bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculating the free energy of self-assembled structures by thermodynamic integration
Authors: Müller Marcus , Daoulas Kostas Ch.
Published: January 2008

We discuss a method for calculating free energy differences between disordered and ordered phases of self-assembling systems utilizing computer simulations. Applying an external, ordering field, we impose a predefined structure onto the fluid in the disordered phase. The structure in the presence of the external, ordering field closely mimics the structure of the ordered phase (in the absence of an ordering field). Self-consistent field theory or density functional theory provides an accurate estimate for choosing the strength of the ordering field. Subsequently, we gradually switch off the external, ordering field and, in turn, increase the control parameter that drives the self-assembly. The free energy difference along this reversible path connecting the disordered and the ordered state is obtained via thermodynamic integration or expanded ensemble simulation techniques. Utilizing Single-Chain-in-Mean-Field simulations of a symmetric diblock copolymer melt we illustrate the method and calculate the free energy difference between the disordered phase and the lamellar structure at an intermediate incompatibility χN=20. Evidence for the first-order character of the order-disorder transition at fixed volume is presented. The transition is located at χODTN=13.65±0.10 for an invariant degree of polymerization of N¯=14884. The magnitude of the shift of the transition from the mean field prediction qualitatively agrees with other simulations.
Novel instrument for surface plasmon polariton tracking in space and time
Authors: Sandtke M. , Engelen R. J. P. , Schoenmaker H. , Attema I. , Dekker H. , Cerjak I. , Korterik J. P. , Segerink F. B. , Kuipers L.
Published: January 2008

We describe the realization of a phase-sensitive and ultrafast near-field microscope, optimized for investigation of surface plasmon polariton propagation. The apparatus consists of a homebuilt near-field microscope that is incorporated in Mach-Zehnder-type interferometer which enables heterodyne detection. We show that this microscope is able to measure dynamical properties of both photonic and plasmonic systems with phase sensitivity.
Drift mode in a bounded plasma having two-ion species
Authors: Ahmad Ali , Sajid M. , Saleem H.
Published: January 2008

The drift wave is investigated in a two-ion species plasma in several different cases. The global drift mode is studied in a plasma bounded in a cylinder having Gaussian density profile corresponding to different poloidal wavenumbers. The frequency of the mode becomes a little larger when it is investigated without including the ion cyclotron wave dynamics. The effect of magnetic shear on the wave propagation along the density gradient is studied in a Cartesian geometry assuming absorbing boundary. It is found that the wave amplitude is reduced when two-ion species are present (with the same concentration) compared to pure electron-ion plasma.
Time-resolved scanning system for double reflectance and transmittance fluorescence imaging of diffusive media
Authors: Brambilla Marco , Spinelli Lorenzo , Pifferi Antonio , Torricelli Alessandro , Cubeddu Rinaldo
Published: January 2008

In this work we present a novel diffuse fluorescence imaging system, based on time-resolved two-wavelength double reflectance and transmittance setup for slab geometry samples. We describe the hardware setup, showing its compactness and versatility and show the results on preliminary measurements on phantoms. We fully assessed the performances and the dynamic ranges of the system. We validated its ability of recovering the optical properties of the bulk medium, for samples with scattering and absorption coefficients similar to those of biological tissues and with thicknesses of about 2cm. Moreover we assess the linearity of the recorded signals against the fluorophore concentration, when it is homogeneously diffused in the phantom or concentrated inside a sealed inclusion. In both cases we observe again a fairly good linearity, over three orders of magnitude, from 10−8M to 10−5M. With the fluorescent inclusion we were also able to assess the imaging capabilities of the system, in terms of spatial resolution, which we appraise in about 3mm, and in terms of imaging sensitivity (the smallest quantity of fluorescent dye distinguishable from the homogeneous background), settled to 200fmol. Since the recorded data are time resolved, we could also estimate the dye fluorescence lifetime and build early and late time gate images. We finally discuss some of the criticalities of the proposed system and the developments we are currently carrying on in order to adapt it for in vivo measurements.
Metal-enhanced e-type fluorescence
Authors: Zhang Yongxia , Aslan Kadir , Previte Michael J. R. , Geddes Chris D.
Published: January 2008

In this letter, we report metal-enhanced e-type fluorescence. Eosin in close proximity to silver island films (SiFs) shows enhanced e-type fluorescence with an approximately two-fold higher intensity observed from SiFs, as compared to a control sample. Our findings suggest two complementary mechanisms for the enhancement: surface plasmons can radiate e-type delayed fluorescence efficiently and enhanced absorption also facilitates enhanced emission from both S1 and T1 states. This observation is helpful in our understanding not only for studying the interactions between plasmons and fluorophores but also for our laboratories continued efforts to develop a unified plasmon-lumophore description.
Surface plasmon coupling on metallic film perforated by two-dimensional rectangular hole array
Authors: Sauvan C. , Billaudeau C. , Collin S. , Bardou N. , Pardo F. , Pelouard J.-L. , Lalanne P.
Published: January 2008

The impact of the periodicity on the dispersion relation of surface modes supported by two dimensional (2D) structured metallic films is experimentally and numerically investigated between 1 and 5μm. A coupling between modes propagating in two nearly orthogonal directions forming an angle of 77° is evidenced for a rectangular array of holes perforated in a gold film. The coupling results in a narrow band gap for nonzero wavevectors and in a coupled mode with a large density of states and a strong radiative damping. We show that the gap location in the (ω,k) space can be precisely tuned by changing the 2D period.
Enhanced microwave absorption in Ni/polyaniline nanocomposites by dual dielectric relaxations
Authors: Dong X. L. , Zhang X. F. , Huang H. , Zuo F.
Published: January 2008

Ni/polyaniline (PANi) nanocomposites were prepared by chemical polymerization, and electromagnetic characteristics were then studied at 2–18GHz. The permittivity of the Ni/PANi nanocomposite presents dual dielectric relaxations with increasing content of PANi to over 15.6wt%, which is ascribed to a cooperative consequence of the core/shell interfaces and the dielectric PANi shells. Additionally, the permeability presents a strong natural resonance around 2–8GHz, which is dominant among microwave magnetic loss. The proper matching of the permittivity and the permeability contributes to enhanced microwave absorption.
Effects of hydrostatic pressure on the magnetism and martensitic transition of Ni–Mn–In magnetic superelastic alloys
Authors: Mañosa Lluís , Moya Xavier , Planes Antoni , Gutfleisch Oliver , Lyubina Julia , Barrio Maria , Tamarit Josep-Lluís , Aksoy Seda , Krenke Thorsten , Acet Mehmet
Published: January 2008

We report magnetization and differential thermal analysis measurements as a function of pressure across the martensitic transition in magnetically superelastic Ni–Mn–In alloys. It is found that the properties of the martensitic transformation are significantly affected by the application of pressure. All transition temperatures shift to higher values with increasing pressure. The largest rate of temperature shift with pressure has been found for Ni50Mn34In16 as a consequence of its small entropy change at the transition. Such a strong pressure dependence of the transition temperature opens up the possibility of inducing the martensitic transition by applying relatively low hydrostatic pressures.
Measurement of electronic structure at nanoscale solid-solid interfaces by surface-sensitive electron spectroscopy
Authors: Wang Hui-Qiong , Altman Eric I. , Henrich Victor E.
Published: January 2008

We explore the use of electron spectroscopy that samples the near-surface region of a crystal to study the electronic structure at the buried interfaces between two dissimilar transition-metal oxides. The interface is probed by comparing experimental ultraviolet photoelectron spectra to model spectra and by taking sequential differences between the experimental spectra as one oxide is grown on another. Using (100) Fe3O4–NiO and Fe3O4–CoO interfaces grown by molecular beam epitaxy, we show that there is a much higher density of electronic states at the Fe3O4–CoO interface than at the Fe3O4–NiO interface. The origin of this difference is discussed.
Kinetics of capillary wetting in nanoporous films in the presence of surface evaporation
Authors: Seker Erkin , Begley Matthew R. , Reed Michael L. , Utz Marcel
Published: January 2008

A liquid in contact with a nanoporous Au film forms a halo of constant width around the droplet. Due to the large surface area-to-volume ratio, one would expect either complete wetting or rejection of the liquid. Instead, a stable halo width is observed, depending on pore size, void fraction, film thickness, and the liquid. This is due to competition between capillary flow and evaporation through the surface of the nanoporous film. A theory is presented that predicts the halo width from the film geometry and liquid properties. Without adjustable parameters, the theory is in good agreement with experimental results.
Diffusion and crystallization mechanisms of Ge∕Au bilayer media for write-once optical disk
Authors: Wu T. H. , Kuo P. C. , Ou S. L. , Chen Jung-Po , Yen Po-Fu , Jeng Tzuan-Ren , Wu Chih-Yuan , Huang Der-Ray
Published: January 2008

Ge ∕ Au bilayer thin films were fabricated by magnetron sputtering method, the temperature dependence of resistance from room temperature to 500°C and concentration depth profiles are measured. From the temperature dependence of resistance measurement, we found two phase change phenomena which occurred at 175 and 360°C. The element concentration depth profiles of the as-deposited and recorded region indicate that the Au–Ge alloy is initially formed at the Ge∕Au interface. The dominant diffusion element is Au atom and the diffusion path is from Au layer to Ge layer. The optimum simulated bit error rate value is about 1.4×0−6 at 9.0mW under two time high definition digital versatile disk (HD DVD) recording speed. The dynamic tests show that this Ge∕Au bilayer films can be applied to one to two times HD DVD-R.
Strong magnetoelectric coupling in Tb–Fe∕Pb(Zr0.52Ti0.48)O3 thin-film heterostructure prepared by low energy cluster beam deposition
Authors: Zhao Shifeng , Wu Yujie , Wan Jian-guo , Dong XinWei , Liu Jun-ming , Wang Guanghou
Published: January 2008

The magnetoelectric Tb–Fe∕Pb(Zr0.52Ti0.48)O3 thin-film heterostructure was prepared by low energy cluster beam deposition. The microstructures, ferroelectric property, leakage current, and magnetization, as well as magnetoelectric effect were investigated for the heterostructure. It is shown that the thin-film heterostructure displays the well-defined microstructure with clear interface. The heterostructure not only exhibits good ferromagnetic and ferroelectric properties, but also possesses strong magnetoelectric effect. The present work provides an ideal avenue to prepare magnetoelectric composite films and facilitates their applications on the microelectromechanical system devices.
Active steering of laser-accelerated ion beams
Authors: Lundh O. , Glinec Y. , Homann C. , Lindau F. , Persson A. , Wahlström C.-G. , Carroll D. C. , McKenna P.
Published: January 2008

A technique for optical control of the spatial distribution of laser-accelerated ion beams is presented. An ultrashort laser pulse, tightly focused to relativistic intensities on a thin foil target, drives a beam of MeV ions. An auxiliary, nanosecond laser pulse drives a shock and locally deforms the initially flat target prior to the main pulse interaction. By changing the properties of the shock-driving laser pulse, the normal direction of the ion emitting surface is locally manipulated and the emission direction is thereby controlled. In the future, this method could be used to achieve dynamic control of the ion beam divergence.
Cathode spot motion in an oblique magnetic field
Authors: Garner Allen L.
Published: January 2008

Improper control of cathode spot (CS) motion can lead to uneven cathode erosion and shorter life, so magnetic fields are often used to direct CS motion. Here, we incorporate an axial magnetic field component into a model for CS retrograde motion based on the difference between the plasma kinetic and self-magnetic pressures. We consider the motion of the positive space charge associated with retrograde motion to generate a current perpendicular to the axial magnetic field, introducing an additional component to CS motion. The predicted angle of CS motion agrees well with the experimental data and a prior model based on electron backflow to the cathode surface.
Setting New Directions in Physics Teaching: PSSC 30 Years Later
Authors: French Anthony P.
Published: January 2008

In 1945 the United States emerged from World War II—into a world profoundly altered by scientific growth. Under the pressure of wartime conditions, sophisticated technology—most notably radar—had been developed by exploiting basic physical principles, such as those of electronics and atomic phenomena, and this technology had proved crucial to the war's outcome. Yet in the postwar US, fewer than 25% of high-school students were studying physics at all, and what physics was taught emphasized rote learning and superficial description. Similar situations existed in the teaching of mathematics and of other sciences.
The Cost-Effectiveness of Physics Journals
Authors: Barschall Henry H.
Published: January 2008

The rapid increase in the prices of physics journals has forced many physics libraries, in the face of static budgets, to cancel some of their subscriptions. Decisions on cancellations are usually based on the research interests of the users of the library, but the decision-making process can be improved if a quantitative measure of the cost-effectiveness of the journals is available. An often-used measure is the cost per printed character; another is the frequency with which articles in the journal are cited, often referred to as the “impact.” The ratio of these two measures is perhaps the best indicator of a journal's cost-effectiveness.
An Outsider's Inside View of the Challenger Inquiry
Authors: Feynman Richard P.
Published: January 2008

A few days after the Challenger accident, on a Friday, I got a call from William Graham, who was the acting director of NASA. Mr. Graham had been a student of mine—at Caltech, and also at the Hughes Aircraft Company, where I gave a series of lectures—and thought maybe I would be of some use to the investigation. When I heard it would be in Washington, my immediate reaction was not to do it. I have a principle of not going anywhere near Washington or having anything to do with government.
Cosmology from Robertson to Today
Authors: Zel'dovich Yakov B.
Published: January 2008

The outstanding contributions of H. P. Robertson to cosmology make giving this memorial lecture a great honor for me—a feeling that is enhanced by reading the list of the eminent previous Robertson lecturers.
The Discovery of Nuclear Fission
Authors: Segrè Emilio G.
Published: January 2008

Few modern discoveries have influenced mankind so rapidly and so profoundly as has nuclear fission, and few have had such an intricate history. Thus it is natural that the discovery of fission by Otto Hahn and Fritz Strassmann in December 1938 is remembered and commemorated in many places on its 50th anniversary. I participated in the early experiments in Rome, and later in the US, and I knew most of the principals well, except for Strassmann. I will try to present a brief outline of the discovery and its antecedents.
New Measurements Standards for 1990
Authors: Taylor Barry N.
Published: January 2008

By international agreement, new practical reference standards for the volt and the ohm, based respectively on the Josephson effect and the quantum Hall effect, will be adopted worldwide on 1 January 1990. Until now, national standards laboratories have been using wirewound resistors as practical reference standards for the ohm. Practical reference standards for the volt, on the other hand, have been based on the Josephson effect since the early 1970s. But four different such standards are in use in different countries, and their values all differ significantly from the volt as defined in the Système International d'Unités (SI), the internationally accepted system of measurement units.
Pathological Science
Authors: Langmuir Irving , Hall Robert N.
Published: January 2008

Irving Langmuir spent many productive years pursuing Nobel-caliber research (see the photo on the opposite page). Over the years, he also explored the subject of what he called “pathological science.” Although he never published his investigations in this area, on 18December 1953 at General Electric's Knolls Atomic Power Laboratory, he gave a colloquium on the subject that will long be remembered by those in his audience. This talk was a colorful account of a particular kind of pitfall into which scientists may stumble.
Physical Properties of High-Tc Superconductors
Authors: Batlogg Bertram
Published: January 2008

Four years of intensive research following J. Georg Bednorz and K. Alex Müller's discovery of high-temperature superconductors has produced about 18 000 publications. An overview of all physical properties is thus beyond the scope of this article, so I will focus on a few topics that are widely perceived to hold the key to understanding these fascinating compounds.
A Dialogue on the Theory of High Tc
Authors: Anderson Philip W. , Schrieffer Robert
Published: January 2008

Anderson: The consensus is that there is absolutely no consensus on the theory of high-Tc superconductivity. I suppose that, in a way, this is true. One can find groups working with some level of conviction on almost every hypothesis, and there are groups from very diverse backgrounds (such as quantum chemistry, electronic structure and many-body physics) working on the problem, groups that have very little meaningful communication with each other. Looked at relative to this scientific Tower of Babel, I suspect you and I are practically speaking the same language. Would you agree?
High-Tc Thin Film and Electronic Devices
Authors: Simon Randy
Published: January 2008

A worldwide effort to develop high-temperature-superconductor thin films and electronic devices began within weeks of the initial discovery in early 1987 of superconductivity above liquid-nitrogen temperature. The ensuing period has seen remarkable progress, spurred by innovations in deposition technology, materials characterization and device design. Prospects for practical electronic applications of superconductivity have driven the development of high-temperature-superconductor thin-film technology at an unprecedented pace. After five years researchers in the field have surmounted many of the initial hurdles in developing the new materials, and they are now working toward the first practical implementations of high-temperature-superconductor electronic technology.
US Energy Transition: On Getting from Here to There
Authors: Gibbons John H. , Blair Peter D.
Published: January 2008

Uncommon events like the Exxon Valdez oil spill, the Three Mile Island nuclear power plant meltdown and the Persian Gulf war as well as such unremitting problems as global climate change and the balance-of-payments deficit point up the urgency of dealing with the nation's energy issues. Congress is now deliberating President Bush's National Energy Strategy. The topic is hardly a new one. In fact, in the words of that immortal American philosopher Yogi Berra, “It's déjà vu all over again.”
Handedness, Origin of Life and Evolution
Authors: Avetisov Vladik A. , Kuz'min Vladimir V. , Goldanskii Vitalii I.
Published: January 2008

At first glance the nucleic acids and proteins that are the basis of life do not stand out in any way among all the possible polymeric structures. If we look at their functions, however, we find one unique feature of these biological polymers: self-replication, the distinctive property of living systems. What is self-replication, and how could this biologically primordial property have originated in an unorganized medium? The solution to the problem of life's origin lies in resolving the paradox of how polymers of rather common structure can exhibit such a distinctive function.
Advice to Beginning Physics Speakers
Authors: Garland James C.
Published: January 2008

If you're a physics graduate student, it's highly likely that before you receive your degree, you'll be asked to give a talk on your research—possibly at an APS meeting, or maybe just to fellow students. And once you finally graduate, you'll undoubtedly find yourself standing behind a podium. Whatever the situation, it's going to matter that your presentation be well received and that your audience depart with a favorable impression.
Health Effects of Low-Level Ionizing Radiation
Authors: Upton Arthur C.
Published: January 2008

The effects of ionizing radiation have received greater study than those of any other environmental agent. Within months after Wilhelm Roentgen's discovery of the x ray in 1895, early radiation workers experienced injurious effects of overexposure to radiation. In the century since, the study of such effects has received continuing impetus from the expanding use of radiation in medicine, science and industry and from the peaceful and military applications of nuclear energy.
The Physicists Intervene
Authors: Swartz Clifford
Published: January 2008

In 1826 Joseph Henry went down from Albany, New York, to visit the United States Military Academy at West Point. He observed that one article very necessary in teaching chemestrys is found in this room. VIZ. a blackboard on which the student is taught the atomic theory and all algebraic formula and chemistry. Indeed, it appears to be one of the principles of teaching in this institution that everything as far as practical should be demonstrated on the blackboard.
Nasa's Small Explorer Program
Authors: Baker Daniel N. , Chin Gordon , Pfaff Robert F.
Published: January 2008

Substantial publicity surrounds NASA's major scientific space missions. The Voyager interplanetary probes enthralled the public as they swept past the outer planets. The Hubble Space Telescope continues to attract great attention because of its ambitious objectives and large cost as well as its technical difficulties. NASA's deep space missions, such as Pioneer, Viking, Magellan, Galileo and Ulysses, and its “moderate” missions such as the Cosmic Background Explorer are further examples of large, longterm projects. Near-Earth spacecraft like the recently launched Gamma Ray Observatory and the many satellites of the planned International Solar Terrestrial Physics program also cost hundreds of millions of dollars. Indeed, with the attention given to programs involving humans in space—Space Station Freedom and the Manned Mission to Mars, for example—it might appear that NASA has only “big ticket” space missions.
Roundtable: New Challenges for the National Labs
Authors: Allen Lew , Buchsbaum Solomon J. , Gibbons John H. , Hecker Siegfried S. , Knapp Edward A. , Yonas Gerold , Lubkin Gloria B. , Goodwin Irwin , Levi Barbara G.
Published: January 2008

The birth of national research laboratories in the US is marked by the founding of the Bureau of Standards at the turn of the 20th century. As the country was about to enter World War I, the government organized the National Advisory Committee for Aeronautics, which actually performed R&D to help the fledgling field of aviation get airborne, and the Naval Consulting Board that quickly fostered the Naval Research Laboratory. Both NACA and NRL were formed to advance the country's defenses. While government labs may have seemed strange in a nation dedicated to free enterprise, the concept of research laboratories was familiar to corporate America. By World War I, research labs were spewing forth new products at General Electric, Westinghouse Electric, DuPont, Eastman Kodak, Corning Glass Works and American Telephone and Telegraph. It was World War II that provided the impetus for a proliferation of government laboratories. One of the earliest was the Radiation Laboratory at MIT, where the British invention of microwave radar was transformed from an engineering curiosity to a practical technology. The Advisory Committee on Uranium, initiated at the urging of prominent physicists in 1939, after nuclear fission was discovered in Germany, led the Army to organize the Manhattan Project in 1943 to produce atomic bombs. The Manhattan Project itself spawned a remarkable network of laboratories to advance nuclear weapons and perform fundamental research: Los Alamos, Oak Ridge, Argonne, Lawrence Radiation Laboratory, Ames, Bettis and Brookhaven. Soon after the war, these labs were designated by Congress as government-owned and contractor-operated, placed under the aegis of the civilian-dominated Atomic Energy Commission and managed by either major universities or industrial firms. Aware of the advantages of using high technology in modern warfare, the armed services had initiated their own laboratories to further their military missions. Some were organized before and during the war, others after the postwar creation of the Defense Department. Six months after the Soviet Union launched its first Sputnik in 1957, NACA was transformed into NASA, which produced another group of national laboratories.
Research Management Today
Authors: Gilman John J.
Published: January 2008

The general problem besetting research management was stated succinctly centuries ago: There is nothing more difficult to take in hand, more perilous to conduct, or more uncertain in its success than to take the lead in the introduction of a new order of things, because the innovator has for enemies all those who have done well under the old condition, and lukewarm defenders in those who may do well under the new.
The 1990s: The Decade of Discovery
Authors: Bahcall John N.
Published: January 2008

Astronomers and astrophysicists have learned that the climates and weather patterns of planets in the solar system are driven by many of the same physical processes that create the Earth's environment; that stars form out of clouds of gas and eventually die either in quiet solitude or spectacular explosions; that most of the common chemical elements are created in explosions of stars; that stars group together in isolated galaxies; that galaxies and clusters of galaxies stretch in sheets and filaments as far as the largest telescopes can see; and that the universe itself was born in a violent explosion some 15×109 years ago. Most amazingly, we have learned that the laws of nature on Earth apply to the farthest reaches of the observable universe.
Radioastronomy in the 1990s
Authors: Kellermann Kenneth I. , Heeschen David S.
Published: January 2008

In the years immediately following World War II, radioastronomers concentrated on following up on the accidental wartime discovery by British and American radar operators of radio bursts from the Sun. However, the continued push toward shorter and shorter radio wavelengths, combined with greatly increased sensitivity and angular resolution, quickly led to a series of remarkable and unexpected discoveries. Radio galaxies, quasars, pulsars, interstellar masers, gravitational lenses and the microwave background radiation—all now familiar topics of the astronomical and popular literature—were discovered serendipitously because of their radio emissions. A new generation of radiotelescopes to be built in the 1990s, together with major improvements in existing instruments, will give even further large gains in sensitivity, angular resolution and image quality, especially in the newly opened millimeter and submillimeter regions of the electromagnetic spectrum.
Time-Scale Invariance in Transport and Relaxation
Authors: Scher Harvey , Shlesinger Michael F. , Bendler John T.
Published: January 2008

An early theme in probability was calculating the fair ante for various games of chance. Nicolas Bernoulli introduced a seemingly innocent game, first published in 1713, that yielded a paradoxical result. The result has become known as the St. Petersburg paradox, because of an analysis written later by Daniel Bernoulli in the Commentary of the St. Petersburg Academy.
Synthesis of Oxide Superconductors
Authors: Sleight Arthur W.
Published: January 2008

From the discovery of oxide superconductors in 1964, there were frequent indications that these materials are metastable. This lack of thermodynamic stability has now become one of the predominant issues in the synthesis of the high-temperature superconductors. Once prepared, metastable superconductors possess sufficient kinetic stability that we generally need have no concern that they will decompose into more stable phases that are not superconducting. Nonetheless, our understanding of the issues relating to the stability of the known superconductors greatly influences our approaches to synthesizing them. Furthermore, understanding the relationship between instabilities and the mechanism of high-Tc superconductivity could be the key to the synthesis of superconductors with even higher critical temperatures.
Space Astronomy and Astrophysics
Authors: Canizares Claude R. , Savage Blair D.
Published: January 2008

Nearly everything we know about the cosmos comes from studying celestial electromagnetic radiation over roughly 16 decades of wavelength from radio to gamma ray. But most radiation is totally absorbed by our atmosphere—only radio and optical waves penetrate to Earth, and even these are subject to distortion or interference. The ability of space astronomy to escape the effects of Earth's atmosphere has literally opened new windows on the heavens, windows through which we have glimpsed a universe far more diverse than previously known and tantalizingly rich with information about its structure and evolution.
Noise in solid-state nanopores
Authors: Smeets R. M. M. , Keyser U. F. , Dekker N. H. , Dekker C.
Published: January 2008

We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (
f
≲ 100 Hz) we observe 1/
f
-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter α = (1.1 ± 0.1) × 10
−4
. In the high-frequency regime (
f
≳ 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency.
Hydrogen peroxide scavenging rescues frataxin deficiency in a
Drosophila
model of Friedreich's ataxia
Authors: Anderson Peter R. , Kirby Kim , Orr William C. , Hilliker Arthur J. , Phillips John P.
Published: January 2008

Friedreich's ataxia (FRDA) is a neurodegenerative disorder arising from a deficit of the mitochondrial iron chaperone, frataxin. Evidence primarily from yeast and mammalian cells is consistent with the hypothesis that a toxic hydroxyl radical generated from hydrogen peroxide (H
2
O
2
) via iron-catalyzed Fenton chemistry at least partially underlies the pathology associated with this disease. However, no whole-organism studies have been presented that directly test this hypothesis. We recently developed a
Drosophila
model that recapitulates the principal hallmarks of FRDA [Anderson PR, Kirby K, Hilliker A, Phillips JP (2005)
Hum Mol Genet
14:3397–3405]. Using the
Drosophila
FRDA model, we now report that ectopic expression of enzymes that scavenge H
2
O
2
suppresses the deleterious phenotypes associated with frataxin deficiency. In contrast, genetic augmentation with enzymes that scavenge superoxide is without effect. Augmentation of endogenous catalase restores the activity of the reactive oxygen species (ROS)-sensitive mitochondrial enzyme, aconitase and enhances resistance to H
2
O
2
exposure, both of which are diminished by frataxin deficiency. Collectively, these data argue that H
2
O
2
is an important pathogenic substrate underlying the phenotypes arising from frataxin deficiency in
Drosophila
and that interventions that reduce this specific ROS can effectively ameliorate these phenotypes. The therapeutic implications of these findings are clear and we believe warrant immediate clinical investigation.
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit
Authors: Simonović Miljan , Steitz Thomas A.
Published: January 2008

Recently, two crystal structures of the
Thermus thermophilus
70S ribosome in the same functional state were determined at 2.8 and 3.7 Å resolution but were different throughout. The most functionally significant structural differences are in the conformation of the peptidyl-transferase center (PTC) and the interface between the PTC and the CCA end of the P-site tRNA. Likewise, the 3.7 Å PTC differed from the functionally equivalent structure of the
Haloarcula marismortui
50S subunit. To ascertain whether the 3.7 Å model does indeed differ from the other two, we performed cross-crystal averaging of the two 70S data sets. The unbiased maps suggest that the conformation of the PTC–CCA in the two 70S crystal forms is identical to that of the 2.8 Å 70S model as well as that of the
H. marismortui
50S subunit. We conclude that the structure of the PTC is the same in the functionally equivalent 70S ribosome and the 50S subunit.
The Sequential Activation of the Yeast HOG and SLT2 Pathways Is Required for Cell Survival to Cell Wall Stress
Authors: Bermejo Clara , Rodríguez Estefanía , García Raúl , Rodríguez-Peña Jose M. , Rodríguez de la Concepción María L. , Rivas Carmen , Arias Patricia , Nombela César , Posas Francesc , Arroyo Javier
Published: January 2008

Yeast mitogen-activated protein kinase (MAPK) signaling pathways transduce external stimuli into cellular responses very precisely. The MAPKs Slt2/Mpk1 and Hog1 regulate transcriptional responses of adaptation to cell wall and osmotic stresses, respectively. Unexpectedly, we observe that the activation of a cell wall integrity (CWI) response to the cell wall damage caused by zymolyase (β-1,3 glucanase) requires both the HOG and SLT2 pathways. Zymolyase activates both MAPKs and Slt2 activation depends on the Sho1 branch of the HOG pathway under these conditions. Moreover, adaptation to zymolyase requires essential components of the CWI pathway, namely the redundant MAPKKs Mkk1/Mkk2, the MAPKKK Bck1, and Pkc1, but it does not require upstream elements, including the sensors and the guanine nucleotide exchange factors of this pathway. In addition, the transcriptional activation of genes involved in adaptation to cell wall stress, like CRH1, depends on the transcriptional factor Rlm1 regulated by Slt2, but not on the transcription factors regulated by Hog1. Consistent with these findings, both MAPK pathways are essential for cell survival under these circumstances because mutant strains deficient in different components of both pathways are hypersensitive to zymolyase. Thus, a sequential activation of two MAPK pathways is required for cellular adaptation to cell wall damage.
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus
Authors: Liao Yu-Chieh , Lee Min-Shi , Ko Chin-Yu , Hsiung Chao A.
Published: January 2008

Motivation: Continual and accumulated mutations in hemagglutinin (HA) protein of influenza A virus generate novel antigenic strains that cause annual epidemics.

Results: We propose a model by incorporating scoring and regression methods to predict antigenic variants. Based on collected sequences of influenza A/H3N2 viruses isolated between 1971 and 2002, our model can be used to accurately predict the antigenic variants in 1999–2004 (agreement rate = 91.67%). Twenty amino acid positions identified in our model contribute significantly to antigenic difference and are potential immunodominant positions.

Contact: hsiung@nhri.org.tw

Supplementary information: The supplementary information includes 62 amino acid sequences of H3N2 viruses and 277 pair-wise antigenic distances.
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
Authors: Kremling A. , Bettenbrock K. , Gilles E. D.
Published: January 2008

Motivation: In Escherichia coli, the phosphoenolpyruvate: carbohydrate phosphotransferase system acts like a sensory element which is able to measure the flux through glycolysis. Since the output of the sensor, the phosphorylated form of protein EIIA, is connected to the activity of the global transcription factor Crp, the kinetic and structural properties of the system are important for the understanding of the overall cellular behavior.

Results: A family of mathematical models is presented, varying with respect to their degree of complexity (number of reactions that are taken into account, number of parameters) that show a structurally and quantitatively robust behavior. The models describe a set of experimental data that relates the output of the sensor to the specific growth rate. A central element that is responsible for the structural robustness is a feed-forward loop in the glycolysis, namely the activation of the pyruvate kinase reaction by a metabolite of the upper part of the glycolysis. The robustness is shown for variations of the measured data as well as for variations of the parameters.

Availability: MATLAB files for model simulations are available on http://www.mpi-magdeburg.mpg.de/people/kre/robust/ A short description of the files provided on this site can be found in the Supporting information.

Contact:  kremling@mpi-magdeburg.mpg.de
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Authors: Khatun Jainab , Hamlett Eric , Giddings Morgan C.
Published: January 2008

Motivation: The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of identification we applied a machine-learning approach using a hidden Markov model (HMM) to capture the complex and often subtle links between a peptide sequence and its MS/MS spectrum.

Model: Our model, HMM_Score, represents ion types as HMM states and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types and the intensity dependence of ion types. The Viterbi algorithm is used to calculate the most probable assignment between ion types in a spectrum and a peptide sequence, then a correction factor is added to account for the propensity of the model to favor longer peptides. An expectation value is calculated based on the model score to assess the significance of each peptide/spectrum match.

Results: We trained and tested HMM_Score on three data sets generated by two different mass spectrometer types. For a reference data set recently reported in the literature and validated using seven identification algorithms, HMM_Score produced 43% more positive identification results at a 1% false positive rate than the best of two other commonly used algorithms, Mascot and X!Tandem. HMM_Score is a highly accurate platform for peptide identification that works well for a variety of mass spectrometer and biological sample types.

Availability: The program is freely available on ProteomeCommons via an OpenSource license. See http://bioinfo.unc.edu/downloads/ for the download link.

Contact:  giddings@unc.edu, giddings@med.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Evidence for population structuring of blue whiting (Micromesistius poutassou) in the Northeast Atlantic
Authors: Was Anna , Gosling Elizabeth , McCrann Karen , Mork Jarle
Published: January 2008

Was, A., Gosling, E., McCrann, K., and Mork, J. 2008. Evidence for population structuring of blue whiting (Micromesistius poutassou) in the Northeast Atlantic. – ICES Journal of Marine Science, 65: 216–225. Many marine fish species are characterized by large population sizes, strong migratory behaviour, high fecundity, and pelagic eggs and larvae that are subject to passive transport by ocean currents, all factors that tend to reduce the rate of development of genetic partitioning among localized populations. The blue whiting (Micromesistius poutassou) is a commercially important gadoid that exhibits all these characteristics, although to date there has been little evidence of genetic heterogeneity except at the latitudinal extremes of its range in the NE Atlantic. Genetic variation was analysed at five microsatellite loci in 16 samples, 14 comprising spawning adults, collected along the continental shelf from 44°N to 60°N, a distance of ∼1900 km. Although pairwise FST values were low (0.0–0.040; mean 0.0097), more than 40% of the estimates were significant, with Celtic Sea and Bay of Biscay samples significantly differentiated from samples from the Porcupine Bank, Hebridean Shelf, Sulisker Bank, and Papa Bank. There was also significant differentiation between samples taken in different years on Rockall Bank. Mantel tests revealed no significant isolation by distance. We used a landscape genetics approach, which combines spatial and genetic information, to detect barriers to gene flow. Four zones of lowered gene flow were identified, generally in concordance with hydrographic patterns, fish spawning behaviour, and the simulated transport of larvae in the NE Atlantic Ocean.
Pathogenesis ofEutypa latain Grapevine: Identification of Virulence Factors and Biochemical Characterization of Cordon Dieback
Authors: Rolshausen P. E. , Greve L. C. , Labavitch J. M. , Mahoney N. E. , Molyneux R. J. , Gubler W. D.
Published: January 2008

Eutypa lata is a vascular pathogen of woody plants. In the present study we (i) determined which component(s) of the cell wall polymers were degraded in naturally infected grapevines and in artificially inoculated grape wood blocks; (ii) compared the pattern of wood decay in the tolerant grape cv. Merlot versus the susceptible cv. Cabernet Sauvignon; and (iii) identified secondary metabolites and hydrolytic enzymes expressed by E. lata during wood degradation. Biochemical analyses and a cytochemical study indicated that glucose-rich polymers were primary targets of E. lata. Structural glucose and xylose of the hemicellulose fraction of the plant cell wall and starch were depleted in infected woods identically in both cultivars. Moreover, the more tolerant cv. Merlot always had more lignin in the wood than the susceptible cv. Cabernet Sauvignon, indicating that this polymer may play a role in disease resistance. In vitro assays demonstrated the production by E. lata of oxidases, glycosidases and starch degrading enzymes. Phytotoxic secondary metabolites were also produced but our data suggest that they may bind to the wood. Finally, we demonstrated that free glucose in liquid cultures repressed primary but not secondary metabolism.
Functional Characterization of PaLAX1, a Putative Auxin Permease, in Heterologous Plant Systems
Authors: Hoyerová Klára , Perry Lucie , Hand Paul , Laňková Martina , Kocábek Tomáš , May Sean , Kottová Jana , Pačes Jan , Napier Richard , Zažímalová Eva
Published: January 2008

We have isolated the cDNA of the gene PaLAX1 from a wild cherry tree (Prunus avium). The gene and its product are highly similar in sequences to both the cDNAs and the corresponding protein products of AUX/LAX-type genes, coding for putative auxin influx carriers. We have prepared and characterized transformed Nicotiana tabacum and Arabidopsis thaliana plants carrying the gene PaLAX1. We have proved that constitutive overexpression of PaLAX1 is accompanied by changes in the content and distribution of free indole-3-acetic acid, the major endogenous auxin. The increase in free indole-3-acetic acid content in transgenic plants resulted in various phenotype changes, typical for the auxin-overproducing plants. The uptake of synthetic auxin, 2,4-dichlorophenoxyacetic acid, was 3 times higher in transgenic lines compared to the wild-type lines and the treatment with the auxin uptake inhibitor 1-naphthoxyacetic acid reverted the changes caused by the expression of PaLAX1. Moreover, the agravitropic response could be restored by expression of PaLAX1 in the mutant aux1 plants, which are deficient in auxin influx carrier activity. Based on our data, we have concluded that the product of the gene PaLAX1 promotes the uptake of auxin into cells, and, as a putative auxin influx carrier, it affects the content and distribution of free endogenous auxin in transgenic plants.
Time flies: the geological record of insects
Authors: JARZEMBOWSKI ED , ROSS ANDREW
Published: January 2008

Two recent databases show that the fossil record of insects is better than commonly supposed, comprising over 1000 families and 5000 genera. Insects (hexapods) first appeared in the Devonian, but by the Permian the number of orders present was similar to that of the present day. However, family data suggest an unsteady increase in diversity during the Phanerozoic, with four main peaks and troughs but no sudden change (supported by genera) at the Cretaceous/Tertiary transition.
Roles of distinct glutamate receptors in induction of anti‐Hebbian long‐term potentiation
Authors: Kullmann Dimitri M. , Lamsa Karri
Published: January 2008

Many glutamatergic synapses on interneurons involved in feedback inhibition in the CA1 region of the hippocampus exhibit an unusual form of long‐term potentiation (LTP) that is induced only if presynaptic glutamate release occurs when the postsynaptic membrane potential is relatively hyperpolarized. We have named this phenomenon ‘anti‐Hebbian’ LTP because it is prevented by postsynaptic depolarization during afferent activity, and hence its induction requirements are opposite to those of Hebbian NMDA receptor‐dependent LTP. This symposium report addresses the roles of distinct glutamate receptors in the induction of anti‐Hebbian LTP. Inwardly rectifying Ca2+‐permeable AMPA receptors mediate fast glutamatergic signalling at synapses that exhibit this form of LTP, and they are highly likely to mediate the instructive signal that triggers the cascade leading to synapse strengthening. NMDA receptors, on the other hand, play no role, nor do they contribute substantially to synaptic transmission at synapses that exhibit anti‐Hebbian LTP. Both kainate and group I metabotropic glutamate receptors are abundant in at least some interneurons in the feedback inhibitory circuit. Delineating the roles of kainate receptors has been hampered by sub‐optimal pharmacological tools. As for group I metabotropic glutamate receptors, their role in anti‐Hebbian LTP is permissive at the very least in some interneuron types, although an instructive role has been suggested in other forms of activity‐dependent plasticity.