bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecohydrologic process networks: 1. Identification
Authors: Ruddell Benjamin L. , Kumar Praveen
Published: March 2009

Ecohydrological systems may be characterized as nonlinear, complex, open dissipative systems. Such systems consist of many coupled processes, and the couplings change depending on the system state or scale in space and time at which the system is analyzed. The arrangement of couplings in a complex system may be represented as a network of information flow and feedback between variables that measure system processes. The occurrence of feedback on such a network provides sufficient conditions for self‐organized and nonlinear behaviors to emerge. We adapt an information‐theoretic statistical method called transfer entropy for the purposes of robustly measuring the directionality, relative strength, statistical significance, and time scale of information flow between pairs of ecohydrological variables using time series data. A process network may be delineated where variables are cast as nodes and information flows as weighted directional links between them. The process network captures key couplings and time scales and represents the state of the complex system as a whole, including functional groups of variables (subsystems) and synchronization resulting from feedbacks. It is therefore able to identify interactions which are not detectable using methods which examine the system using one relationship at a time. We assemble an information flow process network using July 2003 FLUXNET data for a Midwestern corn‐soybean ecohydrological system in a healthy, peak growing season state and compare the results with those using July 2005 data for the same site during a severe drought. We find that the process network during drought is substantially decoupled, and regional‐scale information feedback is reduced during the drought. We conclude that the proposed process network methodology is able to identify the differences between two states of an ecohydrological system on the basis of variations in the pattern of feedback coupling on the network.
Ecohydrologic process networks: 2. Analysis and characterization
Authors: Ruddell Benjamin L. , Kumar Praveen
Published: March 2009

Ecohydrological systems are complex, open dissipative systems characterized by couplings and feedback between subsystems at many scales of space and time. The information flow process network approach is developed to analyze such systems, using time series data to delineate the feedback, time scales, and subsystems that define the complex system's organization. Network statistics are used to measure the statistical feedback, entropy, and net and gross information production of subsystems on the network to study monthly process networks for a Midwestern corn‐soybean ecosystem for the years 1998–2006. Several distinct system states are identified and characterized. Particularly interesting is the midsummer state that is dominated by regional‐scale information feedback and by information flow originating from the ecosystem's photosynthetic activity. In this state, information flows both “top‐down” from synoptic weather systems and “bottom‐up” from the plant photosynthetic activity. A threshold in air temperature separates this summer state where increased organization appears from other system states. The relationship between Shannon entropy and information flow is investigated. It is found that information generally flows from high‐entropy variables to low‐entropy variables, and moderate‐entropy variables participate in feedback.
Eastern U.S. coastal wetlands loss
Authors: Showstack Randy
Published: March 2009

While freshwater wetlands in the United States increased between 1998 and 2004, U.S. coastal watersheds of the Great Lakes, Atlantic Ocean, and Gulf of Mexico lost a total of 59,000 acres each year during the same period, according to “Status and trends of wetlands in the coastal watersheds of the eastern United States, 1998 to 2004,” a report issued on 17 February 2008 by the U.S. National Oceanic and Atmospheric Administration (NOAA) and the U.S. Fish and Wildlife Service.
Jules Aarons (1921–2008)
Authors: Mendillo Michael
Published: March 2009

Jules Aarons, a pioneer in satellite radio beacon studies of the ionosphere, died peacefully at his home in Newton, Mass., on 21 November 2008 at age 87. When considering his college career, Jules was drawn toward the humanities, an interest subsequently redirected by his parents toward science as a more suitable way to earn a living, and then by the U.S. Army Air Corps toward radio technology as a more suitable way to win World War II. Both goals were readily accomplished, perhaps instilling in Jules the value of proper mentorship, that central aspect of his life that so dominates our recollections of him.
Providing Sufficient Streamflows in an Era of Competing Demands: FLOW 2008: Interdisciplinary Solutions to Instream Flow Problems; San Antonio, Texas, 7–9 October 2008
Authors: Gordon Wendy S. , Mayes Kevin , Williams Kathleen
Published: March 2009

The Instream Flow Council (IFC) held its first‐ever conference to forge interdisciplinary solutions to the problem of providing sufficient streamflows for environmental purposes in an era of competing demands for freshwater. Conference participants were drawn from across the United States and Canada and even as far away as China, representing state and provincial fish and wildlife and regulatory agencies, federal agencies including the U.S. Geological Survey and U.S. Environmental Protection Agency, nongovernmental organizations, consultants, industry, academics, and even private citizens. Attendees included biologists, geomorphologists, hydrologists, engineers, attorneys, social scientists, and policy makers. The goals of the meeting were to advance the integration of science and policy related to instream flow and to demonstrate the importance of public dialogue through the engagement of diverse stakeholders in cooperatively solving instream flow problems in the United States and Canada.
Parker Receives 2008 John Adam Fleming Medal
Authors: Jackson Andrew , Parker Robert L.
Published: March 2009

Robert L. Parker was awarded the 2008 John Adam Fleming Medal at the AGU Fall Meeting Honors Ceremony, held 17 December 2008 in San Francisco, Calif. The medal is for “original research and technical leadership in geomagnetism, atmospheric electricity, aeronomy, space physics, and related sciences.”
Fall 2008 Congressional Visits Day Focuses on Underfunding
Authors: Davis Brian
Published: March 2009

“Can't you fill my recruiting schedule with more students?” a company recruiter recently asked Andreas Kronenberg, professor and head of the Department of Geology and Geophysics at Texas A&M University. Kronenberg gave a simple, honest answer: “No.” He shared that anecdote with U.S. Representative Chet Edwards (D‐Tex.) to underscore the fact that a number of college students are majoring in subjects other than geosciences due to the lack of secure funding and jobs in that field. Kronenberg had met with Edwards during AGU's fall 2008 Congressional Visits Day (CVD), a 2‐day program when more than 60 scientists discussed with their legislators the importance of science funding.
Land‐atmosphere coupling and diurnal temperature range over the contiguous United States
Authors: Zhang Jingyong , Wang Wei‐Chyung , Wu Lingyun
Published: March 2009

Soil moisture influences on daily maximum (Tmax) and minimum (Tmin) temperatures, and thus the diurnal temperature range (DTR) in summer, are statistically quantified across the contiguous Unites States using soil moisture from the Global Land Data Assimilation System and observational temperatures. A soil moisture feedback parameter is computed based on lagged covariance ratios. Over the zone from California through the Midwest to the Southeast, the soil moisture exhibits a negative feedback on DTR mainly through its damping effect on Tmax. In contrast, a positive feedback on DTR dominates Arizona and New Mexico as the soil moisture exerts a stronger negative forcing on Tmin relative to Tmax. The feedback‐induced variability accounts for typically 10–20% of the total DTR variance over regions where strong feedbacks are identified. The results provide a useful benchmark for evaluating climate model simulations, although the employed data and method have limitations that should be recognized.
Vaccines, global health and social equity
Authors: Levine Myron M , Robins‐Browne Roy
Published: March 2009

Mortality rates of children less than 5 years old range from <10 per 1000 live births in industrialized countries to >100 in the world's poorest countries. The fact that in New York City infant mortality fell from ∼140 deaths per 1000 live births in 1900 to <60 per 1000 by 1930 indicates what can be achieved through improvements in public health, such as the provision of clean piped water, sewage disposal and fresh refrigeration. For children living in impoverished conditions today, excess mortality is largely due to infectious diseases for which there are effective vaccines. Thus, certain specific vaccines can reduce mortality and morbidity, improve quality of life and contribute to economic development. However, because many vaccines and the means to deliver them are beyond the financial resources of countries with the highest childhood mortality rates, strategies have been devised to provide vaccines to the most needy populations. These strategies include initiatives by the Global Alliance for Vaccines and Immunization, the International Finance Facility for Immunization and the Advanced Market Commitment, which together with various governments, international agencies and charitable foundations are providing funds to make life‐saving vaccines available to the world's most needy children.
IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways inEscherichia coliunder aerobic growth conditions
Authors: Tan Guoqiang , Lu Jianxin , Bitoun Jacob P. , Huang Hao , Ding Huangen
Published: March 2009

IscA/SufA paralogues are the members of the iron-sulfur cluster assembly machinery in Escherichia coli. Whereas deletion of either IscA or SufA has only a mild effect on cell growth, deletion of both IscA and SufA results in a null-growth phenotype in minimal medium under aerobic growth conditions. Here we report that cell growth of the iscA/sufA double mutant (E. coli strain in which both iscA and sufA had been in-frame-deleted) can be partially restored by supplementing with BCAAs (branched-chain amino acids) and thiamin. We further demonstrate that deletion of IscA/SufA paralogues blocks the [4Fe-4S] cluster assembly in IlvD (dihydroxyacid dehydratase) of the BCAA biosynthetic pathway in E. coli cells under aerobic conditions and that addition of the iron-bound IscA/SufA efficiently promotes the [4Fe-4S] cluster assembly in IlvD and restores the enzyme activity in vitro, suggesting that IscA/SufA may act as an iron donor for the [4Fe-4S] cluster assembly under aerobic conditions. Additional studies reveal that IscA/SufA are also required for the [4Fe-4S] cluster assembly in enzyme ThiC of the thiamin-biosynthetic pathway, aconitase B of the citrate acid cycle and endonuclease III of the DNA-base-excision-repair pathway in E. coli under aerobic conditions. Nevertheless, deletion of IscA/SufA does not significantly affect the [2Fe-2S] cluster assembly in the redox transcription factor SoxR, ferredoxin and the siderophore-iron reductase FhuF. The results suggest that the biogenesis of the [4Fe-4S] clusters and the [2Fe-2S] clusters may have distinct pathways and that IscA/SufA paralogues are essential for the [4Fe-4S] cluster assembly, but are dispensable for the [2Fe-2S] cluster assembly in E. coli under aerobic conditions.
An end to 40 years of mistakes in DNA–protein association kinetics?
Authors: Halford Stephen E.
Published: March 2009

Proteins that bind to specific sequences in long DNA molecules have to locate their target sites amid myriad alternative sequences, yet they do so at remarkably rapid rates, sometimes approaching 1010 M−1·s−1. Hence, it has been asserted widely that binding to specific DNA sites can surpass the maximal rate for 3D (three-dimensional) diffusion through solution and that this could only be accounted for by a reduction in the dimensionality of the search for the target in effect by 1D (one-dimensional) diffusion (or ‘sliding’) along the DNA contour. It will be shown here that there is, in fact, no known example of a protein binding to a specific DNA site at a rate above the diffusion limit, and that the rapidity of these reactions is due primarily to electrostatic interactions between oppositely charged molecules. It will also be shown that, contrary to popular belief, reduced dimensionality does not, in general, increase the rate of target-site location but instead reduces it. Finally, it will be demonstrated that proteins locate their target sites primarily by multiple dissociation/reassociation events to other (nearby or distant) sites within the same DNA molecule, and that 1D diffusion is limited to local searches covering ∼50 bp around each landing site.
Probing coupled motions in enzymatic hydrogen tunnelling reactions
Authors: Allemann Rudolf K. , Evans Rhiannon M. , Loveridge E. Joel
Published: March 2009

Much work has gone into understanding the physical basis of the enormous catalytic power of enzymes over the last 50 years or so. Nevertheless, the detailed mechanism used by Nature's catalysts to speed chemical transformations remains elusive. DHFR (dihydrofolate reductase) has served as a paradigm to study the relationship between the structure, function and dynamics of enzymatic transformations. A complex reaction cascade, which involves rearrangements and movements of loops and domains of the enzyme, is used to orientate cofactor and substrate in a reactive configuration from which hydride is transferred by quantum mechanical tunnelling. In the present paper, we review results from experiments that probe the influence of protein dynamics on the chemical step of the reaction catalysed by TmDHFR (DHFR from Thermotoga maritima). This enzyme appears to have evolved an optimal structure that can maintain a catalytically competent conformation under extreme conditions.
Conformational changes in the catalytic cycle of protochlorophyllide oxidoreductase: what lessons can be learnt from dihydrofolate reductase?
Authors: Heyes Derren J. , Scrutton Nigel S.
Published: March 2009

In chlorophyll biosynthesis, the light-activated enzyme, POR (protochlorophyllide oxidoreductase), has been shown to be an excellent model system for studying the role of protein motions during catalysis. The catalytic cycle of POR is understood in detail and comprises an initial photochemical reaction, which is followed by a number of ‘dark’ steps. The latter steps in the reaction cycle have been shown to involve a series of ordered product release and substrate rebinding events and are known to require conformational changes in the protein in order to proceed. However, owing to the current lack of any structural information on the enzyme, the nature of these conformational rearrangements remains poorly understood. By contrast, there is a wealth of structural and kinetic information available on the closely related enzyme dihydrofolate reductase, which is known to have a similar catalytic mechanism to POR. Dihydrofolate reductase is able to adopt an ‘occluded’ and a ‘closed’ structure, depending on which ligand is bound in the active site, and as a result, the catalytic cycle is controlled by a ‘switching’ between these two conformations. By analogy, we suggest that a similar cycling between different conformations may be operating in POR.
Opportunities for mesoporous nanocrystalline SnO2 electrodes in kinetic and catalytic analyses of redox proteins
Authors: Kemp Gemma L. , Marritt Sophie J. , Xiaoe Li , Durrant James R. , Cheesman Myles R. , Butt Julea N.
Published: March 2009

PFV (protein film voltammetry) allows kinetic analysis of redox and coupled-chemical events. However, the voltammograms report on the electron transfer through a flow of electrical current such that simultaneous spectroscopy is required for chemical insights into the species involved. Mesoporous nanocrystalline SnO2 electrodes provide opportunities for such ‘spectroelectrochemical’ analyses through their high surface area and optical transparency at visible wavelengths. Here, we illustrate kinetic and mechanistic insights that may be afforded by working with such electrodes through studies of Escherichia coli NrfA, a pentahaem cytochrome with nitrite and nitric oxide reductase activities. In addition, we demonstrate that the ability to characterize electrocatalytically active protein films by MCD (magnetic circular dichroism) spectroscopy is an advance that should ultimately assist our efforts to resolve catalytic intermediates in many redox enzymes.
Tryptophan 13C nuclear-spin polarization generated by intraprotein electron transfer in a LOV2 domain of the blue-light receptor phototropin
Authors: Eisenreich Wolfgang , Fischer Markus , Römisch-Margl Werner , Joshi Monika , Richter Gerald , Bacher Adelbert , Weber Stefan
Published: March 2009

13C-NMR experiments were performed on photo-excited fully and partially 13C-labelled LOV2 domains of the blue-light receptor phototropin. In the present paper, we report on nuclear-spin polarized tryptophan resonances that are generated by light-induced intraprotein electron transfer to the FMN cofactor. The spectra are discussed with respect to earlier data obtained from 13C-NMR experiments on unlabelled LOV2 domains that have been reconstituted with FMN 13C isotopologues.
Ultrafast catalytic processes and conformational changes in the light-driven enzyme protochlorophyllide oxidoreductase (POR)
Authors: Sytina Olga A. , Heyes Derren J. , Hunter C. Neil , Groot Marie Louise
Published: March 2009

The enzyme POR (protochlorophyllide oxidoreductase), from the family of alcohol dehydrogenases, reduces protochlorophyllide into chlorophyllide on the absorption of light. The reduction involves the transfer of two protons and two electrons and is an important regulatory step in the biosynthesis of chlorophyll. In recent years, due to the availability of large quantities of the pure enzyme, much of the catalytic reaction has been unravelled by using a variety of spectroscopic methods, including ultrafast initial events in catalysis. In addition, it has been demonstrated that a light-activated conformational change of the protein is necessary to activate catalysis. This makes POR a very important model system to study the relationship between structural changes of enzymes and functionality.
The bacterial respiratory nitric oxide reductase
Authors: Watmough Nicholas J. , Field Sarah J. , Hughes Ross J. L. , Richardson David J.
Published: March 2009

The two-subunit cytochrome bc complex (NorBC) isolated from membranes of the model denitrifying soil bacterium Paracoccus denitrificans is the best-characterized example of the bacterial respiratory nitric oxide reductases. These are members of the super-family of haem-copper oxidases and are characterized by the elemental composition of their active site, which contains non-haem iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is catalysed. The reaction requires the presence of two substrate molecules at the active site along with the controlled input of two electrons and two protons from the same side of the membrane. In the present paper, we consider progress towards understanding the pathways of electron and proton transfer in NOR and how this information can be integrated with evidence for the likely modes of substrate binding at the active site to propose a revised and experimentally testable reaction mechanism.
Nucleic acid detection and quantification in the developing world
Authors: Huggett Jim , Green Clare , Zumla Alimuddin
Published: March 2009

Techniques using nucleic acid amplification have not had the same amount of impact on research and clinical diagnosis in the developing world as that observed in the West. This is unsurprising when the costs and infrastructure required to perform nucleic acid amplification are considered. Despite this, nucleic acid amplification is being increasingly used in both research and diagnosis in countries such as Zambia and Tanzania. Scientific research in the developing world is made possible through the support and development of the necessary laboratory infrastructure and the establishment of special transport for the reagents and samples. This has enabled world-leading country-relevant research to be performed by local scientists on subjects ranging from rapid diagnosis of infectious diseases to measuring the RNA gene expression in an immune response. Concomitantly, the challenge presented by the need for tests that are more appropriate for a resource-poor setting has led to a number of newer methodologies for nucleic acid detection, which can be tailored to be performed in the field without the need for training in molecular biology. As nucleic acid amplification techniques become both simpler and cheaper, their impact is likely to play an increasingly crucial role in research and diagnosis in the developing world.
Mutation scanning using high-resolution melting
Authors: Taylor Claire F.
Published: March 2009

Mutation scanning techniques are used to detect sequence variants without the need for prior knowledge of the identity or precise location of the variant, in contrast with genotyping techniques, which determine the status of a specific variant. High-resolution melting is a recently developed method that shows great potential as a mutation scanning technique. Sensitivity and specificity for mutation detection are extremely high and the technique also has advantages of cost and throughput. Practical considerations for successful mutation scanning by high-resolution melting are also discussed in this review.
Functionalized nanoparticles for nucleic acid sequence analysis using optical spectroscopies
Authors: Graham Duncan , Faulds Karen , Thompson David , Mackenzie Fiona , Stokes Robert , Macaskill Alexandra
Published: March 2009

SERRS (surface-enhanced resonance Raman scattering) is a vibrational spectroscopy which allows extremely sensitive and selective detection of labelled DNA sequences with detection limits which rival, and in most cases surpass, that of fluorescence. SERRS relies on a visible chromophore adsorbing on to an enhancing surface. DNA itself is not SERRS-active, as it lacks a suitable visible chromophore and has poor adsorption properties on to the surfaces used for enhancement. The surface normally used for enhancement in these sorts of studies are metallic nanoparticles and, through modification of DNA probes by the addition of suitable SERRS labels, signals can be obtained that are highly sensitive and very selective. The aggregation state of the nanoparticles is critical to the sensitivity, and, in the present paper, we show how straightforward detection of labelled DNA probes can be achieved using SERRS in a quantitative manner and with a variety of different commercially available labels. In a second approach, we show how the properties of aggregation to turn on the SERRS effect can be exploited through DNA hybridization to give identification of a particular DNA sequence. This approach lends itself to closed-tube formats and is a promising way forward for molecular diagnostics using SERRS.
Optical fibre-based detection of DNA hybridization
Authors: Hine Anna V. , Chen Xianfeng , Hughes Marcus D. , Zhou Kaiming , Davies Edward , Sugden Kate , Bennion Ian , Zhang Lin
Published: March 2009

A dual-peak LPFG (long-period fibre grating), inscribed in an optical fibre, has been employed to sense DNA hybridization in real time, over a 1 h period. One strand of the DNA was immobilized on the fibre, while the other was free in solution. After hybridization, the fibre was stripped and repeated detection of hybridization was achieved, so demonstrating reusability of the device. Neither strand of DNA was fluorescently or otherwise labelled. The present paper will provide an overview of our early-stage experimental data and methodology, examine the potential of fibre gratings for use as biosensors to monitor both nucleic acid and other biomolecular interactions and then give a summary of the theory and fabrication of fibre gratings from a biological standpoint. Finally, the potential of improving signal strength and possible future directions of fibre grating biosensors will be addressed.
The SAFE project: towards non-invasive prenatal diagnosis
Authors: Maddocks Deborah G. , Alberry Medhat S. , Attilakos George , Madgett Tracey E. , Choi Kin , Soothill Peter W. , Avent Neil D.
Published: March 2009

After the revolutionary detection of ffDNA (free fetal DNA) in maternal circulation by real-time PCR in 1997 and advances in molecular techniques, NIPD (non-invasive prenatal diagnosis) is now a clinical reality. Non-invasive diagnosis using ffDNA has been implemented, allowing the detection of paternally inherited alleles, sex-linked conditions and some single-gene disorders and is a viable indicator of predisposition to certain obstetric complications [e.g. PET (pre-eclampsia)]. To date, the major use of ffDNA genotyping in the clinic has been for the non-invasive detection of the pregnancies that are at risk of HDFN (haemolytic disease of the fetus and newborn). This has seen numerous clinical services arising across Europe and many large-scale NIPD genotyping studies taking place using maternal plasma. Because of the interest in performing NIPD and the speed at which the research in this area was developing, the SAFE (Special Non-Invasive Advances in Fetal and Neonatal Evaluation) NoE (Network of Excellence) was founded. The SAFE project was set up to implement routine, cost-effective NIPD and neonatal screening through the creation of long-term partnerships within and beyond the European Community and has played a major role in the standardization of non-invasive RHD genotyping. Other research using ffDNA has focused on the amount of ffDNA present in the maternal circulation, with a view to pre-empting various complications of pregnancy. One of the key areas of interest in the non-invasive arena is the prenatal detection of aneuploid pregnancies, particularly Down's syndrome. Owing to the high maternal DNA background, detection of ffDNA from maternal plasma is very difficult; consequently, research in this area is now more focused on ffRNA to produce new biomarkers.
One-dimensional/two-dimensional loss measurements up to high inductions
Authors: Appino Carlo , Fiorillo Fausto , Ragusa Carlo
Published: March 2009

A thermometric-fieldmetric method has been developed by which Fe–Si laminations are characterized under either alternating or rotational excitation up to peak induction Bp=1.85 T in the frequency range 2 Hz≤f≤200 Hz. The measurement is performed on circular samples (diameter=140 mm) under digitally controlled one-dimensional/two-dimensional flux loci. The power losses at high inductions are determined by measurement of the rate of rise of the specimen temperature. Imperfect adiabatic behavior of the material is accounted for by physical modeling of the thermal diffusion process. The low-to-medium induction range, up to Bp∼1.7 T, is covered by conventional fieldmetric measurements, which, in conjunction with the thermometric approach, permit one to achieve a complete characterization of the magnetic sheets versus Bp and f.
High speed magneto-optical valve: Rapid control of the optical transmittance of aqueous solutions by magnetically induced self-assembly of superparamagnetic particle chains
Authors: Park S. Y. , Handa H. , Sandhu A.
Published: March 2009

Magneto-optical effects of magnetorheological fluids are of interest for applications including magnetic field sensors and optical modulators. Here, we describe the rapid control of the optical transmittance of a magnetorheological fluids by rotating columnar arrays of self-assembled superparamagnetic bead (SPB) chains by applying an external field using a permanent magnet. The columnar arrays of chains of magnetic beads acted as optical valves exhibiting distinct “on” and “off” states. For a given magnetic field, the maxima/minima of transmittance occurred when the applied field was parallel/perpendicular to light path and the intensity of light at the maxima varied with the strength of the applied field. Importantly, the response time for rotating the columnar arrays of magnetic chains was very rapid, and in the millisecond range. Our procedure provides a simple means for producing fast, magneto-optical switches that does not require cumbersome and power consuming electromagnetic coils and related peripheral equipment.
Magneto-optic material selectivity in self-assembled BiFeO3–CoFe2O4 biferroic nanostructures
Authors: Postava K. , Hrabovský D. , Životský O. , Pištora J. , Dix N. , Muralidharan R. , Caicedo J. M. , Sánchez F. , Fontcuberta J.
Published: March 2009

Material selective sensitivity of a magneto-optical polar Kerr effect to magnetic contributions from different inclusions in self-organized magnetic nanostructures is presented. The method is supported by modeling of the magneto-optic response based on the effective medium approximation and by hysteresis loop measurement of the multiferroic BiFeO3–CoFe2O4 self-assembled nanostructure. Magneto-optic selective sensitivity is demonstrated and explained as an effect of different complex diagonal and off-diagonal permittivity tensor elements of two materials.
Noise enhanced stability in magnetic systems
Authors: Trapanese Marco
Published: March 2009

In this paper noise enhanced stability in magnetic systems is studied by both an Ising-type model and a Preisach–Arrhenius model as well as a dynamic Preisach model. It is shown that in one nonequilibrium Ising system noise enhanced stability occurs and that dynamic Preisach model has the capability to predict the occurrence of noise enhanced stability in magnetic systems. On the contrary, in a Preisach–Arrhenius model of a single quadrant magnetic material, noise enhanced stability is not detected.
One parameter control of the size of iron oxide nanoparticles synthesized in reverse micelles
Authors: Shultz M. D. , Braxton W. , Taylor C. , Carpenter E. E.
Published: March 2009

Iron oxide nanoparticles were synthesized via reverse micelle methods. The initial iron concentration was varied, while maintaining all other parameters constant, in order to investigate the effect of the iron concentration on the resultant iron oxide nanoparticle size. Increasing the iron concentration from 0.125M to 0.5M yielded an increase in average nanoparticle diameter from 4.71 to 7.95 nm, as measured by transmission electron microscopy. Three other concentrations between 0.125M and 0.5M showed corresponding size variations, all with statistical significance. Magnetic characterization by vibrating sample magnetometry and powder x-ray diffraction was performed to verify proper phase and material. Further insight into the reverse micelle method was acquired along with the ability to tune the nanoparticle size.
Electronic structures and Hall effect in low-doped La0.9Hf0.1MnO3 epitaxial films
Authors: Wang L. , Gao J.
Published: March 2009

The electronic structures of low-doped epitaxial La0.9Hf0.1MnO3 (LHMO) thin films are investigated by x-ray photoemission spectroscopy (XPS) for the first time. XPS spectra of core levels (La 3d, Hf 4f, O 1s, Mn 2p, and Mn 3s) are taken from the cleaned LHMO film surface. Hf 4f spectrum exhibits a typical binding energy (BE=2 eV) of Hf4+. The splitting energy of La 3d core-lever spectrum agrees with the previous reports of other doped LaMnO3 and suggests a trivalent state in the LHMO film. The calculated result of LHMO nominal composition, the shape of Mn 2p spectrum, the separated BE (111.1 eV) between O 1s and Mn 2p2/3 peaks and the splitting energy (6.0 eV) of Mn 3s all reveal that the LHMO compound is in a mixed valence state of Mn2+ and Mn3+, implying an electron-doped conduction mechanism. The magnetic-field dependence of Hall resistivity further confirmed that the carriers in LHMO are electrons.
The influence of the stochastic features of the energy source on the design of an electromagnetic generator
Authors: Trapanese Marco
Published: March 2009

The purpose of this paper is to clarify, in a general way, how the unavoidable randomness of renewable energy sources influences the magnetic design of electric generator. A general model of electromagnetic generator based on the well known d-q axes analysis is given. The energy source is modeled as a stochastic variable and is included in the equations of the system. The equations are solved and, therefore, the energy output of the system is linked to the random characteristic of the energy source. As a result, the magnetic circuit and the parameters of the generator that maximize the energy extraction can be found and generally linked to the stochastic details of the source.
A dynamical systems proof of Kraft–McMillan inequality and its converse for prefix-free codes
Authors: Nagaraj Nithin
Published: March 2009

Uniquely decodable codes are central to lossless data compression in both classical and quantum communication systems. The Kraft–McMillan inequality is a basic result in information theory which gives a necessary and sufficient condition for a code to be uniquely decodable and also has a quantum analogue. In this letter, we provide a novel dynamical systems proof of this inequality and its converse for prefix-free codes (no codeword is a prefix of another—the popular Huffman codes are an example). For constrained sources, the problem is still open.
How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?
Authors: O’Brien Edward P. , Morrison Greg , Brooks Bernard R. , Thirumalai D.
Published: March 2009

Single molecule Förster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average FRET efficiency, ⟨E⟩, the distance distribution P(R) is inferred by assuming that the DSE can be described as a polymer. The single parameter in the appropriate polymer model (Gaussian chain, wormlike chain, or self-avoiding walk) for P(R) is determined by equating the calculated and measured ⟨E⟩. In order to assess the accuracy of this “standard procedure,” we consider the generalized Rouse model (GRM), whose properties [⟨E⟩ and P(R)] can be analytically computed, and the Molecular Transfer Model for protein L for which accurate simulations can be carried out as a function of guanadinium hydrochloride (GdmCl) concentration. Using the precisely computed ⟨E⟩ for the GRM and protein L, we infer P(R) using the standard procedure. We find that the mean end-to-end distance can be accurately inferred (less than 10% relative error) using ⟨E⟩ and polymer models for P(R). However, the value extracted for the radius of gyration (Rg) and the persistence length (lp) are less accurate. For protein L, the errors in the inferred properties increase as the GdmCl concentration increases for all polymer models. The relative error in the inferred Rg and lp, with respect to the exact values, can be as large as 25% at the highest GdmCl concentration. We propose a self-consistency test, requiring measurements of ⟨E⟩ by attaching dyes to different residues in the protein, to assess the validity of describing DSE using the Gaussian model. Application of the self-consistency test to the GRM shows that even for this simple model, which exhibits an order→disorder transition, the Gaussian P(R) is inadequate. Analysis of experimental data of FRET efficiencies with dyes at several locations for the cold shock protein, and simulations results for protein L, for which accurate FRET efficiencies between various locations were computed, shows that at high GdmCl concentrations there are significant deviations in the DSE P(R) from the Gaussian model.
Interband transition energies and carrier distributions of CdxZn1−xTe/ZnTe quantum wires
Authors: You J. H. , Woo J. T. , Kim T. W. , Yoo K. H. , Lee H. S. , Park H. L.
Published: March 2009

Interband transition energies and carrier distributions of the CdxZn1−xTe/ZnTe quantum wires (QWRs) were calculated by using a finite-difference method (FDM) taking into account shape-based strain effects. The shape of the CdxZn1−xTe/ZnTe QWRs was modeled to be approximately a half-ellipsoidal cylinder on the basis of the atomic force microscopy image. The excitonic peak energies corresponding to the ground electronic subband and the ground heavy-hole band (E1-HH1) at several temperatures, as determined from the FDM calculations taking into account strain effects, were in qualitatively reasonable agreement with those corresponding to the (E1-HH1) excitonic transition, as determined from the temperature-dependent photoluminescence spectra.
Gold-implanted shallow conducting layers in polymethylmethacrylate
Authors: Teixeira F. S. , Salvadori M. C. , Cattani M. , Brown I. G.
Published: March 2009

PMMA (polymethylmethacrylate) was ion implanted with gold at very low energy and over a range of different doses using a filtered cathodic arc metal plasma system. A nanometer scale conducting layer was formed, fully buried below the polymer surface at low implantation dose, and evolving to include a gold surface layer as the dose was increased. Depth profiles of the implanted material were calculated using the Dynamic TRIM computer simulation program. The electrical conductivity of the gold-implanted PMMA was measured in situ as a function of dose. Samples formed at a number of different doses were subsequently characterized by Rutherford backscattering spectrometry, and test patterns were formed on the polymer by electron beam lithography. Lithographic patterns were imaged by atomic force microscopy and demonstrated that the contrast properties of the lithography were well maintained in the surface-modified PMMA.
Comment on “Minimax approximation for the decomposition of energy denominators in Laplace-transformed Møller–Plesset perturbation theories” [J. Chem. Phys. 129, 044112 (2008)]
Authors: Kats Danylo , Usvyat Denis , Loibl Stefan , Merz Thomas , Schütz Martin
Published: March 2009

The recently proposed minimax quadrature for Laplace-transformed energy denominators in second order Møller–Plesset perturbation theory is compared to the conventionally used least-squares quadrature. Our test calculations show that the quality of the least-squares quadrature is not inferior compared to minimax. Its computational overhead (required to determine points and weights of the quadrature) is clearly insignificant relative to the subsequent MP2 calculation. For high accuracy and all-electron calculations (correlated core) good starting guesses for the roots are essential.
The role of oxygen in hydrogen sensing by a platinum-gate silicon carbide gas sensor: An ultrahigh vacuum study
Authors: Kahng Yung Ho , Lu Wei , Tobin R. G. , Loloee Reza , Ghosh Ruby N.
Published: March 2009

We report several experiments under ultrahigh vacuum conditions that elucidate the role of oxygen in the functioning of silicon carbide field-effect gas sensors with nonporous platinum gates. The devices studied are shown to be sensitive both to hydrogen and to propene. All of the results are consistent with oxygen acting through its surface reactions with hydrogen. Three specific aspects are highlighted: the need, under some conditions, for oxygen to reset the device to a fully hydrogen-depleted state; competition between hydrogen oxidation and hydrogen diffusion to metal/oxide interface sites, leading to steplike behavior as a function of the oxygen:hydrogen ratio (λ-sensing); and the removal of sulfur contamination by oxygen.
Model for intermediate band solar cells incorporating carrier transport and recombination
Authors: Lin Albert S. , Wang Weiming , Phillips Jamie D.
Published: March 2009

A model for intermediate band solar cells is presented to assess the effect of carrier transport and recombination (CTR) on the efficiency of these devices. The model includes dependencies of physical parameters including optical absorption, carrier lifetime, and carrier transport on the density of intermediate band electronic states. Simulation results using this model indicate that conversion efficiency degrades when the net carrier recombination lifetime is small (range of nanoseconds) or when the device length is long relative to carrier drift length. The intermediate band solar cell model provides a method of determining realistic conversion efficiencies based on experimentally measurable input parameters for CTR. The incorporation of CTR provides insight on the dependence of optimal density of states and energetic position of the intermediate band based on carrier lifetime and mobility. The material ZnTeO (EG=2.3 eV, EI=1.8 eV) is used as a numerical example for the intermediate band solar cell model, where conversion efficiency drops from 30.36% to 19.4% for a 10 μm long device for a recombination lifetime decrease from 1 μs to 5 ns. The optimal impurity concentration is determined to be 1018 cm−3 for an optical absorption cross section of 10−14 cm2. The conversion efficiency of a ZnTe solar cell with a total recombination lifetime of 10 ns is calculated to increase from 14.39% to 26.87% with the incorporation of oxygen.
Mechanisms of the laser plume expansion during the ablation of LiMn2O4
Authors: Canulescu S. , Papadopoulou E. L. , Anglos D. , Lippert Th. , Schneider C. W. , Wokaun A.
Published: March 2009

Films of LiMn2O4 prepared by pulsed laser ablation deposition are typically lithium deficient when grown at background pressures ranging between 10−4 and 20 Pa. The deficiency of light atomic species such as lithium in LiMn2O4 thin films occurs as a result of the different behavior of the species during plume expansion and the deposition of the film at elevated deposition temperatures. The plasma plume evolution in vacuum and 20 Pa oxygen pressure are studied using two spectroscopic techniques: emission spectroscopy and plume imaging. Higher velocities and a wider spatial distribution of lithium atoms are observed in vacuum when compared with manganese and oxygen species. Plume species are slowed down due to collisions with gas molecules when ablating LiMn2O4 in an oxygen atmosphere. As a result, a strong deceleration of the plasma front occurs, and the effect is more pronounced for the light species, e.g., Li. Comparing the spatial manganese and lithium distribution within the plasma, the lithium species are again scattered into a wider angular range. These similar spatial distributions of Li atoms detected in the pressure range between 10−4 and 20 Pa suggest that it is not possible to achieve a congruent lithium transfer to a growing film if the target contains heavier elements besides lithium. The general implications for the ablation of materials containing a combination of light and heavy elements are that as-grown films are inherently deficient with respect to the content of the light elements. If the mass ratio between the light and the heavy elements is not too different, is should be possible to find a set of deposition parameters which will result in the growth of a film with the desired composition.
An ab initio study of the reaction of HOCO radicals with NO2: Addition/elimination mechanism
Authors: Poggi Gabriella , Francisco Joseph S.
Published: March 2009

The reaction between HOCO and NO2 has been examined using the quadratic configuration interaction method to locate the transition states and intermediates involved in the reaction. Analysis of the potential energy surface suggest that two possible intermediates are involved: HOC(O)ONO and HOC(O)NO2. These new species proceed to form the products, HONO+CO2 and HNO2+CO2. Reaction channels leading to the formation of CO are energetically noncompetitive with those yielding CO2. The lower energy pathways produce HONO+CO2 representing new mechanisms for the formation of HONO, through an exchange of carbon and nitrogen centers.
A transverse quantum-box formulation to calculate the electrical conductance of a single-walled carbon nanotube
Authors: Grado-Caffaro M. A. , Grado-Caffaro M.
Published: March 2009

The electron conductance through a single-walled carbon nanotube is determined analytically by using the fact that a potential well transverse to the tube can be considered. In fact, the conduction electrons are conceived as standing waves in the above-mentioned potential well.
Capture and release of traveling intrinsic localized mode in coupled cantilever array
Authors: Kimura Masayuki , Hikihara Takashi
Published: March 2009

A method to manipulate intrinsic localized mode (ILM) is numerically discussed in a nonlinear coupled oscillator array, which is obtained by modeling a microcantilever array. Prior to the manipulation, coexistence and dynamical stability of standing ILMs are first investigated. The stability of coexisting ILMs is determined by a nonlinear coupling coefficient of the array. In addition, the global phase structure, which dominates traveling ILMs, is also changed with the stability. It makes possible to manipulate a traveling ILM by adjusting the nonlinear coupling coefficient. The capture and release manipulation of the traveling ILM is shown numerically.
Frequency tunable gyrotron using backward-wave components
Authors: Chang T. H. , Idehara T. , Ogawa I. , Agusu L. , Kobayashi S.
Published: March 2009

We report a frequency tunable scheme for the gyrotron at millimeter/submillimeter regime. Unlike the step-tunable type where oscillation frequencies change discretely, this scheme continuously adjusts the oscillation frequency as the magnetic field varies. It is a hybrid system, taking the advantages of the backward-wave interaction and the converter-free output structure. The characteristics of backward-wave interaction will be shown. A proof of principle experiment was conducted with a scaled cavity. The result shows the oscillation frequency smoothly transitions over a wide range of 6 GHz from 134 to 140 GHz. With proper design this mechanism is capable of producing medium output power with broad frequency tunability up to the terahertz region.
Magnetoelectric coupling in small Pb(Zr,Ti)O3/terfenol-D laminate composites
Authors: Zhou Jian-Ping , Zhao Wei , Guo Yang-Yang , Liu Peng , Zhang Huai-Wu
Published: March 2009

Electric-field-induced magnetization (EIM) in small Pb(Zr,Ti)O3/terfenol-D bilayered composites was investigated by using double coils, which could conveniently detect the EIM behaviors representing the whole sample and compare the magnetoelectric coupling from different samples. The EIM characteristics with the driving electric field, bias magnetic field, thickness ratio between Pb(Zr,Ti)O3 and terfenol-D, and angle θ between the bias magnetic field and polarization direction were investigated in detail. Part characteristics about magnetic-field-induced electric polarization (MIEP) were studied for comparison. The magnetoelectric variations with the bias magnetic field exhibit hysteresis, forming magnetoelectric hysteresis loops. The EIM coefficients decrease with the thickness ratio, showing an inverse behavior with the MIEP. When the driving electric field frequency is near one of the integer magnetoelectric resonance frequencies, multiple EIM resonances can be inspired. Both MIEP and EIM have evident responses to the driving signal out of the bias magnetic field, offering an approach to the application for the ME composite materials.
Fourier transform infrared spectroscopy of 1-cyclohexyluracil aggregates in CDCl3 solutions
Authors: Biemann Lars , Häber Thomas , Kleinermanns Karl
Published: March 2009

We reinvestigated the self-aggregation of 1-cyclohexyluracil (1CHU) in CDCl3 solutions. Wavelength dependent absolute extinction coefficients of the monomer and of dimers are presented on the basis of a simple deconvolution method. Two isomeric dimer structures coexist in a solution with similar abundance. Our results are supported by RI-B3LYP/TZVP calculations within the conductorlike screening model framework to account for solvent effects in the ab initio calculations.