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Many Orders (many + order)
Selected AbstractsParallel protein folding with STAPLCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 14 2005Shawna Thomas Abstract The protein-folding problem is a study of how a protein dynamically folds to its so-called native state,an energetically stable, three-dimensional conformation. Understanding this process is of great practical importance since some devastating diseases such as Alzheimer's and bovine spongiform encephalopathy (Mad Cow) are associated with the misfolding of proteins. We have developed a new computational technique for studying protein folding that is based on probabilistic roadmap methods for motion planning. Our technique yields an approximate map of a protein's potential energy landscape that contains thousands of feasible folding pathways. We have validated our method against known experimental results. Other simulation techniques, such as molecular dynamics or Monte Carlo methods, require many orders of magnitude more time to produce a single, partial trajectory. In this paper we report on our experiences parallelizing our method using STAPL (Standard Template Adaptive Parallel Library) that is being developed in the Parasol Lab at Texas A&M. An efficient parallel version will enable us to study larger proteins with increased accuracy. We demonstrate how STAPL enables portable efficiency across multiple platforms, ranging from small Linux clusters to massively parallel machines such as IBM's BlueGene/L, without user code modification. Copyright © 2005 John Wiley & Sons, Ltd. [source] Efficient sampling and data reduction techniques for probabilistic seismic lifeline risk assessmentEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 10 2010Nirmal Jayaram Abstract Probabilistic seismic risk assessment for spatially distributed lifelines is less straightforward than for individual structures. While procedures such as the ,PEER framework' have been developed for risk assessment of individual structures, these are not easily applicable to distributed lifeline systems, due to difficulties in describing ground-motion intensity (e.g. spectral acceleration) over a region (in contrast to ground-motion intensity at a single site, which is easily quantified using Probabilistic Seismic Hazard Analysis), and since the link between the ground-motion intensities and lifeline performance is usually not available in closed form. As a result, Monte Carlo simulation (MCS) and its variants are well suited for characterizing ground motions and computing resulting losses to lifelines. This paper proposes a simulation-based framework for developing a small but stochastically representative catalog of earthquake ground-motion intensity maps that can be used for lifeline risk assessment. In this framework, Importance Sampling is used to preferentially sample ,important' ground-motion intensity maps, and K -Means Clustering is used to identify and combine redundant maps in order to obtain a small catalog. The effects of sampling and clustering are accounted for through a weighting on each remaining map, so that the resulting catalog is still a probabilistically correct representation. The feasibility of the proposed simulation framework is illustrated by using it to assess the seismic risk of a simplified model of the San Francisco Bay Area transportation network. A catalog of just 150 intensity maps is generated to represent hazard at 1038 sites from 10 regional fault segments causing earthquakes with magnitudes between five and eight. The risk estimates obtained using these maps are consistent with those obtained using conventional MCS utilizing many orders of magnitudes more ground-motion intensity maps. Therefore, the proposed technique can be used to drastically reduce the computational expense of a simulation-based risk assessment, without compromising the accuracy of the risk estimates. This will facilitate computationally intensive risk analysis of systems such as transportation networks. Finally, the study shows that the uncertainties in the ground-motion intensities and the spatial correlations between ground-motion intensities at various sites must be modeled in order to obtain unbiased estimates of lifeline risk. Copyright © 2010 John Wiley & Sons, Ltd. [source] X-ray computed tomography of peat soils: measuring gas content and peat structureHYDROLOGICAL PROCESSES, Issue 25 2008Nicholas Kettridge Abstract The potential of using X-ray computed tomography (CT) to (i) analyse individual biogenic gas bubbles entrapped within peats and (ii) produce reliable descriptors of peat structure is examined. Existing approaches used to study biogenic gas bubbles measure the gas content of volumes of peat many orders of magnitude larger than most bubbles, and are, therefore, of little use in helping to understand bubble dynamics. In many peatland studies, the description of peat structures is derived from only a few relatively basic metrics; principally the porosity, the bulk density, and the von Post humification scale. CT is applied to identify and quantitatively analyse the size, location and shape of individual gas bubbles entrapped during the saturation of a 200 cm3 sample of S. fuscum. 3421 gas bubbles were identified, ranging in size from 0·1 mm3 to 99·9 mm3. These gas bubbles were non-randomly distributed, clustered predominantly in the vertical plane. When analysing the peat structure, Sphagnum peat and water are shown to be indistinguishable within CT scans. Peat samples were therefore prepared prior to scanning by flushing the peat with lead (II) nitrate solution to increase the linear attenuation of the Sphagnum. Sphagnum stems and branches were analysed, producing metrics of the peat structure; including stem and branch lengths, radii and orientation. In a 100 cm3 sample of S. magellanicum, the length of all Sphagnum stems totalled 1·82 m, with an average radius of 0·65 mm. The Sphagnum stems and branches were both preferentially orientated in the horizontal direction. Copyright © 2008 John Wiley & Sons, Ltd. [source] Modeling power and intermodulation behavior of microwave transistors with unified small-signal/large-signal neural network modelsINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 4 2003F. Giannini Abstract This article presents a detailed procedure to learn a nonlinear model and its derivatives to as many orders as desired with multilayer perceptron (MLP) neural networks. A modular neural network modeling a nonlinear function and its derivatives is introduced. The method has been used for the extraction of the large-signal model of a power MESFET device, modeling the nonlinear relationship of drain-source current Ids as well as gate and drain charge Qg and Qd with respect to intrinsic voltages Vgs and Vds over the whole operational bias region. The neural models have been implemented into a user-defined nonlinear model of a commercial microwave simulator to predict output power performance as well as intermodulation distortion. The accuracy of the device model is verified by harmonic load-pull measurements. This neural network approach has demonstrated to predict nonlinear behavior with enough accuracy even if based only on first-order derivative information. © 2003 Wiley Periodicals, Inc. Int J RF and Microwave CAE 13: 276,284, 2003. [source] Captan: Transition from ,B2' to ,not likely'.JOURNAL OF APPLIED TOXICOLOGY, Issue 5 2007How pesticide registrants affected the EPA Cancer Classification Update Abstract On 24 November 2004 EPA changed the cancer classification of captan from a ,probable human carcinogen' (Category B2) to ,not likely' when used according to label directions. The new cancer classification considers captan to be a potential carcinogen at prolonged high doses that cause cytotoxicity and regenerative cell hyperplasia. These high doses of captan are many orders of magnitude above those likely to be consumed in the diet, or encountered by individuals in occupational or residential settings. This revised cancer classification reflects EPA's implementation of their new cancer guidelines. The procedures involved in the reclassification effort were agreed upon with EPA and involved an Independent Transparent Review as it related to four components that formed the basis of the original 1986 B2 classification: mouse tumors; rat tumors; mutagenicity; and structural similarity to other carcinogens. A Peer Review Panel organized and administered by Toxicology Excellence for Risk Assessment (TERA) met on 2,3 September 2003. The Panel concluded that captan acted through a non-mutagenic threshold mode of action that required prolonged irritation of the duodenal villi as the initial key event. EPA's Cancer Assessment Review Committee (CARC) met on 9 June 2004 and endorsed the Peer Review findings. EPA intended to have the FIFRA Scientific Advisory Panel (SAP) consider the basis for this reclassification but found the science was robust and judged that a SAP review was not warranted. Using the revised classification, the margin of exposure is approximately 1,200,000, supporting the ,not likely' characterization. Copyright © 2007 John Wiley & Sons, Ltd. [source] Estimation of agitator flow shear rateAICHE JOURNAL, Issue 7 2006Jie Wu Abstract Laboratory laser Doppler velocimetry (LDV) measurements were conducted to measure the shear rate coefficient KS of a range of impellers. Equations correlating KS with NQ (flow number) are provided for axial flow and radial flow impellers. Theoretical formulations based on the classic boundary layer theory are developed to estimate the shear rate at the blade surface. Calculations show that the shear rates at the blade surface are many orders of magnitude higher than those in the flow at the impeller outlet. The software code XFOIL was used to illustrate typical distributions of the shear rates along the blade surfaces. Effects of viscosity, non-Newtonian shear-thinning index, agitator design, and scale-up on shear rates are illustrated. © 2006 American Institute of Chemical Engineers AIChE J, 2006 [source] Concepts of scale held by students with visual impairmentJOURNAL OF RESEARCH IN SCIENCE TEACHING, Issue 5 2009M. Gail Jones Abstract This study investigated students' with visual impairment concepts about linear size and scale. Specifically the study examined the accuracy of students' concepts over many orders of magnitude as well as experiences students have had in and out-of-school learning about size and scale. The results of assessments of 17 students with visual impairment were compared to those of students with normal sight. The study showed that students with visual impairment were most accurate for measurements in the human scale and were least accurate with very large and very small scales that cannot be directly experienced. However, when compared to students with normal sight, students with visual impairment were more accurate at large and small scales than their normally sighted peers. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 46: 506,519, 2009 [source] Accuracy of scale conceptions in science: Mental maneuverings across many orders of spatial magnitudeJOURNAL OF RESEARCH IN SCIENCE TEACHING, Issue 10 2006Thomas R. Tretter The use of unifying themes that span the various branches of science is recommended to enhance curricular coherence in science instruction. Conceptions of spatial scale are one such unifying theme. This research explored the accuracy of spatial scale conceptions of science phenomena across a spectrum of 215 participants: fifth grade, seventh grade, ninth grade, twelfth grade, and doctoral students in science. Conceptions spanning sizes from one nanometer to one billion meters were investigated through use of written assessments and individual interviews. Results showed that accuracy of conceptions at small scale were not symmetrical with respect to conceptions at large scale. Large scale accuracy tended to decline in a smooth, uniform fashion as the scale increased, whereas small scale accuracy displayed a discontinuity at the microscopic level. To conceptually interact with scales far removed from human scale, experts used strategies of mentally jumping to a new scale-world. Experts tended not to transition smoothly between the differently scaled worlds but rather to make a discontinuous leap, maintaining abstract linkages between the worlds via mathematics. Implications of these findings for curriculum development and classroom instruction are discussed. © 2006 Wiley Periodicals, Inc. J Res Sci Teach 43: 1061,1085, 2006 [source] Universal scaling in a trapped Fermi super-fluid in the BCS-unitarity crossoverLASER PHYSICS LETTERS, Issue 12 2009S.K. AdhikariArticle first published online: 14 AUG 200 Abstract Using numerical simulation based on a densityfunctional equation for a trapped Fermi super-fluid valid along the BCS-unitarity crossover, we establish robust scaling over many orders of magnitude in the observables of the system as a function of fermion number. This scaling allows to predict the static properties of the system, such as energy, chemical potential, etc., for a large number of fermions, over the crossover, from the knowledge of those for a small number (,4 , 10) of fermions. (© 2009 by Astro Ltd., Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA) [source] Offline, multidetector intensity interferometers , I. TheoryMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2006Aviv Ofir ABSTRACT Stellar amplitude interferometry is limited by the need to have optical distances fixed and known to a fraction of the wavelength. We suggest reviving intensity interferometry, which requires hardware which is many orders of magnitude less accurate, at the cost of more limited sensitivity. We present an algorithm to use the very high redundancy of a uniform linear array to increase the sensitivity of the instrument by more than a 100-fold. When using an array of 100 elements, each almost 100 m in diameter, and conservative technological improvements, we can achieve a limiting magnitude of about mb= 14.4. Digitization, storage, and offline processing of all the data will also enable interferometric image reconstruction from a single observation run, and application of various algorithms at any later time. Coronagraphy, selectively suppressing only the large-scale structure of the source, can be achieved by specific aperture shapes. We conclude that after three decades of abandonment optical intensity interferometry deserves another review. [source] A selective newsvendor approach to order managementNAVAL RESEARCH LOGISTICS: AN INTERNATIONAL JOURNAL, Issue 8 2008Kevin Taaffe Abstract Consider a supplier offering a product to several potential demand sources, each with a unique revenue, size, and probability that it will materialize. Given a long procurement lead time, the supplier must choose the orders to pursue and the total quantity to procure prior to the selling season. We model this as a selective newsvendor problem of maximizing profits where the total (random) demand is given by the set of pursued orders. Given that the dimensionality of a mixed-integer linear programming formulation of the problem increases exponentially with the number of potential orders, we develop both a tailored exact algorithm based on the L-shaped method for two-stage stochastic programming as well as a heuristic method. We also extend our solution approach to account for piecewise-linear cost and revenue functions as well as a multiperiod setting. Extensive experimentation indicates that our exact approach rapidly finds optimal solutions with three times as many orders as a state-of-the-art commercial solver. In addition, our heuristic approach provides average gaps of less than 1% for the largest problems that can be solved exactly. Observing that the gaps decrease as problem size grows, we expect the heuristic approach to work well for large problem instances. © 2008 Wiley Periodicals, Inc. Naval Research Logistics 2008 [source] Selenium Accumulation in Plant FoodsNUTRITION REVIEWS, Issue 6 2005John W. Finley PhD Selenium (Se) is an essential nutrient, and Se deficiency is associated with disease conditions and general impairment of the immune system. Supplementation of Se to humans already consuming the RDA may help to prevent certain cancers. A convincing argument can be made for augmenting the food supply with Se, and Se-enhanced plants may be the best means of accomplishing this. Plants accumulate varying amounts of Se in different chemical forms; some plants accumulate Se in direct relationship to the amount available from the soil, whereas others (Se-accumulators) may accumulate Se in concentrations many orders of magnitude above that in the soil. There are many different chemical forms of Se in plants, and the form partially dictates the metabolism of Se by the animal that consumes the plant. The Se content and the chemical form of Se withinplants may be altered by manipulation of plant genetics or by agricultural production conditions. However, attempts to maximize Se in plants may have unintended consequences and must be carefully monitored. [source] Conductivity of graphite and fullerene under pressures up to 50 GPaPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2003G. V. Tikhomirova Abstract The DC resistance of polycrystalline fullerene C60 and graphite in the temperature range 77,450 K were studied at pressures up to 50 GPa. The AC measurements were performed at room temperature. The temperature and pressure dependences of resistance for both materials are of a similar character. However, the resistance of both materials is different by many orders of magnitude. It is shown that both fullerene and graphite keep some features of their original microscopic structure even at high pressures. [source] Effect of overgrowth conditions on the optical properties of lateral epitaxially overgrown a -plane GaNPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 7-8 2010T. J. Badcock Abstract We investigate the optical properties of lateral epitaxially overgrown non-polar a -plane GaN using photoluminescence and spatially resolved cathodoluminescence spectroscopy. Despite the decreased density of extended defects relative to a -plane templates, in material overgrown at a low V:III ratio (57), the low temperature emission spectrum is very weak and is dominated by impurity bands centred at 2.92 and 2.25 eV. On subsequent overgrowth at a higher V:III ratio (260), the intensity of the near band edge emission increases by many orders of magnitude and a donor-acceptor pair band is seen. We suggest that the dramatic modification of the optical properties is related to the impurity or point-defect incorporation rate at the different V:III ratios employed. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single-molecule FRETBIOPOLYMERS, Issue 7 2008James B. Munro Abstract This article reviews the application of single-molecule fluorescence resonance energy transfer (smFRET) methods to the study of protein synthesis catalyzed by the ribosome. smFRET is a powerful new technique that can be used to investigate dynamic processes within enzymes spanning many orders of magnitude. The application of wide-field smFRET imaging methods to the study of dynamic processes in the ribosome offers a new perspective on the mechanism of protein synthesis. Using this technique, the structural and kinetic parameters of tRNA motions within wild-type and specifically mutated ribosome complexes have been obtained that provide valuable new insights into the mechanism and regulation of translation elongation. The results of these studies are discussed in the context of current knowledge of the ribosome mechanism from both structural and biophysical perspectives. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 565,577, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Reversible and Efficient Materials-based Actuation by Electrolytic Phase TransformationCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 9 2003C.G. Cameron Abstract Electrolytic phase transformation is presented as a means of inducing reversible actuation in devices operating in a wide range of applications and scales. The device exploits the enormous pressure and volume changes that accompany the electrochemical interconversion between liquid and gas phases. With this method, strains beyond 136,000 % and stresses surpassing 200 MPa can be achieved, offering a level of performance many orders of magnitude beyond that of other materials-based strategies. [source] | ||||||||||||||||