterocyclic carbene-catalyzed generation of ester enolate equivalents from α,β-unsaturated aldehydes for enantioselective Diels–Alder reactions
Authors: Kaeobamrung Juthanat , Kozlowski Marisa C. , Bode Jeffrey W.
Published: October 2010

The catalytic generation of chiral ester enolate equivalents from α,β-unsaturated aldehydes with chiral N-hetereocyclic carbene catalysts makes possible highly enantioselective hetero-Diels–Alder reactions. The reactions proceed under simple, mild conditions with both aliphatic and aromatic substituted enals as substrates. Previous attempts to employ these starting materials as enolate precursors gave structurally different products via catalytically generated homoenolate equivalents. Critical to the success of the enolate generation was the strength of the catalytic base used to generate the active N-heterocyclic carbene catalyst. To complement these studies, we have investigated the enolate structure using computational methods and find that it prefers conformations perpendicular to the triazolium core.
Two interacting coiled-coil proteins, WEB1 and PMI2, maintain the chloroplast photorelocation movement velocity in
Arabidopsis
Authors: Kodama Yutaka , Suetsugu Noriyuki , Kong Sam-Geun , Wada Masamitsu
Published: October 2010

Chloroplasts move toward weak light (accumulation response) and away from strong light (avoidance response). The fast and accurate movement of chloroplasts in response to ambient light conditions is essential for efficient photosynthesis and photodamage prevention in chloroplasts. Here, we report that two
Arabidopsis
mutants,

we
ak chloroplast movement under
b
lue light 1

(
web1
) and
web2
, are defective in both the avoidance and the accumulation responses. Map-based cloning revealed that both genes encode coiled-coil proteins and that
WEB2
is identical to the
plastid movement impaired 2
(
PMI2
) gene. The velocities of chloroplast movement in
web1
and
pmi2
were approximately threefold lower than that in the wild type. Defects in the avoidance response of
web1
and
pmi2
were suppressed by mutation of the
J-domain protein required for chloroplast accumulation response 1 (JAC1
) gene, which is essential for the accumulation response; these results indicate that WEB1 and PMI2 play a role in suppressing JAC1 under strong light conditions. A yeast two-hybrid analysis and a nuclear recruitment assay identified a physical interaction between WEB1 and PMI2, and transient expression analysis of CFP-WEB1 and YFP-PMI2 revealed that they colocalized in the cytosol. Bimolecular fluorescence complementation analysis confirmed the interaction of these proteins in the cytosol. Blue light-induced changes in short chloroplast actin filaments (cp-actin filaments) were impaired in both
web1
and
pmi2
. Our findings suggest that a cytosolic WEB1–PMI2 complex maintains the velocity of chloroplast photorelocation movement via cp-actin filament regulation.
Soluble plasma HLA peptidome as a potential source for cancer biomarkers
Authors: Bassani-Sternberg Michal , Barnea Eilon , Beer Ilan , Avivi Irit , Katz Tami , Admon Arie
Published: October 2010

The HLA molecules are membrane-bound transporters that carry peptides from the cytoplasm to the cell surface for surveillance by circulating T lymphocytes. Although low levels of soluble HLA molecules (sHLA) are normally released into the blood, many types of tumor cells release larger amounts of these sHLA molecules, presumably to counter immune surveillance by T cells. Here we demonstrate that these sHLA molecules are still bound with their authentic peptide repertoires, similar to those of the membranal HLA molecules (mHLA). Therefore, a single immunoaffinity purification of the plasma sHLA molecules, starting with a few milliliters of patients’ blood, allows for identification of very large sHLA peptidomes by mass spectrometry, forming a foundation for development of a simple and universal blood-based cancer diagnosis. The new methodology was validated using plasma and tumor cells of multiple-myeloma and leukemia patients, plasma of healthy controls, and with cultured cancer cells. The analyses identified thousands of sHLA peptides, including some cancer-related peptides, present among the sHLA peptidomes of the cancer patients. Furthermore, because the HLA peptides are the degradation products of the cellular proteins, this sHLA peptidomics approach opens the way for investigation of the patterns of protein synthesis and degradation within the tumor cells.
Elementary steps at the surface of ice crystals visualized by advanced optical microscopy
Authors: Sazaki Gen , Zepeda Salvador , Nakatsubo Shunichi , Yokoyama Etsuro , Furukawa Yoshinori
Published: October 2010

Due to the abundance of ice on earth, the phase transition of ice plays crucially important roles in various phenomena in nature. Hence, the molecular-level understanding of ice crystal surfaces holds the key to unlocking the secrets of a number of fields. In this study we demonstrate, by laser confocal microscopy combined with differential interference contrast microscopy, that elementary steps (the growing ends of ubiquitous molecular layers with the minimum height) of ice crystals and their dynamic behavior can be visualized directly at air-ice interfaces. We observed the appearance and lateral growth of two-dimensional islands on ice crystal surfaces. When the steps of neighboring two-dimensional islands coalesced, the contrast of the steps always disappeared completely. We were able to discount the occurrence of steps too small to detect directly because we never observed the associated phenomena that would indicate their presence. In addition, classical two-dimensional nucleation theory does not support the appearance of multilayered two-dimensional islands. Hence, we concluded that two-dimensional islands with elementary height (0.37 and 0.39 nm on basal and prism faces, respectively) were visualized by our optical microscopy. On basal and prism faces, we also observed the spiral growth steps generated by screw dislocations. The distance between adjacent spiral steps on a prism face was about 1/20 of that on a basal face. Hence, the step ledge energy of a prism face was 1/20 of that on a basal face, in accord with the known lower-temperature roughening transition of the prism face.
Ferredoxin:NADPH oxidoreductase is recruited to thylakoids by binding to a polyproline type II helix in a pH-dependent manner
Authors: Alte Ferdinand , Stengel Anna , Benz J. Philipp , Petersen Eike , Soll Jürgen , Groll Michael , Bölter Bettina
Published: October 2010

Ferredoxin:NADPH oxidoreductase (FNR) is a key enzyme of photosynthetic electron transport required for generation of reduction equivalents. Recently, two proteins were found to be involved in membrane-anchoring of FNR by specific interaction via a conserved Ser/Pro-rich motif: Tic62 and Trol. Our crystallographic study reveals that the FNR-binding motif, which forms a polyproline type II helix, induces self-assembly of two FNR monomers into a back-to-back dimer. Because binding occurs opposite to the FNR active sites, its activity is not affected by the interaction. Surface plasmon resonance analyses disclose a high affinity of FNR to the binding motif, which is strongly increased under acidic conditions. The pH of the chloroplast stroma changes dependent on the light conditions from neutral to slightly acidic in complete darkness or to alkaline at saturating light conditions. Recruiting of FNR to the thylakoids could therefore represent a regulatory mechanism to adapt FNR availability/activity to photosynthetic electron flow.
Electron tunneling in respiratory complex I
Authors: Hayashi Tomoyuki , Stuchebrukhov Alexei A.
Published: October 2010

NADH:ubiquinone oxidoreductase (complex I) plays a central role in the respiratory electron transport chain by coupling the transfer of electrons from NADH to ubiquinone to the creation of the proton gradient across the membrane necessary for ATP synthesis. Here the atomistic details of electronic wiring of all Fe/S clusters in complex I are revealed by using the tunneling current theory and computer simulations; both density functional theory and semiempirical electronic structure methods were used to examine antiferromagnetically coupled spin states and corresponding tunneling wave functions. Distinct electron tunneling pathways between neighboring Fe/S clusters are identified; the pathways primarily consist of two cysteine ligands and one additional key residue. Internal water between protein subunits is identified as an essential mediator enhancing the overall electron transfer rate by almost three orders of magnitude to achieve a physiologically significant value. The identified key residues are further characterized by sensitivity of electron transfer rates to their mutations, examined in simulations, and their conservation among complex I homologues. The unusual electronic structure properties of Fe
4
S
4
clusters in complex I explain their remarkable efficiency of electron transfer.
RNA-dependent control of gene amplification
Authors: Heyse Gero , Jönsson Franziska , Chang Wei-Jen , Lipps Hans J.
Published: October 2010

We exploit the unusual genome organization of the ciliate cell to analyze the control of specific gene amplification during a nuclear differentiation process. Ciliates contain two types of nuclei within one cell, the macronucleus and the micronucleus; and after sexual reproduction a new macronucleus is formed from a micronuclear derivative. During macronuclear differentiation, most extensive DNA reorganization, elimination, and fragmentation processes occur, resulting in a macronucleus containing short DNA molecules (nanochromosomes) representing individual genetic units and each being present in high copy number. It is believed that these processes are controlled by small nuclear RNAs but also by a template derived from the old macronucleus. We first describe the exact copy numbers of selected nanochromosomes in the macronucleus, and define the timing during nuclear differentiation at which copy number is determined. This led to the suggestion that DNA processing and copy number control may be closely related mechanisms. Degradation of an RNA template derived from the macronucleus leads to significant decrease in copy number, whereas injection of additional template molecules results in an increase in copy number and enhanced expression of the corresponding gene. These observations can be incorporated into a mechanistic model about an RNA-dependent epigenetic regulation of gene copy number during nuclear differentiation. This highlights that RNA, in addition to its well-known biological functions, can also be involved in the control of gene amplification.
Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14
Authors: Luebben Whitney R. , Sharma Neelam , Nyborg Jennifer K.
Published: October 2010

Histone posttranslational modifications and chromatin dynamics are inextricably linked to eukaryotic gene expression. Among the many modifications that have been characterized, histone tail acetylation is most strongly correlated with transcriptional activation. In
Metazoa
, promoters of transcriptionally active genes are generally devoid of physically repressive nucleosomes, consistent with the contemporaneous binding of the large RNA polymerase II transcription machinery. The histone acetyltransferase p300 is also detected at active gene promoters, flanked by regions of histone hyperacetylation. Although the correlation between histone tail acetylation and gene activation is firmly established, the mechanisms by which acetylation facilitates this fundamental biological process remain poorly understood. To explore the role of acetylation in nucleosome dynamics, we utilized an immobilized template carrying a natural promoter reconstituted with various combinations of wild-type and mutant histones. We find that the histone H3 N-terminal tail is indispensable for activator, p300, and acetyl-CoA-dependent nucleosome eviction mediated by the histone chaperone Nap1. Significantly, we identify H3 lysine 14 as the essential p300 acetylation substrate required for dissociation of the histone octamer from the promoter DNA. Together, a total of 11 unique mutant octamer sets corroborated these observations and revealed a striking correlation between nucleosome eviction and strong activator and acetyl-CoA-dependent transcriptional activation. These novel findings uncover an exclusive role for H3 lysine 14 acetylation in facilitating the ATP-independent and transcription-independent disassembly of promoter nucleosomes by Nap1. Furthermore, these studies directly couple nucleosome disassembly with strong, activator-dependent transcription.
RETRACTED: Phospholipid bilayers are viscoelastic
Authors: Harland Christopher W. , Bradley Miranda J. , Parthasarathy Raghuveer
Published: October 2010

Lipid bilayers provide the structural framework for cellular membranes, and their character as two-dimensional fluids enables the mobility of membrane macromolecules. Though the existence of membrane fluidity is well established, the nature of this fluidity remains poorly characterized. Three-dimensional fluids as diverse as chocolates and cytoskeletal networks show a rich variety of Newtonian and non-Newtonian dynamics that have been illuminated by contemporary rheological techniques. Applying particle-tracking microrheology to freestanding phospholipid bilayers, we find that the membranes are not simply viscous but rather exhibit viscoelasticity, with an elastic modulus that dominates the response above a characteristic frequency that diverges at the fluid–gel (
L

α

 - 
L

β

) phase-transition temperature. These findings fundamentally alter our picture of the nature of lipid bilayers and the mechanics of membrane environments.
Understanding the varied response of the extratropical storm tracks to climate change
Authors: O’Gorman Paul A.
Published: October 2010

Transient eddies in the extratropical storm tracks are a primary mechanism for the transport of momentum, energy, and water in the atmosphere, and as such are a major component of the climate system. Changes in the extratropical storm tracks under global warming would impact these transports, the ocean circulation and carbon cycle, and society through changing weather patterns. I show that the southern storm track intensifies in the multimodel mean of simulations of 21st century climate change, and that the seasonal cycle of storm-track intensity increases in amplitude in both hemispheres. I use observations of the present-day seasonal cycle to confirm the relationship between storm-track intensity and the mean available potential energy of the atmosphere, and show how this quantitative relationship can be used to account for much of the varied response in storm-track intensity to global warming, including substantially different responses in simulations with different climate models. The results suggest that storm-track intensity is not related in a simple way to global-mean surface temperature, so that, for example, a stronger southern storm track in response to present-day global warming does not imply it was also stronger in hothouse climates of the past.