bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidation of subfamily segregation and intramolecular coevolution of the olfactomedin‐like proteins by comprehensive phylogenetic analysis and gene expression pattern assessment
Authors: Zeng Ling-Chun , Han Ze-Guang , Ma Wei-Jun
Published: September 2005

The categorization of genes by structural distinctions relevant to biological characteristics is very important for understanding of gene functions and predicting functional implications of uncharacterized genes. It was absolutely necessary to deploy an effective and efficient strategy to deal with the complexity of the large olfactomedin‐like (OLF) gene family sharing sequence similarity but playing diversified roles in many important biological processes, as the simple highest‐hit homology analysis gave incomprehensive results and led to inappropriate annotation for some uncharacterized OLF members. In light of evolutionary information that may facilitate the classification of the OLF family and proper association of novel OLF genes with characterized homologs, we performed phylogenetic analysis on all 116 OLF proteins currently available, including two novel members cloned by our group. The OLF family segregated into seven subfamilies and members with similar domain compositions or functional properties all fell into relevant subfamilies. Furthermore, our Northern blot analysis and previous studies revealed that the typical human OLF members in each subfamily exhibited tissue‐specific expression patterns, which in turn supported the segregation of the OLF subfamilies with functional divergence. Interestingly, the phylogenetic tree topology for the OLF domains alone was almost identical with that of the full‐length tree representing the unique phylogenetic feature of full‐length OLF proteins and their particular domain compositions. Moreover, each of the major functional domains of OLF proteins kept the same phylogenetic feature in defining similar topology of the tree. It indicates that the OLF domain and the various domains in flanking non‐OLF regions have coevolved and are likely to be functionally interdependent. Expanded by a plausible gene duplication and domain couplings scenario, the OLF family comprises seven evolutionarily and functionally distinct subfamilies, in which each member shares similar structural and functional characteristics including the composition of coevolved and interdependent domains. The phylogenetically classified and preliminarily assessed subfamily framework may greatly facilitate the studying on the OLF proteins. Furthermore, it also demonstrated a feasible and reliable strategy to categorize novel genes and predict the functional implications of uncharacterized proteins based on the comprehensive phylogenetic classification of the subfamilies and their relevance to preliminary functional characteristics.
Characterization of the DNA‐binding site in the ferric uptake regulator protein from Escherichia coli by UV crosslinking and mass spectrometry
Authors: Tiss Ali , Barre Olivier , Michaud-Soret Isabelle , Forest Eric
Published: September 2005

Ferric uptake regulator protein (Fur) is activated by its cofactor iron to a state that binds to a specific DNA sequence called ‘Fur box’. Using mass spectrometry‐based methods, we showed that Tyr 55 of Escherichia coli Fur, as well as the two thymines in positions 18 and 19 of the consensus Fur Box, are involved with binding. A conformational model of the Fur–DNA complex is proposed, in which DNA is in contact with each H4 [A52–A64] Fur helix. We propose that this interaction is a common feature for the Fur‐like proteins, such as Zur and PerR, and their respective DNA boxes.
Analysis of juvenile North Atlantic albacore (Thunnus alalunga) catch per unit effort by surface gears in relation to environmental variables
Authors: Goñi Nicolas , Arrizabalaga Haritz
Published: September 2005

The relationship between the catch per unit effort (cpue) of trolling and baitboat fisheries targeting juvenile North Atlantic albacore (Thunnus alalunga, Bonnaterre, 1788) and several environmental variables was studied. A multiple linear regression and a generalized least squares model (GLS) showed a significant negative relationship between age 2 albacore trolling and baitboat cpue, and the average agitation of the sea and the duration of insolation. No clear relationship was found between the juvenile albacore cpue and sea surface temperature, precipitation, and NAO or Gulf Stream Index. Underlying processes that could explain the negative effect of agitation and insolation are discussed, especially relating to the habitat of age 2 albacore above the seasonal thermocline. Results highlight the necessity of considering environmental variables in the standardization of albacore cpue series used for calibrating age-structured stock assessments.
A comparison of four screening methods for cervical neoplasia
Authors: Wu SuFang , Meng Li , Wang ShiXuan , Ma Ding
Published: September 2005

Objective: To evaluate the sensitivity and accuracy of 4 screening methods for cervical neoplasia. Methods: Cervical samples from 450 women were evaluated for human papillomavirus DNA with a second‐generation hybridization assay. Visual inspection, colposcopy, and liquid‐based cytology were also performed for 273 of these women. The sensitivity, specificity, efficiency, positive predictive value (PPV), negative predictive value (NPV), Youden index, and κ value of the different screening methods were compared. Results: Liquid‐based cytology was superior in specificity (98.63%) and PPV (92.86%) to visual inspection and colposcopy, while human papillomavirus DNA testing was superior in sensitivity (88.89%) and NPV (97.10%) to visual inspection and colposcopy. The best concordance with histologic findings was achieved by using both liquid‐based cytology and viral DNA hybridization. Conclusion: Visual inspection and colposcopy should not be used when screening for early stage cervical lesions. The DNA hybridization assay is the best choice in primary screening, if available. Screening should begin at the age of 20 years.
Using a market‐utility‐based approach to designing public services: A case illustration from United States Forest Service
Authors: Verma Rohit , Louviere Jordan J. , Burke Paul
Published: September 2005

Government and public services have to not only enforce the requirements of the regulatory policies, but also have to satisfy the needs of preferences of their clients and customers. In this paper, we summarize the results of a multi‐year case study conducted to assess the choices of campground users at the Shawnee National Forest (Illinois), which is managed by United States Forest Service. The results show how users’ tradeoff between location, capacity‐related and pricing attributes when choosing a campground. The case study provides guidance for design and development of new services and more effective management of effective resources within the national forest.
INCREASING THE CLIENT ORIENTATION OF MAIZE BREEDING USING FARMER PARTICIPATION IN EASTERN INDIA
Authors: VIRK D. S. , CHAKRABORTY M. , GHOSH J. , PRASAD S. C. , WITCOMBE J. R.
Published: September 2005

A maize-breeding programme was targeted at resource-poor farmers of eastern India using a client-oriented approach (often called participatory plant breeding). Farmers tested a range of varieties in a participatory varietal selection programme but none proved to be very popular. Information from these trials was used in a breeding programme to develop a broadly-based population from three yellow- and three white-grained maize varieties that were either identified in the trials or had traits liked by farmers. The population was subjected to several cycles of random mating. In the C3, C4 and C6 cycles, subpopulations were extracted and subjected to mass selection over several generations in environments that represented well the target population of environments of resource-poor farmers' fields in eastern India for traits identified by farmers. To identify better the required traits, in some generations the selection was carried out by farmers on a research farm under fertility levels that approximated farmers' practice. The improvement of the subpopulations resulted in several varieties that performed well in research station and on-farm trials. One of them, BVM 2, was released in Jharkhand state, India. In multilocational research station trials, it yielded more than the control variety BM 1 but silked earlier. In the less favourable environments of on-farm trials, its yield superiority, in percentage terms, was higher. Farmers perceived BVM 2 to have better grain quality and stover yield than the local varieties. BVM 2 was specifically bred to meet the needs of the clients (resource-poor farmers with no access to irrigation) and has earlier maturity combined with higher grain yield. The returns were higher from this highly client-oriented approach, than by classical breeding, mainly because uptake was faster as a result of research and extension being done in tandem.
A COMPARISON OF THE EFFECTS OF MICRONUTRIENT SEED PRIMING AND SOIL FERTILIZATION ON THE MINERAL NUTRITION OF CHICKPEA (Cicer arietinum), LENTIL (Lens culinaris), RICE (Oryza sativa) AND WHEAT (Triticum aestivum) IN NEPAL
Authors: JOHNSON S. E. , LAUREN J. G. , WELCH R. M. , DUXBURY J. M.
Published: September 2005

Soil deficiencies of zinc (Zn) and boron (B) limit crop production in Nepal. Improving the micronutrient status of plants would increase yield and increase micronutrient content of the seeds, leading to better nutrition of the progeny crop and to improved human micronutrient nutrition. The primary micronutrient problem in grain legumes is B deficiency, while in rice (Oryza sativa), Zn deficiency is more important, and wheat (Triticum aestivum) suffers from both deficiencies. A series of field experiments was carried out over two seasons to compare soil fertilization and micronutrient seed priming as methods of improving Zn and B nutrition of each crop. Micronutrient treatments were evaluated for their effect on grain yield and grain micronutrient content. Soil B fertilization increased B content of the grain of lentil (Lens culinaris), chickpea (Cicer arietinum), and wheat by a factor of two to five, while increasing the yield of chickpea only. Soil fertilization with Zn had no effect on yield of any crop, but resulted in a small increase in Zn in wheat grain. Sowing micronutrient-primed seeds had no effect on yield or micronutrient content of the progeny seeds in most cases. During the first season, the primed chickpea seeds failed to emerge at either site, causing complete yield loss, but this negative effect was not observed in the second season with similar priming treatments at nearby sites, and no effect of priming on yield was observed with any other crop in either season.
THE GEOGRAPHICAL DISTRIBUTION OF ALLELIC DIVERSITY, A PRACTICAL MEANS OF PRESERVING AND USING MINOR ROOT CROP GENETIC RESOURCES
Authors: LEBOT VINCENT , IVANCIC ANTON , ABRAHAM KUTTOLAMADATHIL
Published: September 2005

This paper addresses the preservation and use of minor root crop genetic resources, mostly aroids and yams. Conservation is fraught with difficulty: ex situ collections are expensive to maintain and methods for on-farm conservation have not been studied. Conventional breeding strategies present serious limitations when applied to these species. Furthermore, the evaluation and distribution of improved material are as problematical as its conservation. The similarities shared by these species regarding their domestication, breeding constraints and improvement strategies as well as farmers' needs, are briefly reviewed. Based on these biological constraints, we propose a practical alternative to current conservation and breeding strategies. This approach focuses on the geographical distribution of allelic diversity rather than localized ex situ and/or in situ preservation of genotypes. The practical steps are described and discussed. First, a core sample representing the useful diversity of the species is assembled from accessions selected for their diverse and distant geographic origins, wide genetic distances, quality, agronomic performances and functional sexuality. Second, the geographical distribution of this core sample, in vitro via a transit centre, allows the direct use of selected genotypes by farmers or for breeding purposes. Third, the distribution of genes is realized in the form of clones resulting from segregating progenies and, fourth, farmers select clones with local adaptation.
From countrysides of production to countrysides of consumption?
Authors: SLEE R. W.
Published: September 2005

The UK rural economy is increasingly driven by consumption-based demands rather than by productive land use. Such demands have been an influence on rural land use for many hundreds of years, but a range of factors, including greater wealth and mobility, have reinforced a long-standing trend for the rural economy to be consumption driven. A number of recent economic analyses and more anecdotal sources are used to furnish evidence of the importance of new consumption demands. It is argued that such demands may impact directly on land markets through land purchase for amenity, etc. and indirectly through bringing affluent people into closer proximity to diversified business opportunities. It is argued that these new economic realities are the dominant drivers of economic change and that their recognition might suggest new approaches to the support of strategies to deliver more sustainable rural development.
Evolutionary plant breeding for low input systems
Authors: PHILLIPS S. L. , WOLFE M. S.
Published: September 2005

Heritable variation is at the heart of the process of evolution. However, variation is restricted in breeding for uniform crop populations using the pedigree line approach. Pedigree lines are successful in agriculture because synthetic inputs are used to raise fertility and control weeds, pests and diseases. An alternative method promoted for exploring the value of variation and evolutionary fitness in crops is to create composite cross populations. Composite cross populations are formed by assembling seed stocks with diverse evolutionary origins, recombination of these stocks by hybridization, the bulking of F1 progeny, and subsequent natural selection for mass sorting of the progeny in successive natural cropping environments. Composite cross populations can provide dynamic gene pools, which in turn provide a means of conserving germplasm resources: they can also allow selection of heterogeneous crop varieties. The value of composite cross populations in achieving these aims is dependent on the outcome of mass trials by artificial and natural selection acting upon the heterogeneous mixture. There is evidence to suggest that composite cross populations may be an efficient way of providing heterogeneous crops and of selecting superior pure lines for low input systems characterized by unpredictable stress conditions.
Can Robigus defeat an old enemy? – Yellow rust of wheat
Authors: BOYD L. A.
Published: September 2005

The rust diseases have plagued cereal cultivation from the early days of domestication. Biblical accounts report on the plight of Hebrews resulting from severe rust epidemics, while the ancient Greeks and Romans made offerings to the corn god, Robigus in attempts to defeat these devastating diseases (McIntosh et al. 1995). Man's approaches to fighting plant disease have changed since the time of the Romans, but still the fight continues. While we may have won many battles, the war is not yet over.
Yield formation in Nicaraguan landraces of common bean compared to bred cultivars
Authors: GÓMEZ O. J. , FRANKOW-LINDBERG B. E.
Published: September 2005

Dry matter accumulation and its partitioning to different plant components were studied in six common bean populations (two bred cultivars and four landraces) with different yield potentials. The hypothesis that yield was correlated with leaf area or mass and also with leaf area duration was tested. Leaf area and total above-ground dry matter were sampled weekly between 13 and 62 days after planting (DAP). Yield, yield components and seed yield rate were measured at the final harvest. No differences in total above-ground dry matter were observed among populations up to 62 DAP. Bred cultivars had significantly larger leaf areas than the landraces at the last harvest. Landraces initially partitioned more dry matter to reproductive organs but this was not reflected in higher yields. Temporary differences in growth rate and rate of pod formation were observed among the populations. Landraces, with one exception, tended to grow faster at early stages, and they also reached their maximum number of pods per plant earlier than the bred cultivars. Bred cultivars yielded more than all but one of the landraces. In general, yield was positively correlated with the total number of pods per plant, which in turn was well correlated with leaf area and mass. It was concluded that an increase in leaf area duration and a balanced development of reproductive organs v. other plant components are important traits in conferring improvement in yield of common bean.
Occupational blood and body fluid exposure in an Australian teaching hospital
Authors: BI P. , TULLY P. J. , PEARCE S. , HILLER J. E.
Published: September 2005

To examine work-related blood and body fluid exposure (BBFE) among health-care workers (HCWs), to explore potential risk factors and to provide policy suggestions, a 6-year retrospective study of all reported BBFE among HCWs (1998–2003) was conducted in a 430-bed teaching hospital in Australia. Results showed that BBFE reporting was consistent throughout the study period, with medical staff experiencing the highest rate of sharps injury (10·4%). Hollow-bore needles were implicated in 51·7% of all percutaneous injuries. Most incidents occurred during sharps use (40·4%) or after use but before disposal (27·1%). Nursing staff experienced 68·5% of reported mucocutaneous exposure. Many such exposures occurred in the absence of any protective attire (61·1%). This study indicated that emphasis on work practice, attire, disposal systems and education strategies, as well as the use of safety sharps should be employed to reduce work-related injuries among HCWs in Australia.
Sexual risk for hepatitis B virus infection among hepatitis C virus-negative heroin and cocaine users
Authors: RICH J. D. , ANDERSON B. J. , SCHWARTZAPFEL B. , STEIN M. D.
Published: September 2005

Hepatitis C virus (HCV) and hepatitis B virus (HBV) are highly prevalent, often co-occuring infections among drug users. We examined HBV prevalence and risk behaviour patterns among a group of HCV-negative heroin and/or cocaine users in order to understand HBV risk and prevention opportunities among this unique group. Of 164 people enrolled, 44% had injected drugs. Overall, 24% of participants tested positive for exposure to HBV; drug injectors (28%) were only slightly and not significantly (P=0·287) more likely to test positive than those who had never injected drugs (21%). HBV exposure was significantly associated with multiple indicators of greater sex risk. HBV status was not associated with any demographic characteristic, but participants who reported longer duration of cocaine use were significantly less likely to test positive to exposure for HBV. It appears that HBV risk among HCV-negative drug users in this cohort is primarily due to sexual behaviour.
Modeling magma flow and cooling in dikes: Implications for emplacement of Columbia River flood basalts
Authors: Petcovic Heather L. , Dufek Josef D.
Published: September 2005

The Columbia River flood basalts include some of the world's largest individual lava flows, most of which were fed by the Chief Joseph dike swarm. The majority of dikes are chilled against their wall rock; however, rare dikes caused their wall rock to undergo partial melting. These partial melt zones record the thermal history of magma flow and cooling in the dike and, consequently, the emplacement history of the flow it fed. Here, we examine two‐dimensional thermal models of basalt injection, flow, and cooling in a 10‐m‐thick dike constrained by the field example of the Maxwell Lake dike, a likely feeder to the large‐volume Wapshilla Ridge unit of the Grande Ronde Basalt. Two types of models were developed: static conduction simulations and advective transport simulations. Static conduction simulation results confirm that instantaneous injection and stagnation of a single dike did not produce wall rock melt. Repeated injection generated wall rock melt zones comparable to those observed, yet the regular texture across the dike and its wall rock is inconsistent with repeated brittle injection. Instead, advective flow in the dike for 3–4 years best reproduced the field example. Using this result, we estimate that maximum eruption rates for Wapshilla Ridge flows ranged from 3 to 5 km3 d−1. Local eruption rates were likely lower (minimum 0.1–0.8 km3 d−1), as advective modeling results suggest that other fissure segments as yet unidentified fed the same flow. Consequently, the Maxwell Lake dike probably represents an upper crustal (∼2 km) exposure of a long‐lived point source within the Columbia River flood basalts.
Abrupt climate shifts in Greenland due to displacements of the sea ice edge
Authors: Li Camille , Battisti David S. , Schrag Daniel P. , Tziperman Eli
Published: September 2005

An atmospheric circulation model is used to show that a reduction in sea ice extent in the North Atlantic produces a climatic response consistent with abrupt changes in temperature and snow accumulation recorded in Greenland during the Dansgaard‐Oeschger (D‐O) events of the last glacial period. The model simulations exhibit warming that is especially pronounced in winter and an accumulation increase that occurs primarily in summer, though the fractional accumulation increase is greater in winter. The seasonality of the combined temperature and accumulation changes is also consistent with the oxygen isotope signal, explaining why estimates of the magnitude of D‐O warming from oxygen isotopes are damped relative to direct estimates. Mechanisms for driving such displacements of sea ice could be changes in ocean thermohaline circulation (OTC) or rearrangements of the tropical atmosphere‐ocean system.
Impact of toroidal ULF waves on the outer radiation belt electrons
Authors: Ukhorskiy A. Y. , Takahashi K. , Anderson B. J. , Korth H.
Published: September 2005

Relativistic electron fluxes in the outer radiation belt exhibit highly variable complex behavior. Previous studies have established a strong correlation of electron fluxes and the inner magnetospheric ULF waves in the Pc 3–5 frequency range. Resonant interaction of ULF waves with the drift motion of radiation belt electrons violates their third adiabatic invariant and consequently leads to their radial transport. If the wave‐particle interaction has a stochastic character, then the electron transport is diffusive. The goal of this paper is to analyze the impact of toroidal ULF waves on radiation belt electrons. The study is based on direct measurements of ULF electric fields on the CRRES spacecraft. We show that the electric fields of inner magnetospheric toroidal ULF waves exhibit high asymmetry in magnetic local time and have narrow‐band frequency spectra. Such narrow‐band waves can induce radial diffusion of energetic electrons, if an extrinsic stochasticity is introduced in the system. The quasi‐periodic variations in the solar wind dynamic pressure are identified as a possible source of extrinsic stochasticity. In the asymmetric magnetic field, drifting electrons can interact with both azimuthal and radial electric field components. We derive analytically and then calculate numerically the diffusion rates associated with azimuthal and radial electric field components of the waves. It is shown that even under highly disturbed geomagnetic conditions, when the background field asymmetry is large, the diffusion rates due to the radial field component are small. At the same time, the resonant scattering of energetic electrons by the azimuthal electric field of the waves provides an efficient form of radial diffusion and therefore can play an important role in the dynamics of the outer radiation belt.
Effect of the surface charge on ion transport through nanoslits
Authors: Schoch Reto B. , van Lintel Harald , Renaud Philippe
Published: September 2005

A description of ion transport through geometrically defined nanoslits is presented. It is characterized by the effective surface charge density and was obtained by impedance spectroscopy measurements of electrolytes with different physicochemical properties. The fluid channels were fabricated in a Pyrex–Pyrex field assisted bonding process with an intermediate layer of amorphous silicon. The height of the nanoslits was defined by the 50nm thickness of the amorphous silicon layer. Two microfluidic channels, containing electrodes for the characterization of the nanoslits, maintained fresh liquid on both sides of the nanoapertures. By changing the KCl concentration of the electrolyte, a conductance plateau (in log–log scale) was observed due to the dominance of the effective surface charge density, resulting in an excess of mobile counterions in the nanoslits at low salt concentrations. The effective surface charge density of the Pyrex nanoslits could be modified by changing the pH of the solution. It was verified that at higher pH values the nanoslit conductance increased. Field-effect experiments allowed changing the effective surface charge density as well. The polarity of the external voltage could be chosen such that the effective surface charge density was increased or decreased, resulting in a higher or lower nanoslit conductance. This regulation of ionic flow can be exploited for the fabrication of nanofluidic devices.
Ultrasound-mediated destruction of contrast microbubbles used for medical imaging and drug delivery
Authors: Chatterjee Dhiman , Jain Pankaj , Sarkar Kausik
Published: September 2005

Micron-size bubbles encapsulated by a stabilizing layer of surface-active materials are used in medical ultrasound imaging and drug delivery. Their destruction stimulated by ultrasound in vivo plays a critical role in both applications. We investigate the destruction process of microbubbles in a commercially available contrast agent by measuring the attenuation of ultrasound through it. The measurement is performed with single-cycle bursts from an unfocused transducer (with a center frequency of 5MHz) for varying pressure amplitudes at 50-, 100-, and 200-Hz pulse repetition frequencies (PRF) with duty cycles 0.001%, 0.002%, and 0.004%, respectively. At low excitation, the attenuation is found to increase with time. With increased excitation level, the attenuation level decreases with time, indicating destruction of microbubbles. There is a critical pressure amplitude (∼1.2MPa) for all three PRFs, below which there is no significant bubble destruction. Above the critical pressure amplitudes the rate of destruction depends on excitation levels. But at high-pressure amplitudes the destruction becomes independent of excitation pressure amplitude. The results are interpreted to identify two different mechanisms of bubble destruction by its signature in attenuation, namely, slow dissolution by diffusion and catastrophic shell rupture. The different modes are discussed in detail with their implications in medical applications.
Mesoscale modeling of electrical percolation in fiber-filled systems
Authors: Rahatekar Sameer S. , Hamm Marc , Shaffer Milo S. P. , Elliott James A.
Published: September 2005

The research described in this paper primarily involves mesoscale simulations: dissipative particle dynamics (DPD) of packed assemblies of oriented fibers suspended in a viscous medium. Computer simulations have been performed in order to explore how the aspect ratio and degree of fiber alignment affect the critical volume fraction (percolation threshold) required to achieve electrical conductivity. The fiber network impedance was assessed using Monte Carlo simulations after establishing the structural arrangement with DPD. The predictions are compared with the predictions of classical percolation theory and found to be in close agreement. The approach is thus validated and can be extended to systems that cannot be tackled analytically; in particular, the work is motivated by long-standing interest in materials which display a complex percolation behavior.
Spin-unrestricted linear-scaling electronic structure theory and its application to magnetic carbon-doped boron nitride nanotubes
Authors: Xiang H. J. , Liang W. Z. , Yang Jinlong , Hou J. G. , Zhu Qingshi
Published: September 2005

We present an extension of the density-matrix-based linear-scaling electronic structure theory to incorporate spin degrees of freedom. When the spin multiplicity of the system can be predetermined, the generalization of the existing linear-scaling methods to spin-unrestricted cases is straightforward. However, without calculations it is hard to determine the spin multiplicity of some complex systems, such as many magnetic nanostuctures and some inorganic or bioinorganic molecules. Here we give a general prescription to obtain the spin-unrestricted ground state of open-shell systems. Our methods are implemented into the linear-scaling trace-correcting density-matrix purification algorithm. The numerical atomic-orbital basis, rather than the commonly adopted Gaussian basis functions, is used. The test systems include O2 molecule and magnetic carbon-doped boron nitride (BN)(5,5) and BN(7,6) nanotubes. Using the newly developed method, we find that the magnetic moments in carbon-doped BN nanotubes couple antiferromagnetically with each other. Our results suggest that the linear-scaling spin-unrestricted trace-correcting purification method is very powerful to treat large magnetic systems.
Molecular simulation of polymer assisted protein refolding
Authors: Lu Diannan , Liu Zheng
Published: September 2005

Protein refolding in vitro, the formation of the tertiary structure that enables the protein to display its biological function, can be significantly enhanced by adding a polymer of an appropriate hydrophobicity and concentration into the refolding buffer. A molecular simulation of the refolding of a two-dimensional simple lattice protein was presented. A protein folding map recording the occurrence frequency of specified conformations was derived, from which the refolding thermodynamics and kinetics were interpreted. It is shown that, in the absence of polymer, the protein falls into the “energy trapped” conformations characterized by a high intramolecular hydrophobic interaction, denoted as HH contact, and a high magnitude of the structure overlap function, χ. This makes it difficult for the protein to fold to the native state. The polymer with a suitable chain length, concentration, and hydrophobicity has formed complex with partially folded protein and created diversified intermediates with low χ. This gives more pathways for the protein to fold to the native state. At a given hydrophobicity, the short chain polymer has a broader concentration range where it assists protein folding than those of long chains. The above simulation agrees well with the experimental results reported elsewhere [Cleland et al., J. Biol. Chem. 267, 13327 (1992); ibid., Bio/Technology 10, 1013 (1992); Chen et al., Enzyme Microb. Technol. 32, 120 (2003); Lu et al., Biochem. Eng. J. 24, 55 (2005); ibid., J. Chem. Phys. 122, 134902 (2005); ibid., Biochem. Eng. J. (to be published)] and is of fundamental importance for the design and application of polymers for protein refolding.
Pressure-induced phase change in poly(tetrafluoroethylene) at modest impact velocities
Authors: Rae Philip J. , Brown Eric N. , Clements Bradford E. , Dattelbaum Dana M.
Published: September 2005

Although poly(tetrafluoroethylene) (PTFE) is an unusually ductile polymer, it undergoes an abrupt ductile-brittle transition at modest impact velocities. No previous explanation for this behavior has been found after an extensive literature search. In this paper, we examine the role of a pressure-induced phase transition in PTFE in the dynamic failure of Taylor cylinder samples. There is a known phase transition in PTFE with a marked decrease in volume and compressibility that occurs at 0.5–0.65GPa at 21°C, with the transition pressure inversely related to temperature. Varying the temperature of the samples in the experiment revealed that the phase transition is probably involved in sample failure because the ductile/brittle transition velocity increased for decreasing temperature, despite the material fracture toughness decreasing. Additionally, Taylor tests were carried out on samples of poly(chlorotrifluoroethylene) PCTFE to investigate the behavior of a similar material to PTFE but without a pressure-induced phase transition. PCTFE did not exhibit an abrupt ductile to brittle transition.
Bounds for the scattering length of spin-polarized helium from high-accuracy electronic structure calculations
Authors: Przybytek Michał , Jeziorski Bogumil
Published: September 2005

We developed a series of correlation-consistent, polarized multiple zeta basis sets optimized specifically for the energy of the 2S3 state of helium atom. These basis sets were subsequently augmented with diffuse functions optimized for the van der Waals constants C6 through C14 which determine the asymptotic behavior of the second-order dispersion interaction between 2S3 helium atoms at large interatomic separation R. The resulting bases were applied to compute the Born-Oppenheimer (BO) potential for the lowest Σg+5 state of the helium dimer. The coupled cluster and the full configuration-interaction techniques were employed to account for the electron correlation effects. The cardinal number extrapolation technique was used to obtain the complete-basis-set limit V(R) for the interaction potential and to find its lower VL(R) and upper VU(R) bounds. The resulting potentials were fitted to an analytical function containing accurate van der Waals constants C6 through C12 (including C11). We found that the complete-basis-set BO potential has a well depth De=1048.24±0.36cm−1. The highest rotationless vibrational level is bound by D14=90.2±4.7MHz, much stronger than the previous most accurate estimation of 15.2MHz. The error bounds for De and D14 were obtained using the VL(R) and VU(R) potentials. The S-wave scattering length computed using the VL(R), V(R), and VU(R) potentials (assuming atomic masses) is aL=7.41nm, a=7.54nm, and aU=7.69nm, respectively. We also computed the adiabatic, relativistic, and quantum electrodynamics (QED) corrections to the BO potential. When these corrections are taken into account the values of D14 and of a (both computed assuming nuclear masses) are 87.4±6.7MHz and 7.64±0.20nm; the error bounds reflect now also the uncertainty of the included adiabatic, relativistic, and QED corrections. The value of the scattering length resulting from our investigation lies outside the error bounds of all experimental determinations based on the properties of Bose-Einstein condensate of spin-polarized helium atoms.
A higher-order nonlinear evolution equation for broader bandwidth gravity waves in deep water
Authors: Debsarma Suma , Das K. P.
Published: September 2005

From Zakharov’s integral equation a nonlinear evolution equation for broader bandwidth gravity waves in deep water is obtained, which is one order higher than the corresponding equation derived by Trulsen and Dysthe [“A modified nonlinear Schrödinger equation for broader bandwidth gravity waves on deep water,” Wave Motion 24, 281 (1996)]. The instability regions in the perturbed wave-number space for a uniform Stokes wave obtained from this equation are in surprisingly good agreement with the exact results obtained by McLean et al. [“Three dimensional instability of finite amplitude water waves,” Phys. Rev. Lett. 46, 817 (1981)].
Interpolation of diabatic potential-energy surfaces: Quantum dynamics on ab initio surfaces
Authors: Evenhuis Christian R. , Lin Xin , Zhang Dong H. , Yarkony David , Collins Michael A.
Published: September 2005

A method for constructing diabatic potential-energy matrices from ab initio quantum chemistry data is described and tested for use in exact quantum reactive scattering. The method is a refinement of that presented in a previous paper, in that it accounts for the presence of the nonremovable derivative coupling. The accuracy of quantum dynamics on this type of diabatic potential is tested by comparison with an analytic model and for an ab initio description of the two lowest-energy states of H3.
A density-functional study on the formation of Mo22+
Authors: Pis Diez Reinaldo , Alonso Julio A.
Published: September 2005

The presence of metastable states in the doubly ionized molybdenum dimer is studied using gradient-corrected scalar-relativistic density-functional theory. Seventeen metastable states are found within an energy range of less than 6.5eV. All those states show lifetimes large enough to assure experimental detection. The calculation of the second adiabatic ionization potential of the neutral molybdenum dimer seems to confirm that the doubly ionized dimer is produced by the electron-capture process Mo2++Ar+→Mo22++Ar, in which the ionization potentials of Ar and Mo2+ play a crucial role [K. Franzreb, R. C. Sobers, Jr., J. Lörinçik, and P. Williams, J. Chem. Phys. 120, 7983 (2004)]. Moreover, the present results indicate that other species having ionization potentials between 13.01 and 15.34eV could be used as projectiles to produce Mo22+. It is also shown that Xe+ ions could not react with Mo2+ to produce double ionized dimers. A simple thermodynamic argument is also proposed that seems to increase the possibilities of forming Mo22+ from Mo2+ by using Ar+ as projectile ions.
Hysteresis dispersion scaling of a two-dimensional ferroelectric model
Authors: Wang L.-F. , Liu J.-M.
Published: September 2005

The ferroelectric hysteresis dispersion of a two-dimensional ferroelectric model lattice in an ac electric field of amplitude E0 and frequency ω over a wide range, respectively, is calculated by Monte Carlo simulation based on the Ginzburg-Landau theory on tetragonal-type ferroelectric phase transitions. Given a fixed field amplitude E0, the hysteresis dispersion as a function of field frequency ω shows a single-peaked pattern, which predicts the existence of a characteristic time responsible for domain switching in an external electric field. The scaling analysis demonstrates that given different field amplitudes E0, the hysteresis dispersions can be scaled and the characteristic time depends inversely on the field amplitude E0 over a wide range of E0, but the large deviation occurs as E0 is very small or extremely large.
Comparison of low-temperature GaN, SiO2, and SiNx as gate insulators on AlGaN∕GaN heterostructure field-effect transistors
Authors: Kao C. J. , Chen M. C. , Tun C. J. , Chi G. C. , Sheu J. K. , Lai W. C. , Lee M. L. , Ren F. , Pearton S. J.
Published: September 2005

The performance of AlGaN∕GaN heterostructure field-effect transistors (HFETs) with either uncapped surfaces or with low-temperature (LT) GaN or SiO2 or SiNx as gate insulators is reported. The sheet carrier concentrations of AlGaN∕GaN HFETs with any of these surface insulating layers are similar to each other and in each case about 50% higher than that in an AlGaN∕GaN HFET with a free surface. This result is consistent with the insulator layers providing passivation of surface states that cause the depletion of the channel layer. Due to the closer lattice match with the AlGaN surface layer, the HFET with a LT-GaN layer as the gate insulator shows the best dc and rf device performance, demonstrating that this material is an effective insulator for nitride electronic devices.
Quantitative description of disorder parameters in (GaIn)(NAs) quantum wells from the temperature-dependent photoluminescence spectroscopy
Authors: Rubel O. , Galluppi M. , Baranovskii S. D. , Volz K. , Geelhaar L. , Riechert H. , Thomas P. , Stolz W.
Published: September 2005

Photoluminescence in (GaIn)(NAs) quantum wells designed for laser emission was studied experimentally and theoretically. The observed temperature dependences of the luminescence Stokes shift and of the spectral linewidth evidence the essential role of disorder in the dynamics of the recombining excitations. The spatial and energy disorders can cause a localization of photocreated excitations supposedly in the form of excitons. Theoretical study of the exciton dynamics is performed via kinetic Monte Carlo simulations of exciton hopping and recombination in the manifold of localized states. Direct comparison between experimental spectra and theoretical calculations provides quantitative information on the energy scale of the potential fluctuations in (GaIn)(NAs) quantum wells. The results enable one to quantify the impact of annealing on the concentration of localized states and/or on the localization length of excitons in (GaIn)(NAs) quantum wells.
Optical and morphological investigation of backward-deposited layer induced by laser ablation of steel in ambient air
Authors: Pereira A. , Delaporte P. , Sentis M. , Marine W. , Thomann A. L. , Boulmer-Leborgne C.
Published: September 2005

The irradiation of a steel surface in atmospheric pressure ambient was performed to study the surface nanostructuring resulting from the formation of a backward-deposited layer. The dynamics of the plume expansion and of the nanoparticle deposition process were investigated by in situ time-resolved optical analysis. Scanning electron microscopy and atomic force microscopy were employed to investigate the morphological characteristics of the backward deposited layer. The observations revealed a particular shape of plasma expansion. The latter is characterized by the formation of two vortices at the plasma plume periphery, where a high density of condensed nanoparticles are generated. It is shown that the surface nanostructuring is mainly due to a backward nanoparticles flux which leads to a deposition process during several tens of microseconds. The effects of laser wavelength on nanoparticle formation and surface nanostructuring are presented and discussed.
Electrical transport characteristics of single-layer organic devices from theory and experiment
Authors: Martin S. J. , Walker Alison B. , Campbell A. J. , Bradley D. D. C.
Published: September 2005

An electrical model based on drift diffusion is described. We have explored systematically how the shape of the current density-voltage (J-V) curves is determined by the input parameters, information that isessential when deducing values of these parameters by fitting to experimental data for an ITO/PPV/Al organic light-emitting device (OLED), where ITO is shorthand for indium tin oxide and PPV is poly(phenylene vinylene). Our conclusion is that it is often possible to obtain a unique fit even with several parameters to fit. Our results allowing for a tunneling current show remarkable resemblance to experimental data before and after the contacts are conditioned. We have demonstrated our model on single-layer devices with ITO/PFO/Au and ITO/PEDOT/PFO/Au at room temperature and ITO/TPD/Al over temperatures from 130to290K. PFO is shorthand for poly(9,9′-dialkyl-fluorene-2,7-dyl) and TPD is shorthand for N,N′-diphenyl-N,N′-bis(3-methylphenyl)1-1′-biphenyl-4,4′-diamine. Good fits to experimental data have been obtained, but in the case of the TPD device, only if a larger value for the relative permittivity ϵs than would be expected is used. We infer that a layer of dipoles at the ITO/TPD interface could be responsible for the observed J-V characteristics by locally causing changes in ϵs. The strong temperature dependence of the hole barrier height from fitting J-V characteristics to the experimental data may indicate that the temperature dependence of the thermionic emission model is incorrect.
A quantum-mechanical treatment of phonon scattering in carbon nanotube transistors
Authors: Guo Jing
Published: September 2005

Phonon scattering in carbon nanotube field-effect transistors (CNTFETs) is treated using the nonequilibrium Green’s function formalism with the self-consistent Born approximation. The treatment simultaneously captures the essential physics of phonon scattering and important quantum effects. For a one-dimensional channel, it is computationally as efficient as and physically more rigorous than the so-called “Büttiker probe” approach [Phys. Rev. Lett. 57, 1761 (1986)], which has been widely used in mesoscopic physics. The non-self-consistent simulation results confirm that the short mean-free-path optical phonon (OP) scattering, though expected to dominate even in a short channel CNTFET, essentially has no direct effect on the dc on current under modest gate biases. The self-consistent simulation results indicate that OP scattering, however, can have an indirect effect on the on current through self-consistent electrostatics. Using a high-κ gate insulator suppresses the indirect effect and leads to a dc on current closer to the ballistic limit. The indirect effect in a CNT Schottky barrier FET can be more important than that in a metal-oxide semiconductor FET.
A versatile instrument for in situ combination of scanning probe microscopy and time-of-flight mass spectrometry
Authors: Wetzel A. , Socoliuc A. , Meyer E. , Bennewitz R. , Gnecco E. , Gerber C.
Published: September 2005

A scanning probe microscope is combined with a time-of-flight mass spectrometer that analyzes material from the tip of the probe microscope. Chemical analysis on the nanometer scale is achieved by transferring material from surfaces via the probing tip to the mass spectrometer under ultrahigh vacuum conditions. Fast switching between scanning probe and mass analysis operation is implemented by means of a motorized rotatable probe holder. Electrochemically etched tungsten tips are used as probes for the experiments. Thorough characterization of the tips by means of field-emission measurements is crucial for successful experiments. Quartz tuning forks have been applied as force sensors in force microscopy experiments.
Spin-wave logical gates
Authors: Kostylev M. P. , Serga A. A. , Schneider T. , Leven B. , Hillebrands B.
Published: September 2005

A universal approach to spin-wave logic gates is presented. The feasibility of a spin-wave based NOT gate has been demonstrated experimentally. We propose to use a Mach–Zender-type current-controlled interferometer based on spin-wave propagation in a ferromagnetic film to construct logical gates. We investigate the performance of the main element of such interferometric logical gates—the controlled phase shifter implemented as a spin-wave device.
Use of AlInN layers in optical monitoring of growth of GaN-based structures on free-standing GaN substrates
Authors: Watson I. M. , Liu C. , Gu E. , Dawson M. D. , Edwards P. R. , Martin R. W.
Published: September 2005

When lattice matched to GaN, the AlInN ternary alloy has a refractive index ∼7% lower than that of GaN. This characteristic can be exploited to perform in situ reflectometry during epitaxial growth of GaN-based multilayer structures on free-standing GaN substrates, by insertion of a suitable Al0.82In0.18N layer. The real-time information on growth rates and cumulative layer thicknesses thus obtainable is particularly valuable in the growth of optical resonant cavity structures. We illustrate this capability with reference to the growth of InGaN∕GaN multiple quantum-well structures, including a doubly periodic structure with relatively thick GaN spacer layers between groups of wells. Al0.82In0.18N insertion layers can also assist in the fabrication of resonant cavity structures in postgrowth processing, for example, acting as sacrificial layers in a lift-off process exploiting etch selectivity between Al0.82In0.18N and GaN.