Science.gov

Sample records for large-scale chemical modification

  1. An example of deep crustal brines effecting large-scale chemical modification of the crust during assembly of the Paleoproterozoic Columbia supercontinent

    NASA Astrophysics Data System (ADS)

    Glassley, W. E.; Korstgard, J. A.; Sørensen, K.

    2009-12-01

    The Nagssugtoqidian Mobile Belt (NMB) is a 300 km wide, 800 km long orogenic zone in central Greenland. It is part of the >20,000 km long complex of orogenic belts that formed between 1.7 and 2.0 Gya during assembly of the first supercontinent, Columbia,. The NMB is composed of several major crustal-scale shear zones that intervene between coherent blocks of high-grade metamorphic rocks. By combining detailed field, laboratory and aeromagnetic studies along the most northern of the shear zones (the Nordre Stromfjord Shear Zone - NSSZ), we have been able to document large scale chemical modification of the crust caused by the invasion of brines generated during continent-continent collision. The tectonic framework for this process is the following: 1. At 1,923 +/- 20 Mya: Emplacement of a calc-alkaline complex within and on ca. 2.8 Gya continental crust. The basal cumulate portion of the complex is well preserved and records invasion of multiple magma pulses. Coeval pillow basalts and cogenetic porphyritic mafics are also present. 2. 1,900 to 1,800 Mya: Tectonic emplacement of mafic and ultramafic rocks under high pressure (>2.5 GPa), eclogite facies conditions. The emplacement of these lenses probably occurred prior to or during thrust stacking associated with continent-continent collision. The age of the high pressure metamorphism makes these the oldest known eclogite facies metamorphic rocks in the world. 3. 1760 to 1720 Mya: Development of the transcurrent NSSZ, with displacements in excess of a hundred kilometers. Profound chemical enrichment of potassium and phosphorus along the entire length of the NSSZ unequivocally demonstrates that the shear zone was the focus of massive fluid movement. Detailed analysis of phase relationships documents a P-T path identical in form to that of Alpine metamorphic rocks, but displaced toward higher temperatures. These observations provide compelling evidence that assembly of this segment of Columbia involved subduction of

  2. Metal ion implantation for large scale surface modification

    SciTech Connect

    Brown, I.G.

    1992-10-01

    Intense energetic beams of metal ions can be produced by using a metal vapor vacuum arc as the plasma discharge from which the ion beam is formed. We have developed a number of ion sources of this kind and have built a metal ion implantation facility which can produce repetitively pulsed ion beams with mean ion energy up to several hundred key, pulsed beam current of more than an ampere, and time averaged current of several tens of milliamperes delivered onto a downstream target. We've also done some preliminary work on scaling up this technology to very large size. For example, a 50-cm diameter (2000 cm[sup 2]) set of beam formation electrodes was used to produce a pulsed titanium beam with ion current over 7 amperes at a mean ion energy of 100 key. Separately, a dc embodiment has been used to produce a dc titanium ion beam with current over 600 mA, power supply limited in this work, and up to 6 amperes of dc plasma ion current was maintained for over an hour. In a related program we've developed a plasma immersion method for applying thin metallic and compound films in which the added species is atomically mixed to the substrate. By adding a gas flow to the process, well-bonded compound films can also be formed; metallic films and multilayers as well as oxides and nitrides with mixed transition zones some hundreds of angstroms thick have been synthesized. Here we outline these parallel metal-plasma-based research programs and describe the hardware that we've developed and some of the surface modification research that we've done with it.

  3. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives

    PubMed Central

    Zybailov, Boris L.; Glazko, Galina V.; Jaiswal, Mihir; Raney, Kevin D.

    2014-01-01

    The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one’s attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Despite significant advances in mass spectrometry instrumentation over the last decade, mapping Protein-Protein Interactions (PPIs) using chemical cross-linking remains time consuming and requires substantial expertise, even in the simplest of systems. While robust methodologies and software exist for the analysis of binary PPIs and also for the single protein structure refinement using cross-linking-derived constraints, undertaking a proteome-wide cross-linking study is highly complex. Difficulties include i) identifying cross-linkers of the right length and selectivity that could capture interactions of interest; ii) enrichment of the cross-linked species; iii) identification and validation of the cross-linked peptides and cross-linked sites. In this review we examine existing literature aimed at the large-scale protein cross-linking and discuss possible paths for improvement. We also discuss short-length cross-linkers of broad specificity such as formaldehyde and diazirine-based photo-cross-linkers. These cross-linkers could potentially capture many types of interactions, without strict requirement for a particular amino-acid to be present at a given protein-protein interface. How these shortlength, broad specificity cross-linkers be applied to proteome-wide studies? We will suggest specific advances in methodology, instrumentation and software that are needed to

  4. Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.

    PubMed

    Horlacher, Oliver; Lisacek, Frederique; Müller, Markus

    2016-03-04

    Experimental improvements in post-translational modification (PTM) detection by tandem mass spectrometry (MS/MS) has allowed the identification of vast numbers of PTMs. Open modification searches (OMSs) of MS/MS data, which do not require prior knowledge of the modifications present in the sample, further increased the diversity of detected PTMs. Despite much effort, there is still a lack of functional annotation of PTMs. One possibility to narrow the annotation gap is to mine MS/MS data deposited in public repositories and to correlate the PTM presence with biological meta-information attached to the data. Since the data volume can be quite substantial and contain tens of millions of MS/MS spectra, the data mining tools must be able to cope with big data. Here, we present two tools, Liberator and MzMod, which are built using the MzJava class library and the Apache Spark large scale computing framework. Liberator builds large MS/MS spectrum libraries, and MzMod searches them in an OMS mode. We applied these tools to a recently published set of 25 million spectra from 30 human tissues and present tissue specific PTMs. We also compared the results to the ones obtained with the OMS tool MODa and the search engine X!Tandem.

  5. Modification in drag of turbulent boundary layers resulting from manipulation of large-scale structures

    NASA Technical Reports Server (NTRS)

    Corke, T. C.; Guezennec, Y.; Nagib, H. M.

    1981-01-01

    The effects of placing a parallel-plate turbulence manipulator in a boundary layer are documented through flow visualization and hot wire measurements. The boundary layer manipulator was designed to manage the large scale structures of turbulence leading to a reduction in surface drag. The differences in the turbulent structure of the boundary layer are summarized to demonstrate differences in various flow properties. The manipulator inhibited the intermittent large scale structure of the turbulent boundary layer for at least 70 boundary layer thicknesses downstream. With the removal of the large scale, the streamwise turbulence intensity levels near the wall were reduced. The downstream distribution of the skin friction was also altered by the introduction of the manipulator.

  6. Ensuring Adequate Health and Safety Information for Decision Makers during Large-Scale Chemical Releases

    NASA Astrophysics Data System (ADS)

    Petropoulos, Z.; Clavin, C.; Zuckerman, B.

    2015-12-01

    The 2014 4-Methylcyclohexanemethanol (MCHM) spill in the Elk River of West Virginia highlighted existing gaps in emergency planning for, and response to, large-scale chemical releases in the United States. The Emergency Planning and Community Right-to-Know Act requires that facilities with hazardous substances provide Material Safety Data Sheets (MSDSs), which contain health and safety information on the hazardous substances. The MSDS produced by Eastman Chemical Company, the manufacturer of MCHM, listed "no data available" for various human toxicity subcategories, such as reproductive toxicity and carcinogenicity. As a result of incomplete toxicity data, the public and media received conflicting messages on the safety of the contaminated water from government officials, industry, and the public health community. Two days after the governor lifted the ban on water use, the health department partially retracted the ban by warning pregnant women to continue avoiding the contaminated water, which the Centers for Disease Control and Prevention deemed safe three weeks later. The response in West Virginia represents a failure in risk communication and calls to question if government officials have sufficient information to support evidence-based decisions during future incidents. Research capabilities, like the National Science Foundation RAPID funding, can provide a solution to some of the data gaps, such as information on environmental fate in the case of the MCHM spill. In order to inform policy discussions on this issue, a methodology for assessing the outcomes of RAPID and similar National Institutes of Health grants in the context of emergency response is employed to examine the efficacy of research-based capabilities in enhancing public health decision making capacity. The results of this assessment highlight potential roles rapid scientific research can fill in ensuring adequate health and safety data is readily available for decision makers during large-scale

  7. Biologically inspired large scale chemical sensor arrays and embedded data processing

    NASA Astrophysics Data System (ADS)

    Marco, S.; Gutiérrez-Gálvez, A.; Lansner, A.; Martinez, D.; Rospars, J. P.; Beccherelli, R.; Perera, A.; Pearce, T.; Vershure, P.; Persaud, K.

    2013-05-01

    Biological olfaction outperforms chemical instrumentation in specificity, response time, detection limit, coding capacity, time stability, robustness, size, power consumption, and portability. This biological function provides outstanding performance due, to a large extent, to the unique architecture of the olfactory pathway, which combines a high degree of redundancy, an efficient combinatorial coding along with unmatched chemical information processing mechanisms. The last decade has witnessed important advances in the understanding of the computational primitives underlying the functioning of the olfactory system. EU Funded Project NEUROCHEM (Bio-ICT-FET- 216916) has developed novel computing paradigms and biologically motivated artefacts for chemical sensing taking inspiration from the biological olfactory pathway. To demonstrate this approach, a biomimetic demonstrator has been built featuring a large scale sensor array (65K elements) in conducting polymer technology mimicking the olfactory receptor neuron layer, and abstracted biomimetic algorithms have been implemented in an embedded system that interfaces the chemical sensors. The embedded system integrates computational models of the main anatomic building blocks in the olfactory pathway: the olfactory bulb, and olfactory cortex in vertebrates (alternatively, antennal lobe and mushroom bodies in the insect). For implementation in the embedded processor an abstraction phase has been carried out in which their processing capabilities are captured by algorithmic solutions. Finally, the algorithmic models are tested with an odour robot with navigation capabilities in mixed chemical plumes

  8. SureChEMBL: a large-scale, chemically annotated patent document database

    PubMed Central

    Papadatos, George; Davies, Mark; Dedman, Nathan; Chambers, Jon; Gaulton, Anna; Siddle, James; Koks, Richard; Irvine, Sean A.; Pettersson, Joe; Goncharoff, Nicko; Hersey, Anne; Overington, John P.

    2016-01-01

    SureChEMBL is a publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus; given the wealth of knowledge hidden in patent documents, analysis of SureChEMBL data has immediate applications in drug discovery, medicinal chemistry and other commercial areas of chemical science. Currently, the database contains 17 million compounds extracted from 14 million patent documents. Access is available through a dedicated web-based interface and data downloads at: https://www.surechembl.org/. PMID:26582922

  9. A Turn-Key Approach for Large-Scale Identification of Complex Posttranslational Modifications

    PubMed Central

    2015-01-01

    The conjugation of complex post-translational modifications (PTMs) such as glycosylation and Small Ubiquitin-like Modification (SUMOylation) to a substrate protein can substantially change the resulting peptide fragmentation pattern compared to its unmodified counterpart, making current database search methods inappropriate for the identification of tandem mass (MS/MS) spectra from such modified peptides. Traditionally it has been difficult to develop new algorithms to identify these atypical peptides because of the lack of a large set of annotated spectra from which to learn the altered fragmentation pattern. Using SUMOylation as an example, we propose a novel approach to generate large MS/MS training data from modified peptides and derive an algorithm that learns properties of PTM-specific fragmentation from such training data. Benchmark tests on data sets of varying complexity show that our method is 80–300% more sensitive than current state-of-the-art approaches. The core concepts of our method are readily applicable to developing algorithms for the identifications of peptides with other complex PTMs. PMID:24437954

  10. Synthetically chemical-electrical mechanism for controlling large scale reversible deformation of liquid metal objects

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Sheng, Lei; Liu, Jing

    2014-11-01

    Reversible deformation of a machine holds enormous promise across many scientific areas ranging from mechanical engineering to applied physics. So far, such capabilities are still hard to achieve through conventional rigid materials or depending mainly on elastomeric materials, which however own rather limited performances and require complicated manipulations. Here, we show a basic strategy which is fundamentally different from the existing ones to realize large scale reversible deformation through controlling the working materials via the synthetically chemical-electrical mechanism (SCHEME). Such activity incorporates an object of liquid metal gallium whose surface area could spread up to five times of its original size and vice versa under low energy consumption. Particularly, the alterable surface tension based on combination of chemical dissolution and electrochemical oxidation is ascribed to the reversible shape transformation, which works much more flexible than many former deformation principles through converting electrical energy into mechanical movement. A series of very unusual phenomena regarding the reversible configurational shifts are disclosed with dominant factors clarified. This study opens a generalized way to combine the liquid metal serving as shape-variable element with the SCHEME to compose functional soft machines, which implies huge potential for developing future smart robots to fulfill various complicated tasks.

  11. Synthetically chemical-electrical mechanism for controlling large scale reversible deformation of liquid metal objects.

    PubMed

    Zhang, Jie; Sheng, Lei; Liu, Jing

    2014-11-19

    Reversible deformation of a machine holds enormous promise across many scientific areas ranging from mechanical engineering to applied physics. So far, such capabilities are still hard to achieve through conventional rigid materials or depending mainly on elastomeric materials, which however own rather limited performances and require complicated manipulations. Here, we show a basic strategy which is fundamentally different from the existing ones to realize large scale reversible deformation through controlling the working materials via the synthetically chemical-electrical mechanism (SCHEME). Such activity incorporates an object of liquid metal gallium whose surface area could spread up to five times of its original size and vice versa under low energy consumption. Particularly, the alterable surface tension based on combination of chemical dissolution and electrochemical oxidation is ascribed to the reversible shape transformation, which works much more flexible than many former deformation principles through converting electrical energy into mechanical movement. A series of very unusual phenomena regarding the reversible configurational shifts are disclosed with dominant factors clarified. This study opens a generalized way to combine the liquid metal serving as shape-variable element with the SCHEME to compose functional soft machines, which implies huge potential for developing future smart robots to fulfill various complicated tasks.

  12. Synthetically chemical-electrical mechanism for controlling large scale reversible deformation of liquid metal objects

    PubMed Central

    Zhang, Jie; Sheng, Lei; Liu, Jing

    2014-01-01

    Reversible deformation of a machine holds enormous promise across many scientific areas ranging from mechanical engineering to applied physics. So far, such capabilities are still hard to achieve through conventional rigid materials or depending mainly on elastomeric materials, which however own rather limited performances and require complicated manipulations. Here, we show a basic strategy which is fundamentally different from the existing ones to realize large scale reversible deformation through controlling the working materials via the synthetically chemical-electrical mechanism (SCHEME). Such activity incorporates an object of liquid metal gallium whose surface area could spread up to five times of its original size and vice versa under low energy consumption. Particularly, the alterable surface tension based on combination of chemical dissolution and electrochemical oxidation is ascribed to the reversible shape transformation, which works much more flexible than many former deformation principles through converting electrical energy into mechanical movement. A series of very unusual phenomena regarding the reversible configurational shifts are disclosed with dominant factors clarified. This study opens a generalized way to combine the liquid metal serving as shape-variable element with the SCHEME to compose functional soft machines, which implies huge potential for developing future smart robots to fulfill various complicated tasks. PMID:25408295

  13. Large-scale chemical assembly of atomically thin transistors and circuits

    NASA Astrophysics Data System (ADS)

    Zhao, Mervin; Ye, Yu; Han, Yimo; Xia, Yang; Zhu, Hanyu; Wang, Siqi; Wang, Yuan; Muller, David A.; Zhang, Xiang

    2016-11-01

    Next-generation electronics calls for new materials beyond silicon, aiming at increased functionality, performance and scaling in integrated circuits. In this respect, two-dimensional gapless graphene and semiconducting transition-metal dichalcogenides have emerged as promising candidates due to their atomic thickness and chemical stability. However, difficulties with precise spatial control during their assembly currently impede actual integration into devices. Here, we report on the large-scale, spatially controlled synthesis of heterostructures made of single-layer semiconducting molybdenum disulfide contacting conductive graphene. Transmission electron microscopy studies reveal that the single-layer molybdenum disulfide nucleates at the graphene edges. We demonstrate that such chemically assembled atomic transistors exhibit high transconductance (10 µS), on-off ratio (˜106) and mobility (˜17 cm2 V-1 s-1). The precise site selectivity from atomically thin conducting and semiconducting crystals enables us to exploit these heterostructures to assemble two-dimensional logic circuits, such as an NMOS inverter with high voltage gain (up to 70).

  14. Target-Based Drug Repositioning Using Large-Scale Chemical-Protein Interactome Data.

    PubMed

    Sawada, Ryusuke; Iwata, Hiroaki; Mizutani, Sayaka; Yamanishi, Yoshihiro

    2015-12-28

    Drug repositioning, or the identification of new indications for known drugs, is a useful strategy for drug discovery. In this study, we developed novel computational methods to predict potential drug targets and new drug indications for systematic drug repositioning using large-scale chemical-protein interactome data. We explored the target space of drugs (including primary targets and off-targets) based on chemical structure similarity and phenotypic effect similarity by making optimal use of millions of compound-protein interactions. On the basis of the target profiles of drugs, we constructed statistical models to predict new drug indications for a wide range of diseases with various molecular features. The proposed method outperformed previous methods in terms of interpretability, applicability, and accuracy. Finally, we conducted a comprehensive prediction of the drug-target-disease association network for 8270 drugs and 1401 diseases and showed biologically meaningful examples of newly predicted drug targets and drug indications. The predictive model is useful to understand the mechanisms of the predicted drug indications.

  15. Interaction chromatography for characterization and large-scale fractionation of chemically heterogeneous copolymers

    NASA Astrophysics Data System (ADS)

    Han, Junwon

    The remarkable development of polymer synthesis techniques to make complex polymers with controlled chain architectures has inevitably demanded the advancement of polymer characterization tools to analyze the molecular dispersity in polymeric materials beyond size exclusion chromatography (SEC). In particular, man-made synthetic copolymers that consist of more than one monomer type are disperse mixtures of polymer chains that have distributions in terms of both chemical heterogeneity and chain length (molar mass). While the molecular weight distribution has been quite reliably estimated by the SEC, it is still challenging to properly characterize the chemical composition distribution in the copolymers. Here, I have developed and applied adsorption-based interaction chromatography (IC) techniques as a promising tool to characterize and fractionate polystyrene-based block, random and branched copolymers in terms of their chemical heterogeneity. The first part of this thesis is focused on the adsorption-desorption based purification of PS-b-PMMA diblock copolymers using nanoporous silica. The liquid chromatography analysis and large scale purification are discussed for the PS-b-PMMA block copolymers that have been synthesized by sequential anionic polymerization. SEC and IC are compared to critically analyze the contents of PS homopolymers in the as-synthesized block copolymers. In addition, I have developed an IC technique to provide faster and more reliable information on the chemical heterogeneity in the as-synthesized block copolymers. Finally, a large scale (multi-gram) separation technique is developed to obtain "homopolymer-free" block copolymers via a simple chromatographic filtration technique. By taking advantage of the large specific surface area of nanoporous silica (≈300m 2/g), large scale purification of neat PS-b-PMMA has successfully been achieved by controlling adsorption and desorption of the block copolymers on the silica gel surface using a

  16. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    SciTech Connect

    Sweany, M; Bernstein, A; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, S M

    2011-09-21

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  17. An Efficient Approach for Preprocessing Data from a Large-Scale Chemical Sensor Array

    PubMed Central

    Leo, Marco; Distante, Cosimo; Bernabei, Mara; Persaud, Krishna

    2014-01-01

    In this paper, an artificial olfactory system (Electronic Nose) that mimics the biological olfactory system is introduced. The device consists of a Large-Scale Chemical Sensor Array (16, 384 sensors, made of 24 different kinds of conducting polymer materials) that supplies data to software modules, which perform advanced data processing. In particular, the paper concentrates on the software components consisting, at first, of a crucial step that normalizes the heterogeneous sensor data and reduces their inherent noise. Cleaned data are then supplied as input to a data reduction procedure that extracts the most informative and discriminant directions in order to get an efficient representation in a lower dimensional space where it is possible to more easily find a robust mapping between the observed outputs and the characteristics of the odors in input to the device. Experimental qualitative proofs of the validity of the procedure are given by analyzing data acquired for two different pure analytes and their binary mixtures. Moreover, a classification task is performed in order to explore the possibility of automatically recognizing pure compounds and to predict binary mixture concentrations. PMID:25254304

  18. Large-scale production of megakaryocytes from human pluripotent stem cells by chemically defined forward programming

    PubMed Central

    Moreau, Thomas; Evans, Amanda L.; Vasquez, Louella; Tijssen, Marloes R.; Yan, Ying; Trotter, Matthew W.; Howard, Daniel; Colzani, Maria; Arumugam, Meera; Wu, Wing Han; Dalby, Amanda; Lampela, Riina; Bouet, Guenaelle; Hobbs, Catherine M.; Pask, Dean C.; Payne, Holly; Ponomaryov, Tatyana; Brill, Alexander; Soranzo, Nicole; Ouwehand, Willem H.; Pedersen, Roger A.; Ghevaert, Cedric

    2016-01-01

    The production of megakaryocytes (MKs)—the precursors of blood platelets—from human pluripotent stem cells (hPSCs) offers exciting clinical opportunities for transfusion medicine. Here we describe an original approach for the large-scale generation of MKs in chemically defined conditions using a forward programming strategy relying on the concurrent exogenous expression of three transcription factors: GATA1, FLI1 and TAL1. The forward programmed MKs proliferate and differentiate in culture for several months with MK purity over 90% reaching up to 2 × 105 mature MKs per input hPSC. Functional platelets are generated throughout the culture allowing the prospective collection of several transfusion units from as few as 1 million starting hPSCs. The high cell purity and yield achieved by MK forward programming, combined with efficient cryopreservation and good manufacturing practice (GMP)-compatible culture, make this approach eminently suitable to both in vitro production of platelets for transfusion and basic research in MK and platelet biology. PMID:27052461

  19. TALEN-mediated modification of the bovine genome for large-scale production of human serum albumin.

    PubMed

    Moghaddassi, Shaida; Eyestone, Will; Bishop, Colin E

    2014-01-01

    As an initial step towards creating genetically modified cattle as a biopharming source of recombinant human serum albumin (rHSA), we report modification of the bovine albumin (bA) locus by transcription activator-like effector nuclease (TALEN)-stimulated homology-directed repair (HDR). Pedigreed bovine fibroblasts were co-transfected with TALENs and an 11.5-kb human serum albumin (HSA) minigene donor construct, designed to simultaneously disrupt and replace bovine serum albumin (BSA) expression with controlled rHSA expression in both the liver and the milk. Targeted integration of the HSA minigene was confirmed in transfected fibroblasts at a frequency of approximately 11% and transgenic bovine embryos were produced from targeted fibroblasts using somatic cell nuclear transfer (SCNT). The research delineated here lays the foundation for the future generation of transgenic rHSA cattle with the potential to provide a large-scale, reliable, and quality-controlled source of rHSA.

  20. Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Li, Chien-Ming; Hu, Qiyang; Huang, Yong; Damoiseaux, Robert; Torres, Jorge Z

    2015-03-01

    Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60-70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/).

  1. Modification of input datasets for the Ensemble Streamflow Prediction based on large-scale climatic indices and weather generator

    NASA Astrophysics Data System (ADS)

    Šípek, Václav; Daňhelka, Jan

    2015-09-01

    Ensemble Streamflow Prediction (ESP) provides an efficient tool for seasonal hydrological forecasts. In this study, we propose a new modification of input data series for the ESP system used for the runoff volume prediction with a lead of one month. These series are not represented by short historical weather datasets but by longer generated synthetic weather data series. Before their submission to the hydrological model, their number is restricted by relations among observed meteorological variables (average monthly precipitation and temperature) and large-scale climatic patterns and indices (e.g. North Atlantic Oscillation, sea level pressure values and two geopotential heights). This modification was tested over a four-year testing period using the river basin in central Europe. The LARS-WG weather generator proved to be a suitable tool for the extension of the historical weather records. The modified ESP approach proved to be more efficient in the majority of months compared both to the original ESP method and reference forecast (based on probability distribution of historical discharges). The improvement over traditional ESP was most obvious in the narrower forecast interval of the expected runoff volume. The inefficient forecasts of the modified ESP scheme (compared to traditional ESP) were conditioned by an insufficient restriction of input synthetic weather datasets by the climate forecast.

  2. Modification of the large-scale features of high Reynolds number wall turbulence by passive surface obtrusions

    NASA Astrophysics Data System (ADS)

    Monty, J. P.; Allen, J. J.; Lien, K.; Chong, M. S.

    2011-12-01

    A high Reynolds number boundary-layer wind-tunnel facility at New Mexico State University was fitted with a regularly distributed braille surface. The surface was such that braille dots were closely packed in the streamwise direction and sparsely spaced in the spanwise direction. This novel surface had an unexpected influence on the flow: the energy of the very large-scale features of wall turbulence (approximately six-times the boundary-layer thickness in length) became significantly attenuated, even into the logarithmic region. To the author's knowledge, this is the first experimental study to report a modification of `superstructures' in a rough-wall turbulent boundary layer. The result gives rise to the possibility that flow control through very small, passive surface roughness may be possible at high Reynolds numbers, without the prohibitive drag penalty anticipated heretofore. Evidence was also found for the uninhibited existence of the near-wall cycle, well known to smooth-wall-turbulence researchers, in the spanwise space between roughness elements.

  3. Industrial microbial enzymes: their discovery by screening and use in large-scale production of useful chemicals in Japan.

    PubMed

    Ogawa, Jun; Shimizu, Sakayu

    2002-08-01

    The application of microbial enzymes to large-scale organic synthesis is currently attracting much attention, and has been uniquely developed especially in Japan. The discovery of new microbial enzymes through extensive and persistent screening has brought about many new and simple routes for synthetic processes. The application of these enzymes in so-called 'hybrid processes' of enzymatic and chemical reactions, provide one possible way to solve environmental problems.

  4. Color and chemical properties of oil used for deep frying on a large scale.

    PubMed

    Totani, Nagao; Tateishi, Sayuri; Chiue, Hiroko; Mori, Terutosi

    2012-01-01

    Acid value (AV), polar compound content (PC), carbonyl value (CV) and Gardner color of oil used for deep-frying in kitchens at a supermarket, lunch chain store, restaurant, eating house, and hospital were analyzed. All AVs obtained but one (3.38) were within the limit set by the Food Sanitation Act of Japan (AV ≤ 3, peroxide value ≤ 30). However, some oil samples had a PC over 25%, which is beyond the limit legislated by some European countries. When the relation between the Gardner color and the AV, PC, or CV of the oil was investigated, well correlated logarithmic regression curves were obtained from the oil of all kitchens except the hospital kitchen. However, the use of lard-containing canola oil without oil replenishment in the eating house increased color values rapidly. All of the values obtained from pure vegetable oil used almost daily were plotted on a graph. It was found that kitchen-by-kitchen differences in fryer, vegetable oil, frying temperature, heating time, and amounts and kinds of foods fried did not influence the relation between Gardner color value versus AV, PC or CV. In conclusion, frying vegetable oil used in large-scale kitchens without official inspection can be better controlled with Gardner color determination by the operators and administrators. This would improve the quality of the oil ingested by facility patrons.

  5. Chemical ordering suppresses large-scale electronic phase separation in doped manganites

    NASA Astrophysics Data System (ADS)

    Zhu, Yinyan; Du, Kai; Niu, Jiebin; Lin, Lingfang; Wei, Wengang; Liu, Hao; Lin, Hanxuan; Zhang, Kai; Yang, Tieying; Kou, Yunfang; Shao, Jian; Gao, Xingyu; Xu, Xiaoshan; Wu, Xiaoshan; Dong, Shuai; Yin, Lifeng; Shen, Jian

    2016-04-01

    For strongly correlated oxides, it has been a long-standing issue regarding the role of the chemical ordering of the dopants on the physical properties. Here, using unit cell by unit cell superlattice growth technique, we determine the role of chemical ordering of the Pr dopant in a colossal magnetoresistant (La1-yPry)1-xCaxMnO3 (LPCMO) system, which has been well known for its large length-scale electronic phase separation phenomena. Our experimental results show that the chemical ordering of Pr leads to marked reduction of the length scale of electronic phase separations. Moreover, compared with the conventional Pr-disordered LPCMO system, the Pr-ordered LPCMO system has a metal-insulator transition that is ~100 K higher because the ferromagnetic metallic phase is more dominant at all temperatures below the Curie temperature.

  6. Chemical ordering suppresses large-scale electronic phase separation in doped manganites

    PubMed Central

    Zhu, Yinyan; Du, Kai; Niu, Jiebin; Lin, Lingfang; Wei, Wengang; Liu, Hao; Lin, Hanxuan; Zhang, Kai; Yang, Tieying; Kou, Yunfang; Shao, Jian; Gao, Xingyu; Xu, Xiaoshan; Wu, Xiaoshan; Dong, Shuai; Yin, Lifeng; Shen, Jian

    2016-01-01

    For strongly correlated oxides, it has been a long-standing issue regarding the role of the chemical ordering of the dopants on the physical properties. Here, using unit cell by unit cell superlattice growth technique, we determine the role of chemical ordering of the Pr dopant in a colossal magnetoresistant (La1−yPry)1−xCaxMnO3 (LPCMO) system, which has been well known for its large length-scale electronic phase separation phenomena. Our experimental results show that the chemical ordering of Pr leads to marked reduction of the length scale of electronic phase separations. Moreover, compared with the conventional Pr-disordered LPCMO system, the Pr-ordered LPCMO system has a metal–insulator transition that is ∼100 K higher because the ferromagnetic metallic phase is more dominant at all temperatures below the Curie temperature. PMID:27053071

  7. Estimation Source Parameters of Large-Scale Chemical Surface Explosions and Recent Underground Nuclear Tests

    NASA Astrophysics Data System (ADS)

    Gitterman, Y.; Kim, S.; Hofstetter, R.

    2013-12-01

    Large-scale surface explosions were conducted by the Geophysical Institute of Israel at Sayarim Military Range (SMR), Negev desert: 82 tons of strong HE explosives in August 2009, and 10&100 tons of ANFO explosives in January 2011. The main goal was to provide strong controlled sources in different wind conditions, for calibration of IMS infrasound stations. Numerous dense observations of blast waves were provided by high-pressure, acoustic and seismic sensors at near-source (< 1 km) and close local (1-40 km) distances. The rarely reported Secondary Shock (SS) phenomenon was clearly observed at the all sensors. A novel empirical relationship for the new air-blast parameter - SS time delay - versus distance (both scaled by the cubic root of estimated TNT equivalent charge) was developed and analyzed. The scaled SS delays were found clearly separated for 2009 and 2011 shots, thus demonstrating dependence on the type of explosives with different detonation velocity. Additional acoustic and seismic records from very large (> 2000 tons) ANFO surface shots at White Sands Military Range (WSMR) were analyzed for SS time delay. The Secondary Shocks were revealed on the records in the range 1.5-60 km and showed consistency with the SMR data, thus extending the charge and distance range for the developed SS delay relationship. Obtained results suggest that measured SS delays can provide important information about an explosion source character, and can be used as a new simple cost-effective yield estimator for explosions with known type of explosives. The new results are compared with analogous available data of surface nuclear explosions. Special distinctions in air-blast waves are revealed and analyzed, resulting from the different source phenomenology (energy release). Two underground nuclear explosions conducted by North Korea in 2009 and 2013 were recorded by several stations of Israel Seismic Network. Pronounced minima (spectral nulls) at 1.2-1.3 Hz were revealed in the

  8. Generation of low-frequency electric and magnetic fields during large- scale chemical and nuclear explosions

    SciTech Connect

    Adushkin, V.V.; Dubinya, V.A.; Karaseva, V.A.; Soloviev, S.P.; Surkov, V.V.

    1995-06-01

    We discuss the main parameters of the electric field in the surface layer of the atmosphere and the results of the investigations of the natural electric field variations. Experimental investigations of the electromagnetic field for explosions in air are presented. Electromagnetic signals generated by underground nuclear and chemical explosions are discussed and explosions for 1976--1991 are listed. Long term anomalies of the earth`s electromagnetic field in the vicinity of underground explosions were also investigated. Study of the phenomenon of the irreversible shock magnetization showed that in the zone nearest to the explosion the quasistatic magnetic field decreases in inverse proportion to the distance.

  9. Electronic Properties of Large-scale Graphene Chemical Vapor Synthesized on Nickel and on Sapphire

    NASA Astrophysics Data System (ADS)

    Cao, Helin; Zhang, Liyuan; Chen, Yong; Yu, Qingkai; Li, Hao

    2009-03-01

    We have studied the electronic transport properties of large area few-layer graphene/graphitic films grown by two different chemical vapor based methods. The first type of samples (metal-transfer graphene) is synthesized by carbon segregation from Ni, then transferred to SiO2/Si substrates. The second type of samples is synthesized by direct chemical vapor deposition (CVD) on sapphire. We measured these samples under variable temperatures (from 2K to 300 K) and transverse magnet fields (from 0 to 7 T). For both types of samples, we found a negative magnetoresistance at low field, and carrier mobilities on the order of several hundreds of cm^2/V-s. For metal-transfer graphene in particular, we were able to measure a moderate field effect response, using the highly doped Si substrate as back gate. The observed magnetoresistance shows characteristic features of weak localization, from which we extract various carrier scattering lengths in the metal-transfer graphene samples. Comparison with those measured in mechanically exfoliated graphene suggests possibly different carrier scattering mechanisms for graphene materials prepared with different methods.

  10. Ferromagnetic inks facilitate large scale paper recycling and reduce bleach chemical consumption.

    PubMed

    Zeltner, Martin; Toedtli, Laura M; Hild, Nora; Fuhrer, Roland; Rossier, Michaël; Gerber, Lukas C; Raso, Renzo A; Grass, Robert N; Stark, Wendelin J

    2013-04-23

    Deinking is a fundamental part of paper recycling. As the global paper consumption rises and exceeds even the annual paper production, recycling of this raw material is of high importance. Magnetic ink based on carbon coated magnetic nanoparticles enables an alternative approach to state of the art paper deinking. Magnetic deinking comprises three steps (preselection, washing, and magnetic separation of fibers). Preseparation of printed from nonprinted scraps of paper is feasible and reduces the paper mass which has to be fed into a deinking process. A consecutive washing process removes surficial magnetic ink that can be collected by application of a permanent magnet. Still, printed parts are subjected to a further continuous magnetic deinking step, where magnetic and nonmagnetic paper fibers can be separated. Magnetic deinking of a model print allows recovery of more than 80% of bright fibers without any harsh chemical treatment and the re-collection of more than 82% of magnetic ink.

  11. [Physical, chemical and biological study of dust from large-scale pig farms].

    PubMed

    Raszyk, J

    1986-04-01

    Dust deposition in 16 halls of two large pig-fattening farms with dry or wet feeding systems was analyzed. In the halls with wet feeding the samples contained maximally 28 dust particles up to 10 micron and 17 particles up to 5 micron per cm3 of air, in the halls with dry feeding 220 particles smaller than 10 micron and 205 particles smaller than 5 micron per cm3 of air. The total amino acid content in the dust deposition was 17.440 +/- 1.820 g per 100 g of sample and the content of nitrogen compounds (N X X 6.25, %), was 24.170 +/- 2.910. The contents of chemical elements were as follows (mg per kg): zinc 448 +/- 151; manganese 109.9 +/- 49.5; copper 40.5 +/- 12.1; lead 4.77 +/- +/- 4.79; chromium 1.64 +/- 1.47; cadmium 1.61 +/- 1.62; mercury 0.36 +/- 0.39. Chlorinated carbohydrates and triazine and diazine herbicides were present in the following amounts (mg per kg): HCB 0.0023 +/- 0.0021; Lindane 0.0058 +/- 0.0079; DDE 0.0048 +/- +/- 0.0024; DDT 0.0065 +/- 0.0015; Simazine 0.060 +/- 0.020; Atrazine 0.083 +/- 0.059; Prometryn 0.093 +/- 0.040; Chloridazon 0.036 +/- 0.008; Terbutryn 0.085 +/- 0.029. The content of aflatoxin B1 was 12.89 +/- 9.31 micrograms per kg and the maximum amount of polychlorinated biphenyls was 8 mg per kg. Nitrovin was found out only in the dust of two halls: 4.0 and 7.9 mg per kg. The dust deposition also contained 21 genera and species of moulds, six species of mites, numerous saprophytic bacteria and, in some cases, Staphylococcus aureus. For the time being, no viruses have been detected in the dust samples.

  12. Chemical Protein Modification through Cysteine.

    PubMed

    Gunnoo, Smita B; Madder, Annemieke

    2016-04-01

    The modification of proteins with non-protein entities is important for a wealth of applications, and methods for chemically modifying proteins attract considerable attention. Generally, modification is desired at a single site to maintain homogeneity and to minimise loss of function. Though protein modification can be achieved by targeting some natural amino acid side chains, this often leads to ill-defined and randomly modified proteins. Amongst the natural amino acids, cysteine combines advantageous properties contributing to its suitability for site-selective modification, including a unique nucleophilicity, and a low natural abundance--both allowing chemo- and regioselectivity. Native cysteine residues can be targeted, or Cys can be introduced at a desired site in a protein by means of reliable genetic engineering techniques. This review on chemical protein modification through cysteine should appeal to those interested in modifying proteins for a range of applications.

  13. Chemical modification of semiconductor surfaces

    NASA Technical Reports Server (NTRS)

    Finklea, H. O.

    1981-01-01

    Results of research on the chemical modification of TiO2 powders in the gas phase and the examination of the modified powders by infrared absorption spectroscopy are comprehensively summarized. The range of information obtainable by IR spectroscopy of chemically modified semiconductors, and a definition of the optimum reaction conditions for synthesizing a monolayer of methylsilanes using vapor phase reaction conditions were considered.

  14. Chemical Modification of Polysaccharides

    PubMed Central

    Cumpstey, Ian

    2013-01-01

    This review covers methods for modifying the structures of polysaccharides. The introduction of hydrophobic, acidic, basic, or other functionality into polysaccharide structures can alter the properties of materials based on these substances. The development of chemical methods to achieve this aim is an ongoing area of research that is expected to become more important as the emphasis on using renewable starting materials and sustainable processes increases in the future. The methods covered in this review include ester and ether formation using saccharide oxygen nucleophiles, including enzymatic reactions and aspects of regioselectivity; the introduction of heteroatomic nucleophiles into polysaccharide chains; the oxidation of polysaccharides, including oxidative glycol cleavage, chemical oxidation of primary alcohols to carboxylic acids, and enzymatic oxidation of primary alcohols to aldehydes; reactions of uronic-acid-based polysaccharides; nucleophilic reactions of the amines of chitosan; and the formation of unsaturated polysaccharide derivatives. PMID:24151557

  15. Large-Scale Fabrication of Boron Nitride Nanotubes via a Facile Chemical Vapor Reaction Route and Their Cathodoluminescence Properties

    NASA Astrophysics Data System (ADS)

    Zhong, Bo; Huang, Xiaoxiao; Wen, Guangwu; Yu, Hongming; Zhang, Xiaodong; Zhang, Tao; Bai, Hongwei

    2011-12-01

    Cylinder- and bamboo-shaped boron nitride nanotubes (BNNTs) have been synthesized in large scale via a facile chemical vapor reaction route using ammonia borane as a precursor. The structure and chemical composition of the as-synthesized BNNTs are extensively characterized by X-ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, and selected-area electron diffraction. The cylinder-shaped BNNTs have an average diameter of about 100 nm and length of hundreds of microns, while the bamboo-shaped BNNTs are 100-500 nm in diameter with length up to tens of microns. The formation mechanism of the BNNTs has been explored on the basis of our experimental observations and a growth model has been proposed accordingly. Ultraviolet-visible and cathodoluminescence spectroscopic analyses are performed on the BNNTs. Strong ultraviolet emissions are detected on both morphologies of BNNTs. The band gap of the BNNTs are around 5.82 eV and nearly unaffected by tube morphology. There exist two intermediate bands in the band gap of BNNTs, which could be distinguishably assigned to structural defects and chemical impurities.

  16. Large-scale synthesis of copper nanoparticles by chemically controlled reduction for applications of inkjet-printed electronics

    NASA Astrophysics Data System (ADS)

    Lee, Youngil; Choi, Jun-rak; Jong Lee, Kwi; Stott, Nathan E.; Kim, Donghoon

    2008-10-01

    Copper nanoparticles are being given considerable attention as of late due to their interesting properties and potential applications in many areas of industry. One such exploitable use is as the major constituent of conductive inks and pastes used for printing various electronic components. In this study, copper nanoparticles were synthesized through a relatively large-scale (5 l), high-throughput (0.2 M) process. This facile method occurs through the chemical reduction of copper sulfate with sodium hypophosphite in ethylene glycol within the presence of a polymer surfactant (PVP), which was included to prevent aggregation and give dispersion stability to the resulting colloidal nanoparticles. Reaction yields were determined to be quantitative while particle dispersion yields were between 68 and 73%. The size of the copper nanoparticles could be controlled between 30 and 65 nm by varying the reaction time, reaction temperature, and relative ratio of copper sulfate to the surfactant. Field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM) images of the particles revealed a spherical shape within the reported size regime, and x-ray analysis confirmed the formation of face-centered cubic (FCC) metallic copper. Furthermore, inkjet printing nanocopper inks prepared from the polymer-stabilized copper nanoparticles onto polyimide substrates resulted in metallic copper traces with low electrical resistivities (>=3.6 µΩ cm, or >=2.2 times the resistivity of bulk copper) after a relatively low-temperature sintering process (200 °C for up to 60 min).

  17. Natural background levels and threshold values of chemical species in three large-scale groundwater bodies in Northern Italy.

    PubMed

    Molinari, Antonio; Guadagnini, Laura; Marcaccio, Marco; Guadagnini, Alberto

    2012-05-15

    We analyze natural background levels (NBLs) and threshold values (TVs) of spatially distributed chemical species (NH(4), B and As) which may be a potential pressure and concern in three large scale alluvial and fluvio-deltaic aquifers at different depths of the Apennines and Po river plains in Emilia-Romagna, Northern Italy. Our results are based on statistical methodologies designed to separate the natural and anthropogenic contributions in monitored concentrations by modeling the empirical distribution of the detected concentration with a mixture of probability density functions. Available chemical observations are taken over a 20 years period and are associated with different depths and cover planar investigation scales of the order of hundreds of kilometers. High concentration values detected for NH(4) and B appear to be related to high natural background levels. Due to interaction with the host rock in different geochemical environments we observed that concentration vary in time and space (including in depth) consistently with the hydrogeochemical features and the occurrence of natural attenuation mechanisms in the analyzed reservoirs. Conversely, estimated As NBLs are not consistent with the conceptual model of the hydrogeochemical behavior of the systems analyzed and experimental evidences of As content in aquifer cores. This is due to the inability of these techniques to incorporate the complex dynamics of the processes associated with the specific hydrogeochemical setting. Statistical analyses performed upon aggregating the concentration data according to different time observation windows allow identifying temporal dynamics of NBLs and TVs of target compounds within the observation time frame. Our results highlight the benefit of a dynamic monitoring process and analysis of well demarcated groundwater bodies to update the associated NBLs as a function of the temporal dependence of natural processes occurring in the subsurface. Monitoring protocols could

  18. Large scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Doolin, B. F.

    1975-01-01

    Classes of large scale dynamic systems were discussed in the context of modern control theory. Specific examples discussed were in the technical fields of aeronautics, water resources and electric power.

  19. Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics

    PubMed Central

    Iwata, Michio; Sawada, Ryusuke; Iwata, Hiroaki; Kotera, Masaaki; Yamanishi, Yoshihiro

    2017-01-01

    The identification of the modes of action of bioactive compounds is a major challenge in chemical systems biology of diseases. Genome-wide expression profiling of transcriptional responses to compound treatment for human cell lines is a promising unbiased approach for the mode-of-action analysis. Here we developed a novel approach to elucidate the modes of action of bioactive compounds in a cell-specific manner using large-scale chemically-induced transcriptome data acquired from the Library of Integrated Network-based Cellular Signatures (LINCS), and analyzed 16,268 compounds and 68 human cell lines. First, we performed pathway enrichment analyses of regulated genes to reveal active pathways among 163 biological pathways. Next, we explored potential target proteins (including primary targets and off-targets) with cell-specific transcriptional similarity using chemical–protein interactome. Finally, we predicted new therapeutic indications for 461 diseases based on the target proteins. We showed the usefulness of the proposed approach in terms of prediction coverage, interpretation, and large-scale applicability, and validated the new prediction results experimentally by an in vitro cellular assay. The approach has a high potential for advancing drug discovery and repositioning. PMID:28071740

  20. A review of approaches to estimate wildfire plume injection height within large-scale atmospheric chemical transport models

    NASA Astrophysics Data System (ADS)

    Paugam, R.; Wooster, M.; Freitas, S.; Martin, M. Val

    2016-01-01

    Landscape fires produce smoke containing a very wide variety of chemical species, both gases and aerosols. For larger, more intense fires that produce the greatest amounts of emissions per unit time, the smoke tends initially to be transported vertically or semi-vertically close by the source region, driven by the intense heat and convective energy released by the burning vegetation. The column of hot smoke rapidly entrains cooler ambient air, forming a rising plume within which the fire emissions are transported. The characteristics of this plume, and in particular the height to which it rises before releasing the majority of the smoke burden into the wider atmosphere, are important in terms of how the fire emissions are ultimately transported, since for example winds at different altitudes may be quite different. This difference in atmospheric transport then may also affect the longevity, chemical conversion, and fate of the plumes chemical constituents, with for example very high plume injection heights being associated with extreme long-range atmospheric transport. Here we review how such landscape-scale fire smoke plume injection heights are represented in larger-scale atmospheric transport models aiming to represent the impacts of wildfire emissions on component of the Earth system. In particular we detail (i) satellite Earth observation data sets capable of being used to remotely assess wildfire plume height distributions and (ii) the driving characteristics of the causal fires. We also discuss both the physical mechanisms and dynamics taking place in fire plumes and investigate the efficiency and limitations of currently available injection height parameterizations. Finally, we conclude by suggesting some future parameterization developments and ideas on Earth observation data selection that may be relevant to the instigation of enhanced methodologies aimed at injection height representation.

  1. A review of approaches to estimate wildfire plume injection height within large scale atmospheric chemical transport models - Part 1

    NASA Astrophysics Data System (ADS)

    Paugam, R.; Wooster, M.; Freitas, S. R.; Martin, M. Val

    2015-03-01

    Landscape fires produce smoke containing a very wide variety of chemical species, both gases and aerosols. For larger, more intense fires that produce the greatest amounts of emissions per unit time, the smoke tends initially to be transported vertically or semi-vertically close by the source region, driven by the intense heat and convective energy released by the burning vegetation. The column of hot smoke rapidly entrains cooler ambient air, forming a rising plume within which the fire emissions are transported. This characteristics of this plume, and in particular the height to which it rises before releasing the majority of the smoke burden into the wider atmosphere, are important in terms of how the fire emissions are ultimately transported, since for example winds at different altitudes maybe quite different. This difference in atmospheric transport then may also affect the longevity, chemical conversion and fate of the plumes chemical consituents, with for example very high plume injection heights being associated with extreme long-range atmospheric transport. Here we review how such landscape-scale fire smoke plume injection heights are represented in larger scale atmospheric transport models aiming to represent the impacts of wildfire emissions on component of the Earth system. The use of satellite Earth observation (EO) data is commonly used for this, and detail the EO datasets capable of being used to remotely assess wildfire plume height distributions and the driving characteristics of the causal fires. We also discus both the physical mechanisms and dynamics taking place in fire plumes, and investigate the efficiency and limitations of currently available injection height parameterizations. Finally, we conclude by suggestion some future parameterization developments and ideas on EO data selection that maybe relevant to the instigation of enhanced methodologies aimed at injection height representation.

  2. A facile chemical-mechanical polishing lift-off transfer process toward large scale Cu(In,Ga)Se2 thin-film solar cells on arbitrary substrates

    NASA Astrophysics Data System (ADS)

    Tseng, Kuan-Chun; Yen, Yu-Ting; Thomas, Stuart R.; Tsai, Hung-Wei; Hsu, Cheng-Hung; Tsai, Wen-Chi; Shen, Chang-Hong; Shieh, Jia-Min; Wang, Zhiming M.; Chueh, Yu-Lun

    2016-02-01

    The fabrication of Cu(In,Ga)Se2 (CIGS) solar cells on flexible substrates is a non-trivial task due to thermal and ion diffusion related issues. In order to circumvent these issues, we have developed a chemical-mechanical polishing lift-off (CMPL) transfer process, enabling the direct transfer of CIGS solar cells from conventional soda-lime glass (SLG) onto arbitrary flexible substrates up to 4 cm2 in size. The structural and compositional nature of the pre- and post-transferred films is examined using electron microscopy, X-ray diffraction analysis, Raman and photoluminescence spectroscopy. We demonstrate the fabrication of solar cells on a range of flexible substrates while being able to maintain 75% cell efficiency (η) when compared to pre-transferred solar cells. The results obtained in this work suggest that our transfer process offers a highly promising approach toward large scale fabrication of CIGS-based solar cells on a wide variety of flexible substrates, suitable for use in the large scale CIGS photovoltaic industry.The fabrication of Cu(In,Ga)Se2 (CIGS) solar cells on flexible substrates is a non-trivial task due to thermal and ion diffusion related issues. In order to circumvent these issues, we have developed a chemical-mechanical polishing lift-off (CMPL) transfer process, enabling the direct transfer of CIGS solar cells from conventional soda-lime glass (SLG) onto arbitrary flexible substrates up to 4 cm2 in size. The structural and compositional nature of the pre- and post-transferred films is examined using electron microscopy, X-ray diffraction analysis, Raman and photoluminescence spectroscopy. We demonstrate the fabrication of solar cells on a range of flexible substrates while being able to maintain 75% cell efficiency (η) when compared to pre-transferred solar cells. The results obtained in this work suggest that our transfer process offers a highly promising approach toward large scale fabrication of CIGS-based solar cells on a wide

  3. CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data.

    PubMed

    Russo, Daniel P; Kim, Marlene T; Wang, Wenyi; Pinolini, Daniel; Shende, Sunil; Strickland, Judy; Hartung, Thomas; Zhu, Hao

    2016-10-14

    We have developed a public Chemical In vitro-In vivo Profiling (CIIPro) portal, which can automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds. For compounds with in vivo target activity data (e.g. animal toxicity testing results), the integrated cheminformatics algorithm will optimize the extracted biological data using in vitro-in vivo correlations. The resulting in vitro biological data for target compounds can be used for read-across risk assessment of target compounds. Additionally, the CIIPro portal can identify the most similar compounds based on their optimized bioprofiles. The CIIPro portal provides new powerful assessment capabilities to the scientific community and can be easily integrated with other cheminformatics tools.

  4. Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity.

    PubMed

    Schneider, Nadine; Lowe, Daniel M; Sayle, Roger A; Landrum, Gregory A

    2015-01-26

    Fingerprint methods applied to molecules have proven to be useful for similarity determination and as inputs to machine-learning models. Here, we present the development of a new fingerprint for chemical reactions and validate its usefulness in building machine-learning models and in similarity assessment. Our final fingerprint is constructed as the difference of the atom-pair fingerprints of products and reactants and includes agents via calculated physicochemical properties. We validated the fingerprints on a large data set of reactions text-mined from granted United States patents from the last 40 years that have been classified using a substructure-based expert system. We applied machine learning to build a 50-class predictive model for reaction-type classification that correctly predicts 97% of the reactions in an external test set. Impressive accuracies were also observed when applying the classifier to reactions from an in-house electronic laboratory notebook. The performance of the novel fingerprint for assessing reaction similarity was evaluated by a cluster analysis that recovered 48 out of 50 of the reaction classes with a median F-score of 0.63 for the clusters. The data sets used for training and primary validation as well as all python scripts required to reproduce the analysis are provided in the Supporting Information.

  5. Large scale air pollution estimation method combining land use regression and chemical transport modeling in a geostatistical framework.

    PubMed

    Akita, Yasuyuki; Baldasano, Jose M; Beelen, Rob; Cirach, Marta; de Hoogh, Kees; Hoek, Gerard; Nieuwenhuijsen, Mark; Serre, Marc L; de Nazelle, Audrey

    2014-04-15

    In recognition that intraurban exposure gradients may be as large as between-city variations, recent air pollution epidemiologic studies have become increasingly interested in capturing within-city exposure gradients. In addition, because of the rapidly accumulating health data, recent studies also need to handle large study populations distributed over large geographic domains. Even though several modeling approaches have been introduced, a consistent modeling framework capturing within-city exposure variability and applicable to large geographic domains is still missing. To address these needs, we proposed a modeling framework based on the Bayesian Maximum Entropy method that integrates monitoring data and outputs from existing air quality models based on Land Use Regression (LUR) and Chemical Transport Models (CTM). The framework was applied to estimate the yearly average NO2 concentrations over the region of Catalunya in Spain. By jointly accounting for the global scale variability in the concentration from the output of CTM and the intraurban scale variability through LUR model output, the proposed framework outperformed more conventional approaches.

  6. Self-reported household impacts of large-scale chemical contamination of the public water supply, Charleston, West Virginia, USA.

    PubMed

    Schade, Charles P; Wright, Nasandra; Gupta, Rahul; Latif, David A; Jha, Ayan; Robinson, John

    2015-01-01

    A January 2014 industrial accident contaminated the public water supply of approximately 300,000 homes in and near Charleston, West Virginia (USA) with low levels of a strongly-smelling substance consisting principally of 4-methylcyclohexane methanol (MCHM). The ensuing state of emergency closed schools and businesses. Hundreds of people sought medical care for symptoms they related to the incident. We surveyed 498 households by telephone to assess the episode's health and economic impact as well as public perception of risk communication by responsible officials. Thirty two percent of households (159/498) reported someone with illness believed to be related to the chemical spill, chiefly dermatological or gastrointestinal symptoms. Respondents experienced more frequent symptoms of psychological distress during and within 30 days of the emergency than 90 days later. Sixty-seven respondent households (13%) had someone miss work because of the crisis, missing a median of 3 days of work. Of 443 households reporting extra expenses due to the crisis, 46% spent less than $100, while 10% spent over $500 (estimated average about $206). More than 80% (401/485) households learned of the spill the same day it occurred. More than 2/3 of households complied fully with "do not use" orders that were issued; only 8% reported drinking water against advice. Household assessments of official communications varied by source, with local officials receiving an average "B" rating, whereas some federal and water company communication received a "D" grade. More than 90% of households obtained safe water from distribution centers or stores during the emergency. We conclude that the spill had major economic impact with substantial numbers of individuals reporting incident-related illnesses and psychological distress. Authorities were successful supplying emergency drinking water, but less so with risk communication.

  7. A facile chemical-mechanical polishing lift-off transfer process toward large scale Cu(In,Ga)Se2 thin-film solar cells on arbitrary substrates.

    PubMed

    Tseng, Kuan-Chun; Yen, Yu-Ting; Thomas, Stuart R; Tsai, Hung-Wei; Hsu, Cheng-Hung; Tsai, Wen-Chi; Shen, Chang-Hong; Shieh, Jia-Min; Wang, Zhiming M; Chueh, Yu-Lun

    2016-03-07

    The fabrication of Cu(In,Ga)Se2 (CIGS) solar cells on flexible substrates is a non-trivial task due to thermal and ion diffusion related issues. In order to circumvent these issues, we have developed a chemical-mechanical polishing lift-off (CMPL) transfer process, enabling the direct transfer of CIGS solar cells from conventional soda-lime glass (SLG) onto arbitrary flexible substrates up to 4 cm(2) in size. The structural and compositional nature of the pre- and post-transferred films is examined using electron microscopy, X-ray diffraction analysis, Raman and photoluminescence spectroscopy. We demonstrate the fabrication of solar cells on a range of flexible substrates while being able to maintain 75% cell efficiency (η) when compared to pre-transferred solar cells. The results obtained in this work suggest that our transfer process offers a highly promising approach toward large scale fabrication of CIGS-based solar cells on a wide variety of flexible substrates, suitable for use in the large scale CIGS photovoltaic industry.

  8. Chemical modification of surface properties

    SciTech Connect

    Koel, B.E.; Windham, R.G.

    1987-01-01

    Chemically tailoring materials to have new and unique surface properties has enormous potential in a wide variety of applications for interfacial phenomena in materials science and catalysis. Recent work from our laboratory on model systems designed to explain how changes in geometric and electronic structure of metal surfaces affect surface chemistry are discussed. Specifically, the influence of potassium and bismuth coadsorption with small molecules on a Pt(111) single crystal surface will be described. We will also discuss the chemical reactivity of palladium metal monolayers and thin films which have been recently reported to have dramatically altered geometric and electronic structure. 31 refs., 3 figs.

  9. Thermo-Flow Structure and Epitaxial Uniformity in Large-Scale Metalorganic Chemical Vapor Deposition Reactors with Rotating Susceptor and Inlet Flow Control

    NASA Astrophysics Data System (ADS)

    Soong, Chyi-Yeou; Chyuan, Chung-Hsing; Tzong, Ruey-Yau

    1998-10-01

    The transport phenomena in large-scale metalorganic chemical vapor deposition (MOCVD) reactors with a rotating susceptor are investigated by numerical simulation of thin-film epitaxial growth of gallium arsenide. We are mainly concerned with the thermo-flow structure, its influence on epitaxial growth rate, and the means of improving epilayer flatness. The effects of susceptor rotation and thermo-flow conditions on gas flow, temperature and concentration fields are studied. The present results show the flow structure and transport characteristics in various flow regimes. A parameter map and the associated correlations of boundary curves of the flow-mode transition are proposed. It is demonstrated that the epilayer flatness can be tuned either by properly controlling the vortex strength in a rotation-dominated flow regime and/or by employing an inlet flow control technique proposed in the present work.

  10. Comparison of the effects in the rock mass of large-scale chemical and nuclear explosions. Final technical report, June 9, 1994--October 9, 1994

    SciTech Connect

    Spivak, A.A.

    1995-04-01

    It was found that in the first approximation the mechanical effect of underground nuclear explosion is analogous to the effect of chemical explosion. Really qualitative analysis shows that accompanying mechanical effects of nuclear and chemical explosions are the same: in the both cases explosion consequences are characterized by formation of the camouplet cavity (crater after explosion near free surface), destruction of the rock massif near explosion centre, creation of the stress wave, which forms seismoexplosive effect a long distance from explosion epicentre. Qualitative likeness of underground nuclear explosions and chemical explosions is the base of modelling the mechanical effects of the underground nuclear explosion. In this paper we`ll compare two explosions: nuclear (15-04-84) and chemical (27.06.95) with large power. These explosions were realized at the same geological conditions at Degelen test area, which is a part of the Semipalatinsk Test Site. In the case of the nuclear explosion, the charge was disposed in the face of the deep horizontal gallery. The charge of the chemical explosion was a semisphere from explosives at the rock massif surface. In the both case rock massif behavior after explosions was investigated at underground conditions (in the case of chemical explosion -- in the long underground excavation from explosion epicentre). Mechanical effects from the nuclear and chemical explosions were investigated with the same methods. The changes in geological medium after a large-scale explosive actions will be analyzed in detail too. Investigations of the influence of tectonic energy on the mechanical effects after underground nuclear, explosions represents the main interest. In this paper we`ll discuss this question on the data from underground nuclear explosion, realized 08.09.89 in the deep well at the Balapan test area, at the Semipalatinsk Test Site.

  11. Large-Scale Disasters

    NASA Astrophysics Data System (ADS)

    Gad-El-Hak, Mohamed

    "Extreme" events - including climatic events, such as hurricanes, tornadoes, and drought - can cause massive disruption to society, including large death tolls and property damage in the billions of dollars. Events in recent years have shown the importance of being prepared and that countries need to work together to help alleviate the resulting pain and suffering. This volume presents a review of the broad research field of large-scale disasters. It establishes a common framework for predicting, controlling and managing both manmade and natural disasters. There is a particular focus on events caused by weather and climate change. Other topics include air pollution, tsunamis, disaster modeling, the use of remote sensing and the logistics of disaster management. It will appeal to scientists, engineers, first responders and health-care professionals, in addition to graduate students and researchers who have an interest in the prediction, prevention or mitigation of large-scale disasters.

  12. Chemical Modification of Nanotubes for Composites

    NASA Technical Reports Server (NTRS)

    Samulski, Edward T.

    2003-01-01

    In the production of mesoscopically-engineered materials based on single-walled carbon nanotubes (SWNTs), monitoring the stages of chemical modification will be an important step in the fabrication of usable composite materials. In our research program we developed tools for studying high-temperature composites with a long-term goal of having such instrumentation available for SWNT composite analyses.

  13. Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk.

    PubMed

    Schwämmle, Veit; Aspalter, Claudia-Maria; Sidoli, Simone; Jensen, Ole N

    2014-07-01

    Mass spectrometry (MS) is a powerful analytical method for the identification and quantification of co-existing post-translational modifications in histone proteins. One of the most important challenges in current chromatin biology is to characterize the relationships between co-existing histone marks, the order and hierarchy of their deposition, and their distinct biological functions. We developed the database CrossTalkDB to organize observed and reported co-existing histone marks as revealed by MS experiments of histone proteins and their derived peptides. Statistical assessment revealed sample-specific patterns for the co-frequency of histone post-translational modifications. We implemented a new method to identify positive and negative interplay between pairs of methylation and acetylation marks in proteins. Many of the detected features were conserved between different cell types or exist across species, thereby revealing general rules for cross-talk between histone marks. The observed features are in accordance with previously reported examples of cross-talk. We observed novel types of interplay among acetylated residues, revealing positive cross-talk between nearby acetylated sites but negative cross-talk for distant ones, and for discrete methylation states at Lys-9, Lys-27, and Lys-36 of histone H3, suggesting a more differentiated functional role of methylation beyond the general expectation of enhanced activity at higher methylation states.

  14. Changes in the distribution of the grey mangrove Avicennia marina (Forsk.) using large scale aerial color infrared photographs: are the changes related to habitat modification for mosquito control?

    NASA Astrophysics Data System (ADS)

    Jones, J.; Dale, P. E. R.; Chandica, A. L.; Breitfuss, M. J.

    2004-09-01

    Runnelling, a method of habitat modification used for mosquito management in intertidal saltmarshes in Australia, alters marsh hydrology. The objective of this research was to assess if runnelling had affected the distribution of the grey mangrove ( Avicennia marina (Forsk.)) at a study site in southeast Queensland. Since runnelling is carried out in diverse marshes a second aim was to assess differences in mangrove colonisation in the two main saltmarsh species in the area. These are marine couch [ Sporobolus virginicus (L.) Kunth.] and samphire [ Sarcocornia quinqueflora (Bunge ex Ung.-Stern.)]. Runnels at the study site were in an area dominated by Sporobolus. The mangrove area was measured by classifying digital color infrared (CIR) data obtained from aerial photographs acquired in 1982, which was 3 years before runnelling, and in 1987, 1991 and 1999, 2-14 years after. Changes in the spatial extent of A. marina were identified using difference images produced from post-classification change detection. The results showed that runnels did not significantly influence the distribution of A. marina at the study site. At a more detailed level differences in A. marina establishment in the Sporobolus and Sarcocornia areas were determined from counts of trees on the aerial photographs. There was a greater proportion of mangroves in Sarcocornia than Sporobolus and this increased over time. This may be related to differences in density between the plant species, to grapsid crab activity or to other edaphic conditions. There may be implications for runnelling in Sarcocornia marshes. The large increase observed in A. marina in the area generally is likely to be related to factors such as catchment modification or tidal/sea-level changes. It is concluded that runnelling has not led to mangrove establishment in the Sporobolus dominated saltmarsh.

  15. Large scale traffic simulations

    SciTech Connect

    Nagel, K.; Barrett, C.L. |; Rickert, M. |

    1997-04-01

    Large scale microscopic (i.e. vehicle-based) traffic simulations pose high demands on computational speed in at least two application areas: (i) real-time traffic forecasting, and (ii) long-term planning applications (where repeated {open_quotes}looping{close_quotes} between the microsimulation and the simulated planning of individual person`s behavior is necessary). As a rough number, a real-time simulation of an area such as Los Angeles (ca. 1 million travellers) will need a computational speed of much higher than 1 million {open_quotes}particle{close_quotes} (= vehicle) updates per second. This paper reviews how this problem is approached in different projects and how these approaches are dependent both on the specific questions and on the prospective user community. The approaches reach from highly parallel and vectorizable, single-bit implementations on parallel supercomputers for Statistical Physics questions, via more realistic implementations on coupled workstations, to more complicated driving dynamics implemented again on parallel supercomputers. 45 refs., 9 figs., 1 tab.

  16. Large scale tracking algorithms

    SciTech Connect

    Hansen, Ross L.; Love, Joshua Alan; Melgaard, David Kennett; Karelitz, David B.; Pitts, Todd Alan; Zollweg, Joshua David; Anderson, Dylan Z.; Nandy, Prabal; Whitlow, Gary L.; Bender, Daniel A.; Byrne, Raymond Harry

    2015-01-01

    Low signal-to-noise data processing algorithms for improved detection, tracking, discrimination and situational threat assessment are a key research challenge. As sensor technologies progress, the number of pixels will increase signi cantly. This will result in increased resolution, which could improve object discrimination, but unfortunately, will also result in a significant increase in the number of potential targets to track. Many tracking techniques, like multi-hypothesis trackers, suffer from a combinatorial explosion as the number of potential targets increase. As the resolution increases, the phenomenology applied towards detection algorithms also changes. For low resolution sensors, "blob" tracking is the norm. For higher resolution data, additional information may be employed in the detection and classfication steps. The most challenging scenarios are those where the targets cannot be fully resolved, yet must be tracked and distinguished for neighboring closely spaced objects. Tracking vehicles in an urban environment is an example of such a challenging scenario. This report evaluates several potential tracking algorithms for large-scale tracking in an urban environment.

  17. Studies on purothionin by chemical modifications.

    PubMed

    Wada, K; Ozaki, Y; Matsubara, H; Yoshizumi, H

    1982-01-01

    Purothionin from wheat flour was chemically modified by acetic or succinic anhydride under specific conditions. The complete modification of all amino groups of purothionin caused a large change in the net charge of the molecule, leading to the loss of the toxicity to mice and yeast. The sole tyrosyl residue in purothionin was nitrated by tetranitromethane at neutral pH or iodinated by the lactoperoxidase method. The nitro- and diiodo-derivatives of purothionin showed considerably reduced toxicity. Based on these modification studies we conclude that the positive charges of lysyl residues have an important role in the interaction with the negatively charged cell surface, and that the emergence of the toxicity of purothionin depends on a certain state of the tyrosyl residue.

  18. Gold Nanowires and Their Chemical Modifications

    NASA Astrophysics Data System (ADS)

    Häkkinen, Hannu; Barnett, Robert N.; Landman, Uzi

    2000-03-01

    Atomic structure, electronic structure, and ballistic transport in thin gold nanowires at their final stages before break-up, recently imaged by high-resolution electron microscopy,(H. Ohnishi et al., Nature 395), 780 (1998) are investigated with density functional simulations.(H. Häkkinen et al., J. Phys. Chem. B 103), 8814 (1999) We discuss stretching mechanisms leading to elongated chain-like structures showing dimerization akin to a Peierls transition and retaining conductance close to unity for stretching lengths that exceed considerably a typical interatomic bond length. We also demonstrate a chemical modification of the wire via adsorption of a methyl thiol molecule and discuss its effects on the structure and conductance.

  19. Progressive chemical modification of clastic sediments with burial

    NASA Astrophysics Data System (ADS)

    Curtis, C. D.

    1987-03-01

    The porosity of clastic sediments at deposition varies very approximately between about 45% (sands) and 85% (muds). With burial, consolidation takes place as pore water is progressively eliminated. It would be misleading, however, to attribute alterations in sediment bulk properties to physical processes alone. Very significant mineralogical changes occur and these start soon after burial, especially in mudrocks. Striking heterogeneities such as thin, laterally continuous cemented horizons or discrete concretions are commonly introduced. These shallow burial processes are predominently the result of microbial activity. Thermodynamically unstable mixtures of organic matter and various oxidants [dissolved oxygen, sulphate, nitrate, particulate Fe(III) and Mn(IV)] provide both substrate and energy source for a variety of different microbial ecosystems. Mineralogical consequences include both leaching and the precipitation of carbonate, sulphide, phosphate and silica cements. The type and extent of mineral modification depends strongly on depositional environment variables such as rate of sedimentation and water composition. At greater depths, large scale modification of detrital clay minerals (particularly the smectite-I/S-illite transformation) takes place. Recent work of various kinds, however, has demonstrated that these changes may not be solid state transformations: clay mineral dissolution, transport and precipitation occur much more widely than was formerly supposed. In sandstones, authigenic precipitation of clay minerals from pore solution is much more obviouis. Systematic patterns of precipitation, alteration and replacement have been documented in many sedimentary basins. Porosity and permeability are reduced by cementation and, sometimes, enhanced by mineral dissolution. Whereas the general nature of these chemical reactions is fairly well understood, it is not yet possible to predict with certainty the scale or distribution of mineralogical consequences

  20. Chemical methods for encoding and decoding of posttranslational modifications

    PubMed Central

    Chuh, Kelly N.; Batt, Anna R.; Pratt, Matthew R.

    2016-01-01

    A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full compliment of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come. PMID:26933738

  1. Chemical and structural effects of base modifications in messenger RNA

    NASA Astrophysics Data System (ADS)

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles.

  2. Regional and large-scale patterns in Amazon forest structure and function are mediated by variations in soil physical and chemical properties

    NASA Astrophysics Data System (ADS)

    A, Quesada, C.; Lloyd, J.

    2009-04-01

    Forest structure and dynamics have been noted to vary across the Amazon Basin in an east-west gradient in a pattern which coincides with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. To test this hypothesis and assess the importance of edaphic properties in affect forest structure and dynamics, soil and plant samples were collected in a total of 59 different forest plots across the Amazon Basin. Samples were analysed for exchangeable cations, C, N, pH with various P fractions also determined. Physical properties were also examined and an index of soil physical quality developed. Overall, forest structure and dynamics were found to be strongly and quantitatively related to edaphic conditions. Tree turnover rates emerged to be mostly influenced by soil physical properties whereas forest growth rates were mainly related to a measure of available soil phosphorus, although also dependent on rainfall amount and distribution. On the other hand, large scale variations in forest biomass could not be explained by any of the edaphic properties measured, nor by variation in climate. A new hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining forest disturbance levels, species composition and forest productivity on a Basin wide scale.

  3. Surface chemical modification of waxy maize starch nanocrystals.

    PubMed

    Angellier, Hélène; Molina-Boisseau, Sonia; Belgacem, Mohamed Naceur; Dufresne, Alain

    2005-03-15

    The surface of waxy maize starch nanocrystals obtained from sulfuric acid hydrolysis of native waxy maize starch granules was chemically modified using two different reagents, namely, alkenyl succinic anhydride and phenyl isocyanate. The occurrence of chemical modification was evaluated by FTIR and X-ray photoelectron spectroscopies. Contact angle measurements from which the surface energy of the materials under investigation was deduced showed that chemical modification led to more hydrophobic particles. Chemical modification altered the morphology of particles, as shown by observation by transmission electron microscopy, but not their crystallinity (X-ray diffraction analysis).

  4. Large-scale structural optimization

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.

    1983-01-01

    Problems encountered by aerospace designers in attempting to optimize whole aircraft are discussed, along with possible solutions. Large scale optimization, as opposed to component-by-component optimization, is hindered by computational costs, software inflexibility, concentration on a single, rather than trade-off, design methodology and the incompatibility of large-scale optimization with single program, single computer methods. The software problem can be approached by placing the full analysis outside of the optimization loop. Full analysis is then performed only periodically. Problem-dependent software can be removed from the generic code using a systems programming technique, and then embody the definitions of design variables, objective function and design constraints. Trade-off algorithms can be used at the design points to obtain quantitative answers. Finally, decomposing the large-scale problem into independent subproblems allows systematic optimization of the problems by an organization of people and machines.

  5. A review of the chemical modification techniques of starch.

    PubMed

    Masina, Nonhlanhla; Choonara, Yahya E; Kumar, Pradeep; du Toit, Lisa C; Govender, Mershen; Indermun, Sunaina; Pillay, Viness

    2017-02-10

    Starch is a naturally occurring storage copolymer with unique physicochemical properties. There are, however, some key structural properties of starch that can be modified in order to functionalize the copolymer to meet specific requirements. Specifically, the chemical modification of starch provides a variety of physicochemical benefits, some of which have been used previously to functionalize preformed drug delivery systems. Of the three main chemical modification methods reviewed (namely: oxidation, esterification and etherification), surface chemical oxidation introduces more pertinent physicochemical properties that increase overall drug delivery system efficacy and applicability. Surface oxidation evidently is the more preferable chemical modification method of pre-formed starch particles and has the greatest potential for further development when compared to the other reviewed chemical modification methods. The use of modified starch in clinical trials as well as the potential future implications of these systems is also included in this review.

  6. Galaxy clustering on large scales.

    PubMed Central

    Efstathiou, G

    1993-01-01

    I describe some recent observations of large-scale structure in the galaxy distribution. The best constraints come from two-dimensional galaxy surveys and studies of angular correlation functions. Results from galaxy redshift surveys are much less precise but are consistent with the angular correlations, provided the distortions in mapping between real-space and redshift-space are relatively weak. The galaxy two-point correlation function, rich-cluster two-point correlation function, and galaxy-cluster cross-correlation function are all well described on large scales ( greater, similar 20h-1 Mpc, where the Hubble constant, H0 = 100h km.s-1.Mpc; 1 pc = 3.09 x 10(16) m) by the power spectrum of an initially scale-invariant, adiabatic, cold-dark-matter Universe with Gamma = Omegah approximately 0.2. I discuss how this fits in with the Cosmic Background Explorer (COBE) satellite detection of large-scale anisotropies in the microwave background radiation and other measures of large-scale structure in the Universe. PMID:11607400

  7. Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

    PubMed

    Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

    2016-07-14

    We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

  8. Large-scale synthesis of monodisperse SiC nanoparticles with adjustable size, stoichiometric ratio and properties by fluidized bed chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Liu, Rongzheng; Liu, Malin; Chang, Jiaxing

    2017-02-01

    A facile fluidized bed chemical vapor deposition method was proposed for the synthesis of monodisperse SiC nanoparticles by using the single precursor of hexamethyldisilane (HMDS). SiC nanoparticles with average particle size from 10 to 200 nm were obtained by controlling the temperature and the gas ratio. An experimental chemical vapor deposition phase diagram of SiC in the HMDS-Ar-H2 system was obtained and three regions of SiC-Si, SiC and SiC-C can be distinguished. The BET surface area and the photoluminescence properties of the SiC nanoparticles can be adjusted by changing the nanoparticle size. For the SiC nanospheres with free carbon, a novel hierarchical structure with 5 8 nm SiC nanoparticles embedded into the graphite matrix was obtained. The advantages of fluidized bed technology for the preparation of SiC nanoparticles were proposed based on the features of homogenous reaction zone, narrow temperature distribution, ultra-short reactant residence time and mass production.

  9. Regioselective chemical modification of monoclonal antibodies

    DOEpatents

    Ranadive, Girish; Rosenzweig, Howard S.; Epperly, Michael; Bloomer, William

    1993-01-01

    A method of selectively modifying an immunoglobulin having at least one Fab region and at least one Fc region, each region having an isoelectric point wherein said isoelectric point of the Fab fragment of said immunoglobulin is different than the isoelectric point of the Fc fragment of the immunoglobulin, said method comprising modification of the immunoglobulin at a pH between the respective isoelectric points of the Fab and Fc fragments of the immunoglobulin.

  10. Regioselective chemical modification of monoclonal antibodies

    DOEpatents

    Ranadive, G.; Rozenzweig, H.S.; Epperly, M.; Bloomer, W.

    1993-05-04

    A method is presented of selectively modifying an immunoglobulin having at least one Fab region and at least one Fc region. Each region has an isoelectric point where the isoelectric point of the Fab fragment of the immunoglobulin is different from the isoelectric point of the Fc fragment of the immunoglobulin. The method comprises of a modification of the immunoglobulin at a pH between the respective isoelectric points of the Fab and Fc fragments of the immunoglobulin.

  11. Modification of the upper atmosphere with chemicals found in rocket exhaust

    SciTech Connect

    Bernhardt, P.A.; Zinn, J.; Mendillo, M.; Baumgardner, J.

    1982-01-01

    Rockets, burning above 200 km altitude, release exhaust vapors which react chemically with the plasma comprising the F-region ionosphere. The two major types of atmospheric modification produced by rocket exhaust are: (1) the formation of large scale ionospheric holes, and (2) the enhancement of the airglow emissions. The ionospheric holes are regions tens of kilometers in diameter where the plasma concentration can be reduced by a factor of ten or more. Plasma instabilities may produce irregularities at the edges of the holes. Communication and navigation systems relying on radio propagation through the modified ionosphere may be affected. Airglow enhancements are a result of excited neutral species being produced by chemical reactions between the rocket exhaust and the ionospheric plasma. For example, the 630 nm line from atomic oxygen may increase twenty-fold in intensity over the ambient level. This paper reviews experimental observations and theoretical treatments of ionospheric modification produced by gas releases in the upper atmosphere. Recent experimental measurements of the ionospheric modification by an ATLAS-F launch vehicle are presented. The plans for future experiments are discussed.

  12. Investigating the presence of post-perovskite and large-scale chemical variations in Earth's lower mantle using tomographic-geodynamic model comparisons.

    NASA Astrophysics Data System (ADS)

    Koelemeijer, Paula; Ritsema, Jeroen; Deuss, Arwen; Davies, Rhodri; Schuberth, Bernhard

    2016-04-01

    Tomographic models of the Earth's mantle consistently image two large provinces of low shear-wave velocities (LLSVPs) in the lowermost mantle beneath Africa and the Pacific. Seismic studies also find an increase in the ratio of shear-wave velocity (Vs) to compressional-wave velocity (Vp) variations, accompanied by a significant negative correlation between shear-wave and bulk-sound velocity (Vc) variations, both of which are also observed in the recent SP12RTS model. The LLSVPs have consequently been suggested to represent intrinsically dense piles of thermochemical material. Alternatively, they have been interpreted as poorly imaged clusters of thermal plumes, with the deep mantle post-perovskite (pPv) phase invoked as explanation for the high Vs/Vp ratios and Vs-Vc anti-correlation. Geodynamical calculations of thermal plumes and thermochemical piles predict a fundamentally different style of mantle convection, interface topographies and CMB heat flow. However, to interpret tomographic images using these high-resolution models, the limited resolving power of seismic tomography has to be accounted for. Here, we interpret the observed seismic characteristics of SP12RTS by comparing the velocity structures to synthetic tomography images derived from 3D mantle convection models. As in previous studies, geodynamic models are converted to seismic velocities using mineral physics constraints and subsequently convolved with the tomographic resolution operator. In contrast to these studies, where generally only the shear-wave velocity structure has been compared, we use both the Vs and Vp resolution operator of SP12RTS to allow direct comparisons of the resulting velocity ratios and correlations. We use geodynamic models with and without pPv and/or chemical variations to investigate the cause of the high Vs/Vp ratio and Vs-Vs anti-correlation. Although the tomographic filtering significantly affects the synthetic tomography images, we demonstrate that the patterns

  13. Chemical modifications of renewable cellulosic materials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In agriculture, there is a fair amount of byproducts and waste materials. These materials typically contain significant portions of cellulose and hemicellulose. A good opportunity is to take advantage of these relatively cheap renewable materials, carry out chemical reactions, and increase their v...

  14. Chemical modification of antifungal polyene macrolide antibiotics

    NASA Astrophysics Data System (ADS)

    Solovieva, S. E.; Olsufyeva, E. N.; Preobrazhenskaya, M. N.

    2011-02-01

    The review summarizes advances in the methods for the synthesis of polyene antibiotics (amphotericin B, partricin A, etc.) and investigations of the structure-activity relationship made in the last 15 years. State-of-the-art approaches based on the combination of the chemical synthesis and genetic engineering are considered. Emphasis is given to the design of semisynthetic antifungal agents against chemotherapy-resistant pathogens having the highest therapeutic indices. Recent results of research on the mechanisms of action of polyenes are outlined.

  15. Chemical modifications of liquid natural rubber

    NASA Astrophysics Data System (ADS)

    Azhar, Nur Hanis Adila; Rasid, Hamizah Md; Yusoff, Siti Fairus M.

    2016-11-01

    Liquid natural rubber (LNR) was synthesized via photosentisized degradation of natural rubber (NR). LNR was modified into epoxidized liquid natural rubber (LENR) and hydroxylated liquid natural rubber (LNR-OH) using Na2WO4/CH3COOH/H2O2 catalytic system. Chemical structures of LNR and modified LNRs were characterized using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) and 1H Nuclear Magnetic Resonance (NMR) spectroscopies. Integration of 1H NMR was used to calculate the epoxy content (%) of LENR. 1H NMR detected the formation of LNR-OH after prolonged heating and increased of catalyst in oxidation reaction.

  16. Large-scale PACS implementation.

    PubMed

    Carrino, J A; Unkel, P J; Miller, I D; Bowser, C L; Freckleton, M W; Johnson, T G

    1998-08-01

    The transition to filmless radiology is a much more formidable task than making the request for proposal to purchase a (Picture Archiving and Communications System) PACS. The Department of Defense and the Veterans Administration have been pioneers in the transformation of medical diagnostic imaging to the electronic environment. Many civilian sites are expected to implement large-scale PACS in the next five to ten years. This presentation will related the empirical insights gleaned at our institution from a large-scale PACS implementation. Our PACS integration was introduced into a fully operational department (not a new hospital) in which work flow had to continue with minimal impact. Impediments to user acceptance will be addressed. The critical components of this enormous task will be discussed. The topics covered during this session will include issues such as phased implementation, DICOM (digital imaging and communications in medicine) standard-based interaction of devices, hospital information system (HIS)/radiology information system (RIS) interface, user approval, networking, workstation deployment and backup procedures. The presentation will make specific suggestions regarding the implementation team, operating instructions, quality control (QC), training and education. The concept of identifying key functional areas is relevant to transitioning the facility to be entirely on line. Special attention must be paid to specific functional areas such as the operating rooms and trauma rooms where the clinical requirements may not match the PACS capabilities. The printing of films may be necessary for certain circumstances. The integration of teleradiology and remote clinics into a PACS is a salient topic with respect to the overall role of the radiologists providing rapid consultation. A Web-based server allows a clinician to review images and reports on a desk-top (personal) computer and thus reduce the number of dedicated PACS review workstations. This session

  17. Adsorption and Chemical Modification of Phenols on a Silver Surface.

    PubMed

    Sánchez-Cortés; García-Ramos

    2000-11-01

    The adsorption of phenols of different natures on silver colloidal particles is studied here by surface-enhanced Raman spectroscopy (SERS). The studied compounds can be classified in three groups: (a) cinnamic acic derivatives: caffeic and isoferulic acids; (b) catechol; and (c) the phenols derived from benzoic acid: m- and p-hydroxybenzoic acids and salicylic, vanillic, and gallic acids. The interest of these compounds lies in the fact that they are naturally occurring molecules with significant importance in relation to plant metabolism, soil chemistry, and vegetal food stability. In addition, many of these compounds have antioxidant properties derived from their high affinity toward atmospheric oxygen. They exhibit high reactivity that may be enhanced in the presence of a metal surface such as those employed for SERS spectroscopy. From the SERS results it can be deduced that a clear chemical change of caffeic and gallic acid and catechol occurred. The chemical modification consists mainly of polymerization connected to existence in the molecule of o-diphenol moieties. In the case of m-hydroxybenzoic acid the chemical change may occur at low pH at which a reorientation of the molecule on the surface takes place, while in the o-hydroxybenzoic acid the only chemical change seems to be the internal H bond breakdown induced by the complexation with the metal. Finally, isoferulic and p-hydroxybenzoic acids do not show any chemical modification upon adsorption on the metal, which takes place through the carboxylate group adopting the molecule a standing up orientation. The case of vanillic acid is not so clear, although possible chemical modification is also possible for this adsorbate. From the results found in this work it can be inferred that the factors influencing possible chemical modification are the chemical structure of the adsorbate and its orientation and interaction with the surface. Copyright 2000 Academic Press.

  18. Large-Scale Sequence Comparison.

    PubMed

    Lal, Devi; Verma, Mansi

    2017-01-01

    There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.

  19. Large Scale Magnetostrictive Valve Actuator

    NASA Technical Reports Server (NTRS)

    Richard, James A.; Holleman, Elizabeth; Eddleman, David

    2008-01-01

    Marshall Space Flight Center's Valves, Actuators and Ducts Design and Development Branch developed a large scale magnetostrictive valve actuator. The potential advantages of this technology are faster, more efficient valve actuators that consume less power and provide precise position control and deliver higher flow rates than conventional solenoid valves. Magnetostrictive materials change dimensions when a magnetic field is applied; this property is referred to as magnetostriction. Magnetostriction is caused by the alignment of the magnetic domains in the material s crystalline structure and the applied magnetic field lines. Typically, the material changes shape by elongating in the axial direction and constricting in the radial direction, resulting in no net change in volume. All hardware and testing is complete. This paper will discuss: the potential applications of the technology; overview of the as built actuator design; discuss problems that were uncovered during the development testing; review test data and evaluate weaknesses of the design; and discuss areas for improvement for future work. This actuator holds promises of a low power, high load, proportionally controlled actuator for valves requiring 440 to 1500 newtons load.

  20. Large scale cluster computing workshop

    SciTech Connect

    Dane Skow; Alan Silverman

    2002-12-23

    Recent revolutions in computer hardware and software technologies have paved the way for the large-scale deployment of clusters of commodity computers to address problems heretofore the domain of tightly coupled SMP processors. Near term projects within High Energy Physics and other computing communities will deploy clusters of scale 1000s of processors and be used by 100s to 1000s of independent users. This will expand the reach in both dimensions by an order of magnitude from the current successful production facilities. The goals of this workshop were: (1) to determine what tools exist which can scale up to the cluster sizes foreseen for the next generation of HENP experiments (several thousand nodes) and by implication to identify areas where some investment of money or effort is likely to be needed. (2) To compare and record experimences gained with such tools. (3) To produce a practical guide to all stages of planning, installing, building and operating a large computing cluster in HENP. (4) To identify and connect groups with similar interest within HENP and the larger clustering community.

  1. Physical and Chemical Modification of Starches - A Review.

    PubMed

    Din, Zia-Ud-; Xiong, Hanguo; Fei, Peng

    2015-11-03

    The development of green material in the last decade has been increased which tends to reduce the impact of human on the environment. Starch as an agro-sourced polymer has become much popular recently due to its characteristics such as wide availability, low cost and total compostability without toxic residues. Starch is the most abundant organic compound found in nature after cellulose. Starches are inherently unsuitable for most applications and, therefore, must be modified physically and/or chemically to enhance their positive attributes and/or to minimize their defects. Modification of starches is generally carried out by using physical methods that are simple and inexpensive due to the absence of chemical agents. On the other hand, chemical modification involves the exploitation of hydroxyl group present in the starches that brings about the desired results for the utilization of starches for specific applications. All these techniques have the tendency to produce starches with altered physicochemical properties and modified structural attributes for various food and non-food applications. This paper reviews the recent knowledge and developments using physical modification methods, some chemical modification methods and a combination of both to produce a novel molecule with substantial applications, in food industry along with future perspectives.

  2. Basic biotechnologies essential for the Japanese chemical industry in the 1990's and beyond. Bioreactors, large-scale mammalian cell culture, recombinant DNAs, functional protein systems, and bio-electronic devices

    SciTech Connect

    Fujimura, R.K.

    1992-01-01

    The purpose of the program is to induce private company laboratories to do research considered essential for the development of new technologies. One group of projects initially funded under the program was in the field of biotechnology. More specifically, the biotechnology projects were aimed at developing technologies for the chemical industry for the decade of the 1990's. Various projects dealt with bioreactors, large-scale cell culture, and recombinant DNA. These initial biotechnology projects have now been completed. The report reviews their accomplishments and assesses their possible impact on the Japanese chemical industry. A new project on functional protein complexes was added in 1989. Progress on the nine-year project is also reviewed. Finally, an assessment is provided of the biotechnology components of an unrelated group of projects being administered by the Research and Development Association for Future Electron Devices. The relevant components in the program involve bio-electronic devices and functional protein complexes. The objectives are to mimic biological systems for use in microsensors, information transmission and processing, artificial tissues and organs, robotics, and artificial intelligence.

  3. Material design of plasma-enhanced chemical vapour deposition SiCH films for low-k cap layers in the further scaling of ultra-large-scale integrated devices-Cu interconnects.

    PubMed

    Shimizu, Hideharu; Nagano, Shuji; Uedono, Akira; Tajima, Nobuo; Momose, Takeshi; Shimogaki, Yukihiro

    2013-10-01

    Cap layers for Cu interconnects in ultra-large-scale integrated devices (ULSIs), with a low dielectric constant (k-value) and strong barrier properties against Cu and moisture diffusion, are required for the future further scaling of ULSIs. There is a trade-off, however, between reducing the k-value and maintaining strong barrier properties. Using quantum mechanical simulations and other theoretical computations, we have designed ideal dielectrics: SiCH films with Si-C2H4-Si networks. Such films were estimated to have low porosity and low k; thus they are the key to realizing a cap layer with a low k and strong barrier properties against diffusion. For fabricating these ideal SiCH films, we designed four novel precursors: isobutyl trimethylsilane, diisobutyl dimethylsilane, 1, 1-divinylsilacyclopentane and 5-silaspiro [4,4] noname, based on quantum chemical calculations, because such fabrication is difficult by controlling only the process conditions in plasma-enhanced chemical vapor deposition (PECVD) using conventional precursors. We demonstrated that SiCH films prepared using these newly designed precursors had large amounts of Si-C2H4-Si networks and strong barrier properties. The pore structure of these films was then analyzed by positron annihilation spectroscopy, revealing that these SiCH films actually had low porosity, as we designed. These results validate our material and precursor design concepts for developing a PECVD process capable of fabricating a low-k cap layer.

  4. In the fast lane: large-scale bacterial genome engineering.

    PubMed

    Fehér, Tamás; Burland, Valerie; Pósfai, György

    2012-07-31

    The last few years have witnessed rapid progress in bacterial genome engineering. The long-established, standard ways of DNA synthesis, modification, transfer into living cells, and incorporation into genomes have given way to more effective, large-scale, robust genome modification protocols. Expansion of these engineering capabilities is due to several factors. Key advances include: (i) progress in oligonucleotide synthesis and in vitro and in vivo assembly methods, (ii) optimization of recombineering techniques, (iii) introduction of parallel, large-scale, combinatorial, and automated genome modification procedures, and (iv) rapid identification of the modifications by barcode-based analysis and sequencing. Combination of the brute force of these techniques with sophisticated bioinformatic design and modeling opens up new avenues for the analysis of gene functions and cellular network interactions, but also in engineering more effective producer strains. This review presents a summary of recent technological advances in bacterial genome engineering.

  5. Large-Scale Information Systems

    SciTech Connect

    D. M. Nicol; H. R. Ammerlahn; M. E. Goldsby; M. M. Johnson; D. E. Rhodes; A. S. Yoshimura

    2000-12-01

    Large enterprises are ever more dependent on their Large-Scale Information Systems (LSLS), computer systems that are distinguished architecturally by distributed components--data sources, networks, computing engines, simulations, human-in-the-loop control and remote access stations. These systems provide such capabilities as workflow, data fusion and distributed database access. The Nuclear Weapons Complex (NWC) contains many examples of LSIS components, a fact that motivates this research. However, most LSIS in use grew up from collections of separate subsystems that were not designed to be components of an integrated system. For this reason, they are often difficult to analyze and control. The problem is made more difficult by the size of a typical system, its diversity of information sources, and the institutional complexities associated with its geographic distribution across the enterprise. Moreover, there is no integrated approach for analyzing or managing such systems. Indeed, integrated development of LSIS is an active area of academic research. This work developed such an approach by simulating the various components of the LSIS and allowing the simulated components to interact with real LSIS subsystems. This research demonstrated two benefits. First, applying it to a particular LSIS provided a thorough understanding of the interfaces between the system's components. Second, it demonstrated how more rapid and detailed answers could be obtained to questions significant to the enterprise by interacting with the relevant LSIS subsystems through simulated components designed with those questions in mind. In a final, added phase of the project, investigations were made on extending this research to wireless communication networks in support of telemetry applications.

  6. Improving Recent Large-Scale Pulsar Surveys

    NASA Astrophysics Data System (ADS)

    Cardoso, Rogerio Fernando; Ransom, S.

    2011-01-01

    Pulsars are unique in that they act as celestial laboratories for precise tests of gravity and other extreme physics (Kramer 2004). There are approximately 2000 known pulsars today, which is less than ten percent of pulsars in the Milky Way according to theoretical models (Lorimer 2004). Out of these 2000 known pulsars, approximately ten percent are known millisecond pulsars, objects used for their period stability for detailed physics tests and searches for gravitational radiation (Lorimer 2008). As the field and instrumentation progress, pulsar astronomers attempt to overcome observational biases and detect new pulsars, consequently discovering new millisecond pulsars. We attempt to improve large scale pulsar surveys by examining three recent pulsar surveys. The first, the Green Bank Telescope 350MHz Drift Scan, a low frequency isotropic survey of the northern sky, has yielded a large number of candidates that were visually inspected and identified, resulting in over 34.000 thousands candidates viewed, dozens of detections of known pulsars, and the discovery of a new low-flux pulsar, PSRJ1911+22. The second, the PALFA survey, is a high frequency survey of the galactic plane with the Arecibo telescope. We created a processing pipeline for the PALFA survey at the National Radio Astronomy Observatory in Charlottesville- VA, in addition to making needed modifications upon advice from the PALFA consortium. The third survey examined is a new GBT 820MHz survey devoted to find new millisecond pulsars by observing the target-rich environment of unidentified sources in the FERMI LAT catalogue. By approaching these three pulsar surveys at different stages, we seek to improve the success rates of large scale surveys, and hence the possibility for ground-breaking work in both basic physics and astrophysics.

  7. Chemical modification of alginic acid by ultrasonic irradiation

    NASA Astrophysics Data System (ADS)

    Murdzheva, Dilyana; Denev, Panteley

    2016-03-01

    Abstract: Chemical modification of alginic acid has been done by ultrasonic irradiation to obtain its methylated, ethylated and isopropylated derivatives. The influence of ultrasonic frequency and power on esterification process of alginic acid has been investigated. Alginate derivatives have been characterized by degree of esterification (DE) and IR-FT spectroscopy. It has been found that 45 kHz ultrasonic frequency accelerated modification process as reduced the reaction time from 16 hours to 2 hours. The obtained results showed that ultrasound irradiation increased the reaction efficiency in methanol and depended on the ratio of the M/G.

  8. [Chemical approaches for trapping protein thiols and their oxidative modification].

    PubMed

    Huang, Chu-Sen; Zhu, Wei-Ping; Xu, Yu-Fang; Qian, Xu-Hong

    2012-03-01

    Redox signal transduction, especially the oxidative modification of proein thiols, correlates with many diseases and becomes an expanding research area. However, there was rare method for quick and specific detection of protein thiols and their oxidative modification in living cells. In this article, we review the current chemical strategies for the detection and quantification of protein thiols and related cysteine oxidation. We also look into the future of the development of fluorescent probes for protein thiols and their potential application in the research of reactive cysteine proteomes and early detection of redox-related diseases.

  9. Recent advances in the chemical modification of unsaturated polymers

    NASA Technical Reports Server (NTRS)

    Schulz, D. N.; Turner, S. R.; Golub, M. A.

    1982-01-01

    The present discussion has the objective to update the most comprehensive reviews on the considered subject and to fill in the gaps of less complete, but more modern treatments. Only simple chemical functionalization or structural modification of unsaturated polymers are covered, and the literature of diene polymer modification since 1974 is emphasized. Attention is given to hydrogenation, halogenation and hydrohalogenation, cyclization, cis-trans isomerization, epoxidation, ene and other cycloaddition reactions, sulfonation, carboxylation, phosphonylation, sulfenyl chloride addition, carbene addition, metalation, and silylation. It is pointed out that modern synthetic reagents and catalysts have been advantageously employed to improve process and/or product quality. Synthetic techniques have been refined to allow the selective modification of specific polymer microstructures or blocks.

  10. Needs, opportunities, and options for large scale systems research

    SciTech Connect

    Thompson, G.L.

    1984-10-01

    The Office of Energy Research was recently asked to perform a study of Large Scale Systems in order to facilitate the development of a true large systems theory. It was decided to ask experts in the fields of electrical engineering, chemical engineering and manufacturing/operations research for their ideas concerning large scale systems research. The author was asked to distribute a questionnaire among these experts to find out their opinions concerning recent accomplishments and future research directions in large scale systems research. He was also requested to convene a conference which included three experts in each area as panel members to discuss the general area of large scale systems research. The conference was held on March 26--27, 1984 in Pittsburgh with nine panel members, and 15 other attendees. The present report is a summary of the ideas presented and the recommendations proposed by the attendees.

  11. Chemical modification of oxalate decarboxylase to improve adsorption capacity.

    PubMed

    Lin, Rihui; He, Junbin; Wu, Jia; Cai, Xinghua; Long, Han; Chen, Shengfeng; Liu, Haiqian

    2017-02-03

    In order to enhance the adsorption capacity of oxalate decarboxylase (Oxdc) on calcium oxalate monohydrate crystals and improve the application performance of Oxdc, chemical modification of Oxdc with ethylenediaminetetraacetic dianhydride (EDTAD) was investigated in this work. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography tandem mass spectrometry (LC/MS) analysis results demonstrated that Oxdc and EDTAD have been covalently bound, and suggested that the chemical modification occurred at the free amino of the side chain and the α-amine of the N-terminus of Oxdc. Fluorescene and circular dichroic measurement showed that the structure and conformation of Oxdc were tinily altered after modification by EDTAD. The optimum pH of EDTAD-modified Oxdc was shifted to the alkaline side about 1.5 unit and it has a higher thermostability. The analysis of kinetic parameters indicated that the EDTAD-modified Oxdc showed a higher affinity towards the substrate. Through modification the adsorption capacity of Oxdc onto CaOx monohydrate crystals was increased by 42.42%.

  12. Chemical posttranslational modification of phage-displayed peptides.

    PubMed

    Ng, Simon; Tjhung, Katrina F; Paschal, Beth M; Noren, Christopher J; Derda, Ratmir

    2015-01-01

    Phage-displayed peptide library has fueled the discovery of novel ligands for diverse targets. A new type of phage libraries that displays not only linear and disulfide-constrained cyclic peptides but moieties that cannot be encoded genetically or incorporated easily by bacterial genetic machinery has emerged recently. Chemical posttranslational modification of phage library is one of the simplest approaches to encode nonnatural moieties. It confers the library with new functionality and makes it possible to select and evolve molecules with properties not found in the peptides, for instance, glycopeptides recognized by carbohydrate-binding protein and peptides with photoswitching capability. To this end, we describe the newly emerging techniques to chemically modify the phage library and quantify the efficiency of the reaction with a biotin-capture assay. Finally, we provide the methods to construct N-terminal Ser peptide library that allows site-selective modification of phage.

  13. Engineering small interfering RNAs by strategic chemical modification.

    PubMed

    Bramsen, Jesper B; Kjems, Jørgen

    2013-01-01

    Synthetic small interfering RNAs (siRNAs) have revolutionized functional genomics in mammalian cell cultures due to their reliability, efficiency, and ease of use. This success, however, has not fully translated into siRNA applications in vivo and in siRNA therapeutics where initial optimism has been dampened by a lack of efficient delivery strategies and reports of siRNA off-target effects and immunogenicity. Encouragingly, most aspects of siRNA behavior can be addressed by careful engineering of siRNAs incorporating beneficial chemical modifications into discrete nucleotide positions during siRNA synthesis. Here, we review the literature (Subheadings 1 -3) and provide a quick guide (Subheading 4) to how the performance of siRNA can be improved by chemical modification to suit specific applications in vitro and in vivo.

  14. Large scale DNA microsequencing device

    DOEpatents

    Foote, R.S.

    1997-08-26

    A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.

  15. Large scale DNA microsequencing device

    DOEpatents

    Foote, Robert S.

    1999-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  16. Large scale DNA microsequencing device

    DOEpatents

    Foote, Robert S.

    1997-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  17. Large scale DNA microsequencing device

    DOEpatents

    Foote, R.S.

    1999-08-31

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.

  18. Chemical modification: the key to clinical application of RNA interference?

    PubMed Central

    Corey, David R.

    2007-01-01

    RNA interference provides a potent and specific method for controlling gene expression in human cells. To translate this potential into a broad new family of therapeutics, it is necessary to optimize the efficacy of the RNA-based drugs. As discussed in this Review, it might be possible to achieve this optimization using chemical modifications that improve their in vivo stability, cellular delivery, biodistribution, pharmacokinetics, potency, and specificity. PMID:18060019

  19. Surface chemical modification of fullerene by mechanochemical treatment

    NASA Astrophysics Data System (ADS)

    Todorović Marković, B.; Jokanović, V.; Jovanović, S.; Kleut, D.; Dramićanin, M.; Marković, Z.

    2009-06-01

    In this study different encapsulating agents have been used for chemical modification of fullerenes. Fullerenes have reacted with tetrahydrofuran, sodium dodecyl sulfate, sodium dodecylbenzene sulfonate and ethylene vinyl acetate-ethylene vinyl versatate at room temperature under mechanical milling. The obtained powder has been dispersed in water by ultrasonication. The fullerene based colloids have been characterized by UV-vis, FTIR, Raman spectroscopy and atomic force microscopy. FTIR and Raman analysis have shown the presence of C 60 after surface functionalization.

  20. Selective Chemical Labeling of Natural T Modifications in DNA

    PubMed Central

    2015-01-01

    We present a chemical method to selectively tag and enrich thymine modifications, 5-formyluracil (5-fU) and 5-hydroxymethyluracil (5-hmU), found naturally in DNA. Inherent reactivity differences have enabled us to tag 5-fU chemoselectively over its C modification counterpart, 5-formylcytosine (5-fC). We rationalized the enhanced reactivity of 5-fU compared to 5-fC via ab initio quantum mechanical calculations. We exploited this chemical tagging reaction to provide proof of concept for the enrichment of 5-fU containing DNA from a pool that contains 5-fC or no modification. We further demonstrate that 5-hmU can be chemically oxidized to 5-fU, providing a strategy for the enrichment of 5-hmU. These methods will enable the mapping of 5-fU and 5-hmU in genomic DNA, to provide insights into their functional role and dynamics in biology. PMID:25946119

  1. Chemical modification of the cocoa shell surface using diazonium salts.

    PubMed

    Fioresi, Flavia; Vieillard, Julien; Bargougui, Radhouane; Bouazizi, Nabil; Fotsing, Patrick Nkuigue; Woumfo, Emmanuel Djoufac; Brun, Nicolas; Mofaddel, Nadine; Le Derf, Franck

    2017-05-15

    The outer portion of the cocoa bean, also known as cocoa husk or cocoa shell (CS), is an agrowaste material from the cocoa industry. Even though raw CS is used as food additive, garden mulch, and soil conditioner or even burnt for fuel, this biomass material has hardly ever been investigated for further modification. This article proposes a strategy of chemical modification of cocoa shell to add value to this natural material. The study investigates the grafting of aryl diazonium salt on cocoa shell. Different diazonium salts were grafted on the shell surface and characterized by infrared spectroscopy and scanning electronic microscopy imaging. Strategies were developed to demonstrate the spontaneous grafting of aryl diazonium salt on cocoa shell and to elucidate that lignin is mainly involved in immobilizing the phenyl layer.

  2. Chemical modification of arginine residues in the lactose repressor

    SciTech Connect

    Whitson, P.A.; Matthews, K.S.

    1987-10-06

    The lactose repressor protein was chemically modified with 2,3-butanedione and phenylglyoxal. Arginine reaction was quantitated by either amino aced analysis or incorporation of /sup 14/C-labeled phenylglyoxal. Inducer binding activity was unaffected by the modification of arginine residues, while both operator and nonspecific DNA binding activities were diminished, although to differing degrees. The correlation of the decrease in DNA binding activities with the modification of approx. 1-2 equiv of arginine per monomer suggests increased reactivity of a functionally essential residue(s). For both reagents, operator DNA binding activity was protected by the presence of calf thymus DNA, and the extent of reaction with phenylglyoxal was simultaneously diminished. This protection presumably results from steric restriction of reagent access to an arginine(s) that is (are) essential for DNA binding interactions. These experiments suggest that there is (are) an essential reactive arginine(s) critical for repressor binding to DNA.

  3. Chemical modification of proteins by lipids in diabetes.

    PubMed

    Baynes, John W

    2003-09-01

    Advanced glycation and lipoxidation end-products (AGE/ALE) increase in tissue proteins with age and at an accelerated rate in diabetes. This Review focuses on the nature and source of AGEs/ALEs and the factors affecting their formation in tissue and plasma proteins. Lipids are identified as an important source of chemical modification of proteins in diabetes, and the role of diabetes, dyslipidemia and renal disease in formation of AGEs/ALEs is reviewed. The article concludes with a discussion of ELISA assays for AGEs/ALEs and the merits of measuring AGEs/ALEs in the clinical laboratory.

  4. Chemical modification of proteins during peroxidation of phospholipids.

    PubMed

    Januszewski, Andrzej S; Alderson, Nathan L; Jenkins, Alicia J; Thorpe, Suzanne R; Baynes, John W

    2005-07-01

    Chemical modification of proteins by advanced glycation and lipoxidation end products is implicated in the pathogenesis of macrovascular disease in aging and diabetes. To identify biomarkers of the lipoxidative modification of protein, we studied the oxidation of phospholipids in the presence of the model protein RNase A and compared protein-bound products formed in these reactions with those formed during oxidation of plasma proteins. Metal-catalyzed oxidation of 1-palmitoyl-2-arachidonoyl-phosphatidylcholine or 1-palmitoyl-2-linoleoyl-phosphatidylcholine in the presence of RNase led to the loss of amino groups in RNase and the incorporation of phosphate, hexanoate, pentanedioate, nonanedioate, and palmitate into protein. Protein-bound palmitate and phosphate correlated strongly with one another, and protein-bound pentanedioate and nonanedioate, derived from arachidonate and linoleate, respectively, accounted for approximately 20% of the cross-linking of lipid phosphorus to protein. Similar results were obtained on oxidation of total plasma or isolated LDL. We conclude that alkanedioic acids are quantitatively important linkers of oxidized phospholipids to proteins and that measurement of protein-bound phosphate and long-chain fatty acids may be useful for assessing long-term lipid peroxidative damage to proteins in vivo. Analyses of plasma proteins from control and diabetic patients indicated significant increases in lipoxidative modification of protein in diabetic compared with control subjects.

  5. Acoustic Studies of the Large Scale Ocean Circulation

    NASA Technical Reports Server (NTRS)

    Menemenlis, Dimitris

    1999-01-01

    Detailed knowledge of ocean circulation and its transport properties is prerequisite to an understanding of the earth's climate and of important biological and chemical cycles. Results from two recent experiments, THETIS-2 in the Western Mediterranean and ATOC in the North Pacific, illustrate the use of ocean acoustic tomography for studies of the large scale circulation. The attraction of acoustic tomography is its ability to sample and average the large-scale oceanic thermal structure, synoptically, along several sections, and at regular intervals. In both studies, the acoustic data are compared to, and then combined with, general circulation models, meteorological analyses, satellite altimetry, and direct measurements from ships. Both studies provide complete regional descriptions of the time-evolving, three-dimensional, large scale circulation, albeit with large uncertainties. The studies raise serious issues about existing ocean observing capability and provide guidelines for future efforts.

  6. Large Scale Metal Additive Techniques Review

    SciTech Connect

    Nycz, Andrzej; Adediran, Adeola I; Noakes, Mark W; Love, Lonnie J

    2016-01-01

    In recent years additive manufacturing made long strides toward becoming a main stream production technology. Particularly strong progress has been made in large-scale polymer deposition. However, large scale metal additive has not yet reached parity with large scale polymer. This paper is a review study of the metal additive techniques in the context of building large structures. Current commercial devices are capable of printing metal parts on the order of several cubic feet compared to hundreds of cubic feet for the polymer side. In order to follow the polymer progress path several factors are considered: potential to scale, economy, environment friendliness, material properties, feedstock availability, robustness of the process, quality and accuracy, potential for defects, and post processing as well as potential applications. This paper focuses on current state of art of large scale metal additive technology with a focus on expanding the geometric limits.

  7. Large-scale regions of antimatter

    SciTech Connect

    Grobov, A. V. Rubin, S. G.

    2015-07-15

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era.

  8. Chemically defined media modifications to lower tryptophan oxidation of biopharmaceuticals.

    PubMed

    Hazeltine, Laurie B; Knueven, Kristine M; Zhang, Yan; Lian, Zhirui; Olson, Donald J; Ouyang, Anli

    2016-01-01

    Oxidation of biopharmaceuticals is a major product quality issue with potential impacts on activity and immunogenicity. At Eli Lilly and Company, high tryptophan oxidation was observed for two biopharmaceuticals in development produced in Chinese hamster ovary cells. A switch from historical hydrolysate-containing media to chemically defined media with a reformulated basal powder was thought to be responsible, so mitigation efforts focused on media modification. Shake flask studies identified that increasing tryptophan, copper, and manganese and decreasing cysteine concentrations were individual approaches to lower tryptophan oxidation. When amino acid and metal changes were combined, the modified formulation had a synergistic impact that led to substantially less tryptophan oxidation for both biopharmaceuticals. Similar results were achieved in shake flasks and benchtop bioreactors, demonstrating the potential to implement these modifications at manufacturing scale. The modified formulation did not negatively impact cell growth and viability, product titer, purity, charge variants, or glycan profile. A potential mechanism of action is presented for each amino acid or metal factor based on its role in oxidation chemistry. This work served not only to mitigate the tryptophan oxidation issue in two Lilly biopharmaceuticals in development, but also to increase our knowledge and appreciation for the impact of media components on product quality.

  9. Surface Modification of Nitinol by Chemical and Electrochemical Etching

    NASA Astrophysics Data System (ADS)

    Yang, Zhendi; Wei, Xiaojin; Cao, Peng; Gao, Wei

    2013-07-01

    In this paper, Nitinol, an equiatomic binary alloy of nickel and titanium, was surface modified for its potential biomedical applications by chemical and electrochemical etching. The main objective of the surface modification is to reduce the nickel content on the surface of Nitinol and simultaneously to a rough surface microstructure. As a result, better biocompatibility and better cell attachment would be achieved. The effect of the etching parameters was investigated, using scanning electron microscopy (SEM) equipped with energy dispersive X-ray spectrometry (EDX) and X-ray photoelectron spectrometry (XPS). The corrosion property of modified Nitinol surfaces was investigated by electrochemical work station. After etching, the Ni content in the surface layer has been reduced and the oxidation of Ti has been enhanced.

  10. Chemical composition and physicochemical properties of barley dietary fiber by chemical modification.

    PubMed

    Park, Ka Hwa; Lee, Kwang Yeon; Lee, Hyeon Gyu

    2013-09-01

    Chemical modification of dietary fiber (DF), extracted from whole grain barley, was carried out to obtain cross-linked (CL) DF, carboxymethyl (CM) DF, and hydroxypropyl (HP) DF. The DF components, physicochemical properties, and subsequent influence on the in vitro digestibility of wheat starch gels were comparatively investigated. The redistribution of fiber components from chemically modified DF was observed. An increase in the total DF (TDF) content of CL- and HP-DF was observed, which was mainly due to an increase of insoluble DF. Carboxymethylation led to an appreciable increase of soluble DF (1.17-6.20%) but TDF contents slightly decreased. Chemical modification of barley DF led to increases in arabinose (7.1-11.5%) and xylose (10.7-17.5%), but glucose contents decreased (67.4-79.9%). The treatments, especially carboxymethylation, effectively (P<0.05) increased hydration properties (e.g. water solubility, swelling power, and water absorption index). Substitution of 5% wheat starch with CL-, and HP-DF led to decreased in vitro digestibility in comparison to the control starch. Our results suggest that chemical modification improve the DF characteristics of barley and to exploit its potential application as a functional ingredient in fiber-rich products.

  11. Large-scale cortical networks and cognition.

    PubMed

    Bressler, S L

    1995-03-01

    The well-known parcellation of the mammalian cerebral cortex into a large number of functionally distinct cytoarchitectonic areas presents a problem for understanding the complex cortical integrative functions that underlie cognition. How do cortical areas having unique individual functional properties cooperate to accomplish these complex operations? Do neurons distributed throughout the cerebral cortex act together in large-scale functional assemblages? This review examines the substantial body of evidence supporting the view that complex integrative functions are carried out by large-scale networks of cortical areas. Pathway tracing studies in non-human primates have revealed widely distributed networks of interconnected cortical areas, providing an anatomical substrate for large-scale parallel processing of information in the cerebral cortex. Functional coactivation of multiple cortical areas has been demonstrated by neurophysiological studies in non-human primates and several different cognitive functions have been shown to depend on multiple distributed areas by human neuropsychological studies. Electrophysiological studies on interareal synchronization have provided evidence that active neurons in different cortical areas may become not only coactive, but also functionally interdependent. The computational advantages of synchronization between cortical areas in large-scale networks have been elucidated by studies using artificial neural network models. Recent observations of time-varying multi-areal cortical synchronization suggest that the functional topology of a large-scale cortical network is dynamically reorganized during visuomotor behavior.

  12. 76 FR 50815 - TSCA Inventory Update Reporting Modifications; Chemical Data Reporting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-16

    ... subset of chemical substances listed on the TSCA Inventory. 4. To improve the usefulness of the... Update Reporting Modifications; Chemical Data Reporting; Final Rule #0;#0;Federal Register / Vol. 76 , No... Parts 704, 710, and 711 RIN 2070-AJ43 TSCA Inventory Update Reporting Modifications; Chemical...

  13. Survey on large scale system control methods

    NASA Technical Reports Server (NTRS)

    Mercadal, Mathieu

    1987-01-01

    The problem inherent to large scale systems such as power network, communication network and economic or ecological systems were studied. The increase in size and flexibility of future spacecraft has put those dynamical systems into the category of large scale systems, and tools specific to the class of large systems are being sought to design control systems that can guarantee more stability and better performance. Among several survey papers, reference was found to a thorough investigation on decentralized control methods. Especially helpful was the classification made of the different existing approaches to deal with large scale systems. A very similar classification is used, even though the papers surveyed are somehow different from the ones reviewed in other papers. Special attention is brought to the applicability of the existing methods to controlling large mechanical systems like large space structures. Some recent developments are added to this survey.

  14. Physical and chemical modifications of collagen gels: impact on diffusion.

    PubMed

    Erikson, Arne; Andersen, Hilde Nortvedt; Naess, Stine Nalum; Sikorski, Pawel; Davies, Catharina de Lange

    2008-02-01

    The extracellular matrix (ECM) represents a major barrier for delivery of therapeutic drugs, and the transport is determined by the ECM composition, structure, and distribution. Because of the high interstitial fluid pressure in tumors, diffusion becomes the main transport mechanism through ECM. The purpose of this work was to study the impact of the structure of the collagen network on diffusion, by studying to what extent the orientation and chemical modification of the collagen network influenced diffusion. Collagen gels with a concentration of 0.2-2.0% that is comparable with the amount of collagen in the tumor ECM were used as a model system for ECM. Collagen gels were aligned in a low-strength magnetic field and geometrical confinement, and chemically modified by adding decorin or hyaluronan. Diffusion of dextran 2-MDa molecules in the collagen gels was measured using fluorescence recovery after photobleaching. Alignment of the collagen fibers in our gels was found to have no impact on the diffusion coefficient. Adding decorin reduced the diameter of the collagen fibers, but no effect on diffusion was observed. Hyaluronan also reduced the fiber diameter, and high concentration of hyaluronan (2.5 mg/ml) increased the diffusion coefficient. The results indicate that the structure of the collagen network is not a major factor in determining the diffusion through the ECM. Rather, increasing the concentration of collagen was found to reduce the diffusion coefficient. Concentration of the collagen network is more important than the structure in determining the diffusion coefficient.

  15. Large-scale nanophotonic phased array.

    PubMed

    Sun, Jie; Timurdogan, Erman; Yaacobi, Ami; Hosseini, Ehsan Shah; Watts, Michael R

    2013-01-10

    Electromagnetic phased arrays at radio frequencies are well known and have enabled applications ranging from communications to radar, broadcasting and astronomy. The ability to generate arbitrary radiation patterns with large-scale phased arrays has long been pursued. Although it is extremely expensive and cumbersome to deploy large-scale radiofrequency phased arrays, optical phased arrays have a unique advantage in that the much shorter optical wavelength holds promise for large-scale integration. However, the short optical wavelength also imposes stringent requirements on fabrication. As a consequence, although optical phased arrays have been studied with various platforms and recently with chip-scale nanophotonics, all of the demonstrations so far are restricted to one-dimensional or small-scale two-dimensional arrays. Here we report the demonstration of a large-scale two-dimensional nanophotonic phased array (NPA), in which 64 × 64 (4,096) optical nanoantennas are densely integrated on a silicon chip within a footprint of 576 μm × 576 μm with all of the nanoantennas precisely balanced in power and aligned in phase to generate a designed, sophisticated radiation pattern in the far field. We also show that active phase tunability can be realized in the proposed NPA by demonstrating dynamic beam steering and shaping with an 8 × 8 array. This work demonstrates that a robust design, together with state-of-the-art complementary metal-oxide-semiconductor technology, allows large-scale NPAs to be implemented on compact and inexpensive nanophotonic chips. In turn, this enables arbitrary radiation pattern generation using NPAs and therefore extends the functionalities of phased arrays beyond conventional beam focusing and steering, opening up possibilities for large-scale deployment in applications such as communication, laser detection and ranging, three-dimensional holography and biomedical sciences, to name just a few.

  16. The large-scale distribution of galaxies

    NASA Technical Reports Server (NTRS)

    Geller, Margaret J.

    1989-01-01

    The spatial distribution of galaxies in the universe is characterized on the basis of the six completed strips of the Harvard-Smithsonian Center for Astrophysics redshift-survey extension. The design of the survey is briefly reviewed, and the results are presented graphically. Vast low-density voids similar to the void in Bootes are found, almost completely surrounded by thin sheets of galaxies. Also discussed are the implications of the results for the survey sampling problem, the two-point correlation function of the galaxy distribution, the possibility of detecting large-scale coherent flows, theoretical models of large-scale structure, and the identification of groups and clusters of galaxies.

  17. Robust large-scale parallel nonlinear solvers for simulations.

    SciTech Connect

    Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson

    2005-11-01

    This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any existing linear solver, which makes it simple to write

  18. The workshop on iterative methods for large scale nonlinear problems

    SciTech Connect

    Walker, H.F.; Pernice, M.

    1995-12-01

    The aim of the workshop was to bring together researchers working on large scale applications with numerical specialists of various kinds. Applications that were addressed included reactive flows (combustion and other chemically reacting flows, tokamak modeling), porous media flows, cardiac modeling, chemical vapor deposition, image restoration, macromolecular modeling, and population dynamics. Numerical areas included Newton iterative (truncated Newton) methods, Krylov subspace methods, domain decomposition and other preconditioning methods, large scale optimization and optimal control, and parallel implementations and software. This report offers a brief summary of workshop activities and information about the participants. Interested readers are encouraged to look into an online proceedings available at http://www.usi.utah.edu/logan.proceedings. In this, the material offered here is augmented with hypertext abstracts that include links to locations such as speakers` home pages, PostScript copies of talks and papers, cross-references to related talks, and other information about topics addresses at the workshop.

  19. Management of large-scale technology

    NASA Technical Reports Server (NTRS)

    Levine, A.

    1985-01-01

    Two major themes are addressed in this assessment of the management of large-scale NASA programs: (1) how a high technology agency was a decade marked by a rapid expansion of funds and manpower in the first half and almost as rapid contraction in the second; and (2) how NASA combined central planning and control with decentralized project execution.

  20. Evaluating Large-Scale Interactive Radio Programmes

    ERIC Educational Resources Information Center

    Potter, Charles; Naidoo, Gordon

    2009-01-01

    This article focuses on the challenges involved in conducting evaluations of interactive radio programmes in South Africa with large numbers of schools, teachers, and learners. It focuses on the role such large-scale evaluation has played during the South African radio learning programme's development stage, as well as during its subsequent…

  1. Chemical modification of sputtered amorphous-carbon surfaces

    NASA Astrophysics Data System (ADS)

    Leezenberg, Pieter B.; Johnston, William H.; Tyndall, George W.

    2001-03-01

    Methods to chemically passivate the surfaces of amorphous-carbon films (a-C) produced by dc magnetron sputtering were studied. The chemical composition of carbon surfaces produced via sputtering are dependent upon the environment to which the carbon is exposed immediately following deposition. When the sputtered film is vented to ambient conditions, free radicals produced at the surface during the deposition process are quenched by reaction with oxygen and/or water to form an oxidized, hydrophilic surface. If the sputtered carbon film is, however, exposed to a reactive gas prior to venting to ambient, the chemical nature of the resulting surface can be modified substantially. Specifically, a less highly oxidized and much more hydrophobic carbon surface is produced when the surface free radicals are quenched via either an addition reaction (demonstrated with a fluorinated olefin) or a hydrogen abstraction reaction (demonstrated with two alkyl amines). Chemical modification of amorphous-carbon films can also be accomplished by performing the sputtering in a reactive plasma formed from mixtures of argon with molecular hydrogen, amines, and perfluorocarbons. The elemental composition of these films, and the relative reactivity of the surfaces formed, were investigated via x-ray photoelectron spectroscopy and contact-angle goniometry, respectively. In the case of sputtering with a mixture of argon and hydrogen, increasing the hydrogen flow results in an increase in the amount of hydrogen incorporated into the carbon film and a decrease in the surface free energy. Sputtering in diethylamine produces an amorphous-carbon film into which nitrogen is incorporated. The free energies of the a-C:N surfaces produced in this process are similar to those of the a-C:H films. Sputtering in a fluorocarbon vapor results in the incorporation of fluorine into the film structure and the formation of very low free-energy surfaces. Increasing the concentration of the fluorocarbon in the

  2. Large-Scale Measurement of Absolute Protein Glycosylation Stoichiometry.

    PubMed

    Sun, Shisheng; Zhang, Hui

    2015-07-07

    Protein glycosylation is one of the most important protein modifications. Glycosylation site occupancy alteration has been implicated in human diseases and cancers. However, current glycoproteomic methods focus on the identification and quantification of glycosylated peptides and glycosylation sites but not glycosylation occupancy or glycoform stoichiometry. Here we describe a method for large-scale determination of the absolute glycosylation stoichiometry using three independent relative ratios. Using this method, we determined 117 absolute N-glycosylation occupancies in OVCAR-3 cells. Finally, we investigated the possible functions and the determinants for partial glycosylation.

  3. Large-scale Advanced Propfan (LAP) program

    NASA Technical Reports Server (NTRS)

    Sagerser, D. A.; Ludemann, S. G.

    1985-01-01

    The propfan is an advanced propeller concept which maintains the high efficiencies traditionally associated with conventional propellers at the higher aircraft cruise speeds associated with jet transports. The large-scale advanced propfan (LAP) program extends the research done on 2 ft diameter propfan models to a 9 ft diameter article. The program includes design, fabrication, and testing of both an eight bladed, 9 ft diameter propfan, designated SR-7L, and a 2 ft diameter aeroelastically scaled model, SR-7A. The LAP program is complemented by the propfan test assessment (PTA) program, which takes the large-scale propfan and mates it with a gas generator and gearbox to form a propfan propulsion system and then flight tests this system on the wing of a Gulfstream 2 testbed aircraft.

  4. Condition Monitoring of Large-Scale Facilities

    NASA Technical Reports Server (NTRS)

    Hall, David L.

    1999-01-01

    This document provides a summary of the research conducted for the NASA Ames Research Center under grant NAG2-1182 (Condition-Based Monitoring of Large-Scale Facilities). The information includes copies of view graphs presented at NASA Ames in the final Workshop (held during December of 1998), as well as a copy of a technical report provided to the COTR (Dr. Anne Patterson-Hine) subsequent to the workshop. The material describes the experimental design, collection of data, and analysis results associated with monitoring the health of large-scale facilities. In addition to this material, a copy of the Pennsylvania State University Applied Research Laboratory data fusion visual programming tool kit was also provided to NASA Ames researchers.

  5. Large-scale instabilities of helical flows

    NASA Astrophysics Data System (ADS)

    Cameron, Alexandre; Alexakis, Alexandros; Brachet, Marc-Étienne

    2016-10-01

    Large-scale hydrodynamic instabilities of periodic helical flows of a given wave number K are investigated using three-dimensional Floquet numerical computations. In the Floquet formalism the unstable field is expanded in modes of different spacial periodicity. This allows us (i) to clearly distinguish large from small scale instabilities and (ii) to study modes of wave number q of arbitrarily large-scale separation q ≪K . Different flows are examined including flows that exhibit small-scale turbulence. The growth rate σ of the most unstable mode is measured as a function of the scale separation q /K ≪1 and the Reynolds number Re. It is shown that the growth rate follows the scaling σ ∝q if an AKA effect [Frisch et al., Physica D: Nonlinear Phenomena 28, 382 (1987), 10.1016/0167-2789(87)90026-1] is present or a negative eddy viscosity scaling σ ∝q2 in its absence. This holds both for the Re≪1 regime where previously derived asymptotic results are verified but also for Re=O (1 ) that is beyond their range of validity. Furthermore, for values of Re above a critical value ReSc beyond which small-scale instabilities are present, the growth rate becomes independent of q and the energy of the perturbation at large scales decreases with scale separation. The nonlinear behavior of these large-scale instabilities is also examined in the nonlinear regime where the largest scales of the system are found to be the most dominant energetically. These results are interpreted by low-order models.

  6. Large-Scale Aerosol Modeling and Analysis

    DTIC Science & Technology

    2008-09-30

    aerosol species up to six days in advance anywhere on the globe. NAAPS and COAMPS are particularly useful for forecasts of dust storms in areas...impact cloud processes globally. With increasing dust storms due to climate change and land use changes in desert regions, the impact of the...bacteria in large-scale dust storms is expected to significantly impact warm ice cloud formation, human health, and ecosystems globally. In Niemi et al

  7. The Large Scale Synthesis of Aligned Plate Nanostructures

    NASA Astrophysics Data System (ADS)

    Zhou, Yang; Nash, Philip; Liu, Tian; Zhao, Naiqin; Zhu, Shengli

    2016-07-01

    We propose a novel technique for the large-scale synthesis of aligned-plate nanostructures that are self-assembled and self-supporting. The synthesis technique involves developing nanoscale two-phase microstructures through discontinuous precipitation followed by selective etching to remove one of the phases. The method may be applied to any alloy system in which the discontinuous precipitation transformation goes to completion. The resulting structure may have many applications in catalysis, filtering and thermal management depending on the phase selection and added functionality through chemical reaction with the retained phase. The synthesis technique is demonstrated using the discontinuous precipitation of a γ‧ phase, (Ni, Co)3Al, followed by selective dissolution of the γ matrix phase. The production of the nanostructure requires heat treatments on the order of minutes and can be performed on a large scale making this synthesis technique of great economic potential.

  8. The Large Scale Synthesis of Aligned Plate Nanostructures

    PubMed Central

    Zhou, Yang; Nash, Philip; Liu, Tian; Zhao, Naiqin; Zhu, Shengli

    2016-01-01

    We propose a novel technique for the large-scale synthesis of aligned-plate nanostructures that are self-assembled and self-supporting. The synthesis technique involves developing nanoscale two-phase microstructures through discontinuous precipitation followed by selective etching to remove one of the phases. The method may be applied to any alloy system in which the discontinuous precipitation transformation goes to completion. The resulting structure may have many applications in catalysis, filtering and thermal management depending on the phase selection and added functionality through chemical reaction with the retained phase. The synthesis technique is demonstrated using the discontinuous precipitation of a γ′ phase, (Ni, Co)3Al, followed by selective dissolution of the γ matrix phase. The production of the nanostructure requires heat treatments on the order of minutes and can be performed on a large scale making this synthesis technique of great economic potential. PMID:27439672

  9. Economically viable large-scale hydrogen liquefaction

    NASA Astrophysics Data System (ADS)

    Cardella, U.; Decker, L.; Klein, H.

    2017-02-01

    The liquid hydrogen demand, particularly driven by clean energy applications, will rise in the near future. As industrial large scale liquefiers will play a major role within the hydrogen supply chain, production capacity will have to increase by a multiple of today’s typical sizes. The main goal is to reduce the total cost of ownership for these plants by increasing energy efficiency with innovative and simple process designs, optimized in capital expenditure. New concepts must ensure a manageable plant complexity and flexible operability. In the phase of process development and selection, a dimensioning of key equipment for large scale liquefiers, such as turbines and compressors as well as heat exchangers, must be performed iteratively to ensure technological feasibility and maturity. Further critical aspects related to hydrogen liquefaction, e.g. fluid properties, ortho-para hydrogen conversion, and coldbox configuration, must be analysed in detail. This paper provides an overview on the approach, challenges and preliminary results in the development of efficient as well as economically viable concepts for large-scale hydrogen liquefaction.

  10. Large-Scale Visual Data Analysis

    NASA Astrophysics Data System (ADS)

    Johnson, Chris

    2014-04-01

    Modern high performance computers have speeds measured in petaflops and handle data set sizes measured in terabytes and petabytes. Although these machines offer enormous potential for solving very large-scale realistic computational problems, their effectiveness will hinge upon the ability of human experts to interact with their simulation results and extract useful information. One of the greatest scientific challenges of the 21st century is to effectively understand and make use of the vast amount of information being produced. Visual data analysis will be among our most most important tools in helping to understand such large-scale information. Our research at the Scientific Computing and Imaging (SCI) Institute at the University of Utah has focused on innovative, scalable techniques for large-scale 3D visual data analysis. In this talk, I will present state- of-the-art visualization techniques, including scalable visualization algorithms and software, cluster-based visualization methods and innovate visualization techniques applied to problems in computational science, engineering, and medicine. I will conclude with an outline for a future high performance visualization research challenges and opportunities.

  11. Large-scale neuromorphic computing systems

    NASA Astrophysics Data System (ADS)

    Furber, Steve

    2016-10-01

    Neuromorphic computing covers a diverse range of approaches to information processing all of which demonstrate some degree of neurobiological inspiration that differentiates them from mainstream conventional computing systems. The philosophy behind neuromorphic computing has its origins in the seminal work carried out by Carver Mead at Caltech in the late 1980s. This early work influenced others to carry developments forward, and advances in VLSI technology supported steady growth in the scale and capability of neuromorphic devices. Recently, a number of large-scale neuromorphic projects have emerged, taking the approach to unprecedented scales and capabilities. These large-scale projects are associated with major new funding initiatives for brain-related research, creating a sense that the time and circumstances are right for progress in our understanding of information processing in the brain. In this review we present a brief history of neuromorphic engineering then focus on some of the principal current large-scale projects, their main features, how their approaches are complementary and distinct, their advantages and drawbacks, and highlight the sorts of capabilities that each can deliver to neural modellers.

  12. Experimental Simulations of Large-Scale Collisions

    NASA Technical Reports Server (NTRS)

    Housen, Kevin R.

    2002-01-01

    This report summarizes research on the effects of target porosity on the mechanics of impact cratering. Impact experiments conducted on a centrifuge provide direct simulations of large-scale cratering on porous asteroids. The experiments show that large craters in porous materials form mostly by compaction, with essentially no deposition of material into the ejecta blanket that is a signature of cratering in less-porous materials. The ratio of ejecta mass to crater mass is shown to decrease with increasing crater size or target porosity. These results are consistent with the observation that large closely-packed craters on asteroid Mathilde appear to have formed without degradation to earlier craters.

  13. Large-Scale PV Integration Study

    SciTech Connect

    Lu, Shuai; Etingov, Pavel V.; Diao, Ruisheng; Ma, Jian; Samaan, Nader A.; Makarov, Yuri V.; Guo, Xinxin; Hafen, Ryan P.; Jin, Chunlian; Kirkham, Harold; Shlatz, Eugene; Frantzis, Lisa; McClive, Timothy; Karlson, Gregory; Acharya, Dhruv; Ellis, Abraham; Stein, Joshua; Hansen, Clifford; Chadliev, Vladimir; Smart, Michael; Salgo, Richard; Sorensen, Rahn; Allen, Barbara; Idelchik, Boris

    2011-07-29

    This research effort evaluates the impact of large-scale photovoltaic (PV) and distributed generation (DG) output on NV Energy’s electric grid system in southern Nevada. It analyzes the ability of NV Energy’s generation to accommodate increasing amounts of utility-scale PV and DG, and the resulting cost of integrating variable renewable resources. The study was jointly funded by the United States Department of Energy and NV Energy, and conducted by a project team comprised of industry experts and research scientists from Navigant Consulting Inc., Sandia National Laboratories, Pacific Northwest National Laboratory and NV Energy.

  14. What is a large-scale dynamo?

    NASA Astrophysics Data System (ADS)

    Nigro, G.; Pongkitiwanichakul, P.; Cattaneo, F.; Tobias, S. M.

    2017-01-01

    We consider kinematic dynamo action in a sheared helical flow at moderate to high values of the magnetic Reynolds number (Rm). We find exponentially growing solutions which, for large enough shear, take the form of a coherent part embedded in incoherent fluctuations. We argue that at large Rm large-scale dynamo action should be identified by the presence of structures coherent in time, rather than those at large spatial scales. We further argue that although the growth rate is determined by small-scale processes, the period of the coherent structures is set by mean-field considerations.

  15. Neutrinos and large-scale structure

    SciTech Connect

    Eisenstein, Daniel J.

    2015-07-15

    I review the use of cosmological large-scale structure to measure properties of neutrinos and other relic populations of light relativistic particles. With experiments to measure the anisotropies of the cosmic microwave anisotropies and the clustering of matter at low redshift, we now have securely measured a relativistic background with density appropriate to the cosmic neutrino background. Our limits on the mass of the neutrino continue to shrink. Experiments coming in the next decade will greatly improve the available precision on searches for the energy density of novel relativistic backgrounds and the mass of neutrinos.

  16. Large-scale planar lightwave circuits

    NASA Astrophysics Data System (ADS)

    Bidnyk, Serge; Zhang, Hua; Pearson, Matt; Balakrishnan, Ashok

    2011-01-01

    By leveraging advanced wafer processing and flip-chip bonding techniques, we have succeeded in hybrid integrating a myriad of active optical components, including photodetectors and laser diodes, with our planar lightwave circuit (PLC) platform. We have combined hybrid integration of active components with monolithic integration of other critical functions, such as diffraction gratings, on-chip mirrors, mode-converters, and thermo-optic elements. Further process development has led to the integration of polarization controlling functionality. Most recently, all these technological advancements have been combined to create large-scale planar lightwave circuits that comprise hundreds of optical elements integrated on chips less than a square inch in size.

  17. Colloquium: Large scale simulations on GPU clusters

    NASA Astrophysics Data System (ADS)

    Bernaschi, Massimo; Bisson, Mauro; Fatica, Massimiliano

    2015-06-01

    Graphics processing units (GPU) are currently used as a cost-effective platform for computer simulations and big-data processing. Large scale applications require that multiple GPUs work together but the efficiency obtained with cluster of GPUs is, at times, sub-optimal because the GPU features are not exploited at their best. We describe how it is possible to achieve an excellent efficiency for applications in statistical mechanics, particle dynamics and networks analysis by using suitable memory access patterns and mechanisms like CUDA streams, profiling tools, etc. Similar concepts and techniques may be applied also to other problems like the solution of Partial Differential Equations.

  18. Large scale phononic metamaterials for seismic isolation

    SciTech Connect

    Aravantinos-Zafiris, N.; Sigalas, M. M.

    2015-08-14

    In this work, we numerically examine structures that could be characterized as large scale phononic metamaterials. These novel structures could have band gaps in the frequency spectrum of seismic waves when their dimensions are chosen appropriately, thus raising the belief that they could be serious candidates for seismic isolation structures. Different and easy to fabricate structures were examined made from construction materials such as concrete and steel. The well-known finite difference time domain method is used in our calculations in order to calculate the band structures of the proposed metamaterials.

  19. Large-scale Heterogeneous Network Data Analysis

    DTIC Science & Technology

    2012-07-31

    Data for Multi-Player Influence Maximization on Social Networks.” KDD 2012 (Demo).  Po-Tzu Chang , Yen-Chieh Huang, Cheng-Lun Yang, Shou-De Lin, Pu...Jen Cheng. “Learning-Based Time-Sensitive Re-Ranking for Web Search.” SIGIR 2012 (poster)  Hung -Che Lai, Cheng-Te Li, Yi-Chen Lo, and Shou-De Lin...Exploiting and Evaluating MapReduce for Large-Scale Graph Mining.” ASONAM 2012 (Full, 16% acceptance ratio).  Hsun-Ping Hsieh , Cheng-Te Li, and Shou

  20. Large-scale Intelligent Transporation Systems simulation

    SciTech Connect

    Ewing, T.; Canfield, T.; Hannebutte, U.; Levine, D.; Tentner, A.

    1995-06-01

    A prototype computer system has been developed which defines a high-level architecture for a large-scale, comprehensive, scalable simulation of an Intelligent Transportation System (ITS) capable of running on massively parallel computers and distributed (networked) computer systems. The prototype includes the modelling of instrumented ``smart`` vehicles with in-vehicle navigation units capable of optimal route planning and Traffic Management Centers (TMC). The TMC has probe vehicle tracking capabilities (display position and attributes of instrumented vehicles), and can provide 2-way interaction with traffic to provide advisories and link times. Both the in-vehicle navigation module and the TMC feature detailed graphical user interfaces to support human-factors studies. The prototype has been developed on a distributed system of networked UNIX computers but is designed to run on ANL`s IBM SP-X parallel computer system for large scale problems. A novel feature of our design is that vehicles will be represented by autonomus computer processes, each with a behavior model which performs independent route selection and reacts to external traffic events much like real vehicles. With this approach, one will be able to take advantage of emerging massively parallel processor (MPP) systems.

  1. Local gravity and large-scale structure

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, Roman; Vittorio, Nicola; Wyse, Rosemary F. G.

    1990-01-01

    The magnitude and direction of the observed dipole anisotropy of the galaxy distribution can in principle constrain the amount of large-scale power present in the spectrum of primordial density fluctuations. This paper confronts the data, provided by a recent redshift survey of galaxies detected by the IRAS satellite, with the predictions of two cosmological models with very different levels of large-scale power: the biased Cold Dark Matter dominated model (CDM) and a baryon-dominated model (BDM) with isocurvature initial conditions. Model predictions are investigated for the Local Group peculiar velocity, v(R), induced by mass inhomogeneities distributed out to a given radius, R, for R less than about 10,000 km/s. Several convergence measures for v(R) are developed, which can become powerful cosmological tests when deep enough samples become available. For the present data sets, the CDM and BDM predictions are indistinguishable at the 2 sigma level and both are consistent with observations. A promising discriminant between cosmological models is the misalignment angle between v(R) and the apex of the dipole anisotropy of the microwave background.

  2. Large-scale Globally Propagating Coronal Waves.

    PubMed

    Warmuth, Alexander

    Large-scale, globally propagating wave-like disturbances have been observed in the solar chromosphere and by inference in the corona since the 1960s. However, detailed analysis of these phenomena has only been conducted since the late 1990s. This was prompted by the availability of high-cadence coronal imaging data from numerous spaced-based instruments, which routinely show spectacular globally propagating bright fronts. Coronal waves, as these perturbations are usually referred to, have now been observed in a wide range of spectral channels, yielding a wealth of information. Many findings have supported the "classical" interpretation of the disturbances: fast-mode MHD waves or shocks that are propagating in the solar corona. However, observations that seemed inconsistent with this picture have stimulated the development of alternative models in which "pseudo waves" are generated by magnetic reconfiguration in the framework of an expanding coronal mass ejection. This has resulted in a vigorous debate on the physical nature of these disturbances. This review focuses on demonstrating how the numerous observational findings of the last one and a half decades can be used to constrain our models of large-scale coronal waves, and how a coherent physical understanding of these disturbances is finally emerging.

  3. Large-scale genotoxicity assessments in the marine environment.

    PubMed Central

    Hose, J E

    1994-01-01

    There are a number of techniques for detecting genotoxicity in the marine environment, and many are applicable to large-scale field assessments. Certain tests can be used to evaluate responses in target organisms in situ while others utilize surrogate organisms exposed to field samples in short-term laboratory bioassays. Genotoxicity endpoints appear distinct from traditional toxicity endpoints, but some have chemical or ecotoxicologic correlates. One versatile end point, the frequency of anaphase aberrations, has been used in several large marine assessments to evaluate genotoxicity in the New York Bight, in sediment from San Francisco Bay, and following the Exxon Valdez oil spill. PMID:7713029

  4. Large-scale genotoxicity assessments in the marine environment

    SciTech Connect

    Hose, J.E.

    1994-12-01

    There are a number of techniques for detecting genotoxicity in the marine environment, and many are applicable to large-scale field assessments. Certain tests can be used to evaluate responses in target organisms in situ while others utilize surrogate organisms exposed to field samples in short-term laboratory bioassays. Genotoxicity endpoints appear distinct from traditional toxicity endpoints, but some have chemical or ecotoxicologic correlates. One versatile end point, the frequency of anaphase aberrations, has been used in several large marine assessments to evaluate genotoxicity in the New York Bight, in sediment from San Francisco Bay, and following the Exxon Valdez oil spill. 31 refs., 2 tabs.

  5. Surface chemical and physical modification in stent technology for the treatment of coronary artery disease.

    PubMed

    Nazneen, Feroze; Herzog, Grégoire; Arrigan, Damien W M; Caplice, Noel; Benvenuto, Pasquale; Galvin, Paul; Thompson, Michael

    2012-10-01

    Coronary artery disease (CAD) kills millions of people every year. It results from a narrowing of the arteries (stenosis) supplying blood to the heart. This review discusses the merits and limitations of balloon angioplasty and stent implantation, the most common treatment options for CAD, and the pathophysiology associated with these treatments. The focus of the review is heavily placed on research efforts geared toward the modification of stent surfaces for the improvement of stent-vascular compatibility and the reduction in the occurrence of related pathophysiologies. Such modifications may be chemical or physical, both of which are surveyed here. Chemical modifications may be passive or active, while physical modification of stent surfaces can also provide suitable substrates to manipulate the responses of vascular cells (endothelial, smooth muscle, and fibroblast). The influence of micro- and nanostructured surfaces on the in vitro cell response is discussed. Finally, future perspectives on the combination of chemical and physical modifications of stent surfaces are also presented.

  6. Chemical Posttranslational Modification with Designed Rhodium(II) Catalysts.

    PubMed

    Martin, S C; Minus, M B; Ball, Z T

    2016-01-01

    Natural enzymes use molecular recognition to perform exquisitely selective transformations on nucleic acids, proteins, and natural products. Rhodium(II) catalysts mimic this selectivity, using molecular recognition to allow selective modification of proteins with a variety of functionalized diazo reagents. The rhodium catalysts and the diazo reactivity have been successfully applied to a variety of protein folds, the chemistry succeeds in complex environments such as cell lysate, and a simple protein blot method accurately assesses modification efficiency. The studies with rhodium catalysts provide a new tool to study and probe protein-binding events, as well as a new synthetic approach to protein conjugates for medical, biochemical, or materials applications.

  7. Engineering management of large scale systems

    NASA Technical Reports Server (NTRS)

    Sanders, Serita; Gill, Tepper L.; Paul, Arthur S.

    1989-01-01

    The organization of high technology and engineering problem solving, has given rise to an emerging concept. Reasoning principles for integrating traditional engineering problem solving with system theory, management sciences, behavioral decision theory, and planning and design approaches can be incorporated into a methodological approach to solving problems with a long range perspective. Long range planning has a great potential to improve productivity by using a systematic and organized approach. Thus, efficiency and cost effectiveness are the driving forces in promoting the organization of engineering problems. Aspects of systems engineering that provide an understanding of management of large scale systems are broadly covered here. Due to the focus and application of research, other significant factors (e.g., human behavior, decision making, etc.) are not emphasized but are considered.

  8. Large-scale parametric survival analysis.

    PubMed

    Mittal, Sushil; Madigan, David; Cheng, Jerry Q; Burd, Randall S

    2013-10-15

    Survival analysis has been a topic of active statistical research in the past few decades with applications spread across several areas. Traditional applications usually consider data with only a small numbers of predictors with a few hundreds or thousands of observations. Recent advances in data acquisition techniques and computation power have led to considerable interest in analyzing very-high-dimensional data where the number of predictor variables and the number of observations range between 10(4) and 10(6). In this paper, we present a tool for performing large-scale regularized parametric survival analysis using a variant of the cyclic coordinate descent method. Through our experiments on two real data sets, we show that application of regularized models to high-dimensional data avoids overfitting and can provide improved predictive performance and calibration over corresponding low-dimensional models.

  9. Primer design for large scale sequencing.

    PubMed

    Haas, S; Vingron, M; Poustka, A; Wiemann, S

    1998-06-15

    We have developed PRIDE, a primer design program that automatically designs primers in single contigs or whole sequencing projects to extend the already known sequence and to double strand single-stranded regions. The program is fully integrated into the Staden package (GAP4) and accessible with a graphical user interface. PRIDE uses a fuzzy logic-based system to calculate primer qualities. The computational performance of PRIDE is enhanced by using suffix trees to store the huge amount of data being produced. A test set of 110 sequencing primers and 11 PCR primer pairs has been designed on genomic templates, cDNAs and sequences containing repetitive elements to analyze PRIDE's success rate. The high performance of PRIDE, combined with its minimal requirement of user interaction and its fast algorithm, make this program useful for the large scale design of primers, especially in large sequencing projects.

  10. Large scale preparation of pure phycobiliproteins.

    PubMed

    Padgett, M P; Krogmann, D W

    1987-01-01

    This paper describes simple procedures for the purification of large amounts of phycocyanin and allophycocyanin from the cyanobacterium Microcystis aeruginosa. A homogeneous natural bloom of this organism provided hundreds of kilograms of cells. Large samples of cells were broken by freezing and thawing. Repeated extraction of the broken cells with distilled water released phycocyanin first, then allophycocyanin, and provides supporting evidence for the current models of phycobilisome structure. The very low ionic strength of the aqueous extracts allowed allophycocyanin release in a particulate form so that this protein could be easily concentrated by centrifugation. Other proteins in the extract were enriched and concentrated by large scale membrane filtration. The biliproteins were purified to homogeneity by chromatography on DEAE cellulose. Purity was established by HPLC and by N-terminal amino acid sequence analysis. The proteins were examined for stability at various pHs and exposures to visible light.

  11. Large-Scale Organization of Glycosylation Networks

    NASA Astrophysics Data System (ADS)

    Kim, Pan-Jun; Lee, Dong-Yup; Jeong, Hawoong

    2009-03-01

    Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are frequently attached to proteins and lipids. Glycans participate in fundamental biological processes including molecular trafficking and clearance, cell proliferation and apoptosis, developmental biology, immune response, and pathogenesis. N-linked glycans found on proteins are formed by sequential attachments of monosaccharides with the help of a relatively small number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thus generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigate the large-scale organization of such N-glycosylation pathways in a mammalian cell. The uncovered results give the experimentally-testable predictions for glycosylation process, and can be applied to the engineering of therapeutic glycoproteins.

  12. Efficient, large scale separation of coal macerals

    SciTech Connect

    Dyrkacz, G.R.; Bloomquist, C.A.A.

    1988-01-01

    The authors believe that the separation of macerals by continuous flow centrifugation offers a simple technique for the large scale separation of macerals. With relatively little cost (/approximately/ $10K), it provides an opportunity for obtaining quite pure maceral fractions. Although they have not completely worked out all the nuances of this separation system, they believe that the problems they have indicated can be minimized to pose only minor inconvenience. It cannot be said that this system completely bypasses the disagreeable tedium or time involved in separating macerals, nor will it by itself overcome the mental inertia required to make maceral separation an accepted necessary fact in fundamental coal science. However, they find their particular brand of continuous flow centrifugation is considerably faster than sink/float separation, can provide a good quality product with even one separation cycle, and permits the handling of more material than a conventional sink/float centrifuge separation.

  13. Large scale cryogenic fluid systems testing

    NASA Technical Reports Server (NTRS)

    1992-01-01

    NASA Lewis Research Center's Cryogenic Fluid Systems Branch (CFSB) within the Space Propulsion Technology Division (SPTD) has the ultimate goal of enabling the long term storage and in-space fueling/resupply operations for spacecraft and reusable vehicles in support of space exploration. Using analytical modeling, ground based testing, and on-orbit experimentation, the CFSB is studying three primary categories of fluid technology: storage, supply, and transfer. The CFSB is also investigating fluid handling, advanced instrumentation, and tank structures and materials. Ground based testing of large-scale systems is done using liquid hydrogen as a test fluid at the Cryogenic Propellant Tank Facility (K-site) at Lewis' Plum Brook Station in Sandusky, Ohio. A general overview of tests involving liquid transfer, thermal control, pressure control, and pressurization is given.

  14. Large-scale optimization of neuron arbors

    NASA Astrophysics Data System (ADS)

    Cherniak, Christopher; Changizi, Mark; Won Kang, Du

    1999-05-01

    At the global as well as local scales, some of the geometry of types of neuron arbors-both dendrites and axons-appears to be self-organizing: Their morphogenesis behaves like flowing water, that is, fluid dynamically; waterflow in branching networks in turn acts like a tree composed of cords under tension, that is, vector mechanically. Branch diameters and angles and junction sites conform significantly to this model. The result is that such neuron tree samples globally minimize their total volume-rather than, for example, surface area or branch length. In addition, the arbors perform well at generating the cheapest topology interconnecting their terminals: their large-scale layouts are among the best of all such possible connecting patterns, approaching 5% of optimum. This model also applies comparably to arterial and river networks.

  15. Grid sensitivity capability for large scale structures

    NASA Technical Reports Server (NTRS)

    Nagendra, Gopal K.; Wallerstein, David V.

    1989-01-01

    The considerations and the resultant approach used to implement design sensitivity capability for grids into a large scale, general purpose finite element system (MSC/NASTRAN) are presented. The design variables are grid perturbations with a rather general linking capability. Moreover, shape and sizing variables may be linked together. The design is general enough to facilitate geometric modeling techniques for generating design variable linking schemes in an easy and straightforward manner. Test cases have been run and validated by comparison with the overall finite difference method. The linking of a design sensitivity capability for shape variables in MSC/NASTRAN with an optimizer would give designers a powerful, automated tool to carry out practical optimization design of real life, complicated structures.

  16. Large Scale Quantum Simulations of Nuclear Pasta

    NASA Astrophysics Data System (ADS)

    Fattoyev, Farrukh J.; Horowitz, Charles J.; Schuetrumpf, Bastian

    2016-03-01

    Complex and exotic nuclear geometries collectively referred to as ``nuclear pasta'' are expected to naturally exist in the crust of neutron stars and in supernovae matter. Using a set of self-consistent microscopic nuclear energy density functionals we present the first results of large scale quantum simulations of pasta phases at baryon densities 0 . 03 < ρ < 0 . 10 fm-3, proton fractions 0 . 05

  17. Primer design for large scale sequencing.

    PubMed Central

    Haas, S; Vingron, M; Poustka, A; Wiemann, S

    1998-01-01

    We have developed PRIDE, a primer design program that automatically designs primers in single contigs or whole sequencing projects to extend the already known sequence and to double strand single-stranded regions. The program is fully integrated into the Staden package (GAP4) and accessible with a graphical user interface. PRIDE uses a fuzzy logic-based system to calculate primer qualities. The computational performance of PRIDE is enhanced by using suffix trees to store the huge amount of data being produced. A test set of 110 sequencing primers and 11 PCR primer pairs has been designed on genomic templates, cDNAs and sequences containing repetitive elements to analyze PRIDE's success rate. The high performance of PRIDE, combined with its minimal requirement of user interaction and its fast algorithm, make this program useful for the large scale design of primers, especially in large sequencing projects. PMID:9611248

  18. Large scale study of tooth enamel

    SciTech Connect

    Bodart, F.; Deconninck, G.; Martin, M.Th.

    1981-04-01

    Human tooth enamel contains traces of foreign elements. The presence of these elements is related to the history and the environment of the human body and can be considered as the signature of perturbations which occur during the growth of a tooth. A map of the distribution of these traces on a large scale sample of the population will constitute a reference for further investigations of environmental effects. One hundred eighty samples of teeth were first analysed using PIXE, backscattering and nuclear reaction techniques. The results were analysed using statistical methods. Correlations between O, F, Na, P, Ca, Mn, Fe, Cu, Zn, Pb and Sr were observed and cluster analysis was in progress. The techniques described in the present work have been developed in order to establish a method for the exploration of very large samples of the Belgian population.

  19. Modeling the Internet's large-scale topology

    PubMed Central

    Yook, Soon-Hyung; Jeong, Hawoong; Barabási, Albert-László

    2002-01-01

    Network generators that capture the Internet's large-scale topology are crucial for the development of efficient routing protocols and modeling Internet traffic. Our ability to design realistic generators is limited by the incomplete understanding of the fundamental driving forces that affect the Internet's evolution. By combining several independent databases capturing the time evolution, topology, and physical layout of the Internet, we identify the universal mechanisms that shape the Internet's router and autonomous system level topology. We find that the physical layout of nodes form a fractal set, determined by population density patterns around the globe. The placement of links is driven by competition between preferential attachment and linear distance dependence, a marked departure from the currently used exponential laws. The universal parameters that we extract significantly restrict the class of potentially correct Internet models and indicate that the networks created by all available topology generators are fundamentally different from the current Internet. PMID:12368484

  20. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  1. Voids in the Large-Scale Structure

    NASA Astrophysics Data System (ADS)

    El-Ad, Hagai; Piran, Tsvi

    1997-12-01

    Voids are the most prominent feature of the large-scale structure of the universe. Still, their incorporation into quantitative analysis of it has been relatively recent, owing essentially to the lack of an objective tool to identify the voids and to quantify them. To overcome this, we present here the VOID FINDER algorithm, a novel tool for objectively quantifying voids in the galaxy distribution. The algorithm first classifies galaxies as either wall galaxies or field galaxies. Then, it identifies voids in the wall-galaxy distribution. Voids are defined as continuous volumes that do not contain any wall galaxies. The voids must be thicker than an adjustable limit, which is refined in successive iterations. In this way, we identify the same regions that would be recognized as voids by the eye. Small breaches in the walls are ignored, avoiding artificial connections between neighboring voids. We test the algorithm using Voronoi tesselations. By appropriate scaling of the parameters with the selection function, we apply it to two redshift surveys, the dense SSRS2 and the full-sky IRAS 1.2 Jy. Both surveys show similar properties: ~50% of the volume is filled by voids. The voids have a scale of at least 40 h-1 Mpc and an average -0.9 underdensity. Faint galaxies do not fill the voids, but they do populate them more than bright ones. These results suggest that both optically and IRAS-selected galaxies delineate the same large-scale structure. Comparison with the recovered mass distribution further suggests that the observed voids in the galaxy distribution correspond well to underdense regions in the mass distribution. This confirms the gravitational origin of the voids.

  2. Supporting large-scale computational science

    SciTech Connect

    Musick, R

    1998-10-01

    A study has been carried out to determine the feasibility of using commercial database management systems (DBMSs) to support large-scale computational science. Conventional wisdom in the past has been that DBMSs are too slow for such data. Several events over the past few years have muddied the clarity of this mindset: 1. 2. 3. 4. Several commercial DBMS systems have demonstrated storage and ad-hoc quer access to Terabyte data sets. Several large-scale science teams, such as EOSDIS [NAS91], high energy physics [MM97] and human genome [Kin93] have adopted (or make frequent use of) commercial DBMS systems as the central part of their data management scheme. Several major DBMS vendors have introduced their first object-relational products (ORDBMSs), which have the potential to support large, array-oriented data. In some cases, performance is a moot issue. This is true in particular if the performance of legacy applications is not reduced while new, albeit slow, capabilities are added to the system. The basic assessment is still that DBMSs do not scale to large computational data. However, many of the reasons have changed, and there is an expiration date attached to that prognosis. This document expands on this conclusion, identifies the advantages and disadvantages of various commercial approaches, and describes the studies carried out in exploring this area. The document is meant to be brief, technical and informative, rather than a motivational pitch. The conclusions within are very likely to become outdated within the next 5-7 years, as market forces will have a significant impact on the state of the art in scientific data management over the next decade.

  3. Supporting large-scale computational science

    SciTech Connect

    Musick, R., LLNL

    1998-02-19

    Business needs have driven the development of commercial database systems since their inception. As a result, there has been a strong focus on supporting many users, minimizing the potential corruption or loss of data, and maximizing performance metrics like transactions per second, or TPC-C and TPC-D results. It turns out that these optimizations have little to do with the needs of the scientific community, and in particular have little impact on improving the management and use of large-scale high-dimensional data. At the same time, there is an unanswered need in the scientific community for many of the benefits offered by a robust DBMS. For example, tying an ad-hoc query language such as SQL together with a visualization toolkit would be a powerful enhancement to current capabilities. Unfortunately, there has been little emphasis or discussion in the VLDB community on this mismatch over the last decade. The goal of the paper is to identify the specific issues that need to be resolved before large-scale scientific applications can make use of DBMS products. This topic is addressed in the context of an evaluation of commercial DBMS technology applied to the exploration of data generated by the Department of Energy`s Accelerated Strategic Computing Initiative (ASCI). The paper describes the data being generated for ASCI as well as current capabilities for interacting with and exploring this data. The attraction of applying standard DBMS technology to this domain is discussed, as well as the technical and business issues that currently make this an infeasible solution.

  4. Introducing Large-Scale Innovation in Schools

    NASA Astrophysics Data System (ADS)

    Sotiriou, Sofoklis; Riviou, Katherina; Cherouvis, Stephanos; Chelioti, Eleni; Bogner, Franz X.

    2016-08-01

    Education reform initiatives tend to promise higher effectiveness in classrooms especially when emphasis is given to e-learning and digital resources. Practical changes in classroom realities or school organization, however, are lacking. A major European initiative entitled Open Discovery Space (ODS) examined the challenge of modernizing school education via a large-scale implementation of an open-scale methodology in using technology-supported innovation. The present paper describes this innovation scheme which involved schools and teachers all over Europe, embedded technology-enhanced learning into wider school environments and provided training to teachers. Our implementation scheme consisted of three phases: (1) stimulating interest, (2) incorporating the innovation into school settings and (3) accelerating the implementation of the innovation. The scheme's impact was monitored for a school year using five indicators: leadership and vision building, ICT in the curriculum, development of ICT culture, professional development support, and school resources and infrastructure. Based on about 400 schools, our study produced four results: (1) The growth in digital maturity was substantial, even for previously high scoring schools. This was even more important for indicators such as vision and leadership" and "professional development." (2) The evolution of networking is presented graphically, showing the gradual growth of connections achieved. (3) These communities became core nodes, involving numerous teachers in sharing educational content and experiences: One out of three registered users (36 %) has shared his/her educational resources in at least one community. (4) Satisfaction scores ranged from 76 % (offer of useful support through teacher academies) to 87 % (good environment to exchange best practices). Initiatives such as ODS add substantial value to schools on a large scale.

  5. Large-scale sequential quadratic programming algorithms

    SciTech Connect

    Eldersveld, S.K.

    1992-09-01

    The problem addressed is the general nonlinear programming problem: finding a local minimizer for a nonlinear function subject to a mixture of nonlinear equality and inequality constraints. The methods studied are in the class of sequential quadratic programming (SQP) algorithms, which have previously proved successful for problems of moderate size. Our goal is to devise an SQP algorithm that is applicable to large-scale optimization problems, using sparse data structures and storing less curvature information but maintaining the property of superlinear convergence. The main features are: 1. The use of a quasi-Newton approximation to the reduced Hessian of the Lagrangian function. Only an estimate of the reduced Hessian matrix is required by our algorithm. The impact of not having available the full Hessian approximation is studied and alternative estimates are constructed. 2. The use of a transformation matrix Q. This allows the QP gradient to be computed easily when only the reduced Hessian approximation is maintained. 3. The use of a reduced-gradient form of the basis for the null space of the working set. This choice of basis is more practical than an orthogonal null-space basis for large-scale problems. The continuity condition for this choice is proven. 4. The use of incomplete solutions of quadratic programming subproblems. Certain iterates generated by an active-set method for the QP subproblem are used in place of the QP minimizer to define the search direction for the nonlinear problem. An implementation of the new algorithm has been obtained by modifying the code MINOS. Results and comparisons with MINOS and NPSOL are given for the new algorithm on a set of 92 test problems.

  6. Chemical TOPAZ: Modifications to the heat transfer code TOPAZ: The addition of chemical reaction kinetics and chemical mixtures

    SciTech Connect

    Nichols, A.L. III.

    1990-06-07

    This is a report describing the modifications which have been made to the heat flow code TOPAZ to allow the inclusion of thermally controlled chemical kinetics. This report is broken into parts. The first part is an introduction to the general assumptions and theoretical underpinning that were used to develop the model. The second section describes the changes that have been implemented into the code. The third section is the users manual for the input for the code. The fourth section is a compilation of hints, common errors, and things to be aware of while you are getting started. The fifth section gives a sample problem using the new code. This manual addenda is written with the presumption that most readers are not fluent with chemical concepts. Therefore, we shall in this section endeavor to describe the requirements that must be met before chemistry can occur and how we have modeled the chemistry in the code.

  7. Automated Sequence Preprocessing in a Large-Scale Sequencing Environment

    PubMed Central

    Wendl, Michael C.; Dear, Simon; Hodgson, Dave; Hillier, LaDeana

    1998-01-01

    A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is ∼100,000 sequencing reads per week. PMID:9750196

  8. Chemical Modifications that Affect Nutritional and Functional Properties of Proteins.

    ERIC Educational Resources Information Center

    Richardson, T.; Kester, J. J.

    1984-01-01

    Discusses chemical alterations of selected amino acids resulting from environmental effects (photooxidations, pH extremes, thermally induced effects). Also dicusses use of intentional chemical derivatizations of various functional groups in amino acid residue side chains and how recombinant DNA techniques might be useful in structure/function…

  9. Chemical modification of the tryptophan residue in adrenocorticotropin.

    PubMed

    Canova-Davis, E; Ramachandran, J

    1976-02-24

    The single tryptophan residue in the pituitary hormone adrenocorticotropin was modified selectively by reaction with a variety of substituted o-nitrophenylsulfenyl chlorides. In addition to quantitative modification of the tryptophan residue, the reaction invariably resulted in partial oxidation of the methionine residue to the sulfoxide. The methionine sulfoxide derivative could be separated from the desired product by partition chromatography on Sephadex G-50 in the solvent system 1-butanol-pyridine-0.1% acetic acid (5:3:11). Thus, the 2,4-dinitrophenylsulfenyl, 2-nitro-4-carboxyphenylsulfenyl, and 2-nitro-4-carbamidophenylsulfenyl derivatives of adrenocorticotropin were prepared and characterized. Modifications in the isolation of adrenocorticotropin from ovine pituitaries are also described. The melanocyte stimulating activities of the native hormone and the analogues are discussed.

  10. Importance of the Small-Scale Processes Melting, Plate Boundary Formation and Mineralogy on the Large-Scale, Long-Term Thermo-Chemical Evolution of Earth's Mantle-Plate System

    NASA Astrophysics Data System (ADS)

    Tackley, P.

    2015-12-01

    Seismic observations of the deep Earth reveal the presence of two large low shear velocity provinces (LLSVPs) that are typically inferred to be dense chemically-distinct material, as well as discontinuities that are typically linked to the post-perovskite (pPv) phase transition. Several possible origins of chemically-dense material have been proposed, including recycling of mid-ocean ridge basalt (MORB), primordial differentiation events, crystallisation of a basal magma ocean, or some combination of these creating a basal melange (BAM; Tackley 2012 Earth Sci. Rev.). Each of these possibilities would result in a different composition hence different mineralogy. In order to constrain this we have been running calculations of thermo-chemical mantle evolution over 4.5 billion years that include melting-induced differentiation, plate tectonics induced by strongly temperature-dependent viscosity and plastic yielding, core cooling and compressibility with reasonable assumptions about the pressure-dependence of other material properties. Some of our simulations start from a magma ocean state so initial layering is developed self-consistently. Already-published results (Nakagawa et al., 2009 GCubed, 2010 PEPI, 2012 GCubed) already indicate the importance of exact MORB composition on the amount of MORB segregating above the CMB, which in turn influences mantle thermal structure and the evolution of the core and geodynamo. In more recent results we have been additionally including primordial material. We find that melting-induced differentiation has several first-order effects on the dynamics, including (i) making plate tectonics easier (through stresses associated with lateral variations in crustal thickness) and (ii) reducing heat flux through the CMB (due to the build-up of dense material above the CMB); also (iii) tectonic mode (continuous plate tectonics, episodic lid or stagnant lid) also makes a first-order difference to mantle structure and dynamics. This emphasises

  11. Towards large-scale plasma-assisted synthesis of nanowires

    NASA Astrophysics Data System (ADS)

    Cvelbar, U.

    2011-05-01

    Large quantities of nanomaterials, e.g. nanowires (NWs), are needed to overcome the high market price of nanomaterials and make nanotechnology widely available for general public use and applications to numerous devices. Therefore, there is an enormous need for new methods or routes for synthesis of those nanostructures. Here plasma technologies for synthesis of NWs, nanotubes, nanoparticles or other nanostructures might play a key role in the near future. This paper presents a three-dimensional problem of large-scale synthesis connected with the time, quantity and quality of nanostructures. Herein, four different plasma methods for NW synthesis are presented in contrast to other methods, e.g. thermal processes, chemical vapour deposition or wet chemical processes. The pros and cons are discussed in detail for the case of two metal oxides: iron oxide and zinc oxide NWs, which are important for many applications.

  12. Large-scale self-assembled epitaxial growth of highly-ordered three-dimensional micro/nano single-crystalline PbSe pyramid arrays by selective chemical bath deposition

    NASA Astrophysics Data System (ADS)

    Qiu, Jijun; Weng, Binbin; Li, Lin; Li, Xiaomin; Shi, Zhisheng

    2015-05-01

    Highly ordered three-dimensional micro- and nano- PbSe pyramid arrays were synthesized by using selective epitaxial self-assembled chemical bath deposition method. Each pyramid consists of a very sharp (111) tip with six smooth equivalent {100} facets. Every (100) facet forms an angle of about 54.7° with respect to the (111) facet. The structural features including pyramidal size and period could be precisely tailored by pre-patterned Au mask and etching time. Pyramids are self-assembled on the confined positions by the dual functions of one-dimensional and two-dimensional oriented attachment mechanisms along [110] directions on the (111) surface, following the Gibbs-Curie-Wulff minimum energy principle. This method could effectively create large, bottom-up 3D pyramidal surface patterns in a cost-effective and time-saving manner, which has potential applications in infrared photoconductors, solar cells and light emitting enhancement for display, etc.

  13. Large-scale wind turbine structures

    NASA Technical Reports Server (NTRS)

    Spera, David A.

    1988-01-01

    The purpose of this presentation is to show how structural technology was applied in the design of modern wind turbines, which were recently brought to an advanced stage of development as sources of renewable power. Wind turbine structures present many difficult problems because they are relatively slender and flexible; subject to vibration and aeroelastic instabilities; acted upon by loads which are often nondeterministic; operated continuously with little maintenance in all weather; and dominated by life-cycle cost considerations. Progress in horizontal-axis wind turbines (HAWT) development was paced by progress in the understanding of structural loads, modeling of structural dynamic response, and designing of innovative structural response. During the past 15 years a series of large HAWTs was developed. This has culminated in the recent completion of the world's largest operating wind turbine, the 3.2 MW Mod-5B power plane installed on the island of Oahu, Hawaii. Some of the applications of structures technology to wind turbine will be illustrated by referring to the Mod-5B design. First, a video overview will be presented to provide familiarization with the Mod-5B project and the important components of the wind turbine system. Next, the structural requirements for large-scale wind turbines will be discussed, emphasizing the difficult fatigue-life requirements. Finally, the procedures used to design the structure will be presented, including the use of the fracture mechanics approach for determining allowable fatigue stresses.

  14. Large-scale tides in general relativity

    NASA Astrophysics Data System (ADS)

    Ip, Hiu Yan; Schmidt, Fabian

    2017-02-01

    Density perturbations in cosmology, i.e. spherically symmetric adiabatic perturbations of a Friedmann-Lemaȋtre-Robertson-Walker (FLRW) spacetime, are locally exactly equivalent to a different FLRW solution, as long as their wavelength is much larger than the sound horizon of all fluid components. This fact is known as the "separate universe" paradigm. However, no such relation is known for anisotropic adiabatic perturbations, which correspond to an FLRW spacetime with large-scale tidal fields. Here, we provide a closed, fully relativistic set of evolutionary equations for the nonlinear evolution of such modes, based on the conformal Fermi (CFC) frame. We show explicitly that the tidal effects are encoded by the Weyl tensor, and are hence entirely different from an anisotropic Bianchi I spacetime, where the anisotropy is sourced by the Ricci tensor. In order to close the system, certain higher derivative terms have to be dropped. We show that this approximation is equivalent to the local tidal approximation of Hui and Bertschinger [1]. We also show that this very simple set of equations matches the exact evolution of the density field at second order, but fails at third and higher order. This provides a useful, easy-to-use framework for computing the fully relativistic growth of structure at second order.

  15. Large-scale autostereoscopic outdoor display

    NASA Astrophysics Data System (ADS)

    Reitterer, Jörg; Fidler, Franz; Saint Julien-Wallsee, Ferdinand; Schmid, Gerhard; Gartner, Wolfgang; Leeb, Walter; Schmid, Ulrich

    2013-03-01

    State-of-the-art autostereoscopic displays are often limited in size, effective brightness, number of 3D viewing zones, and maximum 3D viewing distances, all of which are mandatory requirements for large-scale outdoor displays. Conventional autostereoscopic indoor concepts like lenticular lenses or parallax barriers cannot simply be adapted for these screens due to the inherent loss of effective resolution and brightness, which would reduce both image quality and sunlight readability. We have developed a modular autostereoscopic multi-view laser display concept with sunlight readable effective brightness, theoretically up to several thousand 3D viewing zones, and maximum 3D viewing distances of up to 60 meters. For proof-of-concept purposes a prototype display with two pixels was realized. Due to various manufacturing tolerances each individual pixel has slightly different optical properties, and hence the 3D image quality of the display has to be calculated stochastically. In this paper we present the corresponding stochastic model, we evaluate the simulation and measurement results of the prototype display, and we calculate the achievable autostereoscopic image quality to be expected for our concept.

  16. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  17. Food appropriation through large scale land acquisitions

    NASA Astrophysics Data System (ADS)

    Rulli, Maria Cristina; D'Odorico, Paolo

    2014-05-01

    The increasing demand for agricultural products and the uncertainty of international food markets has recently drawn the attention of governments and agribusiness firms toward investments in productive agricultural land, mostly in the developing world. The targeted countries are typically located in regions that have remained only marginally utilized because of lack of modern technology. It is expected that in the long run large scale land acquisitions (LSLAs) for commercial farming will bring the technology required to close the existing crops yield gaps. While the extent of the acquired land and the associated appropriation of freshwater resources have been investigated in detail, the amount of food this land can produce and the number of people it could feed still need to be quantified. Here we use a unique dataset of land deals to provide a global quantitative assessment of the rates of crop and food appropriation potentially associated with LSLAs. We show how up to 300-550 million people could be fed by crops grown in the acquired land, should these investments in agriculture improve crop production and close the yield gap. In contrast, about 190-370 million people could be supported by this land without closing of the yield gap. These numbers raise some concern because the food produced in the acquired land is typically exported to other regions, while the target countries exhibit high levels of malnourishment. Conversely, if used for domestic consumption, the crops harvested in the acquired land could ensure food security to the local populations.

  18. Large scale mechanical metamaterials as seismic shields

    NASA Astrophysics Data System (ADS)

    Miniaci, Marco; Krushynska, Anastasiia; Bosia, Federico; Pugno, Nicola M.

    2016-08-01

    Earthquakes represent one of the most catastrophic natural events affecting mankind. At present, a universally accepted risk mitigation strategy for seismic events remains to be proposed. Most approaches are based on vibration isolation of structures rather than on the remote shielding of incoming waves. In this work, we propose a novel approach to the problem and discuss the feasibility of a passive isolation strategy for seismic waves based on large-scale mechanical metamaterials, including for the first time numerical analysis of both surface and guided waves, soil dissipation effects, and adopting a full 3D simulations. The study focuses on realistic structures that can be effective in frequency ranges of interest for seismic waves, and optimal design criteria are provided, exploring different metamaterial configurations, combining phononic crystals and locally resonant structures and different ranges of mechanical properties. Dispersion analysis and full-scale 3D transient wave transmission simulations are carried out on finite size systems to assess the seismic wave amplitude attenuation in realistic conditions. Results reveal that both surface and bulk seismic waves can be considerably attenuated, making this strategy viable for the protection of civil structures against seismic risk. The proposed remote shielding approach could open up new perspectives in the field of seismology and in related areas of low-frequency vibration damping or blast protection.

  19. Large-scale carbon fiber tests

    NASA Technical Reports Server (NTRS)

    Pride, R. A.

    1980-01-01

    A realistic release of carbon fibers was established by burning a minimum of 45 kg of carbon fiber composite aircraft structural components in each of five large scale, outdoor aviation jet fuel fire tests. This release was quantified by several independent assessments with various instruments developed specifically for these tests. The most likely values for the mass of single carbon fibers released ranged from 0.2 percent of the initial mass of carbon fiber for the source tests (zero wind velocity) to a maximum of 0.6 percent of the initial carbon fiber mass for dissemination tests (5 to 6 m/s wind velocity). Mean fiber lengths for fibers greater than 1 mm in length ranged from 2.5 to 3.5 mm. Mean diameters ranged from 3.6 to 5.3 micrometers which was indicative of significant oxidation. Footprints of downwind dissemination of the fire released fibers were measured to 19.1 km from the fire.

  20. The Modification of Biocellular Chemical Reactions by Environmental Physicochemicals

    NASA Astrophysics Data System (ADS)

    Ishido, M.

    Environmental risk factors affect human biological system to different extent from modification of biochemical reaction to cellular catastrophe. There are considerable public concerns about electromagnetic fields and endocrine disruptors. Their risk assessments have not been fully achieved because of their scientific uncertainty: electromagnetic fields just modify the bioreaction in the restricted cells and endocrine disruptors are quite unique in that their expression is dependent on the exposure periods throughout a life. Thus, we here describe their molecular characterization to establish the new risk assessments for environmental physicochemicals.

  1. Excimer laser induced surface chemical modification of polytetrafluoroethylene

    NASA Astrophysics Data System (ADS)

    Révész, K.; Hopp, B.; Bor, Z.

    1997-02-01

    Polytetrafluoroethylene has a notoriously non adhesive and non reactive character. Its successful surface photochemical modification was performed by irradiating the polytetrafluoroethylene/liquid triethylamine interface with an ArF excimer laser (λ=193 nm). Due to the photochemical treatment the polytetrafluoroethylene surface became more hydrophilic. The water receding contact angle decreased from 94° to 43°. The reaction cross section was determined from the decrease of the contact angles. It was found to be as high as 6.4×10-18 cm2. XPS measurements evidenced the removal of fluorine from the polytetrafluoroethylene, incorporation of alkyl carbon and nitrogen. Photochemical dissociation path of the triethylamine makes probable that it bonded to the fluoropolymer backbone via the α-carbon atom of an ethyl group. A radical, or a photoinduced electron transfer mechanism was suggested to describe this reaction. A selective area electroless plating of silver was performed after pretreating the sample with patterned photomodification. The increased adhesion of the sample was proved by gluing with epoxy resin. As a result of the surface modification the tensile strength of gluing increased by 210× and reached 24% of the value characteristic for the bulk material.

  2. Chemical reporter for visualizing metabolic cross-talk between carbohydrate metabolism and protein modification.

    PubMed

    Zaro, Balyn W; Chuh, Kelly N; Pratt, Matthew R

    2014-09-19

    Metabolic chemical reporters have been largely used to study posttranslational modifications. Generally, it was assumed that these reporters entered one biosynthetic pathway, resulting in labeling of one type of modification. However, because they are metabolized by cells before their addition onto proteins, metabolic chemical reporters potentially provide a unique opportunity to read-out on both modifications of interest and cellular metabolism. We report here the development of a metabolic chemical reporter 1-deoxy-N-pentynyl glucosamine (1-deoxy-GlcNAlk). This small-molecule cannot be incorporated into glycans; however, treatment of mammalian cells results in labeling of a variety proteins and enables their visualization and identification. Competition of this labeling with sodium acetate and an acetyltransferase inhibitor suggests that 1-deoxy-GlcNAlk can enter the protein acetylation pathway. These results demonstrate that metabolic chemical reporters have the potential to isolate and potentially discover cross-talk between metabolic pathways in living cells.

  3. Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples

    PubMed Central

    2010-01-01

    Exposure to a variety of toxins and/or infectious agents leads to disease, degeneration and death, often characterised by circumstances in which cells or tissues do not merely die and cease to function but may be more or less entirely obliterated. It is then legitimate to ask the question as to whether, despite the many kinds of agent involved, there may be at least some unifying mechanisms of such cell death and destruction. I summarise the evidence that in a great many cases, one underlying mechanism, providing major stresses of this type, entails continuing and autocatalytic production (based on positive feedback mechanisms) of hydroxyl radicals via Fenton chemistry involving poorly liganded iron, leading to cell death via apoptosis (probably including via pathways induced by changes in the NF-κB system). While every pathway is in some sense connected to every other one, I highlight the literature evidence suggesting that the degenerative effects of many diseases and toxicological insults converge on iron dysregulation. This highlights specifically the role of iron metabolism, and the detailed speciation of iron, in chemical and other toxicology, and has significant implications for the use of iron chelating substances (probably in partnership with appropriate anti-oxidants) as nutritional or therapeutic agents in inhibiting both the progression of these mainly degenerative diseases and the sequelae of both chronic and acute toxin exposure. The complexity of biochemical networks, especially those involving autocatalytic behaviour and positive feedbacks, means that multiple interventions (e.g. of iron chelators plus antioxidants) are likely to prove most effective. A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions. PMID:20967426

  4. Towards large scale production and separation of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Alvarez, Noe T.

    Since their discovery, carbon nanotubes (CNTs) have boosted the research and applications of nanotechnology; however, many applications of CNTs are inaccessible because they depend upon large-scale CNT production and separations. Type, chirality and diameter control of CNTs determine many of their physical properties, and such control is still not accesible. This thesis studies the fundamentals for scalable selective reactions of HiPCo CNTs as well as the early phase of routes to an inexpensive approach for large-scale CNT production. In the growth part, this thesis covers a complete wet-chemistry process of catalyst and catalyst support deposition for growth of vertically aligned (VA) CNTs. A wet-chemistry preparation process has significant importance for CNT synthesis through chemical vapor deposition (CVD). CVD is by far, the most suitable and inexpensive process for large-scale CNT production when compared to other common processes such as laser ablation and arc discharge. However, its potential has been limited by low-yielding and difficult preparation processes of catalyst and its support, therefore its competitiveness has been reduced. The wet-chemistry process takes advantage of current nanoparticle technology to deposit the catalyst and the catalyst support as a thin film of nanoparticles, making the protocol simple compared to electron beam evaporation and sputtering processes. In the CNT selective reactions part, this thesis studies UV irradiation of individually dispersed HiPCo CNTs that generates auto-selective reactions in the liquid phase with good control over their diameter and chirality. This technique is ideal for large-scale and continuous-process of separations of CNTs by diameter and type. Additionally, an innovative simple catalyst deposition through abrasion is demonstrated. Simple friction between the catalyst and the substrates deposit a high enough density of metal catalyst particles for successful CNT growth. This simple approach has

  5. Tyrosine-Specific Chemical Modification with in Situ Hemin-Activated Luminol Derivatives.

    PubMed

    Sato, Shinichi; Nakamura, Kosuke; Nakamura, Hiroyuki

    2015-11-20

    Tyrosine-specific chemical modification was achieved using in situ hemin-activated luminol derivatives. Tyrosine residues in peptide and protein were modified effectively with N-methylated luminol derivatives under oxidative conditions in the presence of hemin and H2O2. Both single and double modifications of the tyrosine residue occurred in the reaction of angiotensin II with N-methylated luminol derivative 9. Tyrosine-specific chemical modification of the model protein bovine serum albumin (BSA) revealed that the surface-exposed tyrosine residues were selectively modified with 9. We succeeded in the functionalization of several proteins using azide-conjugated compound 18 using alkyne-conjugated probes by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) or dibenzocyclooctyne (DBCO)-mediated copper-free click chemistry. This tyrosine-specific modification was orthogonal to conventional lysine modification by N-hydroxysuccinimide (NHS) ester, and dual functionalization by fluorescence modification of tyrosine residues and PEG modification of lysine residues was achieved without affecting the modification efficiency.

  6. Sensitivity technologies for large scale simulation.

    SciTech Connect

    Collis, Samuel Scott; Bartlett, Roscoe Ainsworth; Smith, Thomas Michael; Heinkenschloss, Matthias; Wilcox, Lucas C.; Hill, Judith C.; Ghattas, Omar; Berggren, Martin Olof; Akcelik, Volkan; Ober, Curtis Curry; van Bloemen Waanders, Bart Gustaaf; Keiter, Eric Richard

    2005-01-01

    Sensitivity analysis is critically important to numerous analysis algorithms, including large scale optimization, uncertainty quantification,reduced order modeling, and error estimation. Our research focused on developing tools, algorithms and standard interfaces to facilitate the implementation of sensitivity type analysis into existing code and equally important, the work was focused on ways to increase the visibility of sensitivity analysis. We attempt to accomplish the first objective through the development of hybrid automatic differentiation tools, standard linear algebra interfaces for numerical algorithms, time domain decomposition algorithms and two level Newton methods. We attempt to accomplish the second goal by presenting the results of several case studies in which direct sensitivities and adjoint methods have been effectively applied, in addition to an investigation of h-p adaptivity using adjoint based a posteriori error estimation. A mathematical overview is provided of direct sensitivities and adjoint methods for both steady state and transient simulations. Two case studies are presented to demonstrate the utility of these methods. A direct sensitivity method is implemented to solve a source inversion problem for steady state internal flows subject to convection diffusion. Real time performance is achieved using novel decomposition into offline and online calculations. Adjoint methods are used to reconstruct initial conditions of a contamination event in an external flow. We demonstrate an adjoint based transient solution. In addition, we investigated time domain decomposition algorithms in an attempt to improve the efficiency of transient simulations. Because derivative calculations are at the root of sensitivity calculations, we have developed hybrid automatic differentiation methods and implemented this approach for shape optimization for gas dynamics using the Euler equations. The hybrid automatic differentiation method was applied to a first

  7. Knocking down highly-ordered large-scale nanowire arrays.

    PubMed

    Pevzner, Alexander; Engel, Yoni; Elnathan, Roey; Ducobni, Tamir; Ben-Ishai, Moshit; Reddy, Koteeswara; Shpaisman, Nava; Tsukernik, Alexander; Oksman, Mark; Patolsky, Fernando

    2010-04-14

    The large-scale assembly of nanowire elements with controlled and uniform orientation and density at spatially well-defined locations on solid substrates presents one of the most significant challenges facing their integration in real-world electronic applications. Here, we present the universal "knocking-down" approach, based on the controlled in-place planarization of nanowire elements, for the formation of large-scale ordered nanowire arrays. The controlled planarization of the nanowires is achieved by the use of an appropriate elastomer-covered rigid-roller device. After being knocked down, each nanowire in the array can be easily addressed electrically, by a simple single photolithographic step, to yield a large number of nanoelectrical devices with an unprecedented high-fidelity rate. The approach allows controlling, in only two simple steps, all possible array parameters, that is, nanowire dimensions, chemical composition, orientation, and density. The resulting knocked-down arrays can be further used for the creation of massive nanoelectronic-device arrays. More than million devices were already fabricated with yields over 98% on substrate areas of up, but not limited to, to 10 cm(2).

  8. Large Scale Flame Spread Environmental Characterization Testing

    NASA Technical Reports Server (NTRS)

    Clayman, Lauren K.; Olson, Sandra L.; Gokoghi, Suleyman A.; Brooker, John E.; Ferkul, Paul V.; Kacher, Henry F.

    2013-01-01

    Under the Advanced Exploration Systems (AES) Spacecraft Fire Safety Demonstration Project (SFSDP), as a risk mitigation activity in support of the development of a large-scale fire demonstration experiment in microgravity, flame-spread tests were conducted in normal gravity on thin, cellulose-based fuels in a sealed chamber. The primary objective of the tests was to measure pressure rise in a chamber as sample material, burning direction (upward/downward), total heat release, heat release rate, and heat loss mechanisms were varied between tests. A Design of Experiments (DOE) method was imposed to produce an array of tests from a fixed set of constraints and a coupled response model was developed. Supplementary tests were run without experimental design to additionally vary select parameters such as initial chamber pressure. The starting chamber pressure for each test was set below atmospheric to prevent chamber overpressure. Bottom ignition, or upward propagating burns, produced rapid acceleratory turbulent flame spread. Pressure rise in the chamber increases as the amount of fuel burned increases mainly because of the larger amount of heat generation and, to a much smaller extent, due to the increase in gaseous number of moles. Top ignition, or downward propagating burns, produced a steady flame spread with a very small flat flame across the burning edge. Steady-state pressure is achieved during downward flame spread as the pressure rises and plateaus. This indicates that the heat generation by the flame matches the heat loss to surroundings during the longer, slower downward burns. One heat loss mechanism included mounting a heat exchanger directly above the burning sample in the path of the plume to act as a heat sink and more efficiently dissipate the heat due to the combustion event. This proved an effective means for chamber overpressure mitigation for those tests producing the most total heat release and thusly was determined to be a feasible mitigation

  9. Chemical modification of corn fiber with ion-exchanging groups

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pretreated corn fiber was chemically modified with quaternary ammonium group or/and sulfonated with 3-chloro-2-hydroxypropanesulfonic acid under vacuum or at ambient pressure. The soluble fraction was dialyzed through 1 kDa MWCO dialysis tubing and the material retained inside the tubing was filtere...

  10. Synchronization of coupled large-scale Boolean networks

    NASA Astrophysics Data System (ADS)

    Li, Fangfei

    2014-03-01

    This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.

  11. Synchronization of coupled large-scale Boolean networks

    SciTech Connect

    Li, Fangfei

    2014-03-15

    This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.

  12. Conjugate gradient methods with sufficient descent condition for large-scale unconstrained optimization

    NASA Astrophysics Data System (ADS)

    Ling, Mei Mei; Leong, Wah June

    2014-12-01

    In this paper, we make a modification to the standard conjugate gradient method so that its search direction satisfies the sufficient descent condition. We prove that the modified conjugate gradient method is globally convergent under Armijo line search. Numerical results show that the proposed conjugate gradient method is efficient compared to some of its standard counterparts for large-scale unconstrained optimization.

  13. Interaction of a cumulus cloud ensemble with the large-scale environment

    NASA Technical Reports Server (NTRS)

    Arakawa, A.; Schubert, W.

    1973-01-01

    Large-scale modification of the environment by cumulus clouds is discussed in terms of entrainment, detrainment, evaporation, and subsidence. Drying, warming, and condensation by vertical displacement of air are considered as well as budget equations for mass, static energy, water vapor, and liquid water.

  14. Large-Scale Graphene Film Deposition for Monolithic Device Fabrication

    NASA Astrophysics Data System (ADS)

    Al-shurman, Khaled

    Since 1958, the concept of integrated circuit (IC) has achieved great technological developments and helped in shrinking electronic devices. Nowadays, an IC consists of more than a million of compacted transistors. The majority of current ICs use silicon as a semiconductor material. According to Moore's law, the number of transistors built-in on a microchip can be double every two years. However, silicon device manufacturing reaches its physical limits. To explain, there is a new trend to shrinking circuitry to seven nanometers where a lot of unknown quantum effects such as tunneling effect can not be controlled. Hence, there is an urgent need for a new platform material to replace Si. Graphene is considered a promising material with enormous potential applications in many electronic and optoelectronics devices due to its superior properties. There are several techniques to produce graphene films. Among these techniques, chemical vapor deposition (CVD) offers a very convenient method to fabricate films for large-scale graphene films. Though CVD method is suitable for large area growth of graphene, the need for transferring a graphene film to silicon-based substrates is required. Furthermore, the graphene films thus achieved are, in fact, not single crystalline. Also, graphene fabrication utilizing Cu and Ni at high growth temperature contaminates the substrate that holds Si CMOS circuitry and CVD chamber as well. So, lowering the deposition temperature is another technological milestone for the successful adoption of graphene in integrated circuits fabrication. In this research, direct large-scale graphene film fabrication on silicon based platform (i.e. SiO2 and Si3N4) at low temperature was achieved. With a focus on low-temperature graphene growth, hot-filament chemical vapor deposition (HF-CVD) was utilized to synthesize graphene film using 200 nm thick nickel film. Raman spectroscopy was utilized to examine graphene formation on the bottom side of the Ni film

  15. Large-Scale Spacecraft Fire Safety Tests

    NASA Technical Reports Server (NTRS)

    Urban, David; Ruff, Gary A.; Ferkul, Paul V.; Olson, Sandra; Fernandez-Pello, A. Carlos; T'ien, James S.; Torero, Jose L.; Cowlard, Adam J.; Rouvreau, Sebastien; Minster, Olivier; Toth, Balazs; Legros, Guillaume; Eigenbrod, Christian; Smirnov, Nickolay; Fujita, Osamu; Jomaas, Grunde

    2014-01-01

    An international collaborative program is underway to address open issues in spacecraft fire safety. Because of limited access to long-term low-gravity conditions and the small volume generally allotted for these experiments, there have been relatively few experiments that directly study spacecraft fire safety under low-gravity conditions. Furthermore, none of these experiments have studied sample sizes and environment conditions typical of those expected in a spacecraft fire. The major constraint has been the size of the sample, with prior experiments limited to samples of the order of 10 cm in length and width or smaller. This lack of experimental data forces spacecraft designers to base their designs and safety precautions on 1-g understanding of flame spread, fire detection, and suppression. However, low-gravity combustion research has demonstrated substantial differences in flame behavior in low-gravity. This, combined with the differences caused by the confined spacecraft environment, necessitates practical scale spacecraft fire safety research to mitigate risks for future space missions. To address this issue, a large-scale spacecraft fire experiment is under development by NASA and an international team of investigators. This poster presents the objectives, status, and concept of this collaborative international project (Saffire). The project plan is to conduct fire safety experiments on three sequential flights of an unmanned ISS re-supply spacecraft (the Orbital Cygnus vehicle) after they have completed their delivery of cargo to the ISS and have begun their return journeys to earth. On two flights (Saffire-1 and Saffire-3), the experiment will consist of a flame spread test involving a meter-scale sample ignited in the pressurized volume of the spacecraft and allowed to burn to completion while measurements are made. On one of the flights (Saffire-2), 9 smaller (5 x 30 cm) samples will be tested to evaluate NASAs material flammability screening tests

  16. Nuclear-pumped lasers for large-scale applications

    SciTech Connect

    Anderson, R.E.; Leonard, E.M.; Shea, R.E.; Berggren, R.R.

    1988-01-01

    Efficient initiation of large-volume chemical lasers may be achieved by neutron induced reactions which produce charged particles in the final state. When a burst mode nuclear reactor is used as the neutron source, both a sufficiently intense neutron flux and a sufficient short initiation pulse may be possible. Proof-of-principle experiments are planned to demonstrate lasing in a direct nuclear-pumped large-volume system: to study the effects of various neutron absorbing materials on laser performance; to study the effects of long initiation pulse lengths; to determine the performance of large-scale optics and the beam quality that may bo obtained; and to assess the performance of alternative designs of burst systems that increase the neutron output and burst repetition rate. 21 refs., 7 figs., 5 tabs.

  17. A large-scale crop protection bioassay data set

    NASA Astrophysics Data System (ADS)

    Gaulton, Anna; Kale, Namrata; van Westen, Gerard J. P.; Bellis, Louisa J.; Bento, A. Patrícia; Davies, Mark; Hersey, Anne; Papadatos, George; Forster, Mark; Wege, Philip; Overington, John P.

    2015-07-01

    ChEMBL is a large-scale drug discovery database containing bioactivity information primarily extracted from scientific literature. Due to the medicinal chemistry focus of the journals from which data are extracted, the data are currently of most direct value in the field of human health research. However, many of the scientific use-cases for the current data set are equally applicable in other fields, such as crop protection research: for example, identification of chemical scaffolds active against a particular target or endpoint, the de-convolution of the potential targets of a phenotypic assay, or the potential targets/pathways for safety liabilities. In order to broaden the applicability of the ChEMBL database and allow more widespread use in crop protection research, an extensive data set of bioactivity data of insecticidal, fungicidal and herbicidal compounds and assays was collated and added to the database.

  18. A large-scale crop protection bioassay data set

    PubMed Central

    Gaulton, Anna; Kale, Namrata; van Westen, Gerard J. P.; Bellis, Louisa J.; Bento, A. Patrícia; Davies, Mark; Hersey, Anne; Papadatos, George; Forster, Mark; Wege, Philip; Overington, John P.

    2015-01-01

    ChEMBL is a large-scale drug discovery database containing bioactivity information primarily extracted from scientific literature. Due to the medicinal chemistry focus of the journals from which data are extracted, the data are currently of most direct value in the field of human health research. However, many of the scientific use-cases for the current data set are equally applicable in other fields, such as crop protection research: for example, identification of chemical scaffolds active against a particular target or endpoint, the de-convolution of the potential targets of a phenotypic assay, or the potential targets/pathways for safety liabilities. In order to broaden the applicability of the ChEMBL database and allow more widespread use in crop protection research, an extensive data set of bioactivity data of insecticidal, fungicidal and herbicidal compounds and assays was collated and added to the database. PMID:26175909

  19. A large-scale crop protection bioassay data set.

    PubMed

    Gaulton, Anna; Kale, Namrata; van Westen, Gerard J P; Bellis, Louisa J; Bento, A Patrícia; Davies, Mark; Hersey, Anne; Papadatos, George; Forster, Mark; Wege, Philip; Overington, John P

    2015-01-01

    ChEMBL is a large-scale drug discovery database containing bioactivity information primarily extracted from scientific literature. Due to the medicinal chemistry focus of the journals from which data are extracted, the data are currently of most direct value in the field of human health research. However, many of the scientific use-cases for the current data set are equally applicable in other fields, such as crop protection research: for example, identification of chemical scaffolds active against a particular target or endpoint, the de-convolution of the potential targets of a phenotypic assay, or the potential targets/pathways for safety liabilities. In order to broaden the applicability of the ChEMBL database and allow more widespread use in crop protection research, an extensive data set of bioactivity data of insecticidal, fungicidal and herbicidal compounds and assays was collated and added to the database.

  20. Method for chemical surface modification of fumed silica particles

    DOEpatents

    Grabbe, Alexis; Michalske, Terry Arthur; Smith, William Larry

    1999-01-01

    Dehydroxylated, silica-containing, glass surfaces are known to be at least partially terminated by strained siloxane rings. According to the invention, a surface of this kind is exposed to a selected silane compound or mixture of silane compounds under reaction-promoting conditions. The ensuing reaction results in opening of the strained siloxane rings, and termination of surface atoms by chemical species, such as organic or organosilicon species, having desirable properties. These species can be chosen to provide qualities such as hydrophobicity, or improved coupling to a polymeric coating.

  1. Method for chemical surface modification of fumed silica particles

    DOEpatents

    Grabbe, A.; Michalske, T.A.; Smith, W.L.

    1999-05-11

    Dehydroxylated, silica-containing, glass surfaces are known to be at least partially terminated by strained siloxane rings. According to the invention, a surface of this kind is exposed to a selected silane compound or mixture of silane compounds under reaction-promoting conditions. The ensuing reaction results in opening of the strained siloxane rings, and termination of surface atoms by chemical species, such as organic or organosilicon species, having desirable properties. These species can be chosen to provide qualities such as hydrophobicity, or improved coupling to a polymeric coating. 11 figs.

  2. Chemical Modification of Boron-Doped Diamond Electrodes for Applications to Biosensors and Biosensing.

    PubMed

    Svítková, Jana; Ignat, Teodora; Švorc, Ľubomír; Labuda, Ján; Barek, Jiří

    2016-05-03

    Boron-doped diamond (BDD) is a prospective electrode material that possesses many exceptional properties including wide potential window, low noise, low and stable background current, chemical and mechanical stability, good biocompatibility, and last but not least exceptional resistance to passivation. These characteristics extend its usability in various areas of electrochemistry as evidenced by increasing number of published articles over the past two decades. The idea of chemically modifying BDD electrodes with molecular species attached to the surface for the purpose of creating a rational design has found promising applications in the past few years. BDD electrodes have appeared to be excellent substrate materials for various chemical modifications and subsequent application to biosensors and biosensing. Hence, this article presents modification strategies that have extended applications of BDD electrodes in electroanalytical chemistry. Different methods and steps of surface modification of this electrode material for biosensing and construction of biosensors are discussed.

  3. In situ vitrification large-scale operational acceptance test analysis

    SciTech Connect

    Buelt, J.L.; Carter, J.G.

    1986-05-01

    A thermal treatment process is currently under study to provide possible enhancement of in-place stabilization of transuranic and chemically contaminated soil sites. The process is known as in situ vitrification (ISV). In situ vitrification is a remedial action process that destroys solid and liquid organic contaminants and incorporates radionuclides into a glass-like material that renders contaminants substantially less mobile and less likely to impact the environment. A large-scale operational acceptance test (LSOAT) was recently completed in which more than 180 t of vitrified soil were produced in each of three adjacent settings. The LSOAT demonstrated that the process conforms to the functional design criteria necessary for the large-scale radioactive test (LSRT) to be conducted following verification of the performance capabilities of the process. The energy requirements and vitrified block size, shape, and mass are sufficiently equivalent to those predicted by the ISV mathematical model to confirm its usefulness as a predictive tool. The LSOAT demonstrated an electrode replacement technique, which can be used if an electrode fails, and techniques have been identified to minimize air oxidation, thereby extending electrode life. A statistical analysis was employed during the LSOAT to identify graphite collars and an insulative surface as successful cold cap subsidence techniques. The LSOAT also showed that even under worst-case conditions, the off-gas system exceeds the flow requirements necessary to maintain a negative pressure on the hood covering the area being vitrified. The retention of simulated radionuclides and chemicals in the soil and off-gas system exceeds requirements so that projected emissions are one to two orders of magnitude below the maximum permissible concentrations of contaminants at the stack.

  4. Nanomaterials processing toward large-scale flexible/stretchable electronics

    NASA Astrophysics Data System (ADS)

    Takahashi, Toshitake

    In recent years, there has been tremendous progress in large-scale mechanically flexible electronics, where electrical components are fabricated on non-crystalline substrates such as plastics and glass. These devices are currently serving as the basis for various applications such as flat-panel displays, smart cards, and wearable electronics. In this thesis, a promising approach using chemically synthesized nanomaterials is explored to overcome various obstacles current technology faces in this field. Here, we use chemically synthesized semiconducting nanowires (NWs) including group IV (Si, Ge), III-V (InAs) and II-IV (CdS, CdSe) NWs, and semiconductor-enriched SWNTs (99 % purity), and developed reliable, controllable, and more importantly uniform assembly methods on 4-inch wafer-scale flexible substrates in the form of either parallel NW arrays or SWNT random networks, which act as the active components in thin film transistors (TFTs). Thusly obtained TFTs composed of nanomaterials show respectable electrical and optical properties such as 1) cut-off frequency, ft ~ 1 GHz and maximum frequency of oscillation, fmax ~ 1.8 GHz from InAs parallel NW array TFTs with channel length of ~ 1.5 μm, 2) photodetectors covering visible wavelengths (500-700 nm) using compositionally graded CdSxSe1-x (0 < x < 1) parallel NW arrays, and 3) carrier mobility of ~ 20 cm2/Vs, which is an order of magnitude larger than conventional TFT materials such as a-Si and organic semiconductors, without sacrificing current on/off ratio (Ion/Ioff ~ 104) from SWNT network TFTs. The capability to uniformly assemble nanomaterials over large-scale flexible substrates enables us to use them for more sophisticated applications. Artificial electronic skin (e-skin) is demonstrated by laminating pressure sensitive rubber on top of nanomaterial-based active matrix backplanes. Furthermore, an x-ray imaging device is also achieved by combining organic photodiodes with this backplane technology.

  5. Sheltering in buildings from large-scale outdoor releases

    SciTech Connect

    Chan, W.R.; Price, P.N.; Gadgil, A.J.

    2004-06-01

    Intentional or accidental large-scale airborne toxic release (e.g. terrorist attacks or industrial accidents) can cause severe harm to nearby communities. Under these circumstances, taking shelter in buildings can be an effective emergency response strategy. Some examples where shelter-in-place was successful at preventing injuries and casualties have been documented [1, 2]. As public education and preparedness are vital to ensure the success of an emergency response, many agencies have prepared documents advising the public on what to do during and after sheltering [3, 4, 5]. In this document, we will focus on the role buildings play in providing protection to occupants. The conclusions to this article are: (1) Under most circumstances, shelter-in-place is an effective response against large-scale outdoor releases. This is particularly true for release of short duration (a few hours or less) and chemicals that exhibit non-linear dose-response characteristics. (2) The building envelope not only restricts the outdoor-indoor air exchange, but can also filter some biological or even chemical agents. Once indoors, the toxic materials can deposit or sorb onto indoor surfaces. All these processes contribute to the effectiveness of shelter-in-place. (3) Tightening of building envelope and improved filtration can enhance the protection offered by buildings. Common mechanical ventilation system present in most commercial buildings, however, should be turned off and dampers closed when sheltering from an outdoor release. (4) After the passing of the outdoor plume, some residuals will remain indoors. It is therefore important to terminate shelter-in-place to minimize exposure to the toxic materials.

  6. Population generation for large-scale simulation

    NASA Astrophysics Data System (ADS)

    Hannon, Andrew C.; King, Gary; Morrison, Clayton; Galstyan, Aram; Cohen, Paul

    2005-05-01

    Computer simulation is used to research phenomena ranging from the structure of the space-time continuum to population genetics and future combat.1-3 Multi-agent simulations in particular are now commonplace in many fields.4, 5 By modeling populations whose complex behavior emerges from individual interactions, these simulations help to answer questions about effects where closed form solutions are difficult to solve or impossible to derive.6 To be useful, simulations must accurately model the relevant aspects of the underlying domain. In multi-agent simulation, this means that the modeling must include both the agents and their relationships. Typically, each agent can be modeled as a set of attributes drawn from various distributions (e.g., height, morale, intelligence and so forth). Though these can interact - for example, agent height is related to agent weight - they are usually independent. Modeling relations between agents, on the other hand, adds a new layer of complexity, and tools from graph theory and social network analysis are finding increasing application.7, 8 Recognizing the role and proper use of these techniques, however, remains the subject of ongoing research. We recently encountered these complexities while building large scale social simulations.9-11 One of these, the Hats Simulator, is designed to be a lightweight proxy for intelligence analysis problems. Hats models a "society in a box" consisting of many simple agents, called hats. Hats gets its name from the classic spaghetti western, in which the heroes and villains are known by the color of the hats they wear. The Hats society also has its heroes and villains, but the challenge is to identify which color hat they should be wearing based on how they behave. There are three types of hats: benign hats, known terrorists, and covert terrorists. Covert terrorists look just like benign hats but act like terrorists. Population structure can make covert hat identification significantly more

  7. Large-scale assembly of colloidal particles

    NASA Astrophysics Data System (ADS)

    Yang, Hongta

    This study reports a simple, roll-to-roll compatible coating technology for producing three-dimensional highly ordered colloidal crystal-polymer composites, colloidal crystals, and macroporous polymer membranes. A vertically beveled doctor blade is utilized to shear align silica microsphere-monomer suspensions to form large-area composites in a single step. The polymer matrix and the silica microspheres can be selectively removed to create colloidal crystals and self-standing macroporous polymer membranes. The thickness of the shear-aligned crystal is correlated with the viscosity of the colloidal suspension and the coating speed, and the correlations can be qualitatively explained by adapting the mechanisms developed for conventional doctor blade coating. Five important research topics related to the application of large-scale three-dimensional highly ordered macroporous films by doctor blade coating are covered in this study. The first topic describes the invention in large area and low cost color reflective displays. This invention is inspired by the heat pipe technology. The self-standing macroporous polymer films exhibit brilliant colors which originate from the Bragg diffractive of visible light form the three-dimensional highly ordered air cavities. The colors can be easily changed by tuning the size of the air cavities to cover the whole visible spectrum. When the air cavities are filled with a solvent which has the same refractive index as that of the polymer, the macroporous polymer films become completely transparent due to the index matching. When the solvent trapped in the cavities is evaporated by in-situ heating, the sample color changes back to brilliant color. This process is highly reversible and reproducible for thousands of cycles. The second topic reports the achievement of rapid and reversible vapor detection by using 3-D macroporous photonic crystals. Capillary condensation of a condensable vapor in the interconnected macropores leads to the

  8. Surface modified MXene Ti3C2 multilayers by aryl diazonium salts leading to large-scale delamination

    NASA Astrophysics Data System (ADS)

    Wang, Hongbing; Zhang, Jianfeng; Wu, Yuping; Huang, Huajie; Li, Gaiye; Zhang, Xin; Wang, Zhuyin

    2016-10-01

    Herein we report a simple and facile method to delaminate MXene Ti3C2 multilayers by the assistance of surface modification using aryl diazonium salts. The basic strategy involved the preparation of layered MAX Ti3AlC2 and the exfoliation of Ti3AlC2 into Ti3C2 multilayers, followed by Na+ intercalation and surface modification using sulfanilic acid diazonium salts. The resulting chemically grafted Ti3C2 flakes were characterized by Fourier transform infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS) to confirm the presence of the surface organic species. Ultraviolet-visible spectroscopy revealed that surface-modified MXene Ti3C2 sheets disperse well in water and the solutions obey Lambert-Beer's law. Scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD) were used to demonstrate the morphology and structure of delaminating MXene Ti3C2 flakes. The results indicated that chemical modification for MXene multilayers by aryl diazonium salts induced swelling that conversely weakened the bonds between MX layers, hence leading to large-scale delamination of multilayered MXene Ti3C2via mild sonication. Advantages of the present approach rely not only on the simplicity and efficiency of the delamination procedure but also on the grafting of aryl groups to MXene surfaces, highly suitable for further applications of the newly discovered two-dimensional materials.

  9. Chemical modification of porous silicon mirror for biosensing applications

    NASA Astrophysics Data System (ADS)

    Palestino Escobedo, G.; Legros, R.; de la Mora Mojica, B.; del Río Portilla, J. A.; Pérez López, J. E.; Gergely, C.

    2007-05-01

    Porous silicon (PSi) nanostructures have remarkable optical properties that can be used for biosensing applications. In this paper we report first on the fabrication of heavily doped p-type PSi with pore diameters in the range of 400-4000 nm. The nonspecific and specific binding of the Glucose Oxidase protein (GOX) was then studied onto the PSi mirrorlike substrate. Adsorption of GOX was tuned by the pH of the protein solution (pI = 4.2) depending of the surface charge. PSi matrixes were first stabilized by thermal oxidation and GOX adsorption was performed once directly on the oxidized PSi surface, and also on previously functionalized PSi surfaces. In the latter case the GOX was coupled to the PSi via the S-H group of the 3-(mercaptopropyl)trimethoxysilane (MPTS). The silane-GOX and GOX interactions on the PSi surface were monitored by the Fourier Transformed Infrared spectra that display characteristic bands of the linked molecules. The interference spectrum shows a large blue shift in the Fabry-Perot interference pattern caused by the change in the refractive index of the medium implying a decrease in the effective optical thickness. Quantitative analysis shows that chemically modified PSi samples admit approximately 24% of GOX. Activity assay proved that the protein preserves its catalyst properties under these adsorption conditions.

  10. Chemical Modification of the Multi-Target Neuroprotective Compound Fisetin

    PubMed Central

    Chiruta, Chandramouli; Schubert, David; Dargusch, Richard; Maher, Pamela

    2012-01-01

    Many factors are implicated in age-related CNS disorders making it unlikely that modulating only a single factor will provide effective treatment. Perhaps a better approach is to identify small molecules that have multiple biological activities relevant to the maintenance of brain function. Recently, we identified an orally active, neuroprotective and cognition-enhancing molecule, the flavonoid fisetin, that is effective in several animal models of CNS disorders. Fisetin has direct antioxidant activity and can also increase the intracellular levels of glutathione (GSH), the major endogenous antioxidant. In addition, fisetin has both neurotrophic and anti-inflammatory activity. However, its relatively high EC50 in cell based assays, low lipophilicity, high tPSA and poor bioavailability suggest that there is room for medicinal chemical improvement. Here we describe a multi-tiered approach to screening that has allowed us to identify fisetin derivatives with significantly enhanced activity in an in vitro neuroprotection model while at the same time maintaining other key activities. PMID:22192055

  11. A method of orbital analysis for large-scale first-principles simulations.

    PubMed

    Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke

    2014-06-28

    An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF4).

  12. A method of orbital analysis for large-scale first-principles simulations

    NASA Astrophysics Data System (ADS)

    Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke

    2014-06-01

    An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF4).

  13. High-throughput solution processing of large-scale graphene.

    PubMed

    Tung, Vincent C; Allen, Matthew J; Yang, Yang; Kaner, Richard B

    2009-01-01

    The electronic properties of graphene, such as high charge carrier concentrations and mobilities, make it a promising candidate for next-generation nanoelectronic devices. In particular, electrons and holes can undergo ballistic transport on the sub-micrometre scale in graphene and do not suffer from the scale limitations of current MOSFET technologies. However, it is still difficult to produce single-layer samples of graphene and bulk processing has not yet been achieved, despite strenuous efforts to develop a scalable production method. Here, we report a versatile solution-based process for the large-scale production of single-layer chemically converted graphene over the entire area of a silicon/SiO(2) wafer. By dispersing graphite oxide paper in pure hydrazine we were able to remove oxygen functionalities and restore the planar geometry of the single sheets. The chemically converted graphene sheets that were produced have the largest area reported to date (up to 20 x 40 microm), making them far easier to process. Field-effect devices have been fabricated by conventional photolithography, displaying currents that are three orders of magnitude higher than previously reported for chemically produced graphene. The size of these sheets enables a wide range of characterization techniques, including optical microscopy, scanning electron microscopy and atomic force microscopy, to be performed on the same specimen.

  14. High-throughput solution processing of large-scale graphene

    NASA Astrophysics Data System (ADS)

    Tung, Vincent C.; Allen, Matthew J.; Yang, Yang; Kaner, Richard B.

    2009-01-01

    The electronic properties of graphene, such as high charge carrier concentrations and mobilities, make it a promising candidate for next-generation nanoelectronic devices. In particular, electrons and holes can undergo ballistic transport on the sub-micrometre scale in graphene and do not suffer from the scale limitations of current MOSFET technologies. However, it is still difficult to produce single-layer samples of graphene and bulk processing has not yet been achieved, despite strenuous efforts to develop a scalable production method. Here, we report a versatile solution-based process for the large-scale production of single-layer chemically converted graphene over the entire area of a silicon/SiO2 wafer. By dispersing graphite oxide paper in pure hydrazine we were able to remove oxygen functionalities and restore the planar geometry of the single sheets. The chemically converted graphene sheets that were produced have the largest area reported to date (up to 20 × 40 µm), making them far easier to process. Field-effect devices have been fabricated by conventional photolithography, displaying currents that are three orders of magnitude higher than previously reported for chemically produced graphene. The size of these sheets enables a wide range of characterization techniques, including optical microscopy, scanning electron microscopy and atomic force microscopy, to be performed on the same specimen.

  15. Neutrino footprint in large scale structure

    NASA Astrophysics Data System (ADS)

    Garay, Carlos Peña; Verde, Licia; Jimenez, Raul

    2017-03-01

    Recent constrains on the sum of neutrino masses inferred by analyzing cosmological data, show that detecting a non-zero neutrino mass is within reach of forthcoming cosmological surveys. Such a measurement will imply a direct determination of the absolute neutrino mass scale. Physically, the measurement relies on constraining the shape of the matter power spectrum below the neutrino free streaming scale: massive neutrinos erase power at these scales. However, detection of a lack of small-scale power from cosmological data could also be due to a host of other effects. It is therefore of paramount importance to validate neutrinos as the source of power suppression at small scales. We show that, independent on hierarchy, neutrinos always show a footprint on large, linear scales; the exact location and properties are fully specified by the measured power suppression (an astrophysical measurement) and atmospheric neutrinos mass splitting (a neutrino oscillation experiment measurement). This feature cannot be easily mimicked by systematic uncertainties in the cosmological data analysis or modifications in the cosmological model. Therefore the measurement of such a feature, up to 1% relative change in the power spectrum for extreme differences in the mass eigenstates mass ratios, is a smoking gun for confirming the determination of the absolute neutrino mass scale from cosmological observations. It also demonstrates the synergy between astrophysics and particle physics experiments.

  16. Multitree Algorithms for Large-Scale Astrostatistics

    NASA Astrophysics Data System (ADS)

    March, William B.; Ozakin, Arkadas; Lee, Dongryeol; Riegel, Ryan; Gray, Alexander G.

    2012-03-01

    this number every week, resulting in billions of objects. At such scales, even linear-time analysis operations present challenges, particularly since statistical analyses are inherently interactive processes, requiring that computations complete within some reasonable human attention span. The quadratic (or worse) runtimes of straightforward implementations become quickly unbearable. Examples of applications. These analysis subroutines occur ubiquitously in astrostatistical work. We list just a few examples. The need to cross-match objects across different catalogs has led to various algorithms, which at some point perform an AllNN computation. 2-point and higher-order spatial correlations for the basis of spatial statistics, and are utilized in astronomy to compare the spatial structures of two datasets, such as an observed sample and a theoretical sample, for example, forming the basis for two-sample hypothesis testing. Friends-of-friends clustering is often used to identify halos in data from astrophysical simulations. Minimum spanning tree properties have also been proposed as statistics of large-scale structure. Comparison of the distributions of different kinds of objects requires accurate density estimation, for which KDE is the overall statistical method of choice. The prediction of redshifts from optical data requires accurate regression, for which kernel regression is a powerful method. The identification of objects of various types in astronomy, such as stars versus galaxies, requires accurate classification, for which KDA is a powerful method. Overview. In this chapter, we will briefly sketch the main ideas behind recent fast algorithms which achieve, for example, linear runtimes for pairwise-distance problems, or similarly dramatic reductions in computational growth. In some cases, the runtime orders for these algorithms are mathematically provable statements, while in others we have only conjectures backed by experimental observations for the time being

  17. Large Scale Reduction of Graphite Oxide Project

    NASA Technical Reports Server (NTRS)

    Calle, Carlos; Mackey, Paul; Falker, John; Zeitlin, Nancy

    2015-01-01

    This project seeks to develop an optical method to reduce graphite oxide into graphene efficiently and in larger formats than currently available. Current reduction methods are expensive, time-consuming or restricted to small, limited formats. Graphene has potential uses in ultracapacitors, energy storage, solar cells, flexible and light-weight circuits, touch screens, and chemical sensors. In addition, graphite oxide is a sustainable material that can be produced from any form of carbon, making this method environmentally friendly and adaptable for in-situ reduction.

  18. Effects of chemical modification on the conformation and biological activity of peanut agglutinin.

    PubMed

    Nonnenmacher, D; Brossmer, R

    1981-03-27

    The effect of chemical modifications on the biological properties of peanut agglutinin was investigated. The free amino groups were modified with succinic anhydride and 1-isothiocyanato-4-benzenesulfonic acid. Though the extent of modification was 95 and 85%, respectively, these derivatives did not lose their sugar binding capacity. The agglutinating activity with neuraminidase-treated human erythrocytes and various tumor cells was reduced. The mitogenic activity tested with neuraminidase-treated human lymphocytes was also diminished The tyrosine residues were modified with tetranitromethane and further with 4-aminophenyl-alpha-D-glucopyranoside and the negatively charged 2-(4-amino-benzyl)-alpha-D-neuraminic acid. The extent of modification was 30, 28 and 6%, respectively. The agglutinating and mitogenic activities were in this case not severely changed. The influence of all these modifications on the conformation was investigated by means of CD studies in the far and near ultraviolet regions.

  19. Global Wildfire Forecasts Using Large Scale Climate Indices

    NASA Astrophysics Data System (ADS)

    Shen, Huizhong; Tao, Shu

    2016-04-01

    Using weather readings, fire early warning can provided forecast 4-6 hour in advance to minimize fire loss. The benefit would be dramatically enhanced if relatively accurate long-term projection can be also provided. Here we present a novel method for predicting global fire season severity (FSS) at least three months in advance using multiple large-scale climate indices (CIs). The predictive ability is proven effective for various geographic locations and resolution. Globally, as well as in most continents, the El Niño Southern Oscillation (ENSO) is the dominant driving force controlling interannual FSS variability, whereas other CIs also play indispensable roles. We found that a moderate El Niño event is responsible for 465 (272-658 as interquartile range) Tg carbon release and an annual increase of 29,500 (24,500-34,800) deaths from inhalation exposure to air pollutants. Southeast Asia accounts for half of the deaths. Both intercorrelation and interaction of WPs and CIs are revealed, suggesting possible climate-induced modification of fire responses to weather conditions. Our models can benefit fire management in response to climate change.

  20. Ectopically tethered CP190 induces large-scale chromatin decondensation

    NASA Astrophysics Data System (ADS)

    Ahanger, Sajad H.; Günther, Katharina; Weth, Oliver; Bartkuhn, Marek; Bhonde, Ramesh R.; Shouche, Yogesh S.; Renkawitz, Rainer

    2014-01-01

    Insulator mediated alteration in higher-order chromatin and/or nucleosome organization is an important aspect of epigenetic gene regulation. Recent studies have suggested a key role for CP190 in such processes. In this study, we analysed the effects of ectopically tethered insulator factors on chromatin structure and found that CP190 induces large-scale decondensation when targeted to a condensed lacO array in mammalian and Drosophila cells. In contrast, dCTCF alone, is unable to cause such a decondensation, however, when CP190 is present, dCTCF recruits it to the lacO array and mediates chromatin unfolding. The CP190 induced opening of chromatin may not be correlated with transcriptional activation, as binding of CP190 does not enhance luciferase activity in reporter assays. We propose that CP190 may mediate histone modification and chromatin remodelling activity to induce an open chromatin state by its direct recruitment or targeting by a DNA binding factor such as dCTCF.

  1. Chemical modification studies on a lectin from Saccharomyces cerevisiae (baker's yeast).

    PubMed Central

    Kundu, M; Basu, J; Ghosh, A; Chakrabarti, P

    1987-01-01

    The effect of chemical modification on a galactose-specific lectin isolated from a fatty acid auxotroph of Saccharomyces cerevisiae was investigated in order to identify the type of amino acids involved in its agglutinating activity. Modification of 50 free amino groups with succinic anhydride or citraconic anhydride led to an almost complete loss of activity. This could not be protected by the inhibitory sugar methyl alpha-D-galactopyranoside. Treatment with N-bromosuccinimide and N-acetylimidazole, for the modification of tryptophan and tyrosine residues, did not affect lectin activity. Modification of carboxy groups with glycine ethyl ester greatly affected lectin activity, although sugars afford partial protection. Modification of four thiol groups with N-ethylmaleimide was accompanied by a loss of 85% of the agglutinating activity, and two thiol groups were found to be present at the sugar-binding site of the lectin. Modification of 18 arginine residues with cyclohexane-1,2-dione and 26 histidine residues with ethoxyformic anhydride led to a loss of lectin activity. However, in these cases, modification was not protected by the abovementioned inhibitory sugar, suggesting the absence of these groups at the sugar-binding site. In all the cases, immunodiffusion studies with modified lectin showed no gross structural changes which could disrupt antigenic sites of the lectin. Images Fig. 5. PMID:3128265

  2. 76 FR 54932 - TSCA Inventory Update Reporting Modifications; Chemical Data Reporting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-06

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY 40 CFR Parts 704, 710, and 711 RIN 2070-AJ43 TSCA Inventory Update Reporting Modifications; Chemical Data Reporting Correction In rule document 2011-19922, appearing on pages 50816-50879 in the...

  3. Surface modification of silicon-containing fluorocarbon films prepared by plasma-enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Jin, Yoonyoung; Desta, Yohannes; Goettert, Jost; Lee, G. S.; Ajmera, P. K.

    2005-07-01

    Surface modification of silicon-containing fluorocarbon (SiCF) films achieved by wet chemical treatments and through x-ray irradiation is examined. The SiCF films were prepared by plasma-enhanced chemical vapor deposition, using gas precursors of tetrafluoromethane and disilane. As-deposited SiCF film composition was analyzed by x-ray photoelectron spectroscopy. Surface modification of SiCF films utilizing n-lithiodiaminoethane wet chemical treatment is discussed. Sessile water-drop contact angle changed from 95°+/-2° before treatment to 32°+/-2° after treatment, indicating a change in the film surface characteristics from hydrophobic to hydrophilic. For x-ray irradiation on the SiCF film with a dose of 27.4 kJ/cm3, the contact angle of the sessile water drop changed from 95°+/-2° before radiation to 39°+/-3° after x-ray exposure. The effect of x-ray exposure on chemical bond structure of SiCF films is studied using Fourier transform infrared measurements. Electroless Cu deposition was performed to test the applicability of the surface modified films. The x-ray irradiation method offers a unique advantage in making possible surface modification in a localized area of high-aspect-ratio microstructures. Fabrication of a Ti-membrane x-ray mask is introduced here for selective surface modification using x-ray irradiation.

  4. Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

    PubMed Central

    2009-01-01

    The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge. PMID:20948633

  5. Large Scale Turbulent Structures in Supersonic Jets

    NASA Technical Reports Server (NTRS)

    Rao, Ram Mohan; Lundgren, Thomas S.

    1997-01-01

    , turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved Direct Numerical Simulation (DNS) of a turbulent jet flow is produced.

  6. Large Scale Turbulent Structures in Supersonic Jets

    NASA Technical Reports Server (NTRS)

    Rao, Ram Mohan; Lundgren, Thomas S.

    1997-01-01

    velocities, turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved DNS of a turbulent jet flow is produced.

  7. Large-scale electrochromic devices for smart windows and absorbers

    NASA Astrophysics Data System (ADS)

    Meisel, Thomas; Braun, Ruediger

    1992-11-01

    Application of smart windows and absorbers demand electrochromic (EC) devices with long term stability and a large scale production technology. The paper presents recent results on preparation of rigid and flexible EC devices with 0.3 X 0.3 m2 active area in a three layer arrangement (polyaniline/polymeric electrolyte/tungsten trioxide). The main items and risks of processing an EC element are discussed. It is shown, that highly conductive, chemical resistant electrodes (sheet resistance 5 (Omega) /sq., transparency 85%) on flexible PMMA and PC substrates can be prepared by low temperature sputtering of indium tin oxide (ITO). Deposition apparatus and parameters are described. Well known standard techniques for the synthesis of EC films like polyaniline and tungsten trioxide are adapted for large surfaces: polyaniline and tungsten trioxide based EC films on ITO glass have been prepared with chemical and electrochemical preparation techniques. Electrode geometry plays an important role for the homogeneity of the grown film. We succeed in minimizing tolerances in optical density over 0.3 X 0.3 m2 down to 2%. The solid polymer electrolyte essentially determines the performance of the EC device. High transmittance, proper conductivity, and strong adhesion, are the main attributes.

  8. Chemical modification of amino acid residues in glycerinated Vorticella stalk and Ca(2+)-induced contractility.

    PubMed

    Kono, R; Ochiai, T; Asai, H

    1997-01-01

    The glycerinated stalk of the peritrich ciliate Vorticella, was treated with various reagents to chemically modify the amino acid residues. The influences of these modifcations on spasmoneme contractility were investigated. First, it was confirmed that the spasmoneme contraction is not inhibited by alteration of SH groups. It was also demonstrated that chemical modification of methionine and tryptophan residues abolishes spasmoneme contractility. The reagents used for chemical modification were N-bromosuccinimide (NBS), chloramine T, and 2-hydroxy-5-nitrobenzyl bromide (HNBB), which abolished spasmoneme contractility at concentrations of 40-50 microM, 200-300 microM, and 4 mM, respectively. These results suggest that, along with Ca2+ binding proteins, there are other as yet to be identified proteins involved in contractility.

  9. Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation.

    PubMed

    Mills, Martin; Arimondo, Paola B; Lacroix, Laurent; Garestier, Thérèse; Klump, Horst; Mergny, Jean-Louis

    2002-01-08

    DNA triple helices offer exciting perspectives toward oligonucleotide-directed control of gene expression. Oligonucleotide analogues are routinely used with modifications in either the backbone or the bases to form more stable triple-helical structures or to prevent their degradation in cells. In this article, different chemical modifications are tested in a model system, which sets up a competition between the purine and pyrimidine motifs. For most modifications, the DeltaH degrees of purine triplex formation is close to zero, implying a nearly temperature-independent affinity constant. In contrast, the pyrimidine triplex is strongly favored at lower temperatures. The stabilization induced by modifications previously known to be favorable to the pyrimidine motif was quantified. Interestingly, modifications favorable to the GT motif (propynyl-U and dU replacing T) were also discovered. In a system where two third strands compete for triplex formation, replacement of the GA or GT strand by a pyrimidine strand may be observed at neutral pH upon lowering the temperature. This purine-to-pyrimidine triplex conversion depends on the chemical nature of the triplex-forming strands and the stability of the corresponding triplexes.

  10. Information Tailoring Enhancements for Large-Scale Social Data

    DTIC Science & Technology

    2016-06-15

    Intelligent Automation Incorporated Information Tailoring Enhancements for Large-Scale...Automation Incorporated Progress Report No. 3 Information Tailoring Enhancements for Large-Scale Social Data Submitted in accordance with...also gathers information about entities from all news articles and displays it on over one million entity pages [5][6], and the information is made

  11. Chemical modifications of Achromobacter collagenase and their influence on the enzymic activity.

    PubMed

    Trocheris, I; Herry, P; Keil-Dlouha, V; Keil, B

    1980-10-01

    A study of the influence of chemical modifications on the activity of Achromobacter iophagus collagenase (EC 3.4.24.8) has led to the following conclusions: a modification of 4 out of 80 COOH groups with carbodiimide led to 90% loss of enzymic activity. A 70% inactivation was found after modification of two tyrosines out of 30 with tetranitromethane. The modification of four to six tryptophans out of 16 with 2-hydroxy-5-nitrobenzyl bromide decreased enzyme activity to 36%. This inactivation is accelerated in the presence of collagen. An increase of reagent/enzyme molar ratio led to a modification of 16 tryptophan residues and denaturation of Acahromobacter collagenase. A modification of two arginines out of 18 with 1,2-cyclohexanedione and eight NH2 groups out of 24 with 2,3-dimethyl maleic anhydride does not change the collagenolytic activity. All NH2 groups become available for 2,3-dimethyl maleic anhydride after dissociation of the dimer. A possible analogy of hydrolytic site of collagenase with that of two other known bacterial metalloproteinases (thermolysin and Bacillus subtilis neutral proteinase (EC 3.4.24.4)) is discussed.

  12. Chemical modifications at Teflon interfaces induced by MeV ion beams

    NASA Astrophysics Data System (ADS)

    Ingemarsson, P. Anders; Keane, Michael P.; Gelius, Ulrik

    1989-10-01

    The effect of MeV ion beams incident on Teflon surfaces was studied by x-ray photoelectron spectroscopy (XPS). Irradiation with 20-MeV 35Cl4+ was carried out at doses ranging from 1012 to 1014 ions/cm2. Residual gas analysis was performed during irradiation to identify molecular fragments released from the Teflon surface. XPS spectra were recorded before and after ion irradiation. On some substrates, gold thin films were evaporated before and after ion bombardment, respectively, to detect possible modifications in thin-film adhesion. Changes in the XPS spectra were interpreted in terms of chemical and structural shifts, and related to the observed adhesion modifications.

  13. Chemical Modification of siRNA Bases to Probe and Enhance RNA Interference

    PubMed Central

    Peacock, Hayden; Kannan, Arunkumar; Beal, Peter A.; Burrows, Cynthia J.

    2011-01-01

    Considerable attention has focused on the use of alternatives to the native ribose and phosphate backbone of small interfering RNAs for therapeutic applications of the RNA interference pathway. In this synopsis, we highlight the less common chemical modifications, namely those of the RNA nucleobases. Base modifications have the potential to lend insight into the mechanism of gene silencing and to lead to novel methods to overcome off-target effects that arise due to deleterious protein binding or mis-targeting of mRNA. PMID:21834582

  14. Chemical and physical modifications to poly(dimethylsiloxane) surfaces affect adhesion of Caco-2 cells.

    PubMed

    Wang, Lin; Sun, Bing; Ziemer, Katherine S; Barabino, Gilda A; Carrier, Rebecca L

    2010-06-15

    Polydimethylsiloxane (PDMS) silicone elastomer is extensively used in soft lithography processes to fabricate microscale or nano scale systems for microfluidic or cell culture applications. Though PDMS is biocompatible, it is not an ideal material for cell culture due to its poor cell adhesion properties. In this study, PDMS surfaces were modified to promote intestinal cell adhesion, in the interest of testing feasibility of using microfabricated PDMS systems for high throughput drug screening. Modification techniques included changing chemical composition of PDMS (i.e., varying curing to mixing agent ratio, and oxidization of PDMS surface by oxygen plasma), surface treatment of PDMS by coating with charged molecules (i.e., poly-D-lysine, L-alpha-phosphatidylcholine, and a layer bylayer coating), and deposition of extracellular matrix (ECM) proteins (i.e., laminin, fibronectin, and collagen). The influence of these modifications on PDMS properties, including elastic modulus and surface properties (wettability, chemical composition, topography, and protein adsorption) were characterized. Modification techniques were all found to change PDMS properties and influence the attachment and proliferation of Caco-2 cells over three days of culture to varying degrees. Generally, Caco-2 cells preferred to attach on collagen-coated, fibronectin-coated, and fibronectin-coated oxygen-plasma treated PDMS. The results highlight the importance of considering multiple physical and chemical factors that may be influenced by biomaterial modification and result in altered cell attachment to microfabricated systems, including surface hydrophobicity, chemical composition, stiffness, and topography. This study provides a foundation for further miniaturization, utilizing soft lithography techniques, of Caco-2 cell-based system for high-throughput screening of drug intestinal absorption during lead optimization in drug discovery. The understanding of different surface modifications on

  15. Glutathione release through connexin hemichannels: Implications for chemical modification of pores permeable to large molecules

    PubMed Central

    Tong, Xuhui; Lopez, William; Ramachandran, Jayalakshmi; Ayad, Wafaa A.; Liu, Yu; Lopez-Rodriguez, Angelica; Harris, Andrew L.

    2015-01-01

    Cysteine-scanning mutagenesis combined with thiol reagent modification is a powerful method with which to define the pore-lining elements of channels and the changes in structure that accompany channel gating. Using the Xenopus laevis oocyte expression system and two-electrode voltage clamp, we performed cysteine-scanning mutagenesis of several pore-lining residues of connexin 26 (Cx26) hemichannels, followed by chemical modification using a methanethiosulfonate (MTS) reagent, to help identify the position of the gate. Unexpectedly, we observed that the effect of MTS modification on the currents was reversed within minutes of washout. Such a reversal should not occur unless reducing agents, which can break the disulfide thiol–MTS linkage, have access to the site of modification. Given the permeability to large metabolites of connexin channels, we tested whether cytosolic glutathione (GSH), the primary cell reducing agent, was reaching the modified sites through the connexin pore. Inhibition of gamma-glutamylcysteine synthetase by buthionine sulfoximine decreased the cytosolic GSH concentration in Xenopus oocytes and reduced reversibility of MTS modification, as did acute treatment with tert-butyl hydroperoxide, which oxidizes GSH. Cysteine modification based on thioether linkages (e.g., maleimides) cannot be reversed by reducing agents and did not reverse with washout. Using reconstituted hemichannels in a liposome-based transport-specific fractionation assay, we confirmed that homomeric Cx26 and Cx32 and heteromeric Cx26/Cx32 are permeable to GSH and other endogenous reductants. These results show that, for wide pores, accessibility of cytosolic reductants can lead to reversal of MTS-based thiol modifications. This potential for reversibility of thiol modification applies to on-cell accessibility studies of connexin channels and other channels that are permeable to large molecules, such as pannexin, CALHM, and VRAC. PMID:26324677

  16. SALSA - a Sectional Aerosol module for Large Scale Applications

    NASA Astrophysics Data System (ADS)

    Kokkola, H.; Korhonen, H.; Lehtinen, K. E. J.; Makkonen, R.; Asmi, A.; Järvenoja, S.; Anttila, T.; Partanen, A.-I.; Kulmala, M.; Järvinen, H.; Laaksonen, A.; Kerminen, V.-M.

    2007-12-01

    The sectional aerosol module SALSA is introduced. The model has been designed to be implemented in large scale climate models, which require both accuracy and computational efficiency. We have used multiple methods to reduce the computational burden of different aerosol processes to optimize the model performance without losing physical features relevant to problematics of climate importance. The optimizations include limiting the chemical compounds and physical processes available in different size sections of aerosol particles; division of the size distribution into size sections using size sections of variable width depending on the sensitivity of microphysical processing to the particles sizes; the total amount of size sections to describe the size distribution is kept to the minimum; furthermore, only the relevant microphysical processes affecting each size section are calculated. The ability of the module to describe different microphysical processes was evaluated against explicit microphysical models and several microphysical models used in air quality models. The results from the current module show good consistency when compared to more explicit models. Also, the module was used to simulate a new particle formation event typical in highly polluted conditions with comparable results to a more explicit model setup.

  17. SALSA - a Sectional Aerosol module for Large Scale Applications

    NASA Astrophysics Data System (ADS)

    Kokkola, H.; Korhonen, H.; Lehtinen, K. E. J.; Makkonen, R.; Asmi, A.; Järvenoja, S.; Anttila, T.; Partanen, A.-I.; Kulmala, M.; Järvinen, H.; Laaksonen, A.; Kerminen, V.-M.

    2008-05-01

    The sectional aerosol module SALSA is introduced. The model has been designed to be implemented in large scale climate models, which require both accuracy and computational efficiency. We have used multiple methods to reduce the computational burden of different aerosol processes to optimize the model performance without losing physical features relevant to problematics of climate importance. The optimizations include limiting the chemical compounds and physical processes available in different size sections of aerosol particles; division of the size distribution into size sections using size sections of variable width depending on the sensitivity of microphysical processing to the particles sizes; the total amount of size sections to describe the size distribution is kept to the minimum; furthermore, only the relevant microphysical processes affecting each size section are calculated. The ability of the module to describe different microphysical processes was evaluated against explicit microphysical models and several microphysical models used in air quality models. The results from the current module show good consistency when compared to more explicit models. Also, the module was used to simulate a new particle formation event typical in highly polluted conditions with comparable results to more explicit model setup.

  18. Challenges for large scale ab initio Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Kent, Paul

    2015-03-01

    Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).

  19. Distribution probability of large-scale landslides in central Nepal

    NASA Astrophysics Data System (ADS)

    Timilsina, Manita; Bhandary, Netra P.; Dahal, Ranjan Kumar; Yatabe, Ryuichi

    2014-12-01

    Large-scale landslides in the Himalaya are defined as huge, deep-seated landslide masses that occurred in the geological past. They are widely distributed in the Nepal Himalaya. The steep topography and high local relief provide high potential for such failures, whereas the dynamic geology and adverse climatic conditions play a key role in the occurrence and reactivation of such landslides. The major geoscientific problems related with such large-scale landslides are 1) difficulties in their identification and delineation, 2) sources of small-scale failures, and 3) reactivation. Only a few scientific publications have been published concerning large-scale landslides in Nepal. In this context, the identification and quantification of large-scale landslides and their potential distribution are crucial. Therefore, this study explores the distribution of large-scale landslides in the Lesser Himalaya. It provides simple guidelines to identify large-scale landslides based on their typical characteristics and using a 3D schematic diagram. Based on the spatial distribution of landslides, geomorphological/geological parameters and logistic regression, an equation of large-scale landslide distribution is also derived. The equation is validated by applying it to another area. For the new area, the area under the receiver operating curve of the landslide distribution probability in the new area is 0.699, and a distribution probability value could explain > 65% of existing landslides. Therefore, the regression equation can be applied to areas of the Lesser Himalaya of central Nepal with similar geological and geomorphological conditions.

  20. Modification of chemical reactivity of enzymatic hydrolysis lignin by ultrasound treatment in dilute alkaline solutions.

    PubMed

    Ma, Zhuoming; Li, Shujun; Fang, Guizhen; Patil, Nikhil; Yan, Ning

    2016-12-01

    In this study, we have explored various ultrasound treatment conditions for structural modification of enzymatic hydrolysis lignin (EHL) for enhanced chemical reactivity. The key structural modifications were characterized by using a combination of analytical methods, including, Fourier Transform-Infrared spectroscopy (FTIR), Proton Nuclear Magnetic Resonance ((1)H NMR), Gel permeation chromatography (GPC), X-ray photoelectron spectroscopy (XPS), and Folin-Ciocalteu (F-C) method. Chemical reactivity of the modified EHL samples was determined by both 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity and their reactivity towards formaldehyde. It was observed that the modified EHL had a higher phenolic hydroxyl group content, a lower molecular weight, a higher reactivity towards formaldehyde, and a greater antioxidant property. The higher reactivity demonstrated by the samples after treatment suggesting that ultrasound is a promising method for modifying enzymatic hydrolysis lignin for value-added applications.

  1. Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases

    PubMed Central

    Raindlová, Veronika; Janoušková, Martina; Slavíčková, Michaela; Perlíková, Pavla; Boháčová, Soňa; Milisavljevič, Nemanja; Šanderová, Hana; Benda, Martin; Barvík, Ivan; Krásný, Libor; Hocek, Michal

    2016-01-01

    DNA templates containing a set of base modifications in the major groove (5-substituted pyrimidines or 7-substituted 7-deazapurines bearing H, methyl, vinyl, ethynyl or phenyl groups) were prepared by PCR using the corresponding base-modified 2′-deoxyribonucleoside triphosphates (dNTPs). The modified templates were used in an in vitro transcription assay using RNA polymerase from Bacillus subtilis and Escherichia coli. Some modified nucleobases bearing smaller modifications (H, Me in 7-deazapurines) were perfectly tolerated by both enzymes, whereas bulky modifications (Ph at any nucleobase) and, surprisingly, uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) were partly tolerated mostly by the E. coli enzyme. In all cases where the transcription proceeded, full length RNA product with correct sequence was obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation. The results are promising for the development of bioorthogonal reactions for artificial chemical switching of the transcription. PMID:27001521

  2. Design of a V/STOL propulsion system for a large-scale fighter model

    NASA Technical Reports Server (NTRS)

    Willis, W. S.

    1981-01-01

    Modifications were made to the existing Large-Scale STOL fighter model to simulate a V/STOL configuration. Modifications include the substitutions of two dimensional lift/cruise exhaust nozzles in the nacelles, and the addition of a third J97 engine in the fuselage to suppy a remote exhaust nozzle simulating a Remote Augmented Lift System. A preliminary design of the inlet and exhaust ducting for the third engine was developed and a detailed design was completed of the hot exhaust ducting and remote nozzle.

  3. Site-specific Chemical Modification of a Glycoprotein Fragment Expressed in Yeast

    PubMed Central

    Xiao, Junpeng; Tolbert, Thomas J.

    2011-01-01

    Site-specific modification of glycoproteins has wide application in both biochemical and biophysical studies. This method describes the conjugation of synthetic molecules to the N-terminus of a glycoprotein fragment: immunoglobulin G subclass 1 fragment crystallizable (IgG1 Fc) by native chemical ligation. The glycosylated IgG1 Fc is expressed in a glycosylation deficient yeast strain. The N-terminal cysteine is generated by the endogenous yeast protease Kex2 in the yeast secretory pathway. The N-terminal cysteine is then conjugated with a biotin thioester to produce a biotinylated, glycosylated IgG1 Fc using native chemical ligation. PMID:21674341

  4. Structural Modification of Metal Oxide Nanoparticles in Chemical Vapor Synthesis and Related Properties

    NASA Astrophysics Data System (ADS)

    Lee, Jai-Sung; Lee, Chang-Woo; Lee, Kyoung-No

    2011-10-01

    This paper overviews recent studies on structural modification of metal oxide nanoparticles occurring in the process of chemical vapour condensation (CVC) and related peculiar properties. Hollow nanostructure is controlled at specific process conditions where the pressure in the reactor and the evaporation temperature play an important role in terms of kinematical equilibrium during particle formation and decomposition of precursors in the CVC reactor. As a natural consequence, particle properties also rely on a large surface area from the hollow nanostructure. In this review paper, phase transformation, chemical reactivity and microstructural evolution of nanoparticles are discussed based on hollow nanostructure.

  5. Altering the interfacial activation mechanism of a lipase by solid-phase selective chemical modification.

    PubMed

    López-Gallego, Fernando; Abian, Olga; Guisán, Jose Manuel

    2012-09-04

    This study presents a combined protein immobilization, directed mutagenesis, and site-selective chemical modification approach, which was used to create a hyperactivated semisynthetic variant of BTL2. Various alkane chains were tethered at three different positions in order to mimic the lipase interfacial activation exogenously triggered by detergents. Optimum results were obtained when a dodecane chain was introduced at position 320 by solid-phase site-selective chemical modification. The resulting semisynthetic variant showed a 2.5-fold higher activity than the wild-type nonmodified variant in aqueous conditions. Remarkably, this is the maximum hyperactivation ever observed for BTL2 in the presence of detergents such as Triton X-100. We present evidence to suggest that the endogenous dodecane chain hyperactivates the enzyme in a similar fashion as an exogenous detergent molecule. In this way, we also observe a faster irreversible enzyme inhibition and an altered detergent sensitivity profile promoted by the site-selective chemical modification. These findings are also supported by fluorescence studies, which reveal that the structural conformation changes of the semisynthetic variant are different to those of the wild type, an effect that is more pronounced in the presence of detergent. Finally, the optimal immobilized semisynthetic variant was successfully applied to the selective synthesis of oxiran-2-yl butyrate. Significantly, this biocatalyst is 12-fold more efficient than the immobilized wild-type enzyme, producing the S-enantiomer with higher enantiospecificity (ee = 92%).

  6. A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

    PubMed Central

    Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

    2009-01-01

    We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

  7. Large-scale epitaxial growth kinetics of graphene: A kinetic Monte Carlo study

    SciTech Connect

    Jiang, Huijun; Hou, Zhonghuai

    2015-08-28

    Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be C{sub 1}-attachment for concave growth-front segments and C{sub 5}-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment.

  8. Mechanisation of large-scale agricultural fields in developing countries - a review.

    PubMed

    Onwude, Daniel I; Abdulstter, Rafia; Gomes, Chandima; Hashim, Norhashila

    2016-09-01

    Mechanisation of large-scale agricultural fields often requires the application of modern technologies such as mechanical power, automation, control and robotics. These technologies are generally associated with relatively well developed economies. The application of these technologies in some developing countries in Africa and Asia is limited by factors such as technology compatibility with the environment, availability of resources to facilitate the technology adoption, cost of technology purchase, government policies, adequacy of technology and appropriateness in addressing the needs of the population. As a result, many of the available resources have been used inadequately by farmers, who continue to rely mostly on conventional means of agricultural production, using traditional tools and equipment in most cases. This has led to low productivity and high cost of production among others. Therefore this paper attempts to evaluate the application of present day technology and its limitations to the advancement of large-scale mechanisation in developing countries of Africa and Asia. Particular emphasis is given to a general understanding of the various levels of mechanisation, present day technology, its management and application to large-scale agricultural fields. This review also focuses on/gives emphasis to future outlook that will enable a gradual, evolutionary and sustainable technological change. The study concludes that large-scale-agricultural farm mechanisation for sustainable food production in Africa and Asia must be anchored on a coherent strategy based on the actual needs and priorities of the large-scale farmers. © 2016 Society of Chemical Industry.

  9. Learning networks for sustainable, large-scale improvement.

    PubMed

    McCannon, C Joseph; Perla, Rocco J

    2009-05-01

    Large-scale improvement efforts known as improvement networks offer structured opportunities for exchange of information and insights into the adaptation of clinical protocols to a variety of settings.

  10. Modified gravity and large scale flows, a review

    NASA Astrophysics Data System (ADS)

    Mould, Jeremy

    2017-02-01

    Large scale flows have been a challenging feature of cosmography ever since galaxy scaling relations came on the scene 40 years ago. The next generation of surveys will offer a serious test of the standard cosmology.

  11. Bayesian hierarchical model for large-scale covariance matrix estimation.

    PubMed

    Zhu, Dongxiao; Hero, Alfred O

    2007-12-01

    Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to "overfitting." We cast the large-scale covariance matrix estimation problem into the Bayesian hierarchical model framework, and introduce dependency between covariance parameters. We demonstrate the advantages of our approaches over the traditional approaches using simulations and OMICS data analysis.

  12. A study of MLFMA for large-scale scattering problems

    NASA Astrophysics Data System (ADS)

    Hastriter, Michael Larkin

    This research is centered in computational electromagnetics with a focus on solving large-scale problems accurately in a timely fashion using first principle physics. Error control of the translation operator in 3-D is shown. A parallel implementation of the multilevel fast multipole algorithm (MLFMA) was studied as far as parallel efficiency and scaling. The large-scale scattering program (LSSP), based on the ScaleME library, was used to solve ultra-large-scale problems including a 200lambda sphere with 20 million unknowns. As these large-scale problems were solved, techniques were developed to accurately estimate the memory requirements. Careful memory management is needed in order to solve these massive problems. The study of MLFMA in large-scale problems revealed significant errors that stemmed from inconsistencies in constants used by different parts of the algorithm. These were fixed to produce the most accurate data possible for large-scale surface scattering problems. Data was calculated on a missile-like target using both high frequency methods and MLFMA. This data was compared and analyzed to determine possible strategies to increase data acquisition speed and accuracy through multiple computation method hybridization.

  13. Thermal stability of Trichoderma reesei c30 cellulase and aspergillus niger; -glucosidase after ph and chemical modification

    SciTech Connect

    Woodward, J.; Whaley, K.S.; Zachry, G.S.; Wohlpart, D.L.

    1981-01-01

    Treatment of Trichoderma reesei C30 cellulase at pH 10.0 for 1 h at room temperature increased its pH and thermal stability. Chemical modification of the free epsilon-amino groups of cellulase at pH 10.0 resulted in no further increase in stability. Such chemical modification, however, decreased the thermal stability of the cellulose-cellulase complex. On the contrary, the chemical modification of Aspergillus niger glucosidase with glutaraldehyde at pH 8.0 increased the thermal stability of this enzyme.

  14. Thermal stability of Trichoderma reesei C30 cellulase and Aspergillus niger. beta. -glucosidase after pH and chemical modification

    SciTech Connect

    Woodward, J.; Whaley, K.S.; Zachry, G.S.; Wohlpart, D.L.

    1981-01-01

    Treatment of Trichoderma reesei C30 cellulase at pH 10.0 for 1 h at room temperature increased its pH and thermal stability. Chemical modification of the free epsilon-amino groups of cellulase at pH 10.0 resulted in no further increase in stability. Such chemical modification, however, decreased the thermal stability of the cellulose-cellulase complex. On the contrary, the chemical modification of Aspergillus niger ..beta..-glucosidase with glutaraldehyde at pH 8.0 increased the thermal stability of this enzyme.

  15. Enhancing surface free energy and hydrophilicity through chemical modification of microstructured titanium implant surfaces.

    PubMed

    Rupp, F; Scheideler, L; Olshanska, N; de Wild, M; Wieland, M; Geis-Gerstorfer, J

    2006-02-01

    Roughness-induced hydrophobicity, well-known from natural plant surfaces and intensively studied toward superhydrophobic surfaces, has currently been identified on microstructured titanium implant surfaces. Studies indicate that microstructuring by sandblasting and acid etching (SLA) enhances the osteogenic properties of titanium. The undesired initial hydrophobicity, however, presumably decelerates primary interactions with the aqueous biosystem. To improve the initial wettability and to retain SLA microstructure, a novel surface modification was tested. This modification differs from SLA by its preparation after acid etching, which was done under protective gas conditions following liquid instead of dry storage. We hypothesized that this modification should have increased wettability due to the prevention of contaminations that occurs during air contact. The main outcome of dynamic wettability measurements was that the novel modification shows increased surface free energy (SFE) and increased hydrophilicity with initial water contact angles of 0 degrees compared to 139.9 degrees for SLA. This hydrophilization was kept even after any drying. Reduced hydrocarbon contaminations were identified to play a possible role in altered surface thermodynamics. Such surfaces aim to retain the hydrophilicity and natural high surface energy of the Ti dioxide surface until surgical implants' insertion and are compared in this in vitro study with structural surface variants of titanium to compare roughness and chemically induced wettability.

  16. Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification.

    PubMed

    Stephanou, Augoustinos S; Roberts, Gareth A; Cooper, Laurie P; Clarke, David J; Thomson, Andrew R; MacKay, C Logan; Nutley, Margaret; Cooper, Alan; Dryden, David T F

    2009-08-21

    The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an approximately 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove approximately 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to approximately 800-fold.

  17. Chemical modification of jute fibers for the production of green-composites.

    PubMed

    Corrales, F; Vilaseca, F; Llop, M; Gironès, J; Méndez, J A; Mutjè, P

    2007-06-18

    Natural fiber reinforced composites is an emerging area in polymer science. Fibers derived from annual plants are considered a potential substitute for non-renewable synthetic fibers like glass and carbon fibers. The hydrophilic nature of natural fibers affects negatively its adhesion to hydrophobic polymeric matrices. To improve the compatibility between both components a surface modification has been proposed. The aim of the study is the chemical modification of jute fibers using a fatty acid derivate (oleoyl chloride) to confer hydrophobicity and resistance to biofibers. This reaction was applied in swelling and non-swelling solvents, pyridine and dichloromethane, respectively. The formation of ester groups, resulting from the reaction of oleoyl chloride with hydroxyl group of cellulose were studied by elemental analysis (EA) and Fourier Transform infrared spectroscopy (FTIR). The characterization methods applied has proved the chemical interaction between the cellulosic material and the coupling agent. The extent of the reactions evaluated by elemental analysis was calculated using two ratios. Finally electron microscopy was applied to evaluate the surface changes of cellulose fibers after modification process.

  18. Cooperative enhancement of deoxyribozyme activity by chemical modification and added cationic copolymer

    PubMed Central

    Saito, Ken; Shimada, Naohiko; Maruyama, Atushi

    2016-01-01

    Abstract Deoxyribozymes (DNAzymes) having RNA-cleaving activity have widely been explored as tools for therapeutic and diagnostic purposes. Both the chemical cleaving step and the turnover step should be improved for enhancing overall activity of DNAzymes. We have shown that cationic copolymer enhanced DNAzyme activity by increasing turnover efficacy. In this paper, effects of the copolymer on DNAzymes modified with locked nucleic acids (LNA) or 2′-O-methylated (2′-OMe) nucleic acids were studied. The copolymer increased activity of these chemically modified DNAzymes. More than 30-fold enhancement in multiple-turnover catalytic activity was observed with 2′-OMe-modified DNAzyme in the presence of the copolymer. DNAzyme catalytic activity was successfully enhanced by cooperation of the added copolymer and chemical modification of DNAzyme. PMID:27877894

  19. Surface modification via wet chemical etching of single-crystalline silicon for photovoltaic application.

    PubMed

    Reshak, A H; Shahimin, M M; Shaari, S; Johan, N

    2013-11-01

    The potential of solar cells have not been fully tapped due to the lack of energy conversion efficiency. There are three important mechanisms in producing high efficiency cells to harvest solar energy; reduction of light reflectance, enhancement of light trapping in the cell and increment of light absorption. The current work represent studies conducted in surface modification of single-crystalline silicon solar cells using wet chemical etching techniques. Two etching types are applied; alkaline etching (KOH:IPA:DI) and acidic etching (HF:HNO3:DI). The alkaline solution resulted in anisotropic profile that leads to the formation of inverted pyramids. While acidic solution formed circular craters along the front surface of silicon wafer. This surface modification will leads to the reduction of light reflectance via texturizing the surface and thereby increases the short circuit current and conversion rate of the solar cells.

  20. Carrier mobility of MoS2 nanoribbons with edge chemical modification.

    PubMed

    Xiao, Jin; Long, Mengqiu; Li, Mingjun; Li, Xinmei; Xu, Hui; Chan, Kwoksum

    2015-03-14

    We have investigated the electronic structures and carrier mobilities of MoS2 monolayer sheets and armchair nanoribbons with chemical modification using the density functional theory combined with the Boltzmann transport method with relaxation time approximation. It is shown that the hole mobility (96.62 cm(2) V(-1) s(-1)) in monolayer sheets is about twice that of the electron mobility (43.96 cm(2) V(-1) s(-1)). The charge mobilities in MoS2 armchair nanoribbons can be regulated by edge modification owing to the changing electronic structures. In pristine armchair nanoribbons, the electron and hole mobilities are about 30 cm(2) V(-1) s(-1) and 25 cm(2) V(-1) s(-1), respectively. When the edges are terminated by H or F atoms, the hole mobility will enhance obviously even 10 times that in pristine ribbons, and the electron mobility is comparable with that in MoS2 sheets.

  1. Chemical modification of coating of Pinus halepensis pollen by ozone exposure.

    PubMed

    Naas, Oumsaad; Mendez, Maxence; Quijada, Melesio; Gosselin, Sylvie; Farah, Jinane; Choukri, Ali; Visez, Nicolas

    2016-07-01

    Pollen coating, located on the exine, includes an extractible lipid fraction. The modification of the pollen coating by air pollutants may have implications on the interactions of pollen with plant stigmas and human cells. Pinus halepensis pollen was exposed to ozone in vitro and the pollen coating was extracted with organic solvent and analyzed by GC-MS. Ozone has induced chemical changes in the coating as observed with an increase in dicarboxylic acids, short-chain fatty acids and aldehydes. 4-Hydroxybenzaldehyde was identified as the main reaction product and its formation was shown to occur both on native pollen and on defatted pollen. 4-Hydroxybenzaldehyde is very likely formed via the ozonolysis of acid coumaric-like monomers constitutive of the sporopollenin. Modification of pollen coating by air pollutants should be accounted for in further studies on effect of pollution on germination and on allergenicity.

  2. Reversible tuning of two-dimensional electron gases in oxide heterostructures by chemical surface modification

    NASA Astrophysics Data System (ADS)

    Lee, H.; Campbell, N.; Ryu, S.; Chang, W.; Irwin, J.; Lindemann, S.; Mahanthappa, M. K.; Rzchowski, M. S.; Eom, C. B.

    2016-11-01

    Reversible control over the electrical properties of the two-dimensional electron gas (2DEG) in oxide heterostructures is a key capability enabling practical applications. Herein, we report an efficient method to reversibly tune the charge carrier density of the 2DEG by surface modification. We demonstrate both increasing and decreasing the carrier density of the LaAlO3/SrTiO3 2DEG interface via application of functional phosphonic acids with molecular dipoles pointing either toward or away from the interface, respectively. In addition, in the case of the enhanced 2DEG, we recovered the initial conduction properties by exposing the samples to a basic solution. The tuning processes were highly reversible over repetitive cycles. These results reveal that the surface modification is an efficient way to tune the carrier density of 2DEG in oxide heterostructures. This simple chemical approach offers a vast range of fabrication possibilities in versatile electronic device applications.

  3. Selective chemical modification of silicon nitride/silicon oxide nanostructures to develop label-free biosensors.

    PubMed

    Bañuls, María-José; González-Pedro, Victoria; Barrios, Carlos A; Puchades, Rosa; Maquieira, Angel

    2010-02-15

    The selective introduction of functional groups on the surface of silicon nitride/silicon oxide nanostructures was studied. Chemical strategies based on organosilane, Si-H and N-H reactivities were assayed. Among these strategies, the use of glutaraldehyde to selectively immobilize biomolecules only on the silicon nitride part of the chip surface was the most effective for the covalent attachment of proteins, maintaining also their bioavailability. The biomolecule surface coverage results up to 80% and the modification is selective versus silicon oxide; the biomolecule attaching only to silicon nitride and leaving the silicon oxide area of the device unmodified. The effectiveness of our novel selective surface modification procedure is also supported by comparing experimental and numerical calculations of the optical performance of a label-free optical ring resonator based on Si(3)N(4)/SiO(2) slot-waveguides.

  4. Physical, Chemical and Biochemical Modifications of Protein-Based Films and Coatings: An Extensive Review

    PubMed Central

    Zink, Joël; Wyrobnik, Tom; Prinz, Tobias; Schmid, Markus

    2016-01-01

    Protein-based films and coatings are an interesting alternative to traditional petroleum-based materials. However, their mechanical and barrier properties need to be enhanced in order to match those of the latter. Physical, chemical, and biochemical methods can be used for this purpose. The aim of this article is to provide an overview of the effects of various treatments on whey, soy, and wheat gluten protein-based films and coatings. These three protein sources have been chosen since they are among the most abundantly used and are well described in the literature. Similar behavior might be expected for other protein sources. Most of the modifications are still not fully understood at a fundamental level, but all the methods discussed change the properties of the proteins and resulting products. Mastering these modifications is an important step towards the industrial implementation of protein-based films. PMID:27563881

  5. Physico-chemical Modification of the Fibrous Filter Nozzles for Purification Processes of Water and Air

    NASA Astrophysics Data System (ADS)

    Bordunov, S. V.; Galtseva, O. V.; Natalinova, N. M.; Rogachev, A. A.; Zhang, Ruizhi

    2017-01-01

    A set of experiments to study physical and chemical modification of the surface of fibers is conducted to expand the area of their application for purification of water, gas and air (including that in conditions of space). The possibility of modification of filter nozzles in the process of fiber formation by particles of coal of BAU type, copper sulfide and silver chloride is experimentally shown. The fraction of the copper sulfide powder less than 50 microns in size was crushed in a spherical mill; it was deposited on fiber at air temperature of 50° C and powder consumption of 0.5 g/l of air. The resulting material contained 6–18 CuS particles per 1 cm of the fiber length. An effective bactericidal fibrous material can be produced using rather cheap material – CuS and relatively cheap natural compounds of sulphides and oxides of heavy metals.

  6. Recursive architecture for large-scale adaptive system

    NASA Astrophysics Data System (ADS)

    Hanahara, Kazuyuki; Sugiyama, Yoshihiko

    1994-09-01

    'Large scale' is one of major trends in the research and development of recent engineering, especially in the field of aerospace structural system. This term expresses the large scale of an artifact in general, however, it also implies the large number of the components which make up the artifact in usual. Considering a large scale system which is especially used in remote space or deep-sea, such a system should be adaptive as well as robust by itself, because its control as well as maintenance by human operators are not easy due to the remoteness. An approach to realizing this large scale, adaptive and robust system is to build the system as an assemblage of components which are respectively adaptive by themselves. In this case, the robustness of the system can be achieved by using a large number of such components and suitable adaptation as well as maintenance strategies. Such a system gathers many research's interest and their studies such as decentralized motion control, configurating algorithm and characteristics of structural elements are reported. In this article, a recursive architecture concept is developed and discussed towards the realization of large scale system which consists of a number of uniform adaptive components. We propose an adaptation strategy based on the architecture and its implementation by means of hierarchically connected processing units. The robustness and the restoration from degeneration of the processing unit are also discussed. Two- and three-dimensional adaptive truss structures are conceptually designed based on the recursive architecture.

  7. EINSTEIN'S SIGNATURE IN COSMOLOGICAL LARGE-SCALE STRUCTURE

    SciTech Connect

    Bruni, Marco; Hidalgo, Juan Carlos; Wands, David

    2014-10-10

    We show how the nonlinearity of general relativity generates a characteristic nonGaussian signal in cosmological large-scale structure that we calculate at all perturbative orders in a large-scale limit. Newtonian gravity and general relativity provide complementary theoretical frameworks for modeling large-scale structure in ΛCDM cosmology; a relativistic approach is essential to determine initial conditions, which can then be used in Newtonian simulations studying the nonlinear evolution of the matter density. Most inflationary models in the very early universe predict an almost Gaussian distribution for the primordial metric perturbation, ζ. However, we argue that it is the Ricci curvature of comoving-orthogonal spatial hypersurfaces, R, that drives structure formation at large scales. We show how the nonlinear relation between the spatial curvature, R, and the metric perturbation, ζ, translates into a specific nonGaussian contribution to the initial comoving matter density that we calculate for the simple case of an initially Gaussian ζ. Our analysis shows the nonlinear signature of Einstein's gravity in large-scale structure.

  8. Crucial roles of reactive chemical species in modification of respiratory syncytial virus by nitrogen gas plasma.

    PubMed

    Sakudo, Akikazu; Toyokawa, Yoichi; Imanishi, Yuichiro; Murakami, Tomoyuki

    2017-05-01

    The exact mechanisms by which nanoparticles, especially those composed of soft materials, are modified by gas plasma remain unclear. Here, we used respiratory syncytial virus (RSV), which has a diameter of 80-350nm, as a model system to identify important factors for gas plasma modification of nanoparticles composed of soft materials. Nitrogen gas plasma, generated by applying a short high-voltage pulse using a static induction (SI) thyristor power supply produced reactive chemical species (RCS) and caused virus inactivation. The plasma treatment altered the viral genomic RNA, while treatment with a relatively low concentration of hydrogen peroxide, which is a neutral chemical species among RCS, effectively inactivated the virus. Furthermore, a zero dimensional kinetic global model of the reaction scheme during gas plasma generation identified the production of various RCS, including neutral chemical species. Our findings suggest the nitrogen gas plasma generates RCS, including neutral species that damage the viral genomic RNA, leading to virus inactivation. Thus, RCS generated by gas plasma appears to be crucial for virus inactivation, suggesting this may constitute an important factor in terms of the efficient modification of nanoparticles composed of soft materials.

  9. DNA-osmium complexes: recent developments in the operative chemical analysis of DNA epigenetic modifications.

    PubMed

    Okamoto, Akimitsu

    2014-09-01

    The development of a reaction for the detection of one epigenetic modification in a long DNA strand is a chemically and biologically challenging research subject. Herein, we report and discuss the formation of 5-methylcytosine-osmium complexes that are used as the basis for a bisulfite-free chemical assay for DNA methylation analysis. Osmium in the oxidized state reacts with C5-methylated pyrimidines in the presence of a bipyridine ligand to give a stable ternary complex. On the basis of this reaction, an adenine derivative with a tethered bipyridine moiety has been designed for sequence-specific osmium complex formation. Osmium complexation is then achieved by hybridization of a short DNA molecule containing this functional nucleotide to a target DNA sequence and results in the formation of a cross-linked structure. This novel concept of methylation-specific reaction, based on a straightforward chemical process, expands the range of methods available for the analysis of epigenetic modifications. Advantages of the described method include amplification-insensitive detection, 5-hydroxymethylcytosine complexation, and visualization through methylation-specific in situ hybridization.

  10. Chemical modifications and bioconjugate reactions of nanomaterials for sensing, imaging, drug delivery and therapy.

    PubMed

    Biju, Vasudevanpillai

    2014-02-07

    As prepared nanomaterials of metals, semiconductors, polymers and carbon often need surface modifications such as ligand exchange, and chemical and bioconjugate reactions for various biosensor, bioanalytical, bioimaging, drug delivery and therapeutic applications. Such surface modifications help us to control the physico-chemical, toxicological and pharmacological properties of nanomaterials. Furthermore, introduction of various reactive functional groups on the surface of nanomaterials allows us to conjugate a spectrum of contrast agents, antibodies, peptides, ligands, drugs and genes, and construct multifunctional and hybrid nanomaterials for the targeted imaging and treatment of cancers. This tutorial review is intended to provide an introduction to newcomers about how chemical and bioconjugate reactions transform the surface of nanomaterials such as silica nanoparticles, gold nanoparticles, gold quantum clusters, semiconductor quantum dots, carbon nanotubes, fullerene and graphene, and accordingly formulate them for applications such as biosensing, bioimaging, drug and gene delivery, chemotherapy, photodynamic therapy and photothermal therapy. Nonetheless, controversial reports and our growing concerns about toxicity and pharmacokinetics of nanomaterials suggest the need for not only rigorous in vivo experiments in animal models but also novel nanomaterials for practical applications in the clinical settings. Further reading of original and review articles cited herein is necessary to buildup in-depth knowledge about the chemistry, bioconjugate chemistry and biological applications of individual nanomaterials.

  11. Novel fluorinated block copolymers by selective chemical modification: Chemistry and thermodynamics

    NASA Astrophysics Data System (ADS)

    Davidock, Drew Alan

    Many applications of polymers utilize multi-component systems. Regardless of whether the components are physically linked together or not, the properties that they possess are directly influenced by their self-assembly behavior. To exploit the full potential of such materials, strict control of the polymer-polymer phase behavior is required. The objective of this dissertation was to study polymer-polymer phase behavior by using post-polymerization chemical modification to vary the incompatibility between the components, altering their self-assembly behavior. Initially in this work, the modification chemistries were developed and refined. Model 4,1-polyisoprene-block-1,2-polybutadiene (PI- b-PB) copolymers were used as the parent material. A selective hydrogenation of the PB block was performed using a homogeneous Ru catalyst to yield a saturated hydrocarbon. The PI block was then modified to various extents by the controlled addition of a difluorocarbene (CF2), generated by the thermal decomposition of hexafluoropropylene oxide (HFPO). The effect of these chemical modifications on the self-assembly behavior of a series of PI-PB copolymers was studied. Small-angle x-ray scattering (SAXS) was used to determine the equilibrium morphologies and domain spacings. Effective interaction parameters (chieff) were determined from the temperature- and composition-dependent domain spacings, and were found to increase by a factor of approximately 370 upon complete modification. The experimental morphological map was constructed, and it was found that the gyroid phase appears to be stable into the strong segregation regime, in contrast to expectations based on self-consistent field theory. The modification of block copolymers for the creation of a universal blend compatibilizer was also explored. By changing the chemical nature of one or both blocks, their affinity for various homopolymers can be altered. The compatibilization of blends of polystyrene (PS) and poly

  12. Simultaneous effect of modified gravity and primordial non-Gaussianity in large scale structure observations

    SciTech Connect

    Mirzatuny, Nareg; Khosravi, Shahram; Baghram, Shant; Moshafi, Hossein E-mail: khosravi@mail.ipm.ir E-mail: hosseinmoshafi@iasbs.ac.ir

    2014-01-01

    In this work we study the simultaneous effect of primordial non-Gaussianity and the modification of the gravity in f(R) framework on large scale structure observations. We show that non-Gaussianity and modified gravity introduce a scale dependent bias and growth rate functions. The deviation from ΛCDM in the case of primordial non-Gaussian models is in large scales, while the growth rate deviates from ΛCDM in small scales for modified gravity theories. We show that the redshift space distortion can be used to distinguish positive and negative f{sub NL} in standard background, while in f(R) theories they are not easily distinguishable. The galaxy power spectrum is generally enhanced in presence of non-Gaussianity and modified gravity. We also obtain the scale dependence of this enhancement. Finally we define galaxy growth rate and galaxy growth rate bias as new observational parameters to constrain cosmology.

  13. Large-Scale Spray Releases: Initial Aerosol Test Results

    SciTech Connect

    Schonewill, Philip P.; Gauglitz, Phillip A.; Bontha, Jagannadha R.; Daniel, Richard C.; Kurath, Dean E.; Adkins, Harold E.; Billing, Justin M.; Burns, Carolyn A.; Davis, James M.; Enderlin, Carl W.; Fischer, Christopher M.; Jenks, Jeromy WJ; Lukins, Craig D.; MacFarlan, Paul J.; Shutthanandan, Janani I.; Smith, Dennese M.

    2012-12-01

    One of the events postulated in the hazard analysis at the Waste Treatment and Immobilization Plant (WTP) and other U.S. Department of Energy (DOE) nuclear facilities is a breach in process piping that produces aerosols with droplet sizes in the respirable range. The current approach for predicting the size and concentration of aerosols produced in a spray leak involves extrapolating from correlations reported in the literature. These correlations are based on results obtained from small engineered spray nozzles using pure liquids with Newtonian fluid behavior. The narrow ranges of physical properties on which the correlations are based do not cover the wide range of slurries and viscous materials that will be processed in the WTP and across processing facilities in the DOE complex. Two key technical areas were identified where testing results were needed to improve the technical basis by reducing the uncertainty due to extrapolating existing literature results. The first technical need was to quantify the role of slurry particles in small breaches where the slurry particles may plug and result in substantially reduced, or even negligible, respirable fraction formed by high-pressure sprays. The second technical need was to determine the aerosol droplet size distribution and volume from prototypic breaches and fluids, specifically including sprays from larger breaches with slurries where data from the literature are scarce. To address these technical areas, small- and large-scale test stands were constructed and operated with simulants to determine aerosol release fractions and generation rates from a range of breach sizes and geometries. The properties of the simulants represented the range of properties expected in the WTP process streams and included water, sodium salt solutions, slurries containing boehmite or gibbsite, and a hazardous chemical simulant. The effect of anti-foam agents was assessed with most of the simulants. Orifices included round holes and

  14. Microstructural modification of nc-Si/SiOx films during plasma-enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Zhang, X. W.

    2005-07-01

    Nanocrystalline-silicon embedded silicon oxide films are prepared by plasma-enhanced chemical vapor deposition (PECVD) at 300 °C without post-heat treatment. Measurements of XPS, IR, XRD, and HREM are performed. Microstructural modifications are found occurring throughout the film deposition. The silica network with a high oxide state is suggested to be formed directly under the abduction of the former deposited layer, rather than processing repeatedly from the original low-oxide state of silica. Nanocrystalline silicon particles with a size of 6-10 nm are embedded in the SiOx film matrix, indicating the potential application in Si-based optoelectronic integrity.

  15. [Bio-based pharmaceutical polymers, possibility of their chemical modification and the applicability of modified polymers].

    PubMed

    Sebe, István; Szabó, Barnabás; Zelkó, Romána

    2012-01-01

    Different types of polymers are widely used in biomedical, pharmaceutical and cosmetic purposes. Their applications are curbed, if the polymers can not break down by the body or if the polymer itself is harmful or decompose to harmful material. Authors provide an overview of different types of pharmaceutical polymers of various sources, of the structural characterization and possibilities of their chemical modification and of the classical and instrumental analytical examination methods. The paper deals with the limitations of the use of biopolymers, as well.

  16. Modulation analysis of large-scale discrete vortices.

    PubMed

    Cisneros, Luis A; Minzoni, Antonmaria A; Panayotaros, Panayotis; Smyth, Noel F

    2008-09-01

    The behavior of large-scale vortices governed by the discrete nonlinear Schrödinger equation is studied. Using a discrete version of modulation theory, it is shown how vortices are trapped and stabilized by the self-consistent Peierls-Nabarro potential that they generate in the lattice. Large-scale circular and polygonal vortices are studied away from the anticontinuum limit, which is the limit considered in previous studies. In addition numerical studies are performed on large-scale, straight structures, and it is found that they are stabilized by a nonconstant mean level produced by standing waves generated at the ends of the structure. Finally, numerical evidence is produced for long-lived, localized, quasiperiodic structures.

  17. Large-scale simulations of complex physical systems

    NASA Astrophysics Data System (ADS)

    Belić, A.

    2007-04-01

    Scientific computing has become a tool as vital as experimentation and theory for dealing with scientific challenges of the twenty-first century. Large scale simulations and modelling serve as heuristic tools in a broad problem-solving process. High-performance computing facilities make possible the first step in this process - a view of new and previously inaccessible domains in science and the building up of intuition regarding the new phenomenology. The final goal of this process is to translate this newly found intuition into better algorithms and new analytical results. In this presentation we give an outline of the research themes pursued at the Scientific Computing Laboratory of the Institute of Physics in Belgrade regarding large-scale simulations of complex classical and quantum physical systems, and present recent results obtained in the large-scale simulations of granular materials and path integrals.

  18. Large-scale velocity structures in turbulent thermal convection.

    PubMed

    Qiu, X L; Tong, P

    2001-09-01

    A systematic study of large-scale velocity structures in turbulent thermal convection is carried out in three different aspect-ratio cells filled with water. Laser Doppler velocimetry is used to measure the velocity profiles and statistics over varying Rayleigh numbers Ra and at various spatial positions across the whole convection cell. Large velocity fluctuations are found both in the central region and near the cell boundary. Despite the large velocity fluctuations, the flow field still maintains a large-scale quasi-two-dimensional structure, which rotates in a coherent manner. This coherent single-roll structure scales with Ra and can be divided into three regions in the rotation plane: (1) a thin viscous boundary layer, (2) a fully mixed central core region with a constant mean velocity gradient, and (3) an intermediate plume-dominated buffer region. The experiment reveals a unique driving mechanism for the large-scale coherent rotation in turbulent convection.

  19. A relativistic signature in large-scale structure

    NASA Astrophysics Data System (ADS)

    Bartolo, Nicola; Bertacca, Daniele; Bruni, Marco; Koyama, Kazuya; Maartens, Roy; Matarrese, Sabino; Sasaki, Misao; Verde, Licia; Wands, David

    2016-09-01

    In General Relativity, the constraint equation relating metric and density perturbations is inherently nonlinear, leading to an effective non-Gaussianity in the dark matter density field on large scales-even if the primordial metric perturbation is Gaussian. Intrinsic non-Gaussianity in the large-scale dark matter overdensity in GR is real and physical. However, the variance smoothed on a local physical scale is not correlated with the large-scale curvature perturbation, so that there is no relativistic signature in the galaxy bias when using the simplest model of bias. It is an open question whether the observable mass proxies such as luminosity or weak lensing correspond directly to the physical mass in the simple halo bias model. If not, there may be observables that encode this relativistic signature.

  20. Toward Improved Support for Loosely Coupled Large Scale Simulation Workflows

    SciTech Connect

    Boehm, Swen; Elwasif, Wael R; Naughton, III, Thomas J; Vallee, Geoffroy R

    2014-01-01

    High-performance computing (HPC) workloads are increasingly leveraging loosely coupled large scale simula- tions. Unfortunately, most large-scale HPC platforms, including Cray/ALPS environments, are designed for the execution of long-running jobs based on coarse-grained launch capabilities (e.g., one MPI rank per core on all allocated compute nodes). This assumption limits capability-class workload campaigns that require large numbers of discrete or loosely coupled simulations, and where time-to-solution is an untenable pacing issue. This paper describes the challenges related to the support of fine-grained launch capabilities that are necessary for the execution of loosely coupled large scale simulations on Cray/ALPS platforms. More precisely, we present the details of an enhanced runtime system to support this use case, and report on initial results from early testing on systems at Oak Ridge National Laboratory.

  1. PKI security in large-scale healthcare networks.

    PubMed

    Mantas, Georgios; Lymberopoulos, Dimitrios; Komninos, Nikos

    2012-06-01

    During the past few years a lot of PKI (Public Key Infrastructures) infrastructures have been proposed for healthcare networks in order to ensure secure communication services and exchange of data among healthcare professionals. However, there is a plethora of challenges in these healthcare PKI infrastructures. Especially, there are a lot of challenges for PKI infrastructures deployed over large-scale healthcare networks. In this paper, we propose a PKI infrastructure to ensure security in a large-scale Internet-based healthcare network connecting a wide spectrum of healthcare units geographically distributed within a wide region. Furthermore, the proposed PKI infrastructure facilitates the trust issues that arise in a large-scale healthcare network including multi-domain PKI infrastructures.

  2. Magnetic Helicity and Large Scale Magnetic Fields: A Primer

    NASA Astrophysics Data System (ADS)

    Blackman, Eric G.

    2015-05-01

    Magnetic fields of laboratory, planetary, stellar, and galactic plasmas commonly exhibit significant order on large temporal or spatial scales compared to the otherwise random motions within the hosting system. Such ordered fields can be measured in the case of planets, stars, and galaxies, or inferred indirectly by the action of their dynamical influence, such as jets. Whether large scale fields are amplified in situ or a remnant from previous stages of an object's history is often debated for objects without a definitive magnetic activity cycle. Magnetic helicity, a measure of twist and linkage of magnetic field lines, is a unifying tool for understanding large scale field evolution for both mechanisms of origin. Its importance stems from its two basic properties: (1) magnetic helicity is typically better conserved than magnetic energy; and (2) the magnetic energy associated with a fixed amount of magnetic helicity is minimized when the system relaxes this helical structure to the largest scale available. Here I discuss how magnetic helicity has come to help us understand the saturation of and sustenance of large scale dynamos, the need for either local or global helicity fluxes to avoid dynamo quenching, and the associated observational consequences. I also discuss how magnetic helicity acts as a hindrance to turbulent diffusion of large scale fields, and thus a helper for fossil remnant large scale field origin models in some contexts. I briefly discuss the connection between large scale fields and accretion disk theory as well. The goal here is to provide a conceptual primer to help the reader efficiently penetrate the literature.

  3. Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining.

    PubMed

    Chen, Haifen; Lonardi, Stefano; Zheng, Jie

    2014-06-01

    Histone modifications play a major role in the regulation of gene expression. Accumulated evidence has shown that histone modifications mediate biological processes such as transcription cooperatively. This has led to the hypothesis of 'histone code' which suggests that combinations of different histone modifications correspond to unique chromatin states and have distinct functions. In this paper, we propose a framework based on association rule mining to discover the potential regulatory relations between histone modifications and gene expression in Plasmodium falciparum. Our approach can output rules with statistical significance. Some of the discovered rules are supported by literature of experimental results. Moreover, we have also discovered de novo rules which can guide further research in epigenetic regulation of transcription. Based on our association rules we build a model to predict gene expression, which outperforms a published Bayesian network model for gene expression prediction by histone modifications. The results of our study reveal mechanisms for histone modifications to regulate transcription in large-scale. Among our findings, the cooperation among histone modifications provides new evidence for the hypothesis of histone code. Furthermore, the rules output by our method can be used to predict the change of gene expression.

  4. Large scale purification of RNA nanoparticles by preparative ultracentrifugation.

    PubMed

    Jasinski, Daniel L; Schwartz, Chad T; Haque, Farzin; Guo, Peixuan

    2015-01-01

    Purification of large quantities of supramolecular RNA complexes is of paramount importance due to the large quantities of RNA needed and the purity requirements for in vitro and in vivo assays. Purification is generally carried out by liquid chromatography (HPLC), polyacrylamide gel electrophoresis (PAGE), or agarose gel electrophoresis (AGE). Here, we describe an efficient method for the large-scale purification of RNA prepared by in vitro transcription using T7 RNA polymerase by cesium chloride (CsCl) equilibrium density gradient ultracentrifugation and the large-scale purification of RNA nanoparticles by sucrose gradient rate-zonal ultracentrifugation or cushioned sucrose gradient rate-zonal ultracentrifugation.

  5. The Evolution of Baryons in Cosmic Large Scale Structure

    NASA Astrophysics Data System (ADS)

    Snedden, Ali; Arielle Phillips, Lara; Mathews, Grant James; Coughlin, Jared; Suh, In-Saeng; Bhattacharya, Aparna

    2015-01-01

    The environments of galaxies play a critical role in their formation and evolution. We study these environments using cosmological simulations with star formation and supernova feedback included. From these simulations, we parse the large scale structure into clusters, filaments and voids using a segmentation algorithm adapted from medical imaging. We trace the star formation history, gas phase and metal evolution of the baryons in the intergalactic medium as function of structure. We find that our algorithm reproduces the baryon fraction in the intracluster medium and that the majority of star formation occurs in cold, dense filaments. We present the consequences this large scale environment has for galactic halos and galaxy evolution.

  6. [Issues of large scale tissue culture of medicinal plant].

    PubMed

    Lv, Dong-Mei; Yuan, Yuan; Zhan, Zhi-Lai

    2014-09-01

    In order to increase the yield and quality of the medicinal plant and enhance the competitive power of industry of medicinal plant in our country, this paper analyzed the status, problem and countermeasure of the tissue culture of medicinal plant on large scale. Although the biotechnology is one of the most efficient and promising means in production of medicinal plant, it still has problems such as stability of the material, safety of the transgenic medicinal plant and optimization of cultured condition. Establishing perfect evaluation system according to the characteristic of the medicinal plant is the key measures to assure the sustainable development of the tissue culture of medicinal plant on large scale.

  7. Large-Scale Graph Processing Analysis using Supercomputer Cluster

    NASA Astrophysics Data System (ADS)

    Vildario, Alfrido; Fitriyani; Nugraha Nurkahfi, Galih

    2017-01-01

    Graph implementation is widely use in various sector such as automotive, traffic, image processing and many more. They produce graph in large-scale dimension, cause the processing need long computational time and high specification resources. This research addressed the analysis of implementation large-scale graph using supercomputer cluster. We impelemented graph processing by using Breadth-First Search (BFS) algorithm with single destination shortest path problem. Parallel BFS implementation with Message Passing Interface (MPI) used supercomputer cluster at High Performance Computing Laboratory Computational Science Telkom University and Stanford Large Network Dataset Collection. The result showed that the implementation give the speed up averages more than 30 times and eficiency almost 90%.

  8. Corridors Increase Plant Species Richness at Large Scales

    SciTech Connect

    Damschen, Ellen I.; Haddad, Nick M.; Orrock,John L.; Tewksbury, Joshua J.; Levey, Douglas J.

    2006-09-01

    Habitat fragmentation is one of the largest threats to biodiversity. Landscape corridors, which are hypothesized to reduce the negative consequences of fragmentation, have become common features of ecological management plans worldwide. Despite their popularity, there is little evidence documenting the effectiveness of corridors in preserving biodiversity at large scales. Using a large-scale replicated experiment, we showed that habitat patches connected by corridors retain more native plant species than do isolated patches, that this difference increases over time, and that corridors do not promote invasion by exotic species. Our results support the use of corridors in biodiversity conservation.

  9. Clearing and Labeling Techniques for Large-Scale Biological Tissues

    PubMed Central

    Seo, Jinyoung; Choe, Minjin; Kim, Sung-Yon

    2016-01-01

    Clearing and labeling techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information with minimal disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. In this review, we provide an overview and comparison of existing clearing and labeling techniques and discuss challenges and opportunities in the investigations of large-scale biological systems. PMID:27239813

  10. Multilayer Graphene with Chemical Modification as Transparent Conducting Electrodes in Organic Light-Emitting Diode.

    PubMed

    Xu, Yilin; Yu, Haojian; Wang, Cong; Cao, Jin; Chen, Yigang; Ma, Zhongquan; You, Ying; Wan, Jixiang; Fang, Xiaohong; Chen, Xiaoyuan

    2017-12-01

    Graphene is a promising candidate for the replacement of the typical transparent electrode indium tin oxide in optoelectronic devices. Currently, the application of polycrystalline graphene films grown by chemical vapor deposition is limited for their low electrical conductivity due to the poor transfer technique. In this work, we developed a new method of preparing tri-layer graphene films with chemical modification and explored the influence of doping and patterning process on the performance of the graphene films as transparent electrodes. In order to demonstrate the application of the tri-layer graphene films in optoelectronics, we fabricated the organic light-emitting diodes (OLEDs) based on them and found that plasma etching is feasible with certain influence on the quality of the graphene films and the performance of the OLEDs.

  11. Chemical modification of cellulose by in situ reactive extrusion in ionic liquid.

    PubMed

    Zhang, Yue; Li, Haifeng; Li, Xinda; Gibril, Magdi E; Yu, Muhuo

    2014-01-01

    In order to prepare the spinning solution of cellulose with high concentration in environmentally friendly solvent, cellulose was chemically modified by in situ reactive extrusion with several chemicals, such as urea, phthalic anhydride (PA), maleic anhydride (MA) and butyl glycidyl ether (BGE) and with ionic liquid namely 1-N-butyl-3-methylimidazolium chloride (BMIMCl) as reaction medium. These four modifiers all in situ grafted onto cellulose and the modification effectiveness was found to decrease in the sequence, MA>PA>BGE>urea. The formation of side chain on cellulose backbone destroyed the regularity of cellulose chains and the hydrogen bond network efficiently. The concentration of modified cellulose in spinning solution can be up to 14-25%, comparing with 9% for unmodified cellulose in BMIMCl. The high solid content results in high efficiency and less energy consumption of fiber production and solvent recycle.

  12. The evolution of adenoviral vectors through genetic and chemical surface modifications.

    PubMed

    Capasso, Cristian; Garofalo, Mariangela; Hirvinen, Mari; Cerullo, Vincenzo

    2014-02-17

    A long time has passed since the first clinical trial with adenoviral (Ad) vectors. Despite being very promising, Ad vectors soon revealed their limitations in human clinical trials. The pre-existing immunity, the marked liver tropism and the high toxicity of first generation Ad (FG-Ad) vectors have been the main challenges for the development of new approaches. Significant effort toward the development of genetically and chemically modified adenoviral vectors has enabled researchers to create more sophisticated vectors for gene therapy, with an improved safety profile and a higher transduction ability of different tissues. In this review, we will describe the latest findings in the high-speed, evolving field of genetic and chemical modifications of adenoviral vectors, a field in which different disciplines, such as biomaterial research, virology and immunology, co-operate synergistically to create better gene therapy tools for modern challenges.

  13. Chemical modification approaches for improved performance of Na-ion battery electrodes

    NASA Astrophysics Data System (ADS)

    Byles, Bryan; Clites, Mallory; Pomerantseva, Ekaterina

    2015-08-01

    Na-ion batteries have received considerable attention in recent years but still face performance challenges such as limited cycle lifetime and low capacities at high current rates. In this work, we propose novel combinations of preand post-synthesis treatments to modify known Na-ion battery electrode materials to achieve enhanced electrochemical performance. We work with two model metal oxide materials to demonstrate the effectiveness of the different treatments. First, wet chemical preintercalation is combined with post-synthesis aging, hydrothermal treatment, and annealing of α-V2O5, resulting in enhanced capacity retention in a Na-ion battery system. The hydrothermal treatment resulted in an increased specific capacity of nearly 300 mAh/g. Second, post-synthesis acid leaching is performed on α- MnO2, also resulting in improved electrochemical capacity. The chemical, structural, and morphological changes brought about by the modifications are fully characterized.

  14. Altering protein surface charge with chemical modification modulates protein-gold nanoparticle aggregation

    NASA Astrophysics Data System (ADS)

    Jamison, Jennifer A.; Bryant, Erika L.; Kadali, Shyam B.; Wong, Michael S.; Colvin, Vicki L.; Matthews, Kathleen S.; Calabretta, Michelle K.

    2011-02-01

    Gold nanoparticles (AuNP) can interact with a wide range of molecules including proteins. Whereas significant attention has focused on modifying the nanoparticle surface to regulate protein-AuNP assembly or influence the formation of the protein "corona," modification of the protein surface as a mechanism to modulate protein-AuNP interaction has been less explored. Here, we examine this possibility utilizing three small globular proteins—lysozyme with high isoelectric point (pI) and established interactions with AuNP; α-lactalbumin with similar tertiary fold to lysozyme but low pI; and myoglobin with a different globular fold and an intermediate pI. We first chemically modified these proteins to alter their charged surface functionalities, and thereby shift protein pI, and then applied multiple methods to assess protein-AuNP assembly. At pH values lower than the anticipated pI of the modified protein, AuNP exposure elicits changes in the optical absorbance of the protein-NP solutions and other properties due to aggregate formation. Above the expected pI, however, protein-AuNP interaction is minimal, and both components remain isolated, presumably because both species are negatively charged. These data demonstrate that protein modification provides a powerful tool for modulating whether nanoparticle-protein interactions result in material aggregation. The results also underscore that naturally occurring protein modifications found in vivo may be critical in defining nanoparticle-protein corona compositions.

  15. Cell adhesive and antifouling polyvinyl chloride surfaces via wet chemical modification.

    PubMed

    Gabriel, Matthias; Strand, Dennis; Vahl, Christian-Friedrich

    2012-09-01

    Polyvinyl chloride (PVC) is one of the most frequently used polymers for the manufacturing of medical devices. Limitations for its usage are based upon unfavorable surface properties of the polymer including its hydrophobicity and lack of functionalities in order to increase its versatility. To address this issue, wet chemical modification of PVC was performed through surface amination using the bifunctional compound ethylene diamine. The reaction was conducted in order to achieve maximum surface amination while leaving the bulk material unaffected. The initial activation step was characterized by means of various methods including contact angle measurements, colorimetric amine quantification, infrared spectroscopy, and gel permeation chromatography. Depth profiles were obtained by a confocal microscopic method using fluorescence labeling. Exclusive surface modification was thus confirmed. To demonstrate biological applications of the presented technique, two examples were chosen: The covalent immobilization of the cell adhesive Asp-Gly-Asp-Ser-peptide (RGD) onto PVC samples yielded a surface that strongly supported cellular adhesion and proliferation of fibroblasts. In contrast, the decoration of PVC with the hydrophilic polymer polyethylene glycol prevented cellular adhesion to a large extent. The impact of these modifications was demonstrated by cell culture experiments.

  16. Chemical modification of cysteine and tyrosine residues in formyltetrahydrofolate synthetase from Clostridium thermoaceticum

    SciTech Connect

    Elliott, J.I.; Ljungdahl, L.G.

    1982-04-01

    The chemical modification of cysteine and tyrosine residues in formyltetrahydrofolate synthetase from Clostridium thermoaceticum has been examined relative to enzymatic activity and reactivity of these groups in the native protein. 4,4'-Dipyridyl disulfide, dansylaziridine, and fluorescein mercuric acetate all reacted with just one of six sulfhydryls per enzyme subunit, resulting in activities of 100, 95 and 70%, respectively. The K/sub m/ values for MgATP, formate, and tetrahydrofolate were unaltered in the modified enzymes. ATP did produce a 2.5-fold reduction in the rate of reaction between the enzyme and 4,4'-dipyridyl disulfide. Tetranitromethane reacted most rapidly with a single sulfhydryl group per subunit to produce a 20 to 30% loss in activity. Subsequent additions of tetranitromethane modified 2.2 tyrosines per subunit which was proportional to the loss of the remaining enzymatic activity. Folic acid, a competitive inhibitor, protected against modification of the tyrosines and the associated activity losses; however, the oxidation of the single sulfhydryl group and the initial 20 to 30% activity loss were unaffected. In the presence of folic acid, higher concentrations of tetranitromethane produced a loss of the remaining activity proportional to the modification of 1.2 tyrosines per subunit. It is proposed that at least 1 tyrosine critical for enzymatic activity is located at or near the folic acid/tetrahydrofolate binding site.

  17. Modification of wheat starch with succinic acid/acetanhydride and azelaic acid/acetanhydride mixtures. II. Chemical and physical properties.

    PubMed

    Ačkar, Durđica; Subarić, Drago; Babić, Jurislav; Miličević, Borislav; Jozinović, Antun

    2014-08-01

    The aim of this research was to investigate the influence of modification with succinic acid/acetanhydride and azelaic acid/acetanhydride mixtures on chemical and physical properties of wheat starch. Starch was isolated from two wheat varieties and modified with mixtures of succinic acid and acetanhydride and azelaic acid and acetanhydride in 4, 6 and 8% (w/w). Total starch content, resistant starch content, degree of modification, changes in FT-IR spectra, colour, gel texture and freeze-thaw stability were determined. Results showed that resistant starch content increased by both investigated modifications, and degree of modification increased proportionally to amount of reagents used. FT-IR analysis of modified starches showed peak around 1,740 cm(-1), characteristic for carbonyl group of ester. Total colour difference caused by modifications was detectable by trained people. Adhesiveness significantly increased, while freeze-thaw stability decreased by both investigated modifications.

  18. Semiconductor Nanocrystal Quantum Dot Synthesis Approaches Towards Large-Scale Industrial Production for Energy Applications

    NASA Astrophysics Data System (ADS)

    Hu, Michael Z.; Zhu, Ting

    2015-12-01

    This paper reviews the experimental synthesis and engineering developments that focused on various green approaches and large-scale process production routes for quantum dots. Fundamental process engineering principles were illustrated. In relation to the small-scale hot injection method, our discussions focus on the non-injection route that could be scaled up with engineering stir-tank reactors. In addition, applications that demand to utilize quantum dots as "commodity" chemicals are discussed, including solar cells and solid-state lightings.

  19. Semiconductor nanocrystal quantum dot synthesis approaches towards large-scale industrial production for energy applications

    SciTech Connect

    Hu, Michael Z.; Zhu, Ting

    2015-12-04

    This study reviews the experimental synthesis and engineering developments that focused on various green approaches and large-scale process production routes for quantum dots. Fundamental process engineering principles were illustrated. In relation to the small-scale hot injection method, our discussions focus on the non-injection route that could be scaled up with engineering stir-tank reactors. In addition, applications that demand to utilize quantum dots as "commodity" chemicals are discussed, including solar cells and solid-state lightings.

  20. Chemical modification of the bifunctional human serum pseudocholinesterase. Effect on the pseudocholinesterase and aryl acylamidase activities.

    PubMed

    Boopathy, R; Balasubramanian, A S

    1985-09-02

    The effect of chemical modification on the pseudocholinesterase and aryl acylamidase activities of purified human serum pseudocholinesterase was examined in the absence and presence of butyrylcholine iodide, the substrate of pseudocholinesterase. Modification by 2-hydroxy-5-nitrobenzyl bromide, N-bromosuccinimide, diethylpyrocarbonate and trinitrobenzenesulfonic acid caused a parallel inactivation of both pseudocholinesterase and aryl acylamidase activities that could be prevented by butyrylcholine iodide. With phenylglyoxal and 2,4-pentanedione as modifiers there was a selective activation of pseudocholinesterase alone with no effect on aryl acylamidase. This activation could be prevented by butyrylcholine iodide. N-Ethylmaleimide and p-hydroxy-mercuribenzoate when used for modification did not have any effect on the enzyme activities. The results suggested essential tryptophan, lysine and histidine residues at a common catalytic site for pseudocholinesterase and aryl acylamidase and an arginine residue (or residues) exclusively for pseudocholinesterase. The use of N-acetylimidazole, tetranitromethane and acetic anhydride as modifiers indicated a biphasic change in both pseudocholinesterase and aryl acylamidase activities. At low concentrations of the modifiers a stimulation in activities and at high concentrations an inactivation was observed. Butyrylcholine iodide or propionylcholine chloride selectively protected the inactivation phase without affecting the activation phase. Protection by the substrates at the inactivation phase resulted in not only a reversal of the enzyme inactivation but also an activation. Spectral studies and hydroxylamine treatment showed that tyrosine residues were modified during the activation phase. The results suggested that the modified tyrosine residues responsible for the activation were not involved in the active site of pseudocholinesterase or aryl acylamidase and that they were more amenable for modification in comparison to

  1. Engineering specific chemical modification sites into a collagen-like protein from Streptococcus pyogenes.

    PubMed

    Stoichevska, Violet; Peng, Yong Y; Vashi, Aditya V; Werkmeister, Jerome A; Dumsday, Geoff J; Ramshaw, John A M

    2017-03-01

    Recombinant bacterial collagens provide a new opportunity for safe biomedical materials. They are readily expressed in Escherichia coli in good yield and can be readily purified by simple approaches. However, recombinant proteins are limited in that direct secondary modification during expression is generally not easily achieved. Thus, inclusion of unusual amino acids, cyclic peptides, sugars, lipids, and other complex functions generally needs to be achieved chemically after synthesis and extraction. In the present study, we have illustrated that bacterial collagens that have had their sequences modified to include cysteine residue(s), which are not normally present in bacterial collagen-like sequences, enable a range of specific chemical modification reactions to be produced. Various model reactions were shown to be effective for modifying the collagens. The ability to include alkyne (or azide) functions allows the extensive range of substitutions that are available via "click" chemistry to be accessed. When bifunctional reagents were used, some crosslinking occurred to give higher molecular weight polymeric proteins, but gels were not formed. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 806-813, 2017.

  2. Chemical modification of glycerinated stalks shows tyrosine residues essential for spasmoneme contraction of Vorticella sp.

    PubMed

    Fang, Jie; Zhang, Bei; Chen, Ning; Asai, Hiroshi

    2004-05-01

    Chemical modification of glycerinated stalks of Vorticella with TNM is used to investigate the role of tyrosine residues in the Ca(2+)-induced contraction of the spasmoneme. Tetranitromethane (TNM) is often employed as a specific reagent for the nitration of tyrosine residues in a protein at neutral and slightly alkaline pHs although TNM can also oxidize cysteine residues in the acidic and neutral pH range. Prior incubation with Ca(2+) of stalks to be treated with TNM can protect the spasmoneme from irreversible denaturation. On the other hand, TNM treatment in the absence of free Ca(2+) causes an irreversible denaturation of the spasmoneme. It was revealed by us that an isolated Ca(2+)-binding protein called spasmin could not bind with Ca(2+) after TNM treatment, even if the treatment was performed in the presence of Ca(2+). In an additional experiment, we confirmed that the chemical modification of cysteine residues in the spasmoneme with N-7-dimethyl-amino-4methyl- coumarinyl- maleimide (DACM) has no effect on the contractibility. These results suggest that tyrosine residues in spasmin are essential for spasmoneme contraction and are protected from TNM in the presence of Ca(2+) when spasmin binds with its receptor protein in the spasmoneme.

  3. Physico-chemical modifications of conjugated linoleic acid for ruminal protection and oxidative stability.

    PubMed

    Moon, Hyun-Seuk; Lee, Hong-Gu; Chung, Chung-Soo; Choi, Yun-Jaie; Cho, Chong-Su

    2008-06-01

    Conjugated linoleic acid (CLA) is a mixture of positional and geometric isomers of octadecadienoic acid [linoleic acid (LA), 18:2n-6]. Although ruminant milk and meat products represent the largest natural source of CLA and therefore, their concentration in ruminant lipids are of interest to human health, chemical or physical modifications of CLA should be needed as a means to enhance oxidative stability, to improve post-ruminal bioavailability, and to increase the clinical application. In fact, CLA are rapidly decomposed to form furan fatty acids when its are oxidized in air, and the effectiveness of dietary supplements of CLA may be related to the extent that their metabolisms by rumen bacteria are avoided. For these reasons, many scientists have examined the effect of manufacturing and protection on the stability of CLA in ruminants and food products. In this review, physico-chemical modifications of CLA for ruminal protection such as calcium salt (Ca), formaldehyde protection (FP), lipid encapsulation (LE), and amide linkage (AL), and for oxidative stability such as green tea catechin (GTC), cyclodextrin (CD), arginine (Arg), amylase, and PEGylation are proposed.

  4. Physico-chemical modifications of conjugated linoleic acid for ruminal protection and oxidative stability

    PubMed Central

    Moon, Hyun-Seuk; Lee, Hong-Gu; Chung, Chung-Soo; Choi, Yun-Jaie; Cho, Chong-Su

    2008-01-01

    Conjugated linoleic acid (CLA) is a mixture of positional and geometric isomers of octadecadienoic acid [linoleic acid (LA), 18:2n-6]. Although ruminant milk and meat products represent the largest natural source of CLA and therefore, their concentration in ruminant lipids are of interest to human health, chemical or physical modifications of CLA should be needed as a means to enhance oxidative stability, to improve post-ruminal bioavailability, and to increase the clinical application. In fact, CLA are rapidly decomposed to form furan fatty acids when its are oxidized in air, and the effectiveness of dietary supplements of CLA may be related to the extent that their metabolisms by rumen bacteria are avoided. For these reasons, many scientists have examined the effect of manufacturing and protection on the stability of CLA in ruminants and food products. In this review, physico-chemical modifications of CLA for ruminal protection such as calcium salt (Ca), formaldehyde protection (FP), lipid encapsulation (LE), and amide linkage (AL), and for oxidative stability such as green tea catechin (GTC), cyclodextrin (CD), arginine (Arg), amylase, and PEGylation are proposed. PMID:18513443

  5. Recent Progress in Chemical Modifications of Chlorophylls and Bacteriochlorophylls for the Applications in Photodynamic Therapy.

    PubMed

    Staron, Jakub; Boron, Bożena; Karcz, Dariusz; Szczygieł, Małgorzata; Fiedor, Leszek

    2015-01-01

    Since photodynamic therapy emerged as a promising cancer treatment, the development of photosensitizers has gained great interest. In this context, the photosynthetic pigments, chlorophylls and bacteriochlorophylls, as excellent natural photosensitizers, attracted much attention. In effect, several (bacterio) chlorophyll-based phototherapeutic agents have been developed and (or are about to) enter the clinics. The aim of this review article is to give a survey of the advances in the synthetic chemistry of these pigments which have been made over the last decade, and which are pertinent to the application of their derivatives as photosensitizers for photodynamic therapy (PDT). The review focuses on the synthetic strategies undertaken to obtain novel derivatives of (bacterio)chlorophylls with both enhanced photosensitizing and tumorlocalizing properties, and also improved photo- and chemical stability. These include modifications of the C- 17-ester moiety, the isocyclic ring, the central binding pocket, and the derivatization of peripheral functionalities at the C-3 and C-7 positions with carbohydrate-, peptide-, and nanoparticle moieties or other residues. The effects of these modifications on essential features of the pigments are discussed, such as the efficiency of reactive oxygen species generation, photostability, phototoxicity and interactions with living organisms. The review is divided into several sections. In the first part, the principles of PDT and photosensitizer action are briefly described. Then the relevant photophysical features of (bacterio)chlorophylls and earlier approaches to their modification are summarized. Next, a more detailed overview of the progress in synthetic methods is given, followed by a discussion of the effects of these modifications on the photophysics of the pigments and on their biological activity.

  6. Sensitivity study of a large-scale air pollution model by using high-performance computations and Monte Carlo algorithms

    NASA Astrophysics Data System (ADS)

    Ostromsky, Tz.; Dimov, I.; Georgieva, R.; Marinov, P.; Zlatev, Z.

    2013-10-01

    In this paper we present some new results of our work on sensitivity analysis of a large-scale air pollution model, more specificly the Danish Eulerian Model (DEM). The main purpose of this study is to analyse the sensitivity of ozone concentrations with respect to the rates of some chemical reactions. The current sensitivity study considers the rates of six important chemical reactions and is done for the areas of several European cities with different geographical locations, climate, industrialization and population density. One of the most widely used variance-based techniques for sensitivity analysis, such as Sobol estimates and their modifications, have been used in this study. A vast number of numerical experiments with a specially adapted for the purpose version of the Danish Eulerian Model (SA-DEM) were carried out to compute global Sobol sensitivity measures. SA-DEM was implemented and run on two powerful cluster supercomputers: IBM Blue Gene/P, the most powerful parallel supercomputer in Bulgaria and IBM MareNostrum III, the most powerful parallel supercomputer in Spain. The refined (480 × 480) mesh version of the model was used in the experiments on MareNostrum III, which is a challenging computational problem even on such a powerful machine. Some optimizations of the code with respect to the parallel efficiency and the memory use were performed. Tables with performance results of a number of numerical experiments on IBM BlueGene/P and on IBM MareNostrum III are presented and analysed.

  7. Large-scale search for dark-matter axions

    SciTech Connect

    Kinion, D; van Bibber, K

    2000-08-30

    We review the status of two ongoing large-scale searches for axions which may constitute the dark matter of our Milky Way halo. The experiments are based on the microwave cavity technique proposed by Sikivie, and marks a ''second-generation'' to the original experiments performed by the Rochester-Brookhaven-Fermilab collaboration, and the University of Florida group.

  8. Measurement, Sampling, and Equating Errors in Large-Scale Assessments

    ERIC Educational Resources Information Center

    Wu, Margaret

    2010-01-01

    In large-scale assessments, such as state-wide testing programs, national sample-based assessments, and international comparative studies, there are many steps involved in the measurement and reporting of student achievement. There are always sources of inaccuracies in each of the steps. It is of interest to identify the source and magnitude of…

  9. Resilience of Florida Keys coral communities following large scale disturbances

    EPA Science Inventory

    The decline of coral reefs in the Caribbean over the last 40 years has been attributed to multiple chronic stressors and episodic large-scale disturbances. This study assessed the resilience of coral communities in two different regions of the Florida Keys reef system between 199...

  10. Large-Scale Machine Learning for Classification and Search

    ERIC Educational Resources Information Center

    Liu, Wei

    2012-01-01

    With the rapid development of the Internet, nowadays tremendous amounts of data including images and videos, up to millions or billions, can be collected for training machine learning models. Inspired by this trend, this thesis is dedicated to developing large-scale machine learning techniques for the purpose of making classification and nearest…

  11. Efficient On-Demand Operations in Large-Scale Infrastructures

    ERIC Educational Resources Information Center

    Ko, Steven Y.

    2009-01-01

    In large-scale distributed infrastructures such as clouds, Grids, peer-to-peer systems, and wide-area testbeds, users and administrators typically desire to perform "on-demand operations" that deal with the most up-to-date state of the infrastructure. However, the scale and dynamism present in the operating environment make it challenging to…

  12. Assuring Quality in Large-Scale Online Course Development

    ERIC Educational Resources Information Center

    Parscal, Tina; Riemer, Deborah

    2010-01-01

    Student demand for online education requires colleges and universities to rapidly expand the number of courses and programs offered online while maintaining high quality. This paper outlines two universities respective processes to assure quality in large-scale online programs that integrate instructional design, eBook custom publishing, Quality…

  13. Large-Scale Assessments and Educational Policies in Italy

    ERIC Educational Resources Information Center

    Damiani, Valeria

    2016-01-01

    Despite Italy's extensive participation in most large-scale assessments, their actual influence on Italian educational policies is less easy to identify. The present contribution aims at highlighting and explaining reasons for the weak and often inconsistent relationship between international surveys and policy-making processes in Italy.…

  14. Improving the Utility of Large-Scale Assessments in Canada

    ERIC Educational Resources Information Center

    Rogers, W. Todd

    2014-01-01

    Principals and teachers do not use large-scale assessment results because the lack of distinct and reliable subtests prevents identifying strengths and weaknesses of students and instruction, the results arrive too late to be used, and principals and teachers need assistance to use the results to improve instruction so as to improve student…

  15. Current Scientific Issues in Large Scale Atmospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Miller, T. L. (Compiler)

    1986-01-01

    Topics in large scale atmospheric dynamics are discussed. Aspects of atmospheric blocking, the influence of transient baroclinic eddies on planetary-scale waves, cyclogenesis, the effects of orography on planetary scale flow, small scale frontal structure, and simulations of gravity waves in frontal zones are discussed.

  16. Large-Scale Innovation and Change in UK Higher Education

    ERIC Educational Resources Information Center

    Brown, Stephen

    2013-01-01

    This paper reflects on challenges universities face as they respond to change. It reviews current theories and models of change management, discusses why universities are particularly difficult environments in which to achieve large scale, lasting change and reports on a recent attempt by the UK JISC to enable a range of UK universities to employ…

  17. Mixing Metaphors: Building Infrastructure for Large Scale School Turnaround

    ERIC Educational Resources Information Center

    Peurach, Donald J.; Neumerski, Christine M.

    2015-01-01

    The purpose of this analysis is to increase understanding of the possibilities and challenges of building educational infrastructure--the basic, foundational structures, systems, and resources--to support large-scale school turnaround. Building educational infrastructure often exceeds the capacity of schools, districts, and state education…

  18. Large-Scale Environmental Influences on Aquatic Animal Health

    EPA Science Inventory

    In the latter portion of the 20th century, North America experienced numerous large-scale mortality events affecting a broad diversity of aquatic animals. Short-term forensic investigations of these events have sometimes characterized a causative agent or condition, but have rare...

  19. A bibliographical surveys of large-scale systems

    NASA Technical Reports Server (NTRS)

    Corliss, W. R.

    1970-01-01

    A limited, partly annotated bibliography was prepared on the subject of large-scale system control. Approximately 400 references are divided into thirteen application areas, such as large societal systems and large communication systems. A first-author index is provided.

  20. Probabilistic Cuing in Large-Scale Environmental Search

    ERIC Educational Resources Information Center

    Smith, Alastair D.; Hood, Bruce M.; Gilchrist, Iain D.

    2010-01-01

    Finding an object in our environment is an important human ability that also represents a critical component of human foraging behavior. One type of information that aids efficient large-scale search is the likelihood of the object being in one location over another. In this study we investigated the conditions under which individuals respond to…

  1. Newton Methods for Large Scale Problems in Machine Learning

    ERIC Educational Resources Information Center

    Hansen, Samantha Leigh

    2014-01-01

    The focus of this thesis is on practical ways of designing optimization algorithms for minimizing large-scale nonlinear functions with applications in machine learning. Chapter 1 introduces the overarching ideas in the thesis. Chapters 2 and 3 are geared towards supervised machine learning applications that involve minimizing a sum of loss…

  2. Large-Scale Physical Separation of Depleted Uranium from Soil

    DTIC Science & Technology

    2012-09-01

    ER D C/ EL T R -1 2 - 2 5 Army Range Technology Program Large-Scale Physical Separation of Depleted Uranium from Soil E nv ir on m en ta l...Separation ................................................................................................................ 2   Project Background...5  2   Materials and Methods

  3. Lessons from Large-Scale Renewable Energy Integration Studies: Preprint

    SciTech Connect

    Bird, L.; Milligan, M.

    2012-06-01

    In general, large-scale integration studies in Europe and the United States find that high penetrations of renewable generation are technically feasible with operational changes and increased access to transmission. This paper describes other key findings such as the need for fast markets, large balancing areas, system flexibility, and the use of advanced forecasting.

  4. Computational Complexity, Efficiency and Accountability in Large Scale Teleprocessing Systems.

    DTIC Science & Technology

    1980-12-01

    COMPLEXITY, EFFICIENCY AND ACCOUNTABILITY IN LARGE SCALE TELEPROCESSING SYSTEMS DAAG29-78-C-0036 STANFORD UNIVERSITY JOHN T. GILL MARTIN E. BELLMAN...solve but easy to check. Ve have also suggested howy sucb random tapes can be simulated by determin- istically generating "pseudorandom" numbers by a

  5. Large-scale silicon optical switches for optical interconnection

    NASA Astrophysics Data System (ADS)

    Qiao, Lei; Tang, Weijie; Chu, Tao

    2016-11-01

    Large-scale optical switches are greatly demanded in building optical interconnections in data centers and high performance computers (HPCs). Silicon optical switches have advantages of being compact and CMOS process compatible, which can be easily monolithically integrated. However, there are difficulties to construct large ports silicon optical switches. One of them is the non-uniformity of the switch units in large scale silicon optical switches, which arises from the fabrication error and causes confusion in finding the unit optimum operation points. In this paper, we proposed a method to detect the optimum operating point in large scale switch with limited build-in power monitors. We also propose methods for improving the unbalanced crosstalk of cross/bar states in silicon electro-optical MZI switches and insertion losses. Our recent progress in large scale silicon optical switches, including 64 × 64 thermal-optical and 32 × 32 electro-optical switches will be introduced. To the best our knowledge, both of them are the largest scale silicon optical switches in their sections, respectively. The switches were fabricated on 340-nm SOI substrates with CMOS 180- nm processes. The crosstalk of the 32 × 32 electro-optic switch was -19.2dB to -25.1 dB, while the value of the 64 × 64 thermal-optic switch was -30 dB to -48.3 dB.

  6. The large scale microwave background anisotropy in decaying particle cosmology

    SciTech Connect

    Panek, M.

    1987-06-01

    We investigate the large-scale anisotropy of the microwave background radiation in cosmological models with decaying particles. The observed value of the quadrupole moment combined with other constraints gives an upper limit on the redshift of the decay z/sub d/ < 3-5. 12 refs., 2 figs.

  7. DESIGN OF LARGE-SCALE AIR MONITORING NETWORKS

    EPA Science Inventory

    The potential effects of air pollution on human health have received much attention in recent years. In the U.S. and other countries, there are extensive large-scale monitoring networks designed to collect data to inform the public of exposure risks to air pollution. A major crit...

  8. Large Scale Survey Data in Career Development Research

    ERIC Educational Resources Information Center

    Diemer, Matthew A.

    2008-01-01

    Large scale survey datasets have been underutilized but offer numerous advantages for career development scholars, as they contain numerous career development constructs with large and diverse samples that are followed longitudinally. Constructs such as work salience, vocational expectations, educational expectations, work satisfaction, and…

  9. The Large-Scale Structure of Scientific Method

    ERIC Educational Resources Information Center

    Kosso, Peter

    2009-01-01

    The standard textbook description of the nature of science describes the proposal, testing, and acceptance of a theoretical idea almost entirely in isolation from other theories. The resulting model of science is a kind of piecemeal empiricism that misses the important network structure of scientific knowledge. Only the large-scale description of…

  10. Ecosystem resilience despite large-scale altered hydro climatic conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Climate change is predicted to increase both drought frequency and duration, and when coupled with substantial warming, will establish a new hydroclimatological paradigm for many regions. Large-scale, warm droughts have recently impacted North America, Africa, Europe, Amazonia, and Australia result...

  11. US National Large-scale City Orthoimage Standard Initiative

    USGS Publications Warehouse

    Zhou, G.; Song, C.; Benjamin, S.; Schickler, W.

    2003-01-01

    The early procedures and algorithms for National digital orthophoto generation in National Digital Orthophoto Program (NDOP) were based on earlier USGS mapping operations, such as field control, aerotriangulation (derived in the early 1920's), the quarter-quadrangle-centered (3.75 minutes of longitude and latitude in geographic extent), 1:40,000 aerial photographs, and 2.5 D digital elevation models. However, large-scale city orthophotos using early procedures have disclosed many shortcomings, e.g., ghost image, occlusion, shadow. Thus, to provide the technical base (algorithms, procedure) and experience needed for city large-scale digital orthophoto creation is essential for the near future national large-scale digital orthophoto deployment and the revision of the Standards for National Large-scale City Digital Orthophoto in National Digital Orthophoto Program (NDOP). This paper will report our initial research results as follows: (1) High-precision 3D city DSM generation through LIDAR data processing, (2) Spatial objects/features extraction through surface material information and high-accuracy 3D DSM data, (3) 3D city model development, (4) Algorithm development for generation of DTM-based orthophoto, and DBM-based orthophoto, (5) True orthophoto generation by merging DBM-based orthophoto and DTM-based orthophoto, and (6) Automatic mosaic by optimizing and combining imagery from many perspectives.

  12. Developing and Understanding Methods for Large-Scale Nonlinear Optimization

    DTIC Science & Technology

    2006-07-24

    algorithms for large-scale uncon- strained and constrained optimization problems, including limited-memory methods for problems with -2- many thousands...34Published in peer-reviewed journals" E. Eskow, B. Bader, R. Byrd, S. Crivelli, T. Head-Gordon, V. Lamberti and R. Schnabel, "An optimization approach to the

  13. International Large-Scale Assessments: What Uses, What Consequences?

    ERIC Educational Resources Information Center

    Johansson, Stefan

    2016-01-01

    Background: International large-scale assessments (ILSAs) are a much-debated phenomenon in education. Increasingly, their outcomes attract considerable media attention and influence educational policies in many jurisdictions worldwide. The relevance, uses and consequences of these assessments are often the focus of research scrutiny. Whilst some…

  14. Extracting Useful Semantic Information from Large Scale Corpora of Text

    ERIC Educational Resources Information Center

    Mendoza, Ray Padilla, Jr.

    2012-01-01

    Extracting and representing semantic information from large scale corpora is at the crux of computer-assisted knowledge generation. Semantic information depends on collocation extraction methods, mathematical models used to represent distributional information, and weighting functions which transform the space. This dissertation provides a…

  15. Large scale structure of the sun's radio corona

    NASA Technical Reports Server (NTRS)

    Kundu, M. R.

    1986-01-01

    Results of studies of large scale structures of the corona at long radio wavelengths are presented, using data obtained with the multifrequency radioheliograph of the Clark Lake Radio Observatory. It is shown that features corresponding to coronal streamers and coronal holes are readily apparent in the Clark Lake maps.

  16. Moon-based Earth Observation for Large Scale Geoscience Phenomena

    NASA Astrophysics Data System (ADS)

    Guo, Huadong; Liu, Guang; Ding, Yixing

    2016-07-01

    The capability of Earth observation for large-global-scale natural phenomena needs to be improved and new observing platform are expected. We have studied the concept of Moon as an Earth observation in these years. Comparing with manmade satellite platform, Moon-based Earth observation can obtain multi-spherical, full-band, active and passive information,which is of following advantages: large observation range, variable view angle, long-term continuous observation, extra-long life cycle, with the characteristics of longevity ,consistency, integrity, stability and uniqueness. Moon-based Earth observation is suitable for monitoring the large scale geoscience phenomena including large scale atmosphere change, large scale ocean change,large scale land surface dynamic change,solid earth dynamic change,etc. For the purpose of establishing a Moon-based Earth observation platform, we already have a plan to study the five aspects as follows: mechanism and models of moon-based observing earth sciences macroscopic phenomena; sensors' parameters optimization and methods of moon-based Earth observation; site selection and environment of moon-based Earth observation; Moon-based Earth observation platform; and Moon-based Earth observation fundamental scientific framework.

  17. Large-scale screening by the automated Wassermann reaction

    PubMed Central

    Wagstaff, W.; Firth, R.; Booth, J. R.; Bowley, C. C.

    1969-01-01

    In view of the drawbacks in the use of the Kahn test for large-scale screening of blood donors, mainly those of human error through work overload and fatiguability, an attempt was made to adapt an existing automated complement-fixation technique for this purpose. This paper reports the successful results of that adaptation. PMID:5776559

  18. Large-scale societal changes and intentionality - an uneasy marriage.

    PubMed

    Bodor, Péter; Fokas, Nikos

    2014-08-01

    Our commentary focuses on juxtaposing the proposed science of intentional change with facts and concepts pertaining to the level of large populations or changes on a worldwide scale. Although we find a unified evolutionary theory promising, we think that long-term and large-scale, scientifically guided - that is, intentional - social change is not only impossible, but also undesirable.

  19. Pre-slow-roll initial conditions: Large scale power suppression and infrared aspects during inflation

    NASA Astrophysics Data System (ADS)

    Lello, Louis; Boyanovsky, Daniel; Holman, Richard

    2014-03-01

    If the large-scale anomalies in the temperature power spectrum of the cosmic microwave background are of primordial origin, they may herald modifications to the slow-roll inflationary paradigm on the largest scales. We study the possibility that the origin of the large-scale power suppression is a modification of initial conditions during slow roll as a result of a pre-slow-roll phase during which the inflaton evolves rapidly. This stage is manifest in a potential in the equations for the Gaussian fluctuations during slow roll and modifies the power spectra of scalar perturbations via an initial condition transfer function T(k). We provide a general analytical study of its large- and small-scale properties and analyze the impact of these initial conditions on the infrared aspects of typical test scalar fields. The infrared behavior of massless minimally coupled test scalar field theories leads to the dynamical generation of mass and anomalous dimensions, both depending nonanalytically on T(0). During inflation, all quanta decay into many quanta even of the same field because of the lack of kinematic thresholds. The decay leads to a quantum entangled state of subhorizon and superhorizon quanta with correlations across the horizon. We find the modifications of the decay width and the entanglement entropy from the initial conditions. In all cases, initial conditions from a "fast-roll" stage that lead to a suppression in the scalar power spectrum at large scales also result in a suppression of the dynamically generated masses, anomalous dimensions and decay widths.

  20. A method of orbital analysis for large-scale first-principles simulations

    SciTech Connect

    Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke

    2014-06-28

    An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF{sub 4})

  1. FEASIBILITY OF LARGE-SCALE OCEAN CO2 SEQUESTRATION

    SciTech Connect

    Dr. Peter Brewer; Dr. James Barry

    2002-09-30

    We have continued to carry out creative small-scale experiments in the deep ocean to investigate the science underlying questions of possible future large-scale deep-ocean CO{sub 2} sequestration as a means of ameliorating greenhouse gas growth rates in the atmosphere. This project is closely linked to additional research funded by the DoE Office of Science, and to support from the Monterey Bay Aquarium Research Institute. The listing of project achievements here over the past year reflects these combined resources. Within the last project year we have: (1) Published a significant workshop report (58 pages) entitled ''Direct Ocean Sequestration Expert's Workshop'', based upon a meeting held at MBARI in 2001. The report is available both in hard copy, and on the NETL web site. (2) Carried out three major, deep ocean, (3600m) cruises to examine the physical chemistry, and biological consequences, of several liter quantities released on the ocean floor. (3) Carried out two successful short cruises in collaboration with Dr. Izuo Aya and colleagues (NMRI, Osaka, Japan) to examine the fate of cold (-55 C) CO{sub 2} released at relatively shallow ocean depth. (4) Carried out two short cruises in collaboration with Dr. Costas Tsouris, ORNL, to field test an injection nozzle designed to transform liquid CO{sub 2} into a hydrate slurry at {approx}1000m depth. (5) In collaboration with Prof. Jill Pasteris (Washington University) we have successfully accomplished the first field test of a deep ocean laser Raman spectrometer for probing in situ the physical chemistry of the CO{sub 2} system. (6) Submitted the first major paper on biological impacts as determined from our field studies. (7) Submitted a paper on our measurements of the fate of a rising stream of liquid CO{sub 2} droplets to Environmental Science & Technology. (8) Have had accepted for publication in Eos the first brief account of the laser Raman spectrometer success. (9) Have had two papers submitted for the

  2. The Revolution and Evolution of Shotgun Proteomics for Large-Scale Proteome Analysis

    PubMed Central

    Yates, John R.

    2013-01-01

    Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules such as a proteins, protein complexes and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications. PMID:23294060

  3. The effect of chemical modification with pyromellitic anhydride on structure, function, and thermal stability of horseradish peroxidase.

    PubMed

    Hassani, Leila

    2012-06-01

    The stability of enzymes remains a critical issue in biotechnology. Compared with the strategies for obtaining stable enzymes, chemical modification is a simple and effective technique. In the present study, chemical modification of horseradish peroxidase (HRP) was carried out with pyromellitic anhydride. HRP has achieved a prominent position in the pharmaceutical, chemical, and biotechnological industries. In this study, the effect of chemical modification on thermal stability, structure, and function of the enzyme was studied by fluorescence, circular dichroism, and absorbance measurements. The results indicated a decrease in compactness of the structure and a considerable enhancement in thermal stability of HRP below 60 °C. It seems the charge replacement and introduction of the bulky group bring about the observed structural and the functional changes.

  4. Large-Scale Impact Cratering and Early Earth Evolution

    NASA Technical Reports Server (NTRS)

    Grieve, R. A. F.; Cintala, M. J.

    1997-01-01

    The surface of the Moon attests to the importance of large-scale impact in its early crustal evolution. Previous models of the effects of a massive bombardment on terrestrial crustal evolution have relied on analogies with the Moon, with allowances for the presence of water and a thinner lithosphere. It is now apparent that strict lunar-terrestrial analogies are incorrect because of the "differential scaling" of crater dimensions and melt volumes with event size and planetary gravity. Impact melt volumes and "ancient cavity dimensions for specific impacts were modeled according to previous procedures. In the terrestrial case, the melt volume (V(sub m)) exceeds that of the transient cavity (V(sub tc)) at diameters > or = 400 km. This condition is reached on the Moon only with transient cavity diameters > or = 3000 km, equivalent to whole Moon melting. The melt volumes in these large impact events are minimum estimates, since, at these sizes, the higher temperature of the target rocks at depth will increase melt production. Using the modification-scaling relation of Croft, a transient cavity diameter of about 400 km in the terrestrial environment corresponds to an expected final impact "basin" diameter of about 900 km. Such a "basin" would be comparable in dimensions to the lunar basin Orientale. This 900-km "basin" on the early Earth, however, would not have had the appearance of Orientale. It would have been essentially a melt pool, and, morphologically, would have had more in common with the palimpsests structures on Callisto and Ganymede. With the terrestrial equivalents to the large multiring basins of the Moon being manifested as muted palimpsest-like structures filled with impact melt, it is unlikely they played a role in establishing the freeboard on the early Earth. The composition of the massive impact melt sheets (> 10 (exp 7) cu km) produced in "basin-forming" events on the early Earth would have most likely ranged from basaltic to more mafic for the

  5. A Decentralized Multivariable Robust Adaptive Voltage and Speed Regulator for Large-Scale Power Systems

    NASA Astrophysics Data System (ADS)

    Okou, Francis A.; Akhrif, Ouassima; Dessaint, Louis A.; Bouchard, Derrick

    2013-05-01

    This papter introduces a decentralized multivariable robust adaptive voltage and frequency regulator to ensure the stability of large-scale interconnnected generators. Interconnection parameters (i.e. load, line and transormer parameters) are assumed to be unknown. The proposed design approach requires the reformulation of conventiaonal power system models into a multivariable model with generator terminal voltages as state variables, and excitation and turbine valve inputs as control signals. This model, while suitable for the application of modern control methods, introduces problems with regards to current design techniques for large-scale systems. Interconnection terms, which are treated as perturbations, do not meet the common matching condition assumption. A new adaptive method for a certain class of large-scale systems is therefore introduces that does not require the matching condition. The proposed controller consists of nonlinear inputs that cancel some nonlinearities of the model. Auxiliary controls with linear and nonlinear components are used to stabilize the system. They compensate unknown parametes of the model by updating both the nonlinear component gains and excitation parameters. The adaptation algorithms involve the sigma-modification approach for auxiliary control gains, and the projection approach for excitation parameters to prevent estimation drift. The computation of the matrix-gain of the controller linear component requires the resolution of an algebraic Riccati equation and helps to solve the perturbation-mismatching problem. A realistic power system is used to assess the proposed controller performance. The results show that both stability and transient performance are considerably improved following a severe contingency.

  6. The effect of chemical modification on the physico-chemical characteristics of halloysite: FTIR, XRF, and XRD studies

    NASA Astrophysics Data System (ADS)

    Szczepanik, Beata; Słomkiewicz, Piotr; Garnuszek, Magdalena; Czech, Kamil; Banaś, Dariusz; Kubala-Kukuś, Aldona; Stabrawa, Ilona

    2015-03-01

    The effect of chemical modification of halloysite from a Polish strip mine "Dunino" on the chemical composition and structure of this clay mineral was studied using infrared spectroscopy (ATR FT-IR), wavelength dispersive X-ray fluorescence (WDXRF), and X-ray powder diffraction (XRPD) methods. The results obtained by the WDXRF technique confirm that the content of silica and alumina was the highest for bleached halloysite samples and the lowest for acid-treated halloysite. A higher content of Fe2O3 in comparison to halloysite samples coming from other countries was observed for raw halloysite samples. XRPD diffraction pattern obtained for raw halloysite confirmed the presence of halloysite, kaolinite, hematite, and calcite minerals in the sample. Bleaching the halloysite removes (or significantly reduces) the content of other minerals present in the raw halloysite. The FT-IR spectra of the studied halloysite samples show in the 3700-3600 cm-1 region well-defined hydroxyl stretching bands characteristic for the kaolin-group minerals and bands associated with the vibrations of the aluminium-silicon skeleton in the 1400-1000 cm-1 region. Modifying halloysite with 4-chloro-aniline causes successive incorporation of amine into the BH sample.

  7. Physical and chemical basics of modification of poly(vinyl chloride) by means of polyisocyanate

    NASA Astrophysics Data System (ADS)

    Islamov, Anvar; Fakhrutdinova, Venera; Abdrakhmanova, Lyailya

    2016-01-01

    This research presents data relating to polyvinyl chloride (PVC) modification by means of reactive oligomer and measures technological, physical and mechanical properties of the modified composites. Polyisocyanate (PIC) has been chosen as the modifying reactive oligomer. It has been shown that insertion of the oligomer has a double effect on PVC. Primarily, PIC produces a plasticizing effect on PVC and in particular leads to an increase in thermal stability and melt flow index at the stage of processing. In addition, the molded PVC composites possess higher strength properties and lower deformability when exposed to temperature because of chemical transformations of PIC in polymer matrix and, as the result, the formation of cross-linked systems takes place. In this case, semi-interpenetrating structures are formed based on cross-linked products of PIC chemical transformations homogeneously distributed in the PVC matrix. It has been determined by means of IR-spectroscopy that the basic products of PIC curing are compounds with urea and biuret groups which leads to modifying effect on PVC especially: increase in strength, thermal and mechanical properties, and chemical resistance.

  8. Effect of chemical modification on molecular structure and functional properties of Musa AAB starch.

    PubMed

    Koteswara Reddy, Chagam; Vidya, P V; Haripriya, Sundaramoorthy

    2015-11-01

    Starch extracted from Musa AAB (poovan banana) was subjected to acetylation, acid-thinning and oxidation. The effect of the treatments on molecular structure and functional properties of starch were analysed. Chemical composition revealed that non-starch components were reduced after chemical treatment. Amylose content of starch decreased on acetylation from 24.16% to 20.90%, whereas it increased to 24.50% and 25.5% on oxidation and acid-thinning, respectively. X-ray diffraction pattern of modified starches showed B-type crystalline structure with peaks at 2θ=5.5°, 15.0°, 17.1° and 23.5°; which were parallel with the pattern observed in case of native starch. Swelling capacity of starch granules was found to reduce by acid-thinning and oxidation but acetylation induced to increase it. The percentage of colour (L*, a* and b*), solubility and water absorption capacities varied significantly from native starch after chemical modification. Changes in gelatinisation temperatures and enthalpy value of starches were observed in modified starches and it is varied according to reaction conditions. Pasting properties of the starches was increased by acetylation and oxidation while acid-thinning reduced it (P<0.05).

  9. Improving dry carbon nanotube actuators by chemical modifications, material hybridization, and proper engineering

    NASA Astrophysics Data System (ADS)

    Biso, Maurizio; Ansaldo, Alberto; Ricci, Davide

    2013-04-01

    Low voltage, dry electrochemical actuators can be prepared by using a gel made of carbon nanotubes and ionic liquid.1 Their performance can be significantly improved by combining physical and chemical modifications with a proper engineering. We demonstrated that multi walled carbon nanotubes can be effectively used for actuators preparation;2 we achieved interesting performance improvements by chemically cross linking carbon nanotubes using both aromatic and aliphatic diamines;3 we introduced a novel hybrid material, made by in-situ chemical polymerization of pyrrole on carbon nanotubes, that further boosts actuation by taking advantage of the peculiar properties of both materials in terms of maximum strain and conductivity;4 we investigated the influence of actuator thickness showing that the generated strain at high frequency is strongly enhanced when thickness is reduced. To overcome limitations set by bimorphs, we designed a novel actuator in which a metal spring, embedded in the solid electrolyte of a bimorph device, is used as a non-actuating counter plate resulting in a three electrode device capable of both linear and bending motion. Finally, we propose a way to model actuators performance in terms of purely material-dependent parameters instead of geometry-dependent ones.5

  10. Visualization of large-scale aqueous solubility data using a novel hierarchical data visualization technique.

    PubMed

    Yamashita, Fumiyoshi; Itoh, Takayuki; Hara, Hideto; Hashida, Mitsuru

    2006-01-01

    It is a difficult task to recognize the trends in molecular physical properties relevant to a specific chemical class and find a way to optimize potential compounds. We present here a novel hierarchical data visualization technique, named "HeiankyoView", to visualize large-scale multidimensional chemical information. HeiankyoView represents hierarchically organized data objects by mapping leaf nodes as colored square icons and nonleaf nodes as rectangular borders. In this way, data objects can be expressed as equishaped icons without overlapping one another in the two-dimensional display space. HeiankyoView has been applied to visualize aqueous solubility data for 908 compounds collected from the published literature. When the results of a recursive partitioning analysis and hierarchical clustering analysis were visualized, the trends hidden in the solubility data could be effectively displayed as intuitively understandable visual images. Most interestingly, the data visualization technique, without any statistical computations, was able to assist us in extracting from such large-scale data meaningful information establishing that ClogP and the molecular weight are critical factors in determining aqueous solubility. Thus, HeiankyoView is a powerful tool to help us understand structure-activity relationships intuitively from a large-scale data set.

  11. Large-scale linear nonparallel support vector machine solver.

    PubMed

    Tian, Yingjie; Ping, Yuan

    2014-02-01

    Twin support vector machines (TWSVMs), as the representative nonparallel hyperplane classifiers, have shown the effectiveness over standard SVMs from some aspects. However, they still have some serious defects restricting their further study and real applications: (1) They have to compute and store the inverse matrices before training, it is intractable for many applications where data appear with a huge number of instances as well as features; (2) TWSVMs lost the sparseness by using a quadratic loss function making the proximal hyperplane close enough to the class itself. This paper proposes a Sparse Linear Nonparallel Support Vector Machine, termed as L1-NPSVM, to deal with large-scale data based on an efficient solver-dual coordinate descent (DCD) method. Both theoretical analysis and experiments indicate that our method is not only suitable for large scale problems, but also performs as good as TWSVMs and SVMs.

  12. Prototype Vector Machine for Large Scale Semi-Supervised Learning

    SciTech Connect

    Zhang, Kai; Kwok, James T.; Parvin, Bahram

    2009-04-29

    Practicaldataminingrarelyfalls exactlyinto the supervisedlearning scenario. Rather, the growing amount of unlabeled data poses a big challenge to large-scale semi-supervised learning (SSL). We note that the computationalintensivenessofgraph-based SSLarises largely from the manifold or graph regularization, which in turn lead to large models that are dificult to handle. To alleviate this, we proposed the prototype vector machine (PVM), a highlyscalable,graph-based algorithm for large-scale SSL. Our key innovation is the use of"prototypes vectors" for effcient approximation on both the graph-based regularizer and model representation. The choice of prototypes are grounded upon two important criteria: they not only perform effective low-rank approximation of the kernel matrix, but also span a model suffering the minimum information loss compared with the complete model. We demonstrate encouraging performance and appealing scaling properties of the PVM on a number of machine learning benchmark data sets.

  13. Electron drift in a large scale solid xenon

    SciTech Connect

    Yoo, J.; Jaskierny, W. F.

    2015-08-21

    A study of charge drift in a large scale optically transparent solid xenon is reported. A pulsed high power xenon light source is used to liberate electrons from a photocathode. The drift speeds of the electrons are measured using a 8.7 cm long electrode in both the liquid and solid phase of xenon. In the liquid phase (163 K), the drift speed is 0.193 ± 0.003 cm/μs while the drift speed in the solid phase (157 K) is 0.397 ± 0.006 cm/μs at 900 V/cm over 8.0 cm of uniform electric fields. Furthermore, it is demonstrated that a factor two faster electron drift speed in solid phase xenon compared to that in liquid in a large scale solid xenon.

  14. Instrumentation Development for Large Scale Hypersonic Inflatable Aerodynamic Decelerator Characterization

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.

    2011-01-01

    Hypersonic Inflatable Aerodynamic Decelerator (HIAD) technology is currently being considered for multiple atmospheric entry applications as the limitations of traditional entry vehicles have been reached. The Inflatable Re-entry Vehicle Experiment (IRVE) has successfully demonstrated this technology as a viable candidate with a 3.0 m diameter vehicle sub-orbital flight. To further this technology, large scale HIADs (6.0 8.5 m) must be developed and tested. To characterize the performance of large scale HIAD technology new instrumentation concepts must be developed to accommodate the flexible nature inflatable aeroshell. Many of the concepts that are under consideration for the HIAD FY12 subsonic wind tunnel test series are discussed below.

  15. GAIA: A WINDOW TO LARGE-SCALE MOTIONS

    SciTech Connect

    Nusser, Adi; Branchini, Enzo; Davis, Marc E-mail: branchin@fis.uniroma3.it

    2012-08-10

    Using redshifts as a proxy for galaxy distances, estimates of the two-dimensional (2D) transverse peculiar velocities of distant galaxies could be obtained from future measurements of proper motions. We provide the mathematical framework for analyzing 2D transverse motions and show that they offer several advantages over traditional probes of large-scale motions. They are completely independent of any intrinsic relations between galaxy properties; hence, they are essentially free of selection biases. They are free from homogeneous and inhomogeneous Malmquist biases that typically plague distance indicator catalogs. They provide additional information to traditional probes that yield line-of-sight peculiar velocities only. Further, because of their 2D nature, fundamental questions regarding vorticity of large-scale flows can be addressed. Gaia, for example, is expected to provide proper motions of at least bright galaxies with high central surface brightness, making proper motions a likely contender for traditional probes based on current and future distance indicator measurements.

  16. Long gradient mode and large-scale structure observables

    NASA Astrophysics Data System (ADS)

    Allahyari, Alireza; Firouzjaee, Javad T.

    2017-03-01

    We extend the study of long-mode perturbations to other large-scale observables such as cosmic rulers, galaxy-number counts, and halo bias. The long mode is a pure gradient mode that is still outside an observer's horizon. We insist that gradient-mode effects on observables vanish. It is also crucial that the expressions for observables are relativistic. This allows us to show that the effects of a gradient mode on the large-scale observables vanish identically in a relativistic framework. To study the potential modulation effect of the gradient mode on halo bias, we derive a consistency condition to the first order in gradient expansion. We find that the matter variance at a fixed physical scale is not modulated by the long gradient mode perturbations when the consistency condition holds. This shows that the contribution of long gradient modes to bias vanishes in this framework.

  17. Lagrangian space consistency relation for large scale structure

    SciTech Connect

    Horn, Bart; Hui, Lam; Xiao, Xiao E-mail: lh399@columbia.edu

    2015-09-01

    Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias and Riotto and Peloso and Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present. The simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.

  18. Large Scale Deformation of the Western US Cordillera

    NASA Technical Reports Server (NTRS)

    Bennett, Richard A.

    2001-01-01

    Destructive earthquakes occur throughout the western US Cordillera (WUSC), not just within the San Andreas fault zone. But because we do not understand the present-day large-scale deformations of the crust throughout the WUSC, our ability to assess the potential for seismic hazards in this region remains severely limited. To address this problem, we are using a large collection of Global Positioning System (GPS) networks which spans the WUSC to precisely quantify present-day large-scale crustal deformations in a single uniform reference frame. Our work can roughly be divided into an analysis of the GPS observations to infer the deformation field across and within the entire plate boundary zone and an investigation of the implications of this deformation field regarding plate boundary dynamics.

  19. Electron drift in a large scale solid xenon

    DOE PAGES

    Yoo, J.; Jaskierny, W. F.

    2015-08-21

    A study of charge drift in a large scale optically transparent solid xenon is reported. A pulsed high power xenon light source is used to liberate electrons from a photocathode. The drift speeds of the electrons are measured using a 8.7 cm long electrode in both the liquid and solid phase of xenon. In the liquid phase (163 K), the drift speed is 0.193 ± 0.003 cm/μs while the drift speed in the solid phase (157 K) is 0.397 ± 0.006 cm/μs at 900 V/cm over 8.0 cm of uniform electric fields. Furthermore, it is demonstrated that a factor twomore » faster electron drift speed in solid phase xenon compared to that in liquid in a large scale solid xenon.« less

  20. LARGE-SCALE MOTIONS IN THE PERSEUS GALAXY CLUSTER

    SciTech Connect

    Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Sanders, J. S.; Mantz, A.; Nulsen, P. E. J.; Takei, Y.

    2012-10-01

    By combining large-scale mosaics of ROSAT PSPC, XMM-Newton, and Suzaku X-ray observations, we present evidence for large-scale motions in the intracluster medium of the nearby, X-ray bright Perseus Cluster. These motions are suggested by several alternating and interleaved X-ray bright, low-temperature, low-entropy arcs located along the east-west axis, at radii ranging from {approx}10 kpc to over a Mpc. Thermodynamic features qualitatively similar to these have previously been observed in the centers of cool-core clusters, and were successfully modeled as a consequence of the gas sloshing/swirling motions induced by minor mergers. Our observations indicate that such sloshing/swirling can extend out to larger radii than previously thought, on scales approaching the virial radius.

  1. The CLASSgal code for relativistic cosmological large scale structure

    SciTech Connect

    Dio, Enea Di; Montanari, Francesco; Durrer, Ruth; Lesgourgues, Julien E-mail: Francesco.Montanari@unige.ch E-mail: Ruth.Durrer@unige.ch

    2013-11-01

    We present accurate and efficient computations of large scale structure observables, obtained with a modified version of the CLASS code which is made publicly available. This code includes all relativistic corrections and computes both the power spectrum C{sub ℓ}(z{sub 1},z{sub 2}) and the corresponding correlation function ξ(θ,z{sub 1},z{sub 2}) of the matter density and the galaxy number fluctuations in linear perturbation theory. For Gaussian initial perturbations, these quantities contain the full information encoded in the large scale matter distribution at the level of linear perturbation theory. We illustrate the usefulness of our code for cosmological parameter estimation through a few simple examples.

  2. Rapid localization of point mutations in PCR products by chemical (HOT) modification.

    PubMed

    Tindall, K R; Whitaker, R A

    1991-01-01

    Our studies of mutational mechanisms in mammalian cells use the AS52 Chinese hamster ovary cell line. AS52 mutants can be selected as 6-thioguanine resistant colonies and mutations are studied at a chromosomally integrated gpt locus. Mutant gpt sequences are amplified using the polymerase chain reaction (PCR) to distinguish deletions from putative point mutations. PCR is efficiently performed from a few thousand lysed cells or from isolated genomic DNA. Amplified mutant PCR fragments carrying putative point mutations are further characterized by localizing the site of the mutation using chemical modification. A heteroduplex molecule consisting of one wild-type and one mutant DNA strand is generated. A base mismatch will be produced at the site of the mutation. Mismatched cytosine or thymine residues are sensitive to modification by hydroxylamine or osmium tetroxide, respectively. The modified DNA heteroduplex is then sensitive to piperidine cleavage. If one strand is 32P-end labeled, then the cleavage product can be separated on a denaturing acrylamide sequencing gel and visualized using autoradiography. Thus, the site of a mutation can be localized to a specific region of the gene, thereby simplifying the DNA sequence analysis and facilitating the rapid generation of mutational sequence spectra.

  3. Mass Spectrometric Quantification of Histone Post-translational Modifications by a Hybrid Chemical Labeling Method

    PubMed Central

    Maile, Tobias M.; Izrael-Tomasevic, Anita; Cheung, Tommy; Guler, Gulfem D.; Tindell, Charles; Masselot, Alexandre; Liang, Jun; Zhao, Feng; Trojer, Patrick; Classon, Marie; Arnott, David

    2015-01-01

    Mass spectrometry is a powerful alternative to antibody-based methods for the analysis of histone post-translational modifications (marks). A key development in this approach was the deliberate propionylation of histones to improve sequence coverage across the lysine-rich and hydrophilic tails that bear most modifications. Several marks continue to be problematic however, particularly di- and tri-methylated lysine 4 of histone H3 which we found to be subject to substantial and selective losses during sample preparation and liquid chromatography-mass spectrometry. We developed a new method employing a “one-pot” hybrid chemical derivatization of histones, whereby an initial conversion of free lysines to their propionylated forms under mild aqueous conditions is followed by trypsin digestion and labeling of new peptide N termini with phenyl isocyanate. High resolution mass spectrometry was used to collect qualitative and quantitative data, and a novel web-based software application (Fishtones) was developed for viewing and quantifying histone marks in the resulting data sets. Recoveries of 53 methyl, acetyl, and phosphoryl marks on histone H3.1 were improved by an average of threefold overall, and over 50-fold for H3K4 di- and tri-methyl marks. The power of this workflow for epigenetic research and drug discovery was demonstrated by measuring quantitative changes in H3K4 trimethylation induced by small molecule inhibitors of lysine demethylases and siRNA knockdown of epigenetic modifiers ASH2L and WDR5. PMID:25680960

  4. Identification of active site residues of Fenugreek β-amylase: chemical modification and in silico approach.

    PubMed

    Srivastava, Garima; Singh, Vinay K; Kayastha, Arvind M

    2014-10-01

    The amino acid sequence of Fenugreek β-amylase is not available in protein data bank. Therefore, an attempt has been made to identify the catalytic amino acid residues of enzyme by employing studies of pH dependence of enzyme catalysis, chemical modification and bioinformatics. Treatment of purified Fenugreek β-amylase with EDAC in presence of glycine methyl ester and sulfhydryl group specific reagents (IAA, NEM and p-CMB), followed a pseudo first-order kinetics and resulted in effective inactivation of enzyme. The reaction with EDAC in presence of NTEE (3-nitro-l-tyrosine ethylester) resulted into modification of two carboxyl groups per molecule of enzyme and presence of one accessible sulfhydryl group at the active site, per molecule of enzyme was ascertained by titration with DTNB. The above results were supported by the prevention of inactivation of enzyme in presence of substrate. Based on MALDI-TOF analysis of purified Fenugreek β-amylase and MASCOT search, β-amylase of Medicago sativa was found to be the best match. To further confirm the amino acid involved in catalysis, homology modelling of β-amylase of M. sativa was performed. The sequence alignment, superimposition of template and target models, along with study of interactions involved in docking of sucrose and maltose at the active site, led to identification of Glu187, Glu381 and Cys344 as active site residues.

  5. Development and Structural Modifications of Cholinesterase Reactivators against Chemical Warfare Agents in Last Decade: A Review.

    PubMed

    Sharma, Rahul; Gupta, Bhanushree; Singh, Namrata; Acharya, J R; Musilek, Kamil; Kuca, Kamil; Ghosh, Kallol Kumar

    2015-01-01

    Organophosphate (OP) pesticides and nerve agents are responsible for suicidal and accidental poisonings. The acute toxicity of nerve agents leads to progressive inhibition of the enzyme acetylcholinesterase (AChE) by phosphylation of serine residue at the active site of gorge. The recent massive destruction of Syrian civilians by nerve gas sarin, has again renewed the research attention of global science fraternity towards nerve agents, their mode of action and most prominently their therapeutic treatment. This review is principally focused on nerve agent intoxication. The common approach to deal with OP-intoxication is, application of antimuscarinic drug (atropine), anticonvulsant drug (diazepam) and clinically used oximes (pralidoxime, trimedoxime, obidoxime and asoxime). However, the existing therapeutic approach is arguable and has several failings to cure all kinds of nerve agent poisonings. Considering this issue, numerous oximes have been synthesized and screened through various in-vitro and in-vivo studies in last decade to overcome the downsides. At present, only a few oximes (bis pyridinum-oximes) exhibit sound efficacy against selective OPs. In spite of extensive efforts, till date no oxime is available as a universal antidote against all the classes of OPs. This review is centered on the recent developments and structural modification of AChE reactivators against nerve agent toxicity. In particular, a deeper look has been taken into chemical modifications of the reactivators by incorporation of different structural moieties targeted towards the increased reactivation affinity and improved blood brain barrier (BBB) penetration.

  6. Fabrication of robust hydrogel coatings on polydimethylsiloxane substrates using micropillar anchor structures with chemical surface modification.

    PubMed

    Zhang, Hongbin; Bian, Chao; Jackson, John K; Khademolhosseini, Farzad; Burt, Helen M; Chiao, Mu

    2014-06-25

    A durable hydrophilic and protein-resistant surface of polydimethylsiloxane (PDMS) based devices is desirable in many biomedical applications such as implantable and microfluidic devices. This paper describes a stable antifouling hydrogel coating on PDMS surfaces. The coating method combines chemical modification and surface microstructure fabrication of PDMS substrates. Three-(trimethoxysilyl)propyl methacrylates containing C═C groups were used to modify PDMS surfaces with micropillar array structures fabricated by a replica molding method. The micropillar structures increase the surface area of PDMS surfaces, which facilitates secure bonding with a hydrogel coating compared to flat PMDS surfaces. The adhesion properties of the hydrogel coating on PDMS substrates were characterized using bending, stretching and water immersion tests. Long-term hydrophilic stability (maintaining a contact angle of 55° for a month) and a low protein adsorption property (35 ng/cm(2) of adsorbed BSA-FITC) of the hydrogel coated PDMS were demonstrated. This coating method is suitable for PDMS modification with most crosslinkable polymers containing C═C groups, which can be useful for improving the anti-biofouling performance of PDMS-based biomedical microdevices.

  7. Nanolithography and nanochemistry: probe-related patterning techniques and chemical modification for nanometer-sized devices.

    PubMed

    Wouters, Daan; Schubert, Ulrich S

    2004-05-03

    The size regime for devices produced by photolithographic techniques is limited. Therefore, other patterning techniques have been intensively studied to create smaller structures. Scanning-probe-based patterning techniques, such as dip-pen lithography, local force-induced patterning, and local-probe oxidation-based techniques are highly promising because of their relative ease and widespread availability. The latter of these is especially interesting because of the possibility of producing nanopatterns for a broad range of chemical and physical modification and functionalization processes; both the production of nanometer-sized electronic devices and the formation of devices involving (bio)molecular recognition and sensor applications is possible. This Review highlights the development of various scanning probe systems and the possibilities of local oxidation methods, as well as giving an overview of state-of-the-art nanometer-sized devices, and a view of future development.

  8. Mechanism of highly improved electrical properties in polypropylene by chemical modification of grafting maleic anhydride

    NASA Astrophysics Data System (ADS)

    Zhou, Yao; Hu, Jun; Dang, Bin; He, Jinliang

    2016-10-01

    This paper reports excellent electrical properties in polypropylene grafted with maleic anhydride (PP-g-MAH) and a related mechanism of the enhanced electrical properties. The chemical structure of PP-g-MAH was analyzed and its effect on space charge accumulation, electrical breakdown strength and DC conductivity was studied. Compared with pure PP, the PP-g-MAH exhibits remarkably suppressed space charge accumulation, enhanced electrical breakdown strength and reduced conduction current. The mechanism enhancing the electrical properties was studied by measuring the trap level distribution. It can be explained that abundant deep traps are introduced in PP-g-MAH with the introduction of polar groups in MAH, which reduces the charge mobility and raises the charge injection barrier so as to suppress space charge accumulation. This investigation would contribute to propose a new material modification strategy for designing high-voltage direct current insulation material in addition to the inclusion of nanoparticles.

  9. Direct tunneling through high-κ amorphous HfO{sub 2}: Effects of chemical modification

    SciTech Connect

    Wang, Yin Yu, Zhizhou; Zahid, Ferdows; Wang, Jian; Liu, Lei; Zhu, Yu; Guo, Hong

    2014-07-14

    We report first principles modeling of quantum tunneling through amorphous HfO{sub 2} dielectric layer of metal-oxide-semiconductor (MOS) nanostructures in the form of n-Si/HfO{sub 2}/Al. In particular, we predict that chemically modifying the amorphous HfO{sub 2} barrier by doping N and Al atoms in the middle region—far from the two interfaces of the MOS structure—can reduce the gate-to-channel tunnel leakage by more than one order of magnitude. Several other types of modification are found to enhance tunneling or induce substantial band bending in the Si, both are not desired from leakage point of view. By analyzing transmission coefficients and projected density of states, the microscopic physics of electron traversing the tunnel barrier with or without impurity atoms in the high-κ dielectric is revealed.

  10. Chemical modifications of algal mannans and xylomannans: effects on antiviral activity.

    PubMed

    Pérez Recalde, Mercedes; Carlucci, María J; Noseda, Miguel D; Matulewicz, María C

    2012-01-01

    The structures of two sulfated xylomannans extracted from the red alga Nemalion helminthoides were determined. These two fractions plus a sulfated mannan, isolated from the same alga and whose structure was previously reported, were subjected to chemical modification. The mannan was oversulfated with SO(3)-pyridine in dimethyl sulfoxide at 60 °C during two and three hours and the xylomannans were subjected to Smith degradation in order to eliminate xylose side-chains. Structural analysis of all derivatives was carried out by methylation analysis and (13)C NMR spectroscopy. Antiviral activity against herpes simplex virus type 1 and 2, and dengue virus type 2 of native and modified mannans and xylomannans was estimated. Anticoagulant effect of the active fractions was also determined.

  11. Enhancing the properties of wood through chemical modification with palmitoyl chloride

    NASA Astrophysics Data System (ADS)

    Prakash, Gowdra K.; Mahadevan, Kittappa M.

    2008-01-01

    Hevea brassiliensis (rubber wood) was esterified with palmitoyl chloride, prepared from the reaction of palmitic acid with thionyl chloride. The weight gain of the wood increased with increasing reaction time and temperature, the esterified wood were evaluated for their photostability and dimensional stability. Fourier transform infrared spectroscopy (FTIR), solid-state cross-polarization/magic angle spinning 13C nuclear magnetic resonance spectroscopy (CP/MAS 13C NMR) were used to elucidate the characteristics of wood after esterification. The dimensional stability and photostability of the wood was improved by esterification. This is an important observation since chemical modification of wood with fatty acid chlorides has been found to induce thermo-plasticity into wood.

  12. Purification, chemical modification and immunostimulating activity of polysaccharides from Tremella aurantialba fruit bodies*

    PubMed Central

    Du, Xiu-ju; Zhang, Jing-song; Yang, Yan; Tang, Qing-jiu; Jia, Wei; Pan, Ying-jie

    2010-01-01

    Ultrafiltration and a series of chromatographic steps were used to isolate and purify polysaccharides from Tremella aurantialba fruit bodies. Three crude fractions (TAP50w, TAP10–50w, and TAP1–10w), five semi-purified fractions (TAPA–TAPE), and one purified fraction (TAPA1) were obtained. A sulfated derivative of TAPA1 (TAPA1-s) was prepared by chemical modification. The immunostimulating activity of the polysaccharide fractions in vitro was determined using the mouse spleen lymphocyte proliferation assay. Of the three crude fractions tested, cell proliferation rates were increased most by TAP50w. Furthermore, TAPA1-s was markedly more stimulatory than TAPA1, indicating that sulfonation was an effective way to enhance the immunostimulating activity of polysaccharide. PMID:20506575

  13. A Cloud Computing Platform for Large-Scale Forensic Computing

    NASA Astrophysics Data System (ADS)

    Roussev, Vassil; Wang, Liqiang; Richard, Golden; Marziale, Lodovico

    The timely processing of massive digital forensic collections demands the use of large-scale distributed computing resources and the flexibility to customize the processing performed on the collections. This paper describes MPI MapReduce (MMR), an open implementation of the MapReduce processing model that outperforms traditional forensic computing techniques. MMR provides linear scaling for CPU-intensive processing and super-linear scaling for indexing-related workloads.

  14. Large-Scale Weather Disturbances in Mars’ Southern Extratropics

    NASA Astrophysics Data System (ADS)

    Hollingsworth, Jeffery L.; Kahre, Melinda A.

    2015-11-01

    Between late autumn and early spring, Mars’ middle and high latitudes within its atmosphere support strong mean thermal gradients between the tropics and poles. Observations from both the Mars Global Surveyor (MGS) and Mars Reconnaissance Orbiter (MRO) indicate that this strong baroclinicity supports intense, large-scale eastward traveling weather systems (i.e., transient synoptic-period waves). These extratropical weather disturbances are key components of the global circulation. Such wave-like disturbances act as agents in the transport of heat and momentum, and generalized scalar/tracer quantities (e.g., atmospheric dust, water-vapor and ice clouds). The character of large-scale, traveling extratropical synoptic-period disturbances in Mars' southern hemisphere during late winter through early spring is investigated using a moderately high-resolution Mars global climate model (Mars GCM). This Mars GCM imposes interactively lifted and radiatively active dust based on a threshold value of the surface stress. The model exhibits a reasonable "dust cycle" (i.e., globally averaged, a dustier atmosphere during southern spring and summer occurs). Compared to their northern-hemisphere counterparts, southern synoptic-period weather disturbances and accompanying frontal waves have smaller meridional and zonal scales, and are far less intense. Influences of the zonally asymmetric (i.e., east-west varying) topography on southern large-scale weather are examined. Simulations that adapt Mars’ full topography compared to simulations that utilize synthetic topographies emulating key large-scale features of the southern middle latitudes indicate that Mars’ transient barotropic/baroclinic eddies are highly influenced by the great impact basins of this hemisphere (e.g., Argyre and Hellas). The occurrence of a southern storm zone in late winter and early spring appears to be anchored to the western hemisphere via orographic influences from the Tharsis highlands, and the Argyre

  15. Health-Terrain: Visualizing Large Scale Health Data

    DTIC Science & Technology

    2015-04-01

    Award Number: W81XWH-13-1-0020 TITLE: Health-Terrain: Visualizing Large Scale Health Data PRINCIPAL INVESTIGATOR: Ph.D. Fang, Shiaofen...ADDRESS. 1. REPORT DATE April 2015 2. REPORT TYPE Annual 3. DATES COVERED 7 MAR 2014 – 6 MAR 2015 4. TITLE AND SUBTITLE Health-Terrain: Visualizing ...1) creating a concept space data model, which represents a schema tailored to support diverse visualizations and provides a uniform ontology that

  16. A Holistic Management Architecture for Large-Scale Adaptive Networks

    DTIC Science & Technology

    2007-09-01

    MANAGEMENT ARCHITECTURE FOR LARGE-SCALE ADAPTIVE NETWORKS by Michael R. Clement September 2007 Thesis Advisor: Alex Bordetsky Second Reader...TECHNOLOGY MANAGEMENT from the NAVAL POSTGRADUATE SCHOOL September 2007 Author: Michael R. Clement Approved by: Dr. Alex ...achieve in life is by His will. Ad Majorem Dei Gloriam. To my parents, my family, and Caitlin: For supporting me, listening to me when I got

  17. Large-Scale Optimization for Bayesian Inference in Complex Systems

    SciTech Connect

    Willcox, Karen; Marzouk, Youssef

    2013-11-12

    The SAGUARO (Scalable Algorithms for Groundwater Uncertainty Analysis and Robust Optimization) Project focused on the development of scalable numerical algorithms for large-scale Bayesian inversion in complex systems that capitalize on advances in large-scale simulation-based optimization and inversion methods. The project was a collaborative effort among MIT, the University of Texas at Austin, Georgia Institute of Technology, and Sandia National Laboratories. The research was directed in three complementary areas: efficient approximations of the Hessian operator, reductions in complexity of forward simulations via stochastic spectral approximations and model reduction, and employing large-scale optimization concepts to accelerate sampling. The MIT--Sandia component of the SAGUARO Project addressed the intractability of conventional sampling methods for large-scale statistical inverse problems by devising reduced-order models that are faithful to the full-order model over a wide range of parameter values; sampling then employs the reduced model rather than the full model, resulting in very large computational savings. Results indicate little effect on the computed posterior distribution. On the other hand, in the Texas--Georgia Tech component of the project, we retain the full-order model, but exploit inverse problem structure (adjoint-based gradients and partial Hessian information of the parameter-to-observation map) to implicitly extract lower dimensional information on the posterior distribution; this greatly speeds up sampling methods, so that fewer sampling points are needed. We can think of these two approaches as ``reduce then sample'' and ``sample then reduce.'' In fact, these two approaches are complementary, and can be used in conjunction with each other. Moreover, they both exploit deterministic inverse problem structure, in the form of adjoint-based gradient and Hessian information of the underlying parameter-to-observation map, to achieve their

  18. Large-scale detection of recombination in nucleotide sequences

    NASA Astrophysics Data System (ADS)

    Chan, Cheong Xin; Beiko, Robert G.; Ragan, Mark A.

    2008-01-01

    Genetic recombination following a genetic transfer event can produce heterogeneous phylogenetic histories within sets of genes that share a common ancestral origin. Delineating recombination events will enhance our understanding in genome evolution. However, the task of detecting recombination is not trivial due to effect of more-recent evolutionary changes that can obscure such event from detection. In this paper, we demonstrate the use of a two-phase strategy for detecting recombination events on a large-scale dataset.

  19. Multimodel Design of Large Scale Systems with Multiple Decision Makers.

    DTIC Science & Technology

    1982-08-01

    virtue. 5- , Lead me from darkneu to light. - Lead me from death to eternal Life. ( Vedic Payer) p. I, MULTIMODEL DESIGN OF LARGE SCALE SYSTEMS WITH...guidance during the course of *: this research . He would also like to thank Professors W. R. Perkins, P. V. Kokotovic, T. Basar, and T. N. Trick for...thesis concludes with Chapter 7 where we summarize the results obtained, outline the main contributions, and indicate directions for future research . 7- I

  20. Turbulent amplification of large-scale magnetic fields

    NASA Technical Reports Server (NTRS)

    Montgomery, D.; Chen, H.

    1984-01-01

    Previously-introduced methods for analytically estimating the effects of small-scale turbulent fluctuations on large-scale dynamics are extended to fully three-dimensional magnetohydrodynamics. The problem becomes algebraically tractable in the presence of sufficiently large spectral gaps. The calculation generalizes 'alpha dynamo' calculations, except that the velocity fluctuations and magnetic fluctuations are treated on an independent and equal footing. Earlier expressions for the 'alpha coefficients' of turbulent magnetic field amplification are recovered as a special case.

  1. Space transportation booster engine thrust chamber technology, large scale injector

    NASA Technical Reports Server (NTRS)

    Schneider, J. A.

    1993-01-01

    The objective of the Large Scale Injector (LSI) program was to deliver a 21 inch diameter, 600,000 lbf thrust class injector to NASA/MSFC for hot fire testing. The hot fire test program would demonstrate the feasibility and integrity of the full scale injector, including combustion stability, chamber wall compatibility (thermal management), and injector performance. The 21 inch diameter injector was delivered in September of 1991.

  2. Relic vector field and CMB large scale anomalies

    SciTech Connect

    Chen, Xingang; Wang, Yi E-mail: yw366@cam.ac.uk

    2014-10-01

    We study the most general effects of relic vector fields on the inflationary background and density perturbations. Such effects are observable if the number of inflationary e-folds is close to the minimum requirement to solve the horizon problem. We show that this can potentially explain two CMB large scale anomalies: the quadrupole-octopole alignment and the quadrupole power suppression. We discuss its effect on the parity anomaly. We also provide analytical template for more detailed data comparison.

  3. The large-scale anisotropy with the PAMELA calorimeter

    NASA Astrophysics Data System (ADS)

    Karelin, A.; Adriani, O.; Barbarino, G.; Bazilevskaya, G.; Bellotti, R.; Boezio, M.; Bogomolov, E.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bruno, A.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; De Donato, C.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A.; Koldashov, S.; Koldobskiy, S.; Krut'kov, S.; Kvashnin, A.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A.; Menn, W.; Mergé, M.; Mikhailov, V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Ricci, M.; Ricciarini, S.; Sarkar, R.; Simon, M.; Scotti, V.; Sparvoli, R.; Spillantini, P.; Stozhkov, Y.; Vacchi, A.; Vannuccini, E.; Vasilyev, G.; Voronov, S.; Yurkin, Y.; Zampa, G.; Zampa, N.

    2015-10-01

    The large-scale anisotropy (or the so-called star-diurnal wave) has been studied using the calorimeter of the space-born experiment PAMELA. The cosmic ray anisotropy has been obtained for the Southern and Northern hemispheres simultaneously in the equatorial coordinate system for the time period 2006-2014. The dipole amplitude and phase have been measured for energies 1-20 TeV n-1.

  4. Supporting large scale applications on networks of workstations

    NASA Technical Reports Server (NTRS)

    Cooper, Robert; Birman, Kenneth P.

    1989-01-01

    Distributed applications on networks of workstations are an increasingly common way to satisfy computing needs. However, existing mechanisms for distributed programming exhibit poor performance and reliability as application size increases. Extension of the ISIS distributed programming system to support large scale distributed applications by providing hierarchical process groups is discussed. Incorporation of hierarchy in the program structure and exploitation of this to limit the communication and storage required in any one component of the distributed system is examined.

  5. The Phoenix series large scale LNG pool fire experiments.

    SciTech Connect

    Simpson, Richard B.; Jensen, Richard Pearson; Demosthenous, Byron; Luketa, Anay Josephine; Ricks, Allen Joseph; Hightower, Marion Michael; Blanchat, Thomas K.; Helmick, Paul H.; Tieszen, Sheldon Robert; Deola, Regina Anne; Mercier, Jeffrey Alan; Suo-Anttila, Jill Marie; Miller, Timothy J.

    2010-12-01

    The increasing demand for natural gas could increase the number and frequency of Liquefied Natural Gas (LNG) tanker deliveries to ports across the United States. Because of the increasing number of shipments and the number of possible new facilities, concerns about the potential safety of the public and property from an accidental, and even more importantly intentional spills, have increased. While improvements have been made over the past decade in assessing hazards from LNG spills, the existing experimental data is much smaller in size and scale than many postulated large accidental and intentional spills. Since the physics and hazards from a fire change with fire size, there are concerns about the adequacy of current hazard prediction techniques for large LNG spills and fires. To address these concerns, Congress funded the Department of Energy (DOE) in 2008 to conduct a series of laboratory and large-scale LNG pool fire experiments at Sandia National Laboratories (Sandia) in Albuquerque, New Mexico. This report presents the test data and results of both sets of fire experiments. A series of five reduced-scale (gas burner) tests (yielding 27 sets of data) were conducted in 2007 and 2008 at Sandia's Thermal Test Complex (TTC) to assess flame height to fire diameter ratios as a function of nondimensional heat release rates for extrapolation to large-scale LNG fires. The large-scale LNG pool fire experiments were conducted in a 120 m diameter pond specially designed and constructed in Sandia's Area III large-scale test complex. Two fire tests of LNG spills of 21 and 81 m in diameter were conducted in 2009 to improve the understanding of flame height, smoke production, and burn rate and therefore the physics and hazards of large LNG spills and fires.

  6. Information Tailoring Enhancements for Large Scale Social Data

    DTIC Science & Technology

    2016-03-15

    Social Data Progress Report No. 2 Reporting Period: December 16, 2015 – March 15, 2016 Contract No. N00014-15-P-5138 Sponsored by ONR...Intelligent Automation Incorporated Progress Report No. 2 Information Tailoring Enhancements for Large-Scale Social Data Submitted in accordance with...robustness. We imporoved the (i) messaging architecture, (ii) data redundancy, and (iii) service availability of Scraawl computational framework

  7. Host Immunity via Mutable Virtualized Large-Scale Network Containers

    DTIC Science & Technology

    2016-07-25

    system for host immunity that combines virtualization , emulation, and mutable network configurations. This system is deployed on a single host, and...entire !Pv4 address space within 5 Host Immunity via Mutable Virtualized Large-Scale Network Containers 45 minutes from a single machine. Second, when...URL, and we call it URL marker. A URL marker records the information about its parent web page’s URL and the user ID who collects the URL. Thus, when

  8. Concurrent Programming Using Actors: Exploiting Large-Scale Parallelism,

    DTIC Science & Technology

    1985-10-07

    ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASK* Artificial Inteligence Laboratory AREA Is WORK UNIT NUMBERS 545 Technology Square...D-R162 422 CONCURRENT PROGRMMIZNG USING f"OS XL?ITP TEH l’ LARGE-SCALE PARALLELISH(U) NASI AC E Al CAMBRIDGE ARTIFICIAL INTELLIGENCE L. G AGHA ET AL...RESOLUTION TEST CHART N~ATIONAL BUREAU OF STANDA.RDS - -96 A -E. __ _ __ __’ .,*- - -- •. - MASSACHUSETTS INSTITUTE OF TECHNOLOGY ARTIFICIAL

  9. Developing and Understanding Methods for Large Scale Nonlinear Optimization

    DTIC Science & Technology

    2001-12-01

    development of new algorithms for large-scale uncon- strained and constrained optimization problems, including limited-memory methods for problems with...analysis of tensor and SQP methods for singular con- strained optimization", to appear in SIAM Journal on Optimization. Published in peer-reviewed...Mathematica, Vol III, Journal der Deutschen Mathematiker-Vereinigung, 1998. S. Crivelli, B. Bader, R. Byrd, E. Eskow, V. Lamberti , R.Schnabel and T

  10. Large-scale Alfvén vortices

    SciTech Connect

    Onishchenko, O. G.; Horton, W.; Scullion, E.; Fedun, V.

    2015-12-15

    The new type of large-scale vortex structures of dispersionless Alfvén waves in collisionless plasma is investigated. It is shown that Alfvén waves can propagate in the form of Alfvén vortices of finite characteristic radius and characterised by magnetic flux ropes carrying orbital angular momentum. The structure of the toroidal and radial velocity, fluid and magnetic field vorticity, the longitudinal electric current in the plane orthogonal to the external magnetic field are discussed.

  11. Analysis plan for 1985 large-scale tests. Technical report

    SciTech Connect

    McMullan, F.W.

    1983-01-01

    The purpose of this effort is to assist DNA in planning for large-scale (upwards of 5000 tons) detonations of conventional explosives in the 1985 and beyond time frame. Primary research objectives were to investigate potential means to increase blast duration and peak pressures. This report identifies and analyzes several candidate explosives. It examines several charge designs and identifies advantages and disadvantages of each. Other factors including terrain and multiburst techniques are addressed as are test site considerations.

  12. Large-scale image-based screening and profiling of cellular phenotypes.

    PubMed

    Bougen-Zhukov, Nicola; Loh, Sheng Yang; Lee, Hwee Kuan; Loo, Lit-Hsin

    2017-02-01

    Cellular phenotypes are observable characteristics of cells resulting from the interactions of intrinsic and extrinsic chemical or biochemical factors. Image-based phenotypic screens under large numbers of basal or perturbed conditions can be used to study the influences of these factors on cellular phenotypes. Hundreds to thousands of phenotypic descriptors can also be quantified from the images of cells under each of these experimental conditions. Therefore, huge amounts of data can be generated, and the analysis of these data has become a major bottleneck in large-scale phenotypic screens. Here, we review current experimental and computational methods for large-scale image-based phenotypic screens. Our focus is on phenotypic profiling, a computational procedure for constructing quantitative and compact representations of cellular phenotypes based on the images collected in these screens. © 2016 International Society for Advancement of Cytometry.

  13. Equivalent common path method in large-scale laser comparator

    NASA Astrophysics Data System (ADS)

    He, Mingzhao; Li, Jianshuang; Miao, Dongjing

    2015-02-01

    Large-scale laser comparator is main standard device that providing accurate, reliable and traceable measurements for high precision large-scale line and 3D measurement instruments. It mainly composed of guide rail, motion control system, environmental parameters monitoring system and displacement measurement system. In the laser comparator, the main error sources are temperature distribution, straightness of guide rail and pitch and yaw of measuring carriage. To minimize the measurement uncertainty, an equivalent common optical path scheme is proposed and implemented. Three laser interferometers are adjusted to parallel with the guide rail. The displacement in an arbitrary virtual optical path is calculated using three displacements without the knowledge of carriage orientations at start and end positions. The orientation of air floating carriage is calculated with displacements of three optical path and position of three retroreflectors which are precisely measured by Laser Tracker. A 4th laser interferometer is used in the virtual optical path as reference to verify this compensation method. This paper analyzes the effect of rail straightness on the displacement measurement. The proposed method, through experimental verification, can improve the measurement uncertainty of large-scale laser comparator.

  14. Dispersal Mutualism Incorporated into Large-Scale, Infrequent Disturbances

    PubMed Central

    Parker, V. Thomas

    2015-01-01

    Because of their influence on succession and other community interactions, large-scale, infrequent natural disturbances also should play a major role in mutualistic interactions. Using field data and experiments, I test whether mutualisms have been incorporated into large-scale wildfire by whether the outcomes of a mutualism depend on disturbance. In this study a seed dispersal mutualism is shown to depend on infrequent, large-scale disturbances. A dominant shrubland plant (Arctostaphylos species) produces seeds that make up a persistent soil seed bank and requires fire to germinate. In post-fire stands, I show that seedlings emerging from rodent caches dominate sites experiencing higher fire intensity. Field experiments show that rodents (Perimyscus californicus, P. boylii) do cache Arctostaphylos fruit and bury most seed caches to a sufficient depth to survive a killing heat pulse that a fire might drive into the soil. While the rodent dispersal and caching behavior itself has not changed compared to other habitats, the environmental transformation caused by wildfire converts the caching burial of seed from a dispersal process to a plant fire adaptive trait, and provides the context for stimulating subsequent life history evolution in the plant host. PMID:26151560

  15. Impact of Large-scale Geological Architectures On Recharge

    NASA Astrophysics Data System (ADS)

    Troldborg, L.; Refsgaard, J. C.; Engesgaard, P.; Jensen, K. H.

    Geological and hydrogeological data constitutes the basis for assessment of ground- water flow pattern and recharge zones. The accessibility and applicability of hard ge- ological data is often a major obstacle in deriving plausible conceptual models. Nev- ertheless focus is often on parameter uncertainty caused by the effect of geological heterogeneity due to lack of hard geological data, thus neglecting the possibility of alternative conceptualizations of the large-scale geological architecture. For a catchment in the eastern part of Denmark we have constructed different geologi- cal models based on different conceptualization of the major geological trends and fa- cies architecture. The geological models are equally plausible in a conceptually sense and they are all calibrated to well head and river flow measurements. Comparison of differences in recharge zones and subsequently well protection zones emphasize the importance of assessing large-scale geological architecture in hydrological modeling on regional scale in a non-deterministic way. Geostatistical modeling carried out in a transitional probability framework shows the possibility of assessing multiple re- alizations of large-scale geological architecture from a combination of soft and hard geological information.

  16. Line segment extraction for large scale unorganized point clouds

    NASA Astrophysics Data System (ADS)

    Lin, Yangbin; Wang, Cheng; Cheng, Jun; Chen, Bili; Jia, Fukai; Chen, Zhonggui; Li, Jonathan

    2015-04-01

    Line segment detection in images is already a well-investigated topic, although it has received considerably less attention in 3D point clouds. Benefiting from current LiDAR devices, large-scale point clouds are becoming increasingly common. Most human-made objects have flat surfaces. Line segments that occur where pairs of planes intersect give important information regarding the geometric content of point clouds, which is especially useful for automatic building reconstruction and segmentation. This paper proposes a novel method that is capable of accurately extracting plane intersection line segments from large-scale raw scan points. The 3D line-support region, namely, a point set near a straight linear structure, is extracted simultaneously. The 3D line-support region is fitted by our Line-Segment-Half-Planes (LSHP) structure, which provides a geometric constraint for a line segment, making the line segment more reliable and accurate. We demonstrate our method on the point clouds of large-scale, complex, real-world scenes acquired by LiDAR devices. We also demonstrate the application of 3D line-support regions and their LSHP structures on urban scene abstraction.

  17. Reliability assessment for components of large scale photovoltaic systems

    NASA Astrophysics Data System (ADS)

    Ahadi, Amir; Ghadimi, Noradin; Mirabbasi, Davar

    2014-10-01

    Photovoltaic (PV) systems have significantly shifted from independent power generation systems to a large-scale grid-connected generation systems in recent years. The power output of PV systems is affected by the reliability of various components in the system. This study proposes an analytical approach to evaluate the reliability of large-scale, grid-connected PV systems. The fault tree method with an exponential probability distribution function is used to analyze the components of large-scale PV systems. The system is considered in the various sequential and parallel fault combinations in order to find all realistic ways in which the top or undesired events can occur. Additionally, it can identify areas that the planned maintenance should focus on. By monitoring the critical components of a PV system, it is possible not only to improve the reliability of the system, but also to optimize the maintenance costs. The latter is achieved by informing the operators about the system component's status. This approach can be used to ensure secure operation of the system by its flexibility in monitoring system applications. The implementation demonstrates that the proposed method is effective and efficient and can conveniently incorporate more system maintenance plans and diagnostic strategies.

  18. Learning Short Binary Codes for Large-scale Image Retrieval.

    PubMed

    Liu, Li; Yu, Mengyang; Shao, Ling

    2017-03-01

    Large-scale visual information retrieval has become an active research area in this big data era. Recently, hashing/binary coding algorithms prove to be effective for scalable retrieval applications. Most existing hashing methods require relatively long binary codes (i.e., over hundreds of bits, sometimes even thousands of bits) to achieve reasonable retrieval accuracies. However, for some realistic and unique applications, such as on wearable or mobile devices, only short binary codes can be used for efficient image retrieval due to the limitation of computational resources or bandwidth on these devices. In this paper, we propose a novel unsupervised hashing approach called min-cost ranking (MCR) specifically for learning powerful short binary codes (i.e., usually the code length shorter than 100 b) for scalable image retrieval tasks. By exploring the discriminative ability of each dimension of data, MCR can generate one bit binary code for each dimension and simultaneously rank the discriminative separability of each bit according to the proposed cost function. Only top-ranked bits with minimum cost-values are then selected and grouped together to compose the final salient binary codes. Extensive experimental results on large-scale retrieval demonstrate that MCR can achieve comparative performance as the state-of-the-art hashing algorithms but with significantly shorter codes, leading to much faster large-scale retrieval.

  19. Homogenization of Large-Scale Movement Models in Ecology

    USGS Publications Warehouse

    Garlick, M.J.; Powell, J.A.; Hooten, M.B.; McFarlane, L.R.

    2011-01-01

    A difficulty in using diffusion models to predict large scale animal population dispersal is that individuals move differently based on local information (as opposed to gradients) in differing habitat types. This can be accommodated by using ecological diffusion. However, real environments are often spatially complex, limiting application of a direct approach. Homogenization for partial differential equations has long been applied to Fickian diffusion (in which average individual movement is organized along gradients of habitat and population density). We derive a homogenization procedure for ecological diffusion and apply it to a simple model for chronic wasting disease in mule deer. Homogenization allows us to determine the impact of small scale (10-100 m) habitat variability on large scale (10-100 km) movement. The procedure generates asymptotic equations for solutions on the large scale with parameters defined by small-scale variation. The simplicity of this homogenization procedure is striking when compared to the multi-dimensional homogenization procedure for Fickian diffusion,and the method will be equally straightforward for more complex models. ?? 2010 Society for Mathematical Biology.

  20. Large-scale quantization from local correlations in space plasmas

    NASA Astrophysics Data System (ADS)

    Livadiotis, George; McComas, David J.

    2014-05-01

    This study examines the large-scale quantization that can characterize the phase space of certain physical systems. Plasmas are such systems where large-scale quantization, ħ*, is caused by Debye shielding that structures correlations between particles. The value of ħ* is constant—some 12 orders of magnitude larger than the Planck constant—across a wide range of space plasmas, from the solar wind in the inner heliosphere to the distant plasma in the inner heliosheath and the local interstellar medium. This paper develops the foundation and advances the understanding of the concept of plasma quantization; in particular, we (i) show the analogy of plasma to Planck quantization, (ii) show the key points of plasma quantization, (iii) construct some basic quantum mechanical concepts for the large-scale plasma quantization, (iv) investigate the correlation between plasma parameters that implies plasma quantization, when it is approximated by a relation between the magnetosonic energy and the plasma frequency, (v) analyze typical space plasmas throughout the heliosphere and show the constancy of plasma quantization over many orders of magnitude in plasma parameters, (vi) analyze Advanced Composition Explorer (ACE) solar wind measurements to develop another measurement of the value of ħ*, and (vii) apply plasma quantization to derive unknown plasma parameters when some key observable is missing.

  1. Channel capacity of next generation large scale MIMO systems

    NASA Astrophysics Data System (ADS)

    Alshammari, A.; Albdran, S.; Matin, M.

    2016-09-01

    Information rate that can be transferred over a given bandwidth is limited by the information theory. Capacity depends on many factors such as the signal to noise ratio (SNR), channel state information (CSI) and the spatial correlation in the propagation environment. It is very important to increase spectral efficiency in order to meet the growing demand for wireless services. Thus, Multiple input multiple output (MIMO) technology has been developed and applied in most of the wireless standards and it has been very successful in increasing capacity and reliability. As the demand is still increasing, attention now is shifting towards large scale multiple input multiple output (MIMO) which has a potential of bringing orders of magnitude of improvement in spectral and energy efficiency. It has been shown that users channels decorrelate after increasing the number of antennas. As a result, inter-user interference can be avoided since energy can be focused on precise directions. This paper investigates the limits of channel capacity for large scale MIMO. We study the relation between spectral efficiency and the number of antenna N. We use time division duplex (TDD) system in order to obtain CSI using training sequence in the uplink. The same CSI is used for the downlink because the channel is reciprocal. Spectral efficiency is measured for channel model that account for small scale fading while ignoring the effect of large scale fading. It is shown the spectral efficiency can be improved significantly when compared to single antenna systems in ideal circumstances.

  2. Sparse approximation through boosting for learning large scale kernel machines.

    PubMed

    Sun, Ping; Yao, Xin

    2010-06-01

    Recently, sparse approximation has become a preferred method for learning large scale kernel machines. This technique attempts to represent the solution with only a subset of original data points also known as basis vectors, which are usually chosen one by one with a forward selection procedure based on some selection criteria. The computational complexity of several resultant algorithms scales as O(NM(2)) in time and O(NM) in memory, where N is the number of training points and M is the number of basis vectors as well as the steps of forward selection. For some large scale data sets, to obtain a better solution, we are sometimes required to include more basis vectors, which means that M is not trivial in this situation. However, the limited computational resource (e.g., memory) prevents us from including too many vectors. To handle this dilemma, we propose to add an ensemble of basis vectors instead of only one at each forward step. The proposed method, closely related to gradient boosting, could decrease the required number M of forward steps significantly and thus a large fraction of computational cost is saved. Numerical experiments on three large scale regression tasks and a classification problem demonstrate the effectiveness of the proposed approach.

  3. Alteration of Large-Scale Chromatin Structure by Estrogen Receptor

    PubMed Central

    Nye, Anne C.; Rajendran, Ramji R.; Stenoien, David L.; Mancini, Michael A.; Katzenellenbogen, Benita S.; Belmont, Andrew S.

    2002-01-01

    The estrogen receptor (ER), a member of the nuclear hormone receptor superfamily important in human physiology and disease, recruits coactivators which modify local chromatin structure. Here we describe effects of ER on large-scale chromatin structure as visualized in live cells. We targeted ER to gene-amplified chromosome arms containing large numbers of lac operator sites either directly, through a lac repressor-ER fusion protein (lac rep-ER), or indirectly, by fusing lac repressor with the ER interaction domain of the coactivator steroid receptor coactivator 1. Significant decondensation of large-scale chromatin structure, comparable to that produced by the ∼150-fold-stronger viral protein 16 (VP16) transcriptional activator, was produced by ER in the absence of estradiol using both approaches. Addition of estradiol induced a partial reversal of this unfolding by green fluorescent protein-lac rep-ER but not by wild-type ER recruited by a lac repressor-SRC570-780 fusion protein. The chromatin decondensation activity did not require transcriptional activation by ER nor did it require ligand-induced coactivator interactions, and unfolding did not correlate with histone hyperacetylation. Ligand-induced coactivator interactions with helix 12 of ER were necessary for the partial refolding of chromatin in response to estradiol using the lac rep-ER tethering system. This work demonstrates that when tethered or recruited to DNA, ER possesses a novel large-scale chromatin unfolding activity. PMID:11971975

  4. Geospatial Optimization of Siting Large-Scale Solar Projects

    SciTech Connect

    Macknick, J.; Quinby, T.; Caulfield, E.; Gerritsen, M.; Diffendorfer, J.; Haines, S.

    2014-03-01

    Recent policy and economic conditions have encouraged a renewed interest in developing large-scale solar projects in the U.S. Southwest. However, siting large-scale solar projects is complex. In addition to the quality of the solar resource, solar developers must take into consideration many environmental, social, and economic factors when evaluating a potential site. This report describes a proof-of-concept, Web-based Geographical Information Systems (GIS) tool that evaluates multiple user-defined criteria in an optimization algorithm to inform discussions and decisions regarding the locations of utility-scale solar projects. Existing siting recommendations for large-scale solar projects from governmental and non-governmental organizations are not consistent with each other, are often not transparent in methods, and do not take into consideration the differing priorities of stakeholders. The siting assistance GIS tool we have developed improves upon the existing siting guidelines by being user-driven, transparent, interactive, capable of incorporating multiple criteria, and flexible. This work provides the foundation for a dynamic siting assistance tool that can greatly facilitate siting decisions among multiple stakeholders.

  5. Assessing salivary cortisol in large-scale, epidemiological research.

    PubMed

    Adam, Emma K; Kumari, Meena

    2009-11-01

    Salivary cortisol measures are increasingly being incorporated into large-scale, population-based, or epidemiological research, in which participants are selected to be representative of particular communities or populations of interest, and sample sizes are in the order of hundreds to tens of thousands of participants. These approaches to studying salivary cortisol provide important advantages but pose a set of challenges. The representative nature of sampling, and large samples sizes associated with population-based research offer high generalizability and power, and the ability to examine cortisol functioning in relation to: (a) a wide range of social environments; (b) a diverse array individuals and groups; and (c) a broad set of pre-disease and disease outcomes. The greater importance of high response rates (to maintain generalizability) and higher costs associated with this type of large-scale research, however, requires special adaptations of existing ambulatory cortisol protocols. These include: using the most efficient sample collection protocol possible that still adequately address the specific cortisol-related questions at hand, and ensuring the highest possible response and compliance rates among those individuals invited to participate. Examples of choices made, response rates obtained, and examples of results obtained from existing epidemiological cortisol studies are offered, as are suggestions for the modeling and interpretation of salivary cortisol data obtained in large-scale epidemiological research.

  6. Large-scale investigation of genomic markers for severe periodontitis.

    PubMed

    Suzuki, Asami; Ji, Guijin; Numabe, Yukihiro; Ishii, Keisuke; Muramatsu, Masaaki; Kamoi, Kyuichi

    2004-09-01

    The purpose of the present study was to investigate the genomic markers for periodontitis, using large-scale single-nucleotide polymorphism (SNP) association studies comparing healthy volunteers and patients with periodontitis. Genomic DNA was obtained from 19 healthy volunteers and 22 patients with severe periodontitis, all of whom were Japanese. The subjects were genotyped at 637 SNPs in 244 genes on a large scale, using the TaqMan polymerase chain reaction (PCR) system. Statistically significant differences in allele and genotype frequencies were analyzed with Fisher's exact test. We found statistically significant differences (P < 0.01) between the healthy volunteers and patients with severe periodontitis in the following genes; gonadotropin-releasing hormone 1 (GNRH1), phosphatidylinositol 3-kinase regulatory 1 (PIK3R1), dipeptidylpeptidase 4 (DPP4), fibrinogen-like 2 (FGL2), and calcitonin receptor (CALCR). These results suggest that SNPs in the GNRH1, PIK3R1, DPP4, FGL2, and CALCR genes are genomic markers for severe periodontitis. Our findings indicate the necessity of analyzing SNPs in genes on a large scale (i.e., genome-wide approach), to identify genomic markers for periodontitis.

  7. Large-scale data mining pilot project in human genome

    SciTech Connect

    Musick, R.; Fidelis, R.; Slezak, T.

    1997-05-01

    This whitepaper briefly describes a new, aggressive effort in large- scale data Livermore National Labs. The implications of `large- scale` will be clarified Section. In the short term, this effort will focus on several @ssion-critical questions of Genome project. We will adapt current data mining techniques to the Genome domain, to quantify the accuracy of inference results, and lay the groundwork for a more extensive effort in large-scale data mining. A major aspect of the approach is that we will be fully-staffed data warehousing effort in the human Genome area. The long term goal is strong applications- oriented research program in large-@e data mining. The tools, skill set gained will be directly applicable to a wide spectrum of tasks involving a for large spatial and multidimensional data. This includes applications in ensuring non-proliferation, stockpile stewardship, enabling Global Ecology (Materials Database Industrial Ecology), advancing the Biosciences (Human Genome Project), and supporting data for others (Battlefield Management, Health Care).

  8. Large-scale biodiversity patterns in freshwater phytoplankton.

    PubMed

    Stomp, Maayke; Huisman, Jef; Mittelbach, Gary G; Litchman, Elena; Klausmeier, Christopher A

    2011-11-01

    Our planet shows striking gradients in the species richness of plants and animals, from high biodiversity in the tropics to low biodiversity in polar and high-mountain regions. Recently, similar patterns have been described for some groups of microorganisms, but the large-scale biogeographical distribution of freshwater phytoplankton diversity is still largely unknown. We examined the species diversity of freshwater phytoplankton sampled from 540 lakes and reservoirs distributed across the continental United States and found strong latitudinal, longitudinal, and altitudinal gradients in phytoplankton biodiversity, demonstrating that microorganisms can show substantial geographic variation in biodiversity. Detailed analysis using structural equation models indicated that these large-scale biodiversity gradients in freshwater phytoplankton diversity were mainly driven by local environmental factors, although there were residual direct effects of latitude, longitude, and altitude as well. Specifically, we found that phytoplankton species richness was an increasing saturating function of lake chlorophyll a concentration, increased with lake surface area and possibly increased with water temperature, resembling effects of productivity, habitat area, and temperature on diversity patterns commonly observed for macroorganisms. In turn, these local environmental factors varied along latitudinal, longitudinal, and altitudinal gradients. These results imply that changes in land use or climate that affect these local environmental factors are likely to have major impacts on large-scale biodiversity patterns of freshwater phytoplankton.

  9. A model of plasma heating by large-scale flow

    NASA Astrophysics Data System (ADS)

    Pongkitiwanichakul, P.; Cattaneo, F.; Boldyrev, S.; Mason, J.; Perez, J. C.

    2015-12-01

    In this work, we study the process of energy dissipation triggered by a slow large-scale motion of a magnetized conducting fluid. Our consideration is motivated by the problem of heating the solar corona, which is believed to be governed by fast reconnection events set off by the slow motion of magnetic field lines anchored in the photospheric plasma. To elucidate the physics governing the disruption of the imposed laminar motion and the energy transfer to small scales, we propose a simplified model where the large-scale motion of magnetic field lines is prescribed not at the footpoints but rather imposed volumetrically. As a result, the problem can be treated numerically with an efficient, highly accurate spectral method, allowing us to use a resolution and statistical ensemble exceeding those of the previous work. We find that, even though the large-scale deformations are slow, they eventually lead to reconnection events that drive a turbulent state at smaller scales. The small-scale turbulence displays many of the universal features of field-guided magnetohydrodynamic turbulence like a well-developed inertial range spectrum. Based on these observations, we construct a phenomenological model that gives the scalings of the amplitude of the fluctuations and the energy-dissipation rate as functions of the input parameters. We find good agreement between the numerical results and the predictions of the model.

  10. Large-scale flow generation by inhomogeneous helicity.

    PubMed

    Yokoi, N; Brandenburg, A

    2016-03-01

    The effect of kinetic helicity (velocity-vorticity correlation) on turbulent momentum transport is investigated. The turbulent kinetic helicity (pseudoscalar) enters the Reynolds stress (mirror-symmetric tensor) expression in the form of a helicity gradient as the coupling coefficient for the mean vorticity and/or the angular velocity (axial vector), which suggests the possibility of mean-flow generation in the presence of inhomogeneous helicity. This inhomogeneous helicity effect, which was previously confirmed at the level of a turbulence- or closure-model simulation, is examined with the aid of direct numerical simulations of rotating turbulence with nonuniform helicity sustained by an external forcing. The numerical simulations show that the spatial distribution of the Reynolds stress is in agreement with the helicity-related term coupled with the angular velocity, and that a large-scale flow is generated in the direction of angular velocity. Such a large-scale flow is not induced in the case of homogeneous turbulent helicity. This result confirms the validity of the inhomogeneous helicity effect in large-scale flow generation and suggests that a vortex dynamo is possible even in incompressible turbulence where there is no baroclinicity effect.

  11. Large-scale flow experiments for managing river systems

    USGS Publications Warehouse

    Konrad, Christopher P.; Olden, Julian D.; Lytle, David A.; Melis, Theodore S.; Schmidt, John C.; Bray, Erin N.; Freeman, Mary C.; Gido, Keith B.; Hemphill, Nina P.; Kennard, Mark J.; McMullen, Laura E.; Mims, Meryl C.; Pyron, Mark; Robinson, Christopher T.; Williams, John G.

    2011-01-01

    Experimental manipulations of streamflow have been used globally in recent decades to mitigate the impacts of dam operations on river systems. Rivers are challenging subjects for experimentation, because they are open systems that cannot be isolated from their social context. We identify principles to address the challenges of conducting effective large-scale flow experiments. Flow experiments have both scientific and social value when they help to resolve specific questions about the ecological action of flow with a clear nexus to water policies and decisions. Water managers must integrate new information into operating policies for large-scale experiments to be effective. Modeling and monitoring can be integrated with experiments to analyze long-term ecological responses. Experimental design should include spatially extensive observations and well-defined, repeated treatments. Large-scale flow manipulations are only a part of dam operations that affect river systems. Scientists can ensure that experimental manipulations continue to be a valuable approach for the scientifically based management of river systems.

  12. Impacts of tropical deforestation. Part II: The role of large-scale dynamics

    SciTech Connect

    Zhang, H.; Henderson-Sellers, A.; McGuffie, K.

    1996-10-01

    This is the second in a pair of papers in which the possible impacts of tropical deforestation are examined using a version of the NCAR CCM1. The emphasis in this paper is on the influence of tropical deforestation on the large-scale climate system. This influence is explored through the examination of the regional moisture budget and through an analysis of the Hadley and Walker circulations. Modification of the model surface parameters to simulate tropical deforestation produces significant modifications of both Hadley and Walker circulations, which result in changes distant from the region of deforestation. A mechanism for propagation to middle and high latitudes of disturbances arising form tropical deforestation is proposed based on Rossby wave propagation mechanisms. These mechanisms, which have also been associated with the extratropical influences of ENSO events, provide a pathway for the dispersion of the tropical disturbances to high latitudes. 27 refs., 20 figs., 1 tab.

  13. Design and Use of a Large-Scale Liquid Helium Conversion System

    NASA Technical Reports Server (NTRS)

    Knudsen, P. N.

    1999-01-01

    A large-scale liquid helium (LHe) to high-pressure (HP) gas conversion system has been implemented at the John F. Kennedy Space Center (KSC). Helium is used by the Space Shuttle, Titan, Atlas, and Delta programs for prelaunch processing, during launch count-down, and for postlaunch securing. The first phase of modifications to the Compressor Converter Facility (CCF), operational in April 1998, allowed the facility to accept bulk liquid helium from tanker containers and to off-load the helium at super-critical pressures. The second phase of modifications, planned to be operational by January 2001, will implement a 227-cubic-meter (m(sup 3)) on-site liquid helium storage system. This paper describes the design and operation of the current system and discusses the design and implementation for the second phase system.

  14. Simulation of large-scale rule-based models

    SciTech Connect

    Hlavacek, William S; Monnie, Michael I; Colvin, Joshua; Faseder, James

    2008-01-01

    Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules. Rules comprehensively, but implicitly, define the individual chemical species and reactions that molecular interactions can potentially generate. Although rules can be automatically processed to define a biochemical reaction network, the network implied by a set of rules is often too large to generate completely or to simulate using conventional procedures. To address this problem, we present DYNSTOC, a general-purpose tool for simulating rule-based models. DYNSTOC implements a null-event algorithm for simulating chemical reactions in a homogenous reaction compartment. The simulation method does not require that a reaction network be specified explicitly in advance, but rather takes advantage of the availability of the reaction rules in a rule-based specification of a network to determine if a randomly selected set of molecular components participates in a reaction during a time step. DYNSTOC reads reaction rules written in the BioNetGen language which is useful for modeling protein-protein interactions involved in signal transduction. The method of DYNSTOC is closely related to that of STOCHSIM. DYNSTOC differs from STOCHSIM by allowing for model specification in terms of BNGL, which extends the range of protein complexes that can be considered in a model. DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods. We demonstrate the ability of DYNSTOC to simulate models accounting for multisite phosphorylation and multivalent binding processes that are characterized by large numbers of reactions. DYNSTOC is free for non-commercial use. The C source code, supporting documentation and example input files are available at .

  15. Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: chemical artifact or post-translational modification?

    PubMed

    Perdivara, Irina; Deterding, Leesa J; Przybylski, Michael; Tomer, Kenneth B

    2010-07-01

    Oxidative modification of tryptophan to kynurenine (KYN) and N-formyl kynurenine (NFK) has been described in mitochondrial proteins associated with redox metabolism, and in human cataract lenses. To a large extent, however, previously reported identifications of these modifications were performed using peptide mass fingerprinting and/or tandem-MS data of proteins separated by gel electrophoresis. To date, it is uncertain whether NFK and KYN may represent sample handling artifacts or exclusively post-translational events. To address the problem of the origin of tryptophan oxidation, we characterized several antibodies by liquid chromatography-tandem mass spectrometry, with and without the use of electrophoretic separation of heavy and light chains. Antibodies are not normally expected to undergo oxidative modifications, however, several tryptophan (Trp) residues on both heavy and light chains were found extensively modified to both doubly oxidized Trp and KYN following SDS-PAGE separation and in-gel digestion. In contrast, those residues were observed as non-modified upon in-solution digestion. These results indicate that Trp oxidation may occur as an artifact in proteins separated by SDS-PAGE, and their presence should be carefully interpreted, especially when gel electrophoretic separation methods are employed.

  16. New probes of Cosmic Microwave Background large-scale anomalies

    NASA Astrophysics Data System (ADS)

    Aiola, Simone

    Fifty years of Cosmic Microwave Background (CMB) data played a crucial role in constraining the parameters of the LambdaCDM model, where Dark Energy, Dark Matter, and Inflation are the three most important pillars not yet understood. Inflation prescribes an isotropic universe on large scales, and it generates spatially-correlated density fluctuations over the whole Hubble volume. CMB temperature fluctuations on scales bigger than a degree in the sky, affected by modes on super-horizon scale at the time of recombination, are a clean snapshot of the universe after inflation. In addition, the accelerated expansion of the universe, driven by Dark Energy, leaves a hardly detectable imprint in the large-scale temperature sky at late times. Such fundamental predictions have been tested with current CMB data and found to be in tension with what we expect from our simple LambdaCDM model. Is this tension just a random fluke or a fundamental issue with the present model? In this thesis, we present a new framework to probe the lack of large-scale correlations in the temperature sky using CMB polarization data. Our analysis shows that if a suppression in the CMB polarization correlations is detected, it will provide compelling evidence for new physics on super-horizon scale. To further analyze the statistical properties of the CMB temperature sky, we constrain the degree of statistical anisotropy of the CMB in the context of the observed large-scale dipole power asymmetry. We find evidence for a scale-dependent dipolar modulation at 2.5sigma. To isolate late-time signals from the primordial ones, we test the anomalously high Integrated Sachs-Wolfe effect signal generated by superstructures in the universe. We find that the detected signal is in tension with the expectations from LambdaCDM at the 2.5sigma level, which is somewhat smaller than what has been previously argued. To conclude, we describe the current status of CMB observations on small scales, highlighting the

  17. Foundational perspectives on causality in large-scale brain networks.

    PubMed

    Mannino, Michael; Bressler, Steven L

    2015-12-01

    A profusion of recent work in cognitive neuroscience has been concerned with the endeavor to uncover causal influences in large-scale brain networks. However, despite the fact that many papers give a nod to the important theoretical challenges posed by the concept of causality, this explosion of research has generally not been accompanied by a rigorous conceptual analysis of the nature of causality in the brain. This review provides both a descriptive and prescriptive account of the nature of causality as found within and between large-scale brain networks. In short, it seeks to clarify the concept of causality in large-scale brain networks both philosophically and scientifically. This is accomplished by briefly reviewing the rich philosophical history of work on causality, especially focusing on contributions by David Hume, Immanuel Kant, Bertrand Russell, and Christopher Hitchcock. We go on to discuss the impact that various interpretations of modern physics have had on our understanding of causality. Throughout all this, a central focus is the distinction between theories of deterministic causality (DC), whereby causes uniquely determine their effects, and probabilistic causality (PC), whereby causes change the probability of occurrence of their effects. We argue that, given the topological complexity of its large-scale connectivity, the brain should be considered as a complex system and its causal influences treated as probabilistic in nature. We conclude that PC is well suited for explaining causality in the brain for three reasons: (1) brain causality is often mutual; (2) connectional convergence dictates that only rarely is the activity of one neuronal population uniquely determined by another one; and (3) the causal influences exerted between neuronal populations may not have observable effects. A number of different techniques are currently available to characterize causal influence in the brain. Typically, these techniques quantify the statistical

  18. Foundational perspectives on causality in large-scale brain networks

    NASA Astrophysics Data System (ADS)

    Mannino, Michael; Bressler, Steven L.

    2015-12-01

    A profusion of recent work in cognitive neuroscience has been concerned with the endeavor to uncover causal influences in large-scale brain networks. However, despite the fact that many papers give a nod to the important theoretical challenges posed by the concept of causality, this explosion of research has generally not been accompanied by a rigorous conceptual analysis of the nature of causality in the brain. This review provides both a descriptive and prescriptive account of the nature of causality as found within and between large-scale brain networks. In short, it seeks to clarify the concept of causality in large-scale brain networks both philosophically and scientifically. This is accomplished by briefly reviewing the rich philosophical history of work on causality, especially focusing on contributions by David Hume, Immanuel Kant, Bertrand Russell, and Christopher Hitchcock. We go on to discuss the impact that various interpretations of modern physics have had on our understanding of causality. Throughout all this, a central focus is the distinction between theories of deterministic causality (DC), whereby causes uniquely determine their effects, and probabilistic causality (PC), whereby causes change the probability of occurrence of their effects. We argue that, given the topological complexity of its large-scale connectivity, the brain should be considered as a complex system and its causal influences treated as probabilistic in nature. We conclude that PC is well suited for explaining causality in the brain for three reasons: (1) brain causality is often mutual; (2) connectional convergence dictates that only rarely is the activity of one neuronal population uniquely determined by another one; and (3) the causal influences exerted between neuronal populations may not have observable effects. A number of different techniques are currently available to characterize causal influence in the brain. Typically, these techniques quantify the statistical

  19. PROPERTIES IMPORTANT TO MIXING FOR WTP LARGE SCALE INTEGRATED TESTING

    SciTech Connect

    Koopman, D.; Martino, C.; Poirier, M.

    2012-04-26

    Large Scale Integrated Testing (LSIT) is being planned by Bechtel National, Inc. to address uncertainties in the full scale mixing performance of the Hanford Waste Treatment and Immobilization Plant (WTP). Testing will use simulated waste rather than actual Hanford waste. Therefore, the use of suitable simulants is critical to achieving the goals of the test program. External review boards have raised questions regarding the overall representativeness of simulants used in previous mixing tests. Accordingly, WTP requested the Savannah River National Laboratory (SRNL) to assist with development of simulants for use in LSIT. Among the first tasks assigned to SRNL was to develop a list of waste properties that matter to pulse-jet mixer (PJM) mixing of WTP tanks. This report satisfies Commitment 5.2.3.1 of the Department of Energy Implementation Plan for Defense Nuclear Facilities Safety Board Recommendation 2010-2: physical properties important to mixing and scaling. In support of waste simulant development, the following two objectives are the focus of this report: (1) Assess physical and chemical properties important to the testing and development of mixing scaling relationships; (2) Identify the governing properties and associated ranges for LSIT to achieve the Newtonian and non-Newtonian test objectives. This includes the properties to support testing of sampling and heel management systems. The test objectives for LSIT relate to transfer and pump out of solid particles, prototypic integrated operations, sparger operation, PJM controllability, vessel level/density measurement accuracy, sampling, heel management, PJM restart, design and safety margin, Computational Fluid Dynamics (CFD) Verification and Validation (V and V) and comparison, performance testing and scaling, and high temperature operation. The slurry properties that are most important to Performance Testing and Scaling depend on the test objective and rheological classification of the slurry (i

  20. 75 FR 51843 - In the Matter of Certain Large Scale Integrated Circuit Semiconductor Chips and Products...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-23

    ... Matter of Certain Large Scale Integrated Circuit Semiconductor Chips and Products Containing the Same... certain large scale integrated circuit semiconductor chips and products containing same by reason...

  1. A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

    PubMed Central

    Bramsen, Jesper B.; Pakula, Malgorzata M.; Hansen, Thomas B.; Bus, Claus; Langkjær, Niels; Odadzic, Dalibor; Smicius, Romualdas; Wengel, Suzy L.; Chattopadhyaya, Jyoti; Engels, Joachim W.; Herdewijn, Piet; Wengel, Jesper; Kjems, Jørgen

    2010-01-01

    Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low. PMID:20453030

  2. Physico-chemical modification of polyolefins irradiated by swift heavy ions

    NASA Astrophysics Data System (ADS)

    Apel, P. Yu.; Didyk, A. Yu.; Salina, A. G.

    1996-02-01

    The physico-chemical modifications of polypropylene (PP) and polyethylene (PE) induced by 1 MeV/u Xe ions were studied. The irradiated samples were investigated ex situ by means of ultraviolet (UV) spectroscopy, solubility measurements and gel permeation chromatography (GPC). The formation of double bonds, dienes and trienes was observed both in PE and PP. The efficiency of the generation of unsaturated chemical bonds was found to depend on small amounts of aromatic additives in PP. Similarly, the track etch rate in PP increases with increasing concentration of antioxidant molecules. Rough estimates of radiolytic yields of different structures were carried out on the basis of the UV and GPC measurements. It is apparent that there are two basically different processes induced by swift heavy ions passing through the polyolefin: (a) local intratrack reactions; (b) reactions induced by active species leaving the tracks and diffusing into surrounding matrix. The former process leads to the formation of etchable damage. The latter one may cause a mutual influence of tracks even at fairly low ion fluences.

  3. Ultrastructural demonstration of chemical modification of melanogenesis in hairless mouse skin

    SciTech Connect

    Nishimura, M.; Gellin, G.A.; Hoshino, S.; Epstein, J.H.; Epstein, W.L.; Fukuyama, K.

    1982-02-01

    We investigated chemical and physical modifications of the genetically determined ultrastructure of melanosomes. The flank skin of hairless mice was treated with ultraviolet energy (UV) shorter than 320 nm or with a combination of a photosensitizer and UV (PUVA treatment). All melanosomes in the induced melanocytes and those in resident melanocytes in the ear skin showed eumelanogenesis, although the degree of melanin deposition differed considerably according to the induction process. Eumelanogenesis was most advanced in the resident melanocytes while PUVA-induced melanocytes showed more immature premelanosomes. We then topically applied 4-tertiary butyl catechol on the skin. The depigmenting agent caused an appearance of pheomelanosomes. The alteration in melanogenesis was seen most distinctly in premelanosomes of the PUVA-induced cells. Altered ultrastructure was also observed in matured melanosomes; this change was most apparent in the resident melanocytes. These findings indicate that cells with eumelanogenesis may undergo pheomelanogenesis. The present study demonstrated effects of chemicals on genetically determined function of melanocytes by quantitative analysis of melanosome ultrastructure.

  4. Chemical modifications accompanying blueschist facies metamorphism of Franciscan conglomerates, Diablo Range, California

    USGS Publications Warehouse

    Moore, Diane E.; Liou, J.G.; King, B.-S.

    1981-01-01

    As part of an investigation of blueschist-facies mineral parageneses in pebbles and matrix of some Franciscan metaconglomerates of the Diablo Range, California, textural and major-element chemical analyses were conducted on a number of igneous pebbles that comprise a range of rock types from granite and dacite to gabbro and basalt. Compositions of the igneous pebbles differ significantly from common igneous rocks, particularly with respect to Ca, K, Na, Si and H2O. The SiO2 and H2O contents are characteristically high and the K2O contents low. The CaO and Na2O contents may be relatively enriched or reduced in different pebbles. The igneous pebbles show little evidence of alteration prior to their incorporation into the Franciscan conglomerates, and the chemical modifications are considered to have been produced during metamorphism of the conglomerates to (lawsonite + albite + aragonite ?? jadeite)-bearing assemblages. The observed variations in the pebbles are shown to be functions of: (1) bulk chemistry; (2) the igneous mineral assemblage; (3) the stable metamorphic mineral assemblage; and (4) the composition of pore fluids in the conglomerates. The relative proportions of Mg and Fe in most of the pebbles apparently have been unaffected by the metamorphism, and these parameters, along with other textural and chemical factors, were used to determine the petrogenetic affinities of the igneous pebbles. The plutonic and most of the volcanic pebbles correspond to calc-alkaline rock series, whereas a few volcanic pebbles show apparent Fe-enrichment characteristic of tholeiitic rocks. A continental margin arc-batholith complex would be the best source for these igneous detrital assemblages. Conglomerates in local areas differ in igneous lithologies from conglomerates in other areas and probably differ somewhat in age, perhaps reflecting varying degrees of unroofing of such a complex during deposition of Franciscan sediments. ?? 1981.

  5. Large-Scale Hybrid Motor Testing. Chapter 10

    NASA Technical Reports Server (NTRS)

    Story, George

    2006-01-01

    Hybrid rocket motors can be successfully demonstrated at a small scale virtually anywhere. There have been many suitcase sized portable test stands assembled for demonstration of hybrids. They show the safety of hybrid rockets to the audiences. These small show motors and small laboratory scale motors can give comparative burn rate data for development of different fuel/oxidizer combinations, however questions that are always asked when hybrids are mentioned for large scale applications are - how do they scale and has it been shown in a large motor? To answer those questions, large scale motor testing is required to verify the hybrid motor at its true size. The necessity to conduct large-scale hybrid rocket motor tests to validate the burn rate from the small motors to application size has been documented in several place^'^^.^. Comparison of small scale hybrid data to that of larger scale data indicates that the fuel burn rate goes down with increasing port size, even with the same oxidizer flux. This trend holds for conventional hybrid motors with forward oxidizer injection and HTPB based fuels. While the reason this is occurring would make a great paper or study or thesis, it is not thoroughly understood at this time. Potential causes include the fact that since hybrid combustion is boundary layer driven, the larger port sizes reduce the interaction (radiation, mixing and heat transfer) from the core region of the port. This chapter focuses on some of the large, prototype sized testing of hybrid motors. The largest motors tested have been AMROC s 250K-lbf thrust motor at Edwards Air Force Base and the Hybrid Propulsion Demonstration Program s 250K-lbf thrust motor at Stennis Space Center. Numerous smaller tests were performed to support the burn rate, stability and scaling concepts that went into the development of those large motors.

  6. Large-scale smart passive system for civil engineering applications

    NASA Astrophysics Data System (ADS)

    Jung, Hyung-Jo; Jang, Dong-Doo; Lee, Heon-Jae; Cho, Sang-Won

    2008-03-01

    The smart passive system consisting of a magnetorheological (MR) damper and an electromagnetic induction (EMI) part has been recently proposed. An EMI part can generate the input current for an MR damper from vibration of a structure according to Faraday's law of electromagnetic induction. The control performance of the smart passive system has been demonstrated mainly by numerical simulations. It was verified from the numerical results that the system could be effective to reduce the structural responses in the cases of civil engineering structures such as buildings and bridges. On the other hand, the experimental validation of the system is not sufficiently conducted yet. In this paper, the feasibility of the smart passive system to real-scale structures is investigated. To do this, the large-scale smart passive system is designed, manufactured, and tested. The system consists of the large-capacity MR damper, which has a maximum force level of approximately +/-10,000N, a maximum stroke level of +/-35mm and the maximum current level of 3 A, and the large-scale EMI part, which is designed to generate sufficient induced current for the damper. The applicability of the smart passive system to large real-scale structures is examined through a series of shaking table tests. The magnitudes of the induced current of the EMI part with various sinusoidal excitation inputs are measured. According to the test results, the large-scale EMI part shows the possibility that it could generate the sufficient current or power for changing the damping characteristics of the large-capacity MR damper.

  7. Solving large scale structure in ten easy steps with COLA

    SciTech Connect

    Tassev, Svetlin; Zaldarriaga, Matias; Eisenstein, Daniel J. E-mail: matiasz@ias.edu

    2013-06-01

    We present the COmoving Lagrangian Acceleration (COLA) method: an N-body method for solving for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). Unlike standard N-body methods, the COLA method can straightforwardly trade accuracy at small-scales in order to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing, as those catalogs are essential for performing detailed error analysis for ongoing and future surveys of LSS. As an illustration, we ran a COLA-based N-body code on a box of size 100 Mpc/h with particles of mass ≈ 5 × 10{sup 9}M{sub s}un/h. Running the code with only 10 timesteps was sufficient to obtain an accurate description of halo statistics down to halo masses of at least 10{sup 11}M{sub s}un/h. This is only at a modest speed penalty when compared to mocks obtained with LPT. A standard detailed N-body run is orders of magnitude slower than our COLA-based code. The speed-up we obtain with COLA is due to the fact that we calculate the large-scale dynamics exactly using LPT, while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos. Achieving a similar level of accuracy in halo statistics without the COLA method requires at least 3 times more timesteps than when COLA is employed.

  8. Infectious diseases in large-scale cat hoarding investigations.

    PubMed

    Polak, K C; Levy, J K; Crawford, P C; Leutenegger, C M; Moriello, K A

    2014-08-01

    Animal hoarders accumulate animals in over-crowded conditions without adequate nutrition, sanitation, and veterinary care. As a result, animals rescued from hoarding frequently have a variety of medical conditions including respiratory infections, gastrointestinal disease, parasitism, malnutrition, and other evidence of neglect. The purpose of this study was to characterize the infectious diseases carried by clinically affected cats and to determine the prevalence of retroviral infections among cats in large-scale cat hoarding investigations. Records were reviewed retrospectively from four large-scale seizures of cats from failed sanctuaries from November 2009 through March 2012. The number of cats seized in each case ranged from 387 to 697. Cats were screened for feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) in all four cases and for dermatophytosis in one case. A subset of cats exhibiting signs of upper respiratory disease or diarrhea had been tested for infections by PCR and fecal flotation for treatment planning. Mycoplasma felis (78%), calicivirus (78%), and Streptococcus equi subspecies zooepidemicus (55%) were the most common respiratory infections. Feline enteric coronavirus (88%), Giardia (56%), Clostridium perfringens (49%), and Tritrichomonas foetus (39%) were most common in cats with diarrhea. The seroprevalence of FeLV and FIV were 8% and 8%, respectively. In the one case in which cats with lesions suspicious for dermatophytosis were cultured for Microsporum canis, 69/76 lesional cats were culture-positive; of these, half were believed to be truly infected and half were believed to be fomite carriers. Cats from large-scale hoarding cases had high risk for enteric and respiratory infections, retroviruses, and dermatophytosis. Case responders should be prepared for mass treatment of infectious diseases and should implement protocols to prevent transmission of feline or zoonotic infections during the emergency response and when

  9. Statistical analysis of large-scale neuronal recording data

    PubMed Central

    Reed, Jamie L.; Kaas, Jon H.

    2010-01-01

    Relating stimulus properties to the response properties of individual neurons and neuronal networks is a major goal of sensory research. Many investigators implant electrode arrays in multiple brain areas and record from chronically implanted electrodes over time to answer a variety of questions. Technical challenges related to analyzing large-scale neuronal recording data are not trivial. Several analysis methods traditionally used by neurophysiologists do not account for dependencies in the data that are inherent in multi-electrode recordings. In addition, when neurophysiological data are not best modeled by the normal distribution and when the variables of interest may not be linearly related, extensions of the linear modeling techniques are recommended. A variety of methods exist to analyze correlated data, even when data are not normally distributed and the relationships are nonlinear. Here we review expansions of the Generalized Linear Model designed to address these data properties. Such methods are used in other research fields, and the application to large-scale neuronal recording data will enable investigators to determine the variable properties that convincingly contribute to the variances in the observed neuronal measures. Standard measures of neuron properties such as response magnitudes can be analyzed using these methods, and measures of neuronal network activity such as spike timing correlations can be analyzed as well. We have done just that in recordings from 100-electrode arrays implanted in the primary somatosensory cortex of owl monkeys. Here we illustrate how one example method, Generalized Estimating Equations analysis, is a useful method to apply to large-scale neuronal recordings. PMID:20472395

  10. The Large-Scale Current System During Auroral Substorms

    NASA Astrophysics Data System (ADS)

    Gjerloev, Jesper

    2015-04-01

    The substorm process has been discussed for more than four decades and new empirical large-scale models continue to be published. The continued activity implies both the importance and the complexity of the problem. We recently published a new model of the large-scale substorm current system (Gjerloev and Hoffman, JGR, 2014). Based on data from >100 ground magnetometers (obtained from SuperMAG), 116 isolated substorms, global auroral images (obtained by the Polar VIS Earth Camera) and a careful normalization technique we derived an empirical model of the ionospheric equivalent current system. Our model yield some unexpected features that appear inconsistent with the classical single current wedge current system. One of these features is a distinct latitudinal shift of the westward electrojet (WEJ) current between the pre- and post-midnight region and we find evidence that these two WEJ regions are quasi disconnected. This, and other observational facts, led us to propose a modified 3D current system configuration that consists of 2 wedge type systems: a current wedge in the pre-midnight region (bulge current wedge), and another current wedge system in the post-midnight region (oval current wedge). The two wedge systems are shifted in latitude but overlap in local time in the midnight region. Our model is at considerable variance with previous global models and conceptual schematics of the large-scale substorm current system. We speculate that the data coverage, the methodologies and the techniques used in these previous global studies are the cause of the differences in solutions. In this presentation we present our model, compare with other published models and discuss possible causes for the differences.

  11. Solving large scale structure in ten easy steps with COLA

    NASA Astrophysics Data System (ADS)

    Tassev, Svetlin; Zaldarriaga, Matias; Eisenstein, Daniel J.

    2013-06-01

    We present the COmoving Lagrangian Acceleration (COLA) method: an N-body method for solving for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). Unlike standard N-body methods, the COLA method can straightforwardly trade accuracy at small-scales in order to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing, as those catalogs are essential for performing detailed error analysis for ongoing and future surveys of LSS. As an illustration, we ran a COLA-based N-body code on a box of size 100 Mpc/h with particles of mass ≈ 5 × 109Msolar/h. Running the code with only 10 timesteps was sufficient to obtain an accurate description of halo statistics down to halo masses of at least 1011Msolar/h. This is only at a modest speed penalty when compared to mocks obtained with LPT. A standard detailed N-body run is orders of magnitude slower than our COLA-based code. The speed-up we obtain with COLA is due to the fact that we calculate the large-scale dynamics exactly using LPT, while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos. Achieving a similar level of accuracy in halo statistics without the COLA method requires at least 3 times more timesteps than when COLA is employed.

  12. Improving Design Efficiency for Large-Scale Heterogeneous Circuits

    NASA Astrophysics Data System (ADS)

    Gregerson, Anthony

    Despite increases in logic density, many Big Data applications must still be partitioned across multiple computing devices in order to meet their strict performance requirements. Among the most demanding of these applications is high-energy physics (HEP), which uses complex computing systems consisting of thousands of FPGAs and ASICs to process the sensor data created by experiments at particles accelerators such as the Large Hadron Collider (LHC). Designing such computing systems is challenging due to the scale of the systems, the exceptionally high-throughput and low-latency performance constraints that necessitate application-specific hardware implementations, the requirement that algorithms are efficiently partitioned across many devices, and the possible need to update the implemented algorithms during the lifetime of the system. In this work, we describe our research to develop flexible architectures for implementing such large-scale circuits on FPGAs. In particular, this work is motivated by (but not limited in scope to) high-energy physics algorithms for the Compact Muon Solenoid (CMS) experiment at the LHC. To make efficient use of logic resources in multi-FPGA systems, we introduce Multi-Personality Partitioning, a novel form of the graph partitioning problem, and present partitioning algorithms that can significantly improve resource utilization on heterogeneous devices while also reducing inter-chip connections. To reduce the high communication costs of Big Data applications, we also introduce Information-Aware Partitioning, a partitioning method that analyzes the data content of application-specific circuits, characterizes their entropy, and selects circuit partitions that enable efficient compression of data between chips. We employ our information-aware partitioning method to improve the performance of the hardware validation platform for evaluating new algorithms for the CMS experiment. Together, these research efforts help to improve the efficiency

  13. LARGE-SCALE CO2 TRANSPORTATION AND DEEP OCEAN SEQUESTRATION

    SciTech Connect

    Hamid Sarv

    1999-03-01

    Technical and economical feasibility of large-scale CO{sub 2} transportation and ocean sequestration at depths of 3000 meters or grater was investigated. Two options were examined for transporting and disposing the captured CO{sub 2}. In one case, CO{sub 2} was pumped from a land-based collection center through long pipelines laid on the ocean floor. Another case considered oceanic tanker transport of liquid carbon dioxide to an offshore floating structure for vertical injection to the ocean floor. In the latter case, a novel concept based on subsurface towing of a 3000-meter pipe, and attaching it to the offshore structure was considered. Budgetary cost estimates indicate that for distances greater than 400 km, tanker transportation and offshore injection through a 3000-meter vertical pipe provides the best method for delivering liquid CO{sub 2} to deep ocean floor depressions. For shorter distances, CO{sub 2} delivery by parallel-laid, subsea pipelines is more cost-effective. Estimated costs for 500-km transport and storage at a depth of 3000 meters by subsea pipelines and tankers were 1.5 and 1.4 dollars per ton of stored CO{sub 2}, respectively. At these prices, economics of ocean disposal are highly favorable. Future work should focus on addressing technical issues that are critical to the deployment of a large-scale CO{sub 2} transportation and disposal system. Pipe corrosion, structural design of the transport pipe, and dispersion characteristics of sinking CO{sub 2} effluent plumes have been identified as areas that require further attention. Our planned activities in the next Phase include laboratory-scale corrosion testing, structural analysis of the pipeline, analytical and experimental simulations of CO{sub 2} discharge and dispersion, and the conceptual economic and engineering evaluation of large-scale implementation.

  14. Large scale MoS2 nanosheet logic circuits integrated by photolithography on glass

    NASA Astrophysics Data System (ADS)

    Kwon, Hyeokjae; Jeon, Pyo Jin; Kim, Jin Sung; Kim, Tae-Young; Yun, Hoyeol; Lee, Sang Wook; Lee, Takhee; Im, Seongil

    2016-12-01

    We demonstrate 500 × 500 μm2 large scale polygrain MoS2 nanosheets and field effect transistor (FET) circuits integrated using those nanosheets, which are initially grown on SiO2/p+-Si by chemical vapor deposition but transferred onto glass substrate to be patterned by photolithography. In fact, large scale growth of two-dimensional MoS2 and its conventional way of patterning for integrated devices have remained as one of the unresolved important issues. In the present study, we achieved maximum linear mobility of ˜9 cm2 V-1 s-1 from single-domain MoS2 FET on SiO2/p+-Si substrate and 0.5˜3.0 cm2 V-1 s-1 from large scale MoS2 sheet transferred onto glass. Such reduced mobility is attributed to the transfer process-induced wrinkles and crevices, domain boundaries, residue on MoS2, and loss of the back gate-charging effects that might exist due to SiO2/p+-Si substrate. Among 16 MoS2-based FETs, 13 devices successfully work (yield was more than 80%) producing NOT, NOR, and NAND logic circuits. Inverter (NOT gate) shows quite a high voltage gain over 12 at a supply voltage of 5 V, also displaying 60 μs switching speed in kilohertz dynamics.

  15. Large-Scale periodic solar velocities: An observational study

    NASA Technical Reports Server (NTRS)

    Dittmer, P. H.

    1977-01-01

    Observations of large-scale solar velocities were made using the mean field telescope and Babcock magnetograph of the Stanford Solar Observatory. Observations were made in the magnetically insensitive ion line at 5124 A, with light from the center (limb) of the disk right (left) circularly polarized, so that the magnetograph measures the difference in wavelength between center and limb. Computer calculations are made of the wavelength difference produced by global pulsations for spherical harmonics up to second order and of the signal produced by displacing the solar image relative to polarizing optics or diffraction grating.

  16. Large-scale sodium spray fire code validation (SOFICOV) test

    SciTech Connect

    Jeppson, D.W.; Muhlestein, L.D.

    1985-01-01

    A large-scale, sodium, spray fire code validation test was performed in the HEDL 850-m/sup 3/ Containment System Test Facility (CSTF) as part of the Sodium Spray Fire Code Validation (SOFICOV) program. Six hundred fifty eight kilograms of sodium spray was sprayed in an air atmosphere for a period of 2400 s. The sodium spray droplet sizes and spray pattern distribution were estimated. The containment atmosphere temperature and pressure response, containment wall temperature response and sodium reaction rate with oxygen were measured. These results are compared to post-test predictions using SPRAY and NACOM computer codes.

  17. UAV Data Processing for Large Scale Topographical Mapping

    NASA Astrophysics Data System (ADS)

    Tampubolon, W.; Reinhardt, W.

    2014-06-01

    Large scale topographical mapping in the third world countries is really a prominent challenge in geospatial industries nowadays. On one side the demand is significantly increasing while on the other hand it is constrained by limited budgets available for mapping projects. Since the advent of Act Nr.4/yr.2011 about Geospatial Information in Indonesia, large scale topographical mapping has been on high priority for supporting the nationwide development e.g. detail spatial planning. Usually large scale topographical mapping relies on conventional aerial survey campaigns in order to provide high resolution 3D geospatial data sources. Widely growing on a leisure hobby, aero models in form of the so-called Unmanned Aerial Vehicle (UAV) bring up alternative semi photogrammetric aerial data acquisition possibilities suitable for relatively small Area of Interest (AOI) i.e. <5,000 hectares. For detail spatial planning purposes in Indonesia this area size can be used as a mapping unit since it usually concentrates on the basis of sub district area (kecamatan) level. In this paper different camera and processing software systems will be further analyzed for identifying the best optimum UAV data acquisition campaign components in combination with the data processing scheme. The selected AOI is covering the cultural heritage of Borobudur Temple as one of the Seven Wonders of the World. A detailed accuracy assessment will be concentrated within the object feature of the temple at the first place. Feature compilation involving planimetric objects (2D) and digital terrain models (3D) will be integrated in order to provide Digital Elevation Models (DEM) as the main interest of the topographic mapping activity. By doing this research, incorporating the optimum amount of GCPs in the UAV photo data processing will increase the accuracy along with its high resolution in 5 cm Ground Sampling Distance (GSD). Finally this result will be used as the benchmark for alternative geospatial

  18. Large scale obscuration and related climate effects open literature bibliography

    SciTech Connect

    Russell, N.A.; Geitgey, J.; Behl, Y.K.; Zak, B.D.

    1994-05-01

    Large scale obscuration and related climate effects of nuclear detonations first became a matter of concern in connection with the so-called ``Nuclear Winter Controversy`` in the early 1980`s. Since then, the world has changed. Nevertheless, concern remains about the atmospheric effects of nuclear detonations, but the source of concern has shifted. Now it focuses less on global, and more on regional effects and their resulting impacts on the performance of electro-optical and other defense-related systems. This bibliography reflects the modified interest.

  19. Water-based scintillators for large-scale liquid calorimetry

    SciTech Connect

    Winn, D.R.; Raftery, D.

    1985-02-01

    We have investigated primary and secondary solvent intermediates in search of a recipe to create a bulk liquid scintillator with water as the bulk solvent and common fluors as the solutes. As we are not concerned with energy resolution below 1 MeV in large-scale experiments, light-output at the 10% level of high-quality organic solvent based scintillators is acceptable. We have found encouraging performance from industrial surfactants as primary solvents for PPO and POPOP. This technique may allow economical and environmentally safe bulk scintillator for kiloton-sized high energy calorimetry.

  20. Enabling Large-Scale Biomedical Analysis in the Cloud

    PubMed Central

    Lin, Ying-Chih; Yu, Chin-Sheng; Lin, Yen-Jen

    2013-01-01

    Recent progress in high-throughput instrumentations has led to an astonishing growth in both volume and complexity of biomedical data collected from various sources. The planet-size data brings serious challenges to the storage and computing technologies. Cloud computing is an alternative to crack the nut because it gives concurrent consideration to enable storage and high-performance computing on large-scale data. This work briefly introduces the data intensive computing system and summarizes existing cloud-based resources in bioinformatics. These developments and applications would facilitate biomedical research to make the vast amount of diversification data meaningful and usable. PMID:24288665

  1. Large scale mortality of nestling ardeids caused by nematode infection.

    PubMed

    Wiese, J H; Davidson, W R; Nettles, V F

    1977-10-01

    During the summer of 1976, an epornitic of verminous peritonitis caused by Eustrongylides ignotus resulted in large scale mortality of young herons and egrets on Pea Patch Island, Delaware. Mortality was highest (84%) in snowy egret nestlings ( Egretta thula ) and less severe in great egrets ( Casmerodius albus ), Louisiana herons ( Hydranassa tricolor ), little blue herons ( Florida caerulea ), and black crowned night herons ( Nycticorax nycticorax ). Most deaths occured within the first 4 weeks after hatching. Migration of E. ignotus resulted in multiple perforations of the visceral organs, escape of intestinal contents into the body cavity and subsequent bacterial peritonitis. Killifish ( Fundulus heteroclitus ) served as the source of infective larvae.

  2. Integrated High Accuracy Portable Metrology for Large Scale Structural Testing

    NASA Astrophysics Data System (ADS)

    Klaas, Andrej; Richardson, Paul; Burguete, Richard; Harris, Linden

    2014-06-01

    As the performance and accuracy of analysis tools increases bespoke solutions are more regularly being requested to perform high-accuracy measurement on structural tests to validate these methods. These can include optical methods and full-field techniques in place of the more traditional point measurements. As each test is unique it presents its own individual challenges.In this paper two recent, large scale tests performed by Airbus, will be presented and the metrology solutions that were identified for them will be discussed.

  3. Large-scale normal fluid circulation in helium superflows

    NASA Astrophysics Data System (ADS)

    Galantucci, Luca; Sciacca, Michele; Barenghi, Carlo F.

    2017-01-01

    We perform fully coupled numerical simulations of helium II pure superflows in a channel, with vortex-line density typical of experiments. Peculiar to our model is the computation of the back-reaction of the superfluid vortex motion on the normal fluid and the presence of solid boundaries. We recover the uniform vortex-line density experimentally measured employing second sound resonators and we show that pure superflow in helium II is associated with a large-scale circulation of the normal fluid which can be detected using existing particle-tracking visualization techniques.

  4. Clusters as cornerstones of large-scale structure.

    NASA Astrophysics Data System (ADS)

    Gottlöber, S.; Retzlaff, J.; Turchaninov, V.

    1997-04-01

    Galaxy clusters are one of the best tracers of large-scale structure in the Universe on scales well above 100 Mpc. The authors investigate here the clustering properties of a redshift sample of Abell/ACO clusters and compare the observational sample with mock samples constructed from N-body simulations on the basis of four different cosmological models. The authors discuss the power spectrum, the Minkowski functionals and the void statistics of these samples and conclude, that the SCDM and TCDM models are ruled out whereas the ACDM and BSI models are in agreement with the observational data.

  5. Large-Scale Patterns of Filament Channels and Filaments

    NASA Astrophysics Data System (ADS)

    Mackay, Duncan

    2016-07-01

    In this review the properties and large-scale patterns of filament channels and filaments will be considered. Initially, the global formation locations of filament channels and filaments are discussed, along with their hemispheric pattern. Next, observations of the formation of filament channels and filaments are described where two opposing views are considered. Finally, the wide range of models that have been constructed to consider the formation of filament channels and filaments over long time-scales are described, along with the origin of the hemispheric pattern of filaments.

  6. Quantum computation for large-scale image classification

    NASA Astrophysics Data System (ADS)

    Ruan, Yue; Chen, Hanwu; Tan, Jianing; Li, Xi

    2016-10-01

    Due to the lack of an effective quantum feature extraction method, there is currently no effective way to perform quantum image classification or recognition. In this paper, for the first time, a global quantum feature extraction method based on Schmidt decomposition is proposed. A revised quantum learning algorithm is also proposed that will classify images by computing the Hamming distance of these features. From the experimental results derived from the benchmark database Caltech 101, and an analysis of the algorithm, an effective approach to large-scale image classification is derived and proposed against the background of big data.

  7. Large Scale Composite Manufacturing for Heavy Lift Launch Vehicles

    NASA Technical Reports Server (NTRS)

    Stavana, Jacob; Cohen, Leslie J.; Houseal, Keth; Pelham, Larry; Lort, Richard; Zimmerman, Thomas; Sutter, James; Western, Mike; Harper, Robert; Stuart, Michael

    2012-01-01

    Risk reduction for the large scale composite manufacturing is an important goal to produce light weight components for heavy lift launch vehicles. NASA and an industry team successfully employed a building block approach using low-cost Automated Tape Layup (ATL) of autoclave and Out-of-Autoclave (OoA) prepregs. Several large, curved sandwich panels were fabricated at HITCO Carbon Composites. The aluminum honeycomb core sandwich panels are segments of a 1/16th arc from a 10 meter cylindrical barrel. Lessons learned highlight the manufacturing challenges required to produce light weight composite structures such as fairings for heavy lift launch vehicles.

  8. Solving Large-scale Eigenvalue Problems in SciDACApplications

    SciTech Connect

    Yang, Chao

    2005-06-29

    Large-scale eigenvalue problems arise in a number of DOE applications. This paper provides an overview of the recent development of eigenvalue computation in the context of two SciDAC applications. We emphasize the importance of Krylov subspace methods, and point out its limitations. We discuss the value of alternative approaches that are more amenable to the use of preconditioners, and report the progression using the multi-level algebraic sub-structuring techniques to speed up eigenvalue calculation. In addition to methods for linear eigenvalue problems, we also examine new approaches to solving two types of non-linear eigenvalue problems arising from SciDAC applications.

  9. Analysis Plan for 1985 Large-Scale Tests.

    DTIC Science & Technology

    1983-01-01

    KEY WORDS (Continue on reverse side it necessary mnd Identify by block number) Large-Scale Blasting Agents Multiburst ANFO S:,ock Waves 20. ABSTRACT...CONSIDERATIONS 6 1.5 MULTIBURST TECHNIQUES 6 1.6 TEST SITE CONSIDERATIONS 6 2 CANDIDATE EXPLOSIVES 8 2.1 INTRODUCTION 82.2 ANFO 8 2.2.1 Bulk (Loose) ANFO 11...2.2.2 Bagged ANFO 13 2.3 APEX 1360 15 2.4 NITRIC ACID AND NITROPROPANE 17 2.5 NITROPROPANENITRATE (NPN) 19 2.6 DBA - 22M 21 2.7 HARDENING EMULSION 22 2.8

  10. Frequency domain multiplexing for large-scale bolometer arrays

    SciTech Connect

    Spieler, Helmuth

    2002-05-31

    The development of planar fabrication techniques for superconducting transition-edge sensors has brought large-scale arrays of 1000 pixels or more to the realm of practicality. This raises the problem of reading out a large number of sensors with a tractable number of connections. A possible solution is frequency-domain multiplexing. I summarize basic principles, present various circuit topologies, and discuss design trade-offs, noise performance, cross-talk and dynamic range. The design of a practical device and its readout system is described with a discussion of fabrication issues, practical limits and future prospects.

  11. A Modular Ring Architecture for Large Scale Neural Network Implementations

    NASA Astrophysics Data System (ADS)

    Jump, Lance B.; Ligomenides, Panos A.

    1989-11-01

    Constructing fully parallel, large scale, neural networks is complicated by the problems of providing for massive interconnectivity and of overcoming fan in/out limitations in area-efficient VLSI/WSI realizations. A modular, bus switched, neural ring architecture employing primitive ring (pRing) processors is proposed, which solves the fan in/out and connectivity problems by a dynamically reconfigurable communication ring that synchronously serves identical, radially connected, processing elements. It also allows cost versus performance trade-offs by the assignment of variable numbers of logical neurons to each physical processing element.

  12. Design of a large-scale CFB boiler

    SciTech Connect

    Darling, S.; Li, S.

    1997-12-31

    Many CFB boilers sized 100--150 MWe are in operation, and several others sized 150--250 MWe are in operation or under construction. The next step for CFB technology is the 300--400 MWe size range. This paper will describe Foster Wheeler`s large-scale CFB boiler experience and the design for a 300 MWe CFB boiler. The authors will show how the design incorporates Foster Wheeler`s unique combination of extensive utility experience and CFB boiler experience. All the benefits of CFB technology which include low emissions, fuel flexibility, low maintenance and competitive cost are now available in the 300--400 MWe size range.

  13. Simplified DGS procedure for large-scale genome structural study.

    PubMed

    Jung, Yong-Chul; Xu, Jia; Chen, Jun; Kim, Yeong; Winchester, David; Wang, San Ming

    2009-11-01

    Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.

  14. Large-Scale Compton Imaging for Wide-Area Surveillance

    SciTech Connect

    Lange, D J; Manini, H A; Wright, D M

    2006-03-01

    We study the performance of a large-scale Compton imaging detector placed in a low-flying aircraft, used to search wide areas for rad/nuc threat sources. In this paper we investigate the performance potential of equipping aerial platforms with gamma-ray detectors that have photon sensitivity up to a few MeV. We simulate the detector performance, and present receiver operating characteristics (ROC) curves for a benchmark scenario using a {sup 137}Cs source. The analysis uses a realistic environmental background energy spectrum and includes air attenuation.

  15. Decentrally stabilizable linear and bilinear large-scale systems

    NASA Technical Reports Server (NTRS)

    Siljak, D. D.; Vukcevic, M. B.

    1977-01-01

    Two classes of large-scale systems are identified, which can always be stabilized by decentralized feedback control. For the class of systems composed of interconnected linear subsystems, we can choose local controllers for the subsystems to achieve stability of the overall system. The same linear feedback scheme can be used to stabilize a class of linear systems with bilinear interconnections. In this case, however, the scheme is used to establish a finite region of stability for the overall system. The stabilization algorithm is applied to the design of a control system for the Large-Space Telescope.

  16. Large-scale structure from wiggly cosmic strings

    NASA Astrophysics Data System (ADS)

    Vachaspati, Tanmay; Vilenkin, Alexander

    1991-08-01

    Recent simulations of the evolution of cosmic strings indicate the presence of small-scale structure on the strings. It is shown that wakes produced by such 'wiggly' cosmic strings can result in the efficient formation of large-scale structure and large streaming velocities in the universe without significantly affecting the microwave-background isotropy. It is also argued that the motion of strings will lead to the generation of a primordial magnetic field. The most promising version of this scenario appears to be the one in which the universe is dominated by light neutrinos.

  17. Structure and function of large-scale brain systems.

    PubMed

    Koziol, Leonard F; Barker, Lauren A; Joyce, Arthur W; Hrin, Skip

    2014-01-01

    This article introduces the functional neuroanatomy of large-scale brain systems. Both the structure and functions of these brain networks are presented. All human behavior is the result of interactions within and between these brain systems. This system of brain function completely changes our understanding of how cognition and behavior are organized within the brain, replacing the traditional lesion model. Understanding behavior within the context of brain network interactions has profound implications for modifying abstract constructs such as attention, learning, and memory. These constructs also must be understood within the framework of a paradigm shift, which emphasizes ongoing interactions within a dynamically changing environment.

  18. Chemical modification of lysine and arginine residues of bovine heart 2-oxoglutarate dehydrogenase: effect on the enzyme activity and regulation.

    PubMed

    Ostrovtsova, S A

    1998-01-01

    Chemical modification of arginine and lysine residues of bovine heart 2-oxoglutarate dehydrogenase with phenylglyoxal and pyridoxal 5'-phosphate inactivated the enzyme, indicating the importance of these residues for the catalysis. Inactivation caused by pyridoxal 5'-phosphate was prevented in the presence of thiamine pyrophosphate and Mg2+ allowing the assumption that lysine residues participate in binding of the cofactor.

  19. The combustion behavior of large scale lithium titanate battery

    PubMed Central

    Huang, Peifeng; Wang, Qingsong; Li, Ke; Ping, Ping; Sun, Jinhua

    2015-01-01

    Safety problem is always a big obstacle for lithium battery marching to large scale application. However, the knowledge on the battery combustion behavior is limited. To investigate the combustion behavior of large scale lithium battery, three 50 Ah Li(NixCoyMnz)O2/Li4Ti5O12 batteries under different state of charge (SOC) were heated to fire. The flame size variation is depicted to analyze the combustion behavior directly. The mass loss rate, temperature and heat release rate are used to analyze the combustion behavior in reaction way deeply. Based on the phenomenon, the combustion process is divided into three basic stages, even more complicated at higher SOC with sudden smoke flow ejected. The reason is that a phase change occurs in Li(NixCoyMnz)O2 material from layer structure to spinel structure. The critical temperatures of ignition are at 112–121°C on anode tab and 139 to 147°C on upper surface for all cells. But the heating time and combustion time become shorter with the ascending of SOC. The results indicate that the battery fire hazard increases with the SOC. It is analyzed that the internal short and the Li+ distribution are the main causes that lead to the difference. PMID:25586064

  20. Very large-scale motions in a turbulent pipe flow

    NASA Astrophysics Data System (ADS)

    Lee, Jae Hwa; Jang, Seong Jae; Sung, Hyung Jin

    2011-11-01

    Direct numerical simulation of a turbulent pipe flow with ReD=35000 was performed to investigate the spatially coherent structures associated with very large-scale motions. The corresponding friction Reynolds number, based on pipe radius R, is R+=934, and the computational domain length is 30 R. The computed mean flow statistics agree well with previous DNS data at ReD=44000 and 24000. Inspection of the instantaneous fields and two-point correlation of the streamwise velocity fluctuations showed that the very long meandering motions exceeding 25R exist in logarithmic and wake regions, and the streamwise length scale is almost linearly increased up to y/R ~0.3, while the structures in the turbulent boundary layer only reach up to the edge of the log-layer. Time-resolved instantaneous fields revealed that the hairpin packet-like structures grow with continuous stretching along the streamwise direction and create the very large-scale structures with meandering in the spanwise direction, consistent with the previous conceptual model of Kim & Adrian (1999). This work was supported by the Creative Research Initiatives of NRF/MEST of Korea (No. 2011-0000423).

  1. Topographically Engineered Large Scale Nanostructures for Plasmonic Biosensing

    PubMed Central

    Xiao, Bo; Pradhan, Sangram K.; Santiago, Kevin C.; Rutherford, Gugu N.; Pradhan, Aswini K.

    2016-01-01

    We demonstrate that a nanostructured metal thin film can achieve enhanced transmission efficiency and sharp resonances and use a large-scale and high-throughput nanofabrication technique for the plasmonic structures. The fabrication technique combines the features of nanoimprint and soft lithography to topographically construct metal thin films with nanoscale patterns. Metal nanogratings developed using this method show significantly enhanced optical transmission (up to a one-order-of-magnitude enhancement) and sharp resonances with full width at half maximum (FWHM) of ~15nm in the zero-order transmission using an incoherent white light source. These nanostructures are sensitive to the surrounding environment, and the resonance can shift as the refractive index changes. We derive an analytical method using a spatial Fourier transformation to understand the enhancement phenomenon and the sensing mechanism. The use of real-time monitoring of protein-protein interactions in microfluidic cells integrated with these nanostructures is demonstrated to be effective for biosensing. The perpendicular transmission configuration and large-scale structures provide a feasible platform without sophisticated optical instrumentation to realize label-free surface plasmon resonance (SPR) sensing. PMID:27072067

  2. Semantic overlay network for large-scale spatial information indexing

    NASA Astrophysics Data System (ADS)

    Zou, Zhiqiang; Wang, Yue; Cao, Kai; Qu, Tianshan; Wang, Zhongmin

    2013-08-01

    The increased demand for online services of spatial information poses new challenges to the combined filed of Computer Science and Geographic Information Science. Amongst others, these include fast indexing of spatial data in distributed networks. In this paper we propose a novel semantic overlay network for large-scale multi-dimensional spatial information indexing, called SON_LSII, which has a hybrid structure integrating a semantic quad-tree and Chord ring. The SON_LSII is a small world overlay network that achieves a very competitive trade-off between indexing efficiency and maintenance overhead. To create SON_LSII, we use an effective semantic clustering strategy that considers two aspects, i.e., the semantic of spatial information that peer holds in overlay network and physical network performances. Based on SON_LSII, a mapping method is used to reduce the multi-dimensional features into a single dimension and an efficient indexing algorithm is presented to support complex range queries of the spatial information with a massive number of concurrent users. The results from extensive experiments demonstrate that SON_LSII is superior to existing overlay networks in various respects, including scalability, maintenance, rate of indexing hits, indexing logical hops, and adaptability. Thus, the proposed SON_LSII can be used for large-scale spatial information indexing.

  3. The combustion behavior of large scale lithium titanate battery.

    PubMed

    Huang, Peifeng; Wang, Qingsong; Li, Ke; Ping, Ping; Sun, Jinhua

    2015-01-14

    Safety problem is always a big obstacle for lithium battery marching to large scale application. However, the knowledge on the battery combustion behavior is limited. To investigate the combustion behavior of large scale lithium battery, three 50 Ah Li(Ni(x)Co(y)Mn(z))O2/Li(4)Ti(5)O(12) batteries under different state of charge (SOC) were heated to fire. The flame size variation is depicted to analyze the combustion behavior directly. The mass loss rate, temperature and heat release rate are used to analyze the combustion behavior in reaction way deeply. Based on the phenomenon, the combustion process is divided into three basic stages, even more complicated at higher SOC with sudden smoke flow ejected. The reason is that a phase change occurs in Li(Ni(x)Co(y)Mn(z))O2 material from layer structure to spinel structure. The critical temperatures of ignition are at 112-121 °C on anode tab and 139 to 147 °C on upper surface for all cells. But the heating time and combustion time become shorter with the ascending of SOC. The results indicate that the battery fire hazard increases with the SOC. It is analyzed that the internal short and the Li(+) distribution are the main causes that lead to the difference.

  4. Maestro: An Orchestration Framework for Large-Scale WSN Simulations

    PubMed Central

    Riliskis, Laurynas; Osipov, Evgeny

    2014-01-01

    Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation. PMID:24647123

  5. Large-Scale Low-Boom Inlet Test Overview

    NASA Technical Reports Server (NTRS)

    Hirt, Stefanie

    2011-01-01

    This presentation provides a high level overview of the Large-Scale Low-Boom Inlet Test and was presented at the Fundamental Aeronautics 2011 Technical Conference. In October 2010 a low-boom supersonic inlet concept with flow control was tested in the 8'x6' supersonic wind tunnel at NASA Glenn Research Center (GRC). The primary objectives of the test were to evaluate the inlet stability and operability of a large-scale low-boom supersonic inlet concept by acquiring performance and flowfield validation data, as well as evaluate simple, passive, bleedless inlet boundary layer control options. During this effort two models were tested: a dual stream inlet intended to model potential flight hardware and a single stream design to study a zero-degree external cowl angle and to permit surface flow visualization of the vortex generator flow control on the internal centerbody surface. The tests were conducted by a team of researchers from NASA GRC, Gulfstream Aerospace Corporation, University of Illinois at Urbana-Champaign, and the University of Virginia

  6. Wall turbulence manipulation by large-scale streamwise vortices

    NASA Astrophysics Data System (ADS)

    Iuso, Gaetano; Onorato, Michele; Spazzini, Pier Giorgio; di Cicca, Gaetano Maria

    2002-12-01

    This paper describes an experimental study of the manipulation of a fully developed turbulent channel flow through large-scale streamwise vortices originated by vortex generator jets distributed along the wall in the spanwise direction. Apart from the interest in flow management itself, an important aim of the research is to observe the response of the flow to external perturbations as a technique for investigating the structure of turbulence. Considerable mean and fluctuating skin friction reductions, locally as high as 30% and 50% respectively, were measured for an optimal forcing flow intensity. Mean and fluctuating velocity profiles are also greatly modified by the manipulating large-scale vortices; in particular, attenuation of the turbulence intensity was measured. Moreover the flow manipulation caused an increase in longitudinal coherence of the wall organized motions, accompanied by a reduced frequency of burst events, demonstrated by a reduction of the velocity time derivative PDFs and by an higher intermittency. A strong transversal periodic organization of the flow field was observed, including some typical behaviours in each of the periodic boxes originated by the interaction of the vortex pairs. Results are interpreted and discussed in terms of management of the near-wall turbulent structures and with reference to the wall turbulence regeneration mechanisms suggested in the literature.

  7. Power suppression at large scales in string inflation

    SciTech Connect

    Cicoli, Michele; Downes, Sean; Dutta, Bhaskar E-mail: sddownes@physics.tamu.edu

    2013-12-01

    We study a possible origin of the anomalous suppression of the power spectrum at large angular scales in the cosmic microwave background within the framework of explicit string inflationary models where inflation is driven by a closed string modulus parameterizing the size of the extra dimensions. In this class of models the apparent power loss at large scales is caused by the background dynamics which involves a sharp transition from a fast-roll power law phase to a period of Starobinsky-like slow-roll inflation. An interesting feature of this class of string inflationary models is that the number of e-foldings of inflation is inversely proportional to the string coupling to a positive power. Therefore once the string coupling is tuned to small values in order to trust string perturbation theory, enough e-foldings of inflation are automatically obtained without the need of extra tuning. Moreover, in the less tuned cases the sharp transition responsible for the power loss takes place just before the last 50-60 e-foldings of inflation. We illustrate these general claims in the case of Fibre Inflation where we study the strength of this transition in terms of the attractor dynamics, finding that it induces a pivot from a blue to a redshifted power spectrum which can explain the apparent large scale power loss. We compute the effects of this pivot for example cases and demonstrate how magnitude and duration of this effect depend on model parameters.

  8. IP over optical multicasting for large-scale video delivery

    NASA Astrophysics Data System (ADS)

    Jin, Yaohui; Hu, Weisheng; Sun, Weiqiang; Guo, Wei

    2007-11-01

    In the IPTV systems, multicasting will play a crucial role in the delivery of high-quality video services, which can significantly improve bandwidth efficiency. However, the scalability and the signal quality of current IPTV can barely compete with the existing broadcast digital TV systems since it is difficult to implement large-scale multicasting with end-to-end guaranteed quality of service (QoS) in packet-switched IP network. China 3TNet project aimed to build a high performance broadband trial network to support large-scale concurrent streaming media and interactive multimedia services. The innovative idea of 3TNet is that an automatic switched optical networks (ASON) with the capability of dynamic point-to-multipoint (P2MP) connections replaces the conventional IP multicasting network in the transport core, while the edge remains an IP multicasting network. In this paper, we will introduce the network architecture and discuss challenges in such IP over Optical multicasting for video delivery.

  9. Evaluating Unmanned Aerial Platforms for Cultural Heritage Large Scale Mapping

    NASA Astrophysics Data System (ADS)

    Georgopoulos, A.; Oikonomou, C.; Adamopoulos, E.; Stathopoulou, E. K.

    2016-06-01

    When it comes to large scale mapping of limited areas especially for cultural heritage sites, things become critical. Optical and non-optical sensors are developed to such sizes and weights that can be lifted by such platforms, like e.g. LiDAR units. At the same time there is an increase in emphasis on solutions that enable users to get access to 3D information faster and cheaper. Considering the multitude of platforms, cameras and the advancement of algorithms in conjunction with the increase of available computing power this challenge should and indeed is further investigated. In this paper a short review of the UAS technologies today is attempted. A discussion follows as to their applicability and advantages, depending on their specifications, which vary immensely. The on-board cameras available are also compared and evaluated for large scale mapping. Furthermore a thorough analysis, review and experimentation with different software implementations of Structure from Motion and Multiple View Stereo algorithms, able to process such dense and mostly unordered sequence of digital images is also conducted and presented. As test data set, we use a rich optical and thermal data set from both fixed wing and multi-rotor platforms over an archaeological excavation with adverse height variations and using different cameras. Dense 3D point clouds, digital terrain models and orthophotos have been produced and evaluated for their radiometric as well as metric qualities.

  10. High Speed Networking and Large-scale Simulation in Geodynamics

    NASA Technical Reports Server (NTRS)

    Kuang, Weijia; Gary, Patrick; Seablom, Michael; Truszkowski, Walt; Odubiyi, Jide; Jiang, Weiyuan; Liu, Dong

    2004-01-01

    Large-scale numerical simulation has been one of the most important approaches for understanding global geodynamical processes. In this approach, peta-scale floating point operations (pflops) are often required to carry out a single physically-meaningful numerical experiment. For example, to model convective flow in the Earth's core and generation of the geomagnetic field (geodynamo), simulation for one magnetic free-decay time (approximately 15000 years) with a modest resolution of 150 in three spatial dimensions would require approximately 0.2 pflops. If such a numerical model is used to predict geomagnetic secular variation over decades and longer, with e.g. an ensemble Kalman filter assimilation approach, approximately 30 (and perhaps more) independent simulations of similar scales would be needed for one data assimilation analysis. Obviously, such a simulation would require an enormous computing resource that exceeds the capacity of a single facility currently available at our disposal. One solution is to utilize a very fast network (e.g. 10Gb optical networks) and available middleware (e.g. Globus Toolkit) to allocate available but often heterogeneous resources for such large-scale computing efforts. At NASA GSFC, we are experimenting with such an approach by networking several clusters for geomagnetic data assimilation research. We shall present our initial testing results in the meeting.

  11. Maestro: an orchestration framework for large-scale WSN simulations.

    PubMed

    Riliskis, Laurynas; Osipov, Evgeny

    2014-03-18

    Contemporary wireless sensor networks (WSNs) have evolved into large and complex systems and are one of the main technologies used in cyber-physical systems and the Internet of Things. Extensive research on WSNs has led to the development of diverse solutions at all levels of software architecture, including protocol stacks for communications. This multitude of solutions is due to the limited computational power and restrictions on energy consumption that must be accounted for when designing typical WSN systems. It is therefore challenging to develop, test and validate even small WSN applications, and this process can easily consume significant resources. Simulations are inexpensive tools for testing, verifying and generally experimenting with new technologies in a repeatable fashion. Consequently, as the size of the systems to be tested increases, so does the need for large-scale simulations. This article describes a tool called Maestro for the automation of large-scale simulation and investigates the feasibility of using cloud computing facilities for such task. Using tools that are built into Maestro, we demonstrate a feasible approach for benchmarking cloud infrastructure in order to identify cloud Virtual Machine (VM)instances that provide an optimal balance of performance and cost for a given simulation.

  12. Detecting differential protein expression in large-scale population proteomics

    SciTech Connect

    Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

    2014-06-17

    Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

  13. Brief Mental Training Reorganizes Large-Scale Brain Networks

    PubMed Central

    Tang, Yi-Yuan; Tang, Yan; Tang, Rongxiang; Lewis-Peacock, Jarrod A.

    2017-01-01

    Emerging evidences have shown that one form of mental training—mindfulness meditation, can improve attention, emotion regulation and cognitive performance through changing brain activity and structural connectivity. However, whether and how the short-term mindfulness meditation alters large-scale brain networks are not well understood. Here, we applied a novel data-driven technique, the multivariate pattern analysis (MVPA) to resting-state fMRI (rsfMRI) data to identify changes in brain activity patterns and assess the neural mechanisms induced by a brief mindfulness training—integrative body–mind training (IBMT), which was previously reported in our series of randomized studies. Whole brain rsfMRI was performed on an undergraduate group who received 2 weeks of IBMT with 30 min per session (5 h training in total). Classifiers were trained on measures of functional connectivity in this fMRI data, and they were able to reliably differentiate (with 72% accuracy) patterns of connectivity from before vs. after the IBMT training. After training, an increase in positive functional connections (60 connections) were detected, primarily involving bilateral superior/middle occipital gyrus, bilateral frontale operculum, bilateral superior temporal gyrus, right superior temporal pole, bilateral insula, caudate and cerebellum. These results suggest that brief mental training alters the functional connectivity of large-scale brain networks at rest that may involve a portion of the neural circuitry supporting attention, cognitive and affective processing, awareness and sensory integration and reward processing. PMID:28293180

  14. Large Scale Organization of a Near Wall Turbulent Boundary Layer

    NASA Astrophysics Data System (ADS)

    Stanislas, Michel; Dekou Tiomajou, Raoul Florent; Foucaut, Jean Marc

    2016-11-01

    This study lies in the context of large scale coherent structures investigation in a near wall turbulent boundary layer. An experimental database at high Reynolds numbers (Re θ = 9830 and Re θ = 19660) was obtained in the LML wind tunnel with stereo-PIV at 4 Hz and hot wire anemometry at 30 kHz. A Linear Stochastic Estimation procedure, is used to reconstruct a 3 component field resolved in space and time. Algorithms were developed to extract coherent structures from the reconstructed field. A sample of 3D view of the structures is depicted in Figure 1. Uniform momentum regions are characterized with their mean hydraulic diameter in the YZ plane, their life time and their contribution to Reynolds stresses. The vortical motions are characterized by their position, radius, circulation and vorticity in addition to their life time and their number computed at a fixed position from the wall. The spatial organization of the structures was investigated through a correlation of their respective indicative functions in the spanwise direction. The simplified large scale model that arise is compared to the ones available in the literature. Streamwise low (green) and high (yellow) uniform momentum regions with positive (red) and negative (blue) vortical motions. This work was supported by Campus International pour la Sécurité et l'Intermodalité des Transports.

  15. Ecohydrological modeling for large-scale environmental impact assessment.

    PubMed

    Woznicki, Sean A; Nejadhashemi, A Pouyan; Abouali, Mohammad; Herman, Matthew R; Esfahanian, Elaheh; Hamaamin, Yaseen A; Zhang, Zhen

    2016-02-01

    Ecohydrological models are frequently used to assess the biological integrity of unsampled streams. These models vary in complexity and scale, and their utility depends on their final application. Tradeoffs are usually made in model scale, where large-scale models are useful for determining broad impacts of human activities on biological conditions, and regional-scale (e.g. watershed or ecoregion) models provide stakeholders greater detail at the individual stream reach level. Given these tradeoffs, the objective of this study was to develop large-scale stream health models with reach level accuracy similar to regional-scale models thereby allowing for impacts assessments and improved decision-making capabilities. To accomplish this, four measures of biological integrity (Ephemeroptera, Plecoptera, and Trichoptera taxa (EPT), Family Index of Biotic Integrity (FIBI), Hilsenhoff Biotic Index (HBI), and fish Index of Biotic Integrity (IBI)) were modeled based on four thermal classes (cold, cold-transitional, cool, and warm) of streams that broadly dictate the distribution of aquatic biota in Michigan. The Soil and Water Assessment Tool (SWAT) was used to simulate streamflow and water quality in seven watersheds and the Hydrologic Index Tool was used to calculate 171 ecologically relevant flow regime variables. Unique variables were selected for each thermal class using a Bayesian variable selection method. The variables were then used in development of adaptive neuro-fuzzy inference systems (ANFIS) models of EPT, FIBI, HBI, and IBI. ANFIS model accuracy improved when accounting for stream thermal class rather than developing a global model.

  16. The Impact of Large Scale Environments on Cluster Entropy Profiles

    NASA Astrophysics Data System (ADS)

    Trierweiler, Isabella; Su, Yuanyuan

    2017-01-01

    We perform a systematic analysis of 21 clusters imaged by the Suzaku satellite to determine the relation between the richness of cluster environments and entropy at large radii. Entropy profiles for clusters are expected to follow a power-law, but Suzaku observations show that the entropy profiles of many clusters are significantly flattened beyond 0.3 Rvir. While the entropy at the outskirts of clusters is thought to be highly dependent on the large scale cluster environment, the exact nature of the environment/entropy relation is unclear. Using the Sloan Digital Sky Survey and 6dF Galaxy Survey, we study the 20 Mpc large scale environment for all clusters in our sample. We find no strong relation between the entropy deviations at the virial radius and the total luminosity of the cluster surroundings, indicating that accretion and mergers have a more complex and indirect influence on the properties of the gas at large radii. We see a possible anti-correlation between virial temperature and richness of the cluster environment and find that density excess appears to play a larger role in the entropy flattening than temperature, suggesting that clumps of gas can lower entropy.

  17. The effective field theory of cosmological large scale structures

    SciTech Connect

    Carrasco, John Joseph M.; Hertzberg, Mark P.; Senatore, Leonardo

    2012-09-20

    Large scale structure surveys will likely become the next leading cosmological probe. In our universe, matter perturbations are large on short distances and small at long scales, i.e. strongly coupled in the UV and weakly coupled in the IR. To make precise analytical predictions on large scales, we develop an effective field theory formulated in terms of an IR effective fluid characterized by several parameters, such as speed of sound and viscosity. These parameters, determined by the UV physics described by the Boltzmann equation, are measured from N-body simulations. We find that the speed of sound of the effective fluid is c2s ≈ 10–6c2 and that the viscosity contributions are of the same order. The fluid describes all the relevant physics at long scales k and permits a manifestly convergent perturbative expansion in the size of the matter perturbations δ(k) for all the observables. As an example, we calculate the correction to the power spectrum at order δ(k)4. As a result, the predictions of the effective field theory are found to be in much better agreement with observation than standard cosmological perturbation theory, already reaching percent precision at this order up to a relatively short scale k ≃ 0.24h Mpc–1.

  18. Large-scale Direct Targeting for Drug Repositioning and Discovery

    PubMed Central

    Zheng, Chunli; Guo, Zihu; Huang, Chao; Wu, Ziyin; Li, Yan; Chen, Xuetong; Fu, Yingxue; Ru, Jinlong; Ali Shar, Piar; Wang, Yuan; Wang, Yonghua

    2015-01-01

    A system-level identification of drug-target direct interactions is vital to drug repositioning and discovery. However, the biological means on a large scale remains challenging and expensive even nowadays. The available computational models mainly focus on predicting indirect interactions or direct interactions on a small scale. To address these problems, in this work, a novel algorithm termed weighted ensemble similarity (WES) has been developed to identify drug direct targets based on a large-scale of 98,327 drug-target relationships. WES includes: (1) identifying the key ligand structural features that are highly-related to the pharmacological properties in a framework of ensemble; (2) determining a drug’s affiliation of a target by evaluation of the overall similarity (ensemble) rather than a single ligand judgment; and (3) integrating the standardized ensemble similarities (Z score) by Bayesian network and multi-variate kernel approach to make predictions. All these lead WES to predict drug direct targets with external and experimental test accuracies of 70% and 71%, respectively. This shows that the WES method provides a potential in silico model for drug repositioning and discovery. PMID:26155766

  19. Modulation of energetic coherent motions by large-scale topography

    NASA Astrophysics Data System (ADS)

    Lai, Wing; Hamed, Ali M.; Troolin, Dan; Chamorro, Leonardo P.

    2016-11-01

    The distinctive characteristics and dynamics of the large-scale coherent motions induced over 2D and 3D large-scale wavy walls were explored experimentally with time-resolved volumetric PIV, and selected wall-normal high-resolution stereo PIV in a refractive-index-matching channel. The 2D wall consists of a sinusoidal wave in the streamwise direction with amplitude to wavelength ratio a/ λx = 0.05, while the 3D wall has an additional wave in the spanwise direction with a/ λy = 0.1. The ?ow was characterized at Re 8000, based on the bulk velocity and the channel half height. The walls are such that the amplitude to boundary layer thickness ratio is a/ δ99 0.1, which resemble geophysical-like topography. Insight on the dynamics of the coherent motions, Reynolds stress and spatial interaction of sweep and ejection events will be discussed in terms of the wall topography modulation.

  20. Very-large-scale coherent motions in open channel flows

    NASA Astrophysics Data System (ADS)

    Zhong, Qiang; Hussain, Fazle; Li, Dan-Xun

    2016-11-01

    Very-large-scale coherent structures (VLSSs) - whose characteristic length is of the order of 10 h (h is the water depth) - are found to exist in the log and outer layers near the bed of open channel flows. For decades researchers have speculated that large coherent structures may exist in open channel flows. However, conclusive evidence is still lacking. The present study employed pre-multiplied velocity power spectral and co-spectral analyses of time-resolved PIV data obtained in open channel flows. In all cases, two modes - large-scale structures (of the order of h) and VLSSs - dominate the log and outer layers of the turbulent boundary layer. More than half of TKE and 40% of the Reynolds shear stress in the log and outer layers are contributed by VLSSs. The strength difference of VLSSs between open and closed channel flows leads to pronounced redistribution of TKE near the free surface of open channel flows, which is a unique phenomenon that sets the open channel flows apart from other wall-bounded turbulent flows. Funded by China Postdoctoral Science Foundation (No.2015M580105), National Natural Science Foundation of China (No.51127006).

  1. Resonant plankton patchiness induced by large-scale turbulent flow

    NASA Astrophysics Data System (ADS)

    McKiver, William J.; Neufeld, Zoltán

    2011-01-01

    Here we study how large-scale variability of oceanic plankton is affected by mesoscale turbulence in a spatially heterogeneous environment. We consider a phytoplankton-zooplankton (PZ) ecosystem model, with different types of zooplankton grazing functions, coupled to a turbulent flow described by the two-dimensional Navier-Stokes equations, representing large-scale horizontal transport in the ocean. We characterize the system using a dimensionless parameter, γ=TB/TF, which is the ratio of the ecosystem biological time scale TB and the flow time scale TF. Through numerical simulations, we examine how the PZ system depends on the time-scale ratio γ and find that the variance of both species changes significantly, with maximum phytoplankton variability at intermediate mixing rates. Through an analysis of the linearized population dynamics, we find an analytical solution based on the forced harmonic oscillator, which explains the behavior of the ecosystem, where there is resonance between the advection and the ecosystem predator-prey dynamics when the forcing time scales match the ecosystem time scales. We also examine the dependence of the power spectra on γ and find that the resonance behavior leads to different spectral slopes for phytoplankton and zooplankton, in agreement with observations.

  2. Resonant plankton patchiness induced by large-scale turbulent flow.

    PubMed

    McKiver, William J; Neufeld, Zoltán

    2011-01-01

    Here we study how large-scale variability of oceanic plankton is affected by mesoscale turbulence in a spatially heterogeneous environment. We consider a phytoplankton-zooplankton (PZ) ecosystem model, with different types of zooplankton grazing functions, coupled to a turbulent flow described by the two-dimensional Navier-Stokes equations, representing large-scale horizontal transport in the ocean. We characterize the system using a dimensionless parameter, γ=T(B)/T(F), which is the ratio of the ecosystem biological time scale T(B) and the flow time scale T(F). Through numerical simulations, we examine how the PZ system depends on the time-scale ratio γ and find that the variance of both species changes significantly, with maximum phytoplankton variability at intermediate mixing rates. Through an analysis of the linearized population dynamics, we find an analytical solution based on the forced harmonic oscillator, which explains the behavior of the ecosystem, where there is resonance between the advection and the ecosystem predator-prey dynamics when the forcing time scales match the ecosystem time scales. We also examine the dependence of the power spectra on γ and find that the resonance behavior leads to different spectral slopes for phytoplankton and zooplankton, in agreement with observations.

  3. Large-scale anisotropy in stably stratified rotating flows

    SciTech Connect

    Marino, R.; Mininni, P. D.; Rosenberg, D. L.; Pouquet, A.

    2014-08-28

    We present results from direct numerical simulations of the Boussinesq equations in the presence of rotation and/or stratification, both in the vertical direction. The runs are forced isotropically and randomly at small scales and have spatial resolutions of up to $1024^3$ grid points and Reynolds numbers of $\\approx 1000$. We first show that solutions with negative energy flux and inverse cascades develop in rotating turbulence, whether or not stratification is present. However, the purely stratified case is characterized instead by an early-time, highly anisotropic transfer to large scales with almost zero net isotropic energy flux. This is consistent with previous studies that observed the development of vertically sheared horizontal winds, although only at substantially later times. However, and unlike previous works, when sufficient scale separation is allowed between the forcing scale and the domain size, the total energy displays a perpendicular (horizontal) spectrum with power law behavior compatible with $\\sim k_\\perp^{-5/3}$, including in the absence of rotation. In this latter purely stratified case, such a spectrum is the result of a direct cascade of the energy contained in the large-scale horizontal wind, as is evidenced by a strong positive flux of energy in the parallel direction at all scales including the largest resolved scales.

  4. Large-scale anisotropy in stably stratified rotating flows

    DOE PAGES

    Marino, R.; Mininni, P. D.; Rosenberg, D. L.; ...

    2014-08-28

    We present results from direct numerical simulations of the Boussinesq equations in the presence of rotation and/or stratification, both in the vertical direction. The runs are forced isotropically and randomly at small scales and have spatial resolutions of up tomore » $1024^3$ grid points and Reynolds numbers of $$\\approx 1000$$. We first show that solutions with negative energy flux and inverse cascades develop in rotating turbulence, whether or not stratification is present. However, the purely stratified case is characterized instead by an early-time, highly anisotropic transfer to large scales with almost zero net isotropic energy flux. This is consistent with previous studies that observed the development of vertically sheared horizontal winds, although only at substantially later times. However, and unlike previous works, when sufficient scale separation is allowed between the forcing scale and the domain size, the total energy displays a perpendicular (horizontal) spectrum with power law behavior compatible with $$\\sim k_\\perp^{-5/3}$$, including in the absence of rotation. In this latter purely stratified case, such a spectrum is the result of a direct cascade of the energy contained in the large-scale horizontal wind, as is evidenced by a strong positive flux of energy in the parallel direction at all scales including the largest resolved scales.« less

  5. The effect of large scale inhomogeneities on the luminosity distance

    NASA Astrophysics Data System (ADS)

    Brouzakis, Nikolaos; Tetradis, Nikolaos; Tzavara, Eleftheria

    2007-02-01

    We study the form of the luminosity distance as a function of redshift in the presence of large scale inhomogeneities, with sizes of order 10 Mpc or larger. We approximate the Universe through the Swiss-cheese model, with each spherical region described by the Lemaitre Tolman Bondi metric. We study the propagation of light beams in this background, assuming that the locations of the source and the observer are random. We derive the optical equations for the evolution of the beam area and shear. Through their integration we determine the configurations that can lead to an increase of the luminosity distance relative to the homogeneous cosmology. We find that this can be achieved if the Universe is composed of spherical void-like regions, with matter concentrated near their surface. For inhomogeneities consistent with the observed large scale structure, the relative increase of the luminosity distance is of the order of a few per cent at redshifts near 1, and falls short of explaining the substantial increase required by the supernova data. On the other hand, the effect we describe is important for the correct determination of the energy content of the Universe from observations.

  6. Exact-Differential Large-Scale Traffic Simulation

    SciTech Connect

    Hanai, Masatoshi; Suzumura, Toyotaro; Theodoropoulos, Georgios; Perumalla, Kalyan S

    2015-01-01

    Analyzing large-scale traffics by simulation needs repeating execution many times with various patterns of scenarios or parameters. Such repeating execution brings about big redundancy because the change from a prior scenario to a later scenario is very minor in most cases, for example, blocking only one of roads or changing the speed limit of several roads. In this paper, we propose a new redundancy reduction technique, called exact-differential simulation, which enables to simulate only changing scenarios in later execution while keeping exactly same results as in the case of whole simulation. The paper consists of two main efforts: (i) a key idea and algorithm of the exact-differential simulation, (ii) a method to build large-scale traffic simulation on the top of the exact-differential simulation. In experiments of Tokyo traffic simulation, the exact-differential simulation shows 7.26 times as much elapsed time improvement in average and 2.26 times improvement even in the worst case as the whole simulation.

  7. Halo detection via large-scale Bayesian inference

    NASA Astrophysics Data System (ADS)

    Merson, Alexander I.; Jasche, Jens; Abdalla, Filipe B.; Lahav, Ofer; Wandelt, Benjamin; Jones, D. Heath; Colless, Matthew

    2016-08-01

    We present a proof-of-concept of a novel and fully Bayesian methodology designed to detect haloes of different masses in cosmological observations subject to noise and systematic uncertainties. Our methodology combines the previously published Bayesian large-scale structure inference algorithm, HAmiltonian Density Estimation and Sampling algorithm (HADES), and a Bayesian chain rule (the Blackwell-Rao estimator), which we use to connect the inferred density field to the properties of dark matter haloes. To demonstrate the capability of our approach, we construct a realistic galaxy mock catalogue emulating the wide-area 6-degree Field Galaxy Survey, which has a median redshift of approximately 0.05. Application of HADES to the catalogue provides us with accurately inferred three-dimensional density fields and corresponding quantification of uncertainties inherent to any cosmological observation. We then use a cosmological simulation to relate the amplitude of the density field to the probability of detecting a halo with mass above a specified threshold. With this information, we can sum over the HADES density field realisations to construct maps of detection probabilities and demonstrate the validity of this approach within our mock scenario. We find that the probability of successful detection of haloes in the mock catalogue increases as a function of the signal to noise of the local galaxy observations. Our proposed methodology can easily be extended to account for more complex scientific questions and is a promising novel tool to analyse the cosmic large-scale structure in observations.

  8. Brief Mental Training Reorganizes Large-Scale Brain Networks.

    PubMed

    Tang, Yi-Yuan; Tang, Yan; Tang, Rongxiang; Lewis-Peacock, Jarrod A

    2017-01-01

    Emerging evidences have shown that one form of mental training-mindfulness meditation, can improve attention, emotion regulation and cognitive performance through changing brain activity and structural connectivity. However, whether and how the short-term mindfulness meditation alters large-scale brain networks are not well understood. Here, we applied a novel data-driven technique, the multivariate pattern analysis (MVPA) to resting-state fMRI (rsfMRI) data to identify changes in brain activity patterns and assess the neural mechanisms induced by a brief mindfulness training-integrative body-mind training (IBMT), which was previously reported in our series of randomized studies. Whole brain rsfMRI was performed on an undergraduate group who received 2 weeks of IBMT with 30 min per session (5 h training in total). Classifiers were trained on measures of functional connectivity in this fMRI data, and they were able to reliably differentiate (with 72% accuracy) patterns of connectivity from before vs. after the IBMT training. After training, an increase in positive functional connections (60 connections) were detected, primarily involving bilateral superior/middle occipital gyrus, bilateral frontale operculum, bilateral superior temporal gyrus, right superior temporal pole, bilateral insula, caudate and cerebellum. These results suggest that brief mental training alters the functional connectivity of large-scale brain networks at rest that may involve a portion of the neural circuitry supporting attention, cognitive and affective processing, awareness and sensory integration and reward processing.

  9. Large-scale columnar vortices in rotating turbulence

    NASA Astrophysics Data System (ADS)

    Yokoyama, Naoto; Takaoka, Masanori

    2016-11-01

    In the rotating turbulence, flow structures are affected by the angular velocity of the system's rotation. When the angular velocity is small, three-dimensional statistically-isotropic flow, which has the Kolmogorov spectrum all over the inertial subrange, is formed. When the angular velocity increases, the flow becomes two-dimensional anisotropic, and the energy spectrum has a power law k-2 in the small wavenumbers in addition to the Kolmogorov spectrum in the large wavenumbers. When the angular velocity decreases, the flow returns to the isotropic one. It is numerically found that the transition between the isotropic and anisotropic flows is hysteretic; the critical angular velocity at which the flow transitions from the anisotropic one to the isotropic one, and that of the reverse transition are different. It is also observed that the large-scale columnar structures in the anisotropic flow depends on the external force which maintains a statistically-steady state. In some cases, small-scale anticyclonic structures are aligned in a columnar structure apart from the cyclonic Taylor column. The formation mechanism of the large-scale columnar structures will be discussed. This work was partially supported by JSPS KAKENHI.

  10. Large scale CMB anomalies from thawing cosmic strings

    SciTech Connect

    Ringeval, Christophe; Yamauchi, Daisuke; Yokoyama, Jun'ichi; Bouchet, François R. E-mail: yamauchi@resceu.s.u-tokyo.ac.jp E-mail: bouchet@iap.fr

    2016-02-01

    Cosmic strings formed during inflation are expected to be either diluted over super-Hubble distances, i.e., invisible today, or to have crossed our past light cone very recently. We discuss the latter situation in which a few strings imprint their signature in the Cosmic Microwave Background (CMB) Anisotropies after recombination. Being almost frozen in the Hubble flow, these strings are quasi static and evade almost all of the previously derived constraints on their tension while being able to source large scale anisotropies in the CMB sky. Using a local variance estimator on thousand of numerically simulated Nambu-Goto all sky maps, we compute the expected signal and show that it can mimic a dipole modulation at large angular scales while being negligible at small angles. Interestingly, such a scenario generically produces one cold spot from the thawing of a cosmic string loop. Mixed with anisotropies of inflationary origin, we find that a few strings of tension GU = O(1) × 10{sup −6} match the amplitude of the dipole modulation reported in the Planck satellite measurements and could be at the origin of other large scale anomalies.

  11. A visual backchannel for large-scale events.

    PubMed

    Dörk, Marian; Gruen, Daniel; Williamson, Carey; Carpendale, Sheelagh

    2010-01-01

    We introduce the concept of a Visual Backchannel as a novel way of following and exploring online conversations about large-scale events. Microblogging communities, such as Twitter, are increasingly used as digital backchannels for timely exchange of brief comments and impressions during political speeches, sport competitions, natural disasters, and other large events. Currently, shared updates are typically displayed in the form of a simple list, making it difficult to get an overview of the fast-paced discussions as it happens in the moment and how it evolves over time. In contrast, our Visual Backchannel design provides an evolving, interactive, and multi-faceted visual overview of large-scale ongoing conversations on Twitter. To visualize a continuously updating information stream, we include visual saliency for what is happening now and what has just happened, set in the context of the evolving conversation. As part of a fully web-based coordinated-view system we introduce Topic Streams, a temporally adjustable stacked graph visualizing topics over time, a People Spiral representing participants and their activity, and an Image Cloud encoding the popularity of event photos by size. Together with a post listing, these mutually linked views support cross-filtering along topics, participants, and time ranges. We discuss our design considerations, in particular with respect to evolving visualizations of dynamically changing data. Initial feedback indicates significant interest and suggests several unanticipated uses.

  12. Development of Large-Scale Functional Brain Networks in Children

    PubMed Central

    Supekar, Kaustubh; Musen, Mark; Menon, Vinod

    2009-01-01

    The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7–9 y) and 22 young-adults (ages 19–22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar “small-world” organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism. PMID:19621066

  13. Systematic renormalization of the effective theory of Large Scale Structure

    SciTech Connect

    Abolhasani, Ali Akbar; Mirbabayi, Mehrdad; Pajer, Enrico

    2016-05-31

    A perturbative description of Large Scale Structure is a cornerstone of our understanding of the observed distribution of matter in the universe. Renormalization is an essential and defining step to make this description physical and predictive. Here we introduce a systematic renormalization procedure, which neatly associates counterterms to the UV-sensitive diagrams order by order, as it is commonly done in quantum field theory. As a concrete example, we renormalize the one-loop power spectrum and bispectrum of both density and velocity. In addition, we present a series of results that are valid to all orders in perturbation theory. First, we show that while systematic renormalization requires temporally non-local counterterms, in practice one can use an equivalent basis made of local operators. We give an explicit prescription to generate all counterterms allowed by the symmetries. Second, we present a formal proof of the well-known general argument that the contribution of short distance perturbations to large scale density contrast δ and momentum density π(k) scale as k{sup 2} and k, respectively. Third, we demonstrate that the common practice of introducing counterterms only in the Euler equation when one is interested in correlators of δ is indeed valid to all orders.

  14. Scalable WIM: effective exploration in large-scale astrophysical environments.

    PubMed

    Li, Yinggang; Fu, Chi-Wing; Hanson, Andrew J

    2006-01-01

    Navigating through large-scale virtual environments such as simulations of the astrophysical Universe is difficult. The huge spatial range of astronomical models and the dominance of empty space make it hard for users to travel across cosmological scales effectively, and the problem of wayfinding further impedes the user's ability to acquire reliable spatial knowledge of astronomical contexts. We introduce a new technique called the scalable world-in-miniature (WIM) map as a unifying interface to facilitate travel and wayfinding in a virtual environment spanning gigantic spatial scales: Power-law spatial scaling enables rapid and accurate transitions among widely separated regions; logarithmically mapped miniature spaces offer a global overview mode when the full context is too large; 3D landmarks represented in the WIM are enhanced by scale, positional, and directional cues to augment spatial context awareness; a series of navigation models are incorporated into the scalable WIM to improve the performance of travel tasks posed by the unique characteristics of virtual cosmic exploration. The scalable WIM user interface supports an improved physical navigation experience and assists pragmatic cognitive understanding of a visualization context that incorporates the features of large-scale astronomy.

  15. Extending SME to Handle Large-Scale Cognitive Modeling.

    PubMed

    Forbus, Kenneth D; Ferguson, Ronald W; Lovett, Andrew; Gentner, Dedre

    2016-06-20

    Analogy and similarity are central phenomena in human cognition, involved in processes ranging from visual perception to conceptual change. To capture this centrality requires that a model of comparison must be able to integrate with other processes and handle the size and complexity of the representations required by the tasks being modeled. This paper describes extensions to Structure-Mapping Engine (SME) since its inception in 1986 that have increased its scope of operation. We first review the basic SME algorithm, describe psychological evidence for SME as a process model, and summarize its role in simulating similarity-based retrieval and generalization. Then we describe five techniques now incorporated into the SME that have enabled it to tackle large-scale modeling tasks: (a) Greedy merging rapidly constructs one or more best interpretations of a match in polynomial time: O(n(2) log(n)); (b) Incremental operation enables mappings to be extended as new information is retrieved or derived about the base or target, to model situations where information in a task is updated over time; (c) Ubiquitous predicates model the varying degrees to which items may suggest alignment; (d) Structural evaluation of analogical inferences models aspects of plausibility judgments; (e) Match filters enable large-scale task models to communicate constraints to SME to influence the mapping process. We illustrate via examples from published studies how these enable it to capture a broader range of psychological phenomena than before.

  16. A study of synthetic large scales in turbulent boundary layers

    NASA Astrophysics Data System (ADS)

    Duvvuri, Subrahmanyam; Luhar, Mitul; Barnard, Casey; Sheplak, Mark; McKeon, Beverley

    2013-11-01

    Synthetic spanwise-constant spatio-temporal disturbances are excited in a turbulent boundary layer through a spatially impulsive patch of dynamic wall-roughness. The downstream flow response is studied through hot wire anemometry, pressure measurements at the wall and direct measurements of wall-shear-stress made using a novel micro-machined capacitive floating element sensor. These measurements are phase-locked to the input perturbation to recover the synthetic large-scale motion and characterize its structure and wall signature. The phase relationship between the synthetic large scale and small scale activity provides further insights into the apparent amplitude modulation effect between them, and the dynamics of wall-bounded turbulent flows in general. Results from these experiments will be discussed in the context of the critical-layer behavior revealed by the resolvent analysis of McKeon & Sharma (J Fluid Mech, 2010), and compared with similar earlier work by Jacobi & McKeon (J Fluid Mech, 2011). Model predictions are shown to be in broad agreement with experiments. The support of AFOSR grant #FA 9550-12-1-0469, Resnick Institute Graduate Research Fellowship (S.D.) and Sandia Graduate Fellowship (C.B.) are gratefully acknowledged.

  17. Leveraging large-scale behavioral profiling in zebrafish to explore neuroactive polypharmacology

    PubMed Central

    McCarroll, Matthew N; Gendelev, Leo; Keiser, Michael J; Kokel, David

    2016-01-01

    Many psychiatric drugs modulate the nervous system through multi-target mechanisms. However, systematic identification of multi-target compounds has been difficult using traditional in vitro screening assays. New approaches to phenotypic profiling in zebrafish can help researchers identify novel compounds with complex polypharmacology. For example, large-scale behavior-based chemical screens can rapidly identify large numbers of structurally diverse and phenotype-related compounds. Once these compounds have been identified, a systems-level analysis of their structures may help to identify statistically enriched target pathways. Together, systematic behavioral profiling and multi-target predictions may help researchers identify new behavior-modifying pathways and CNS therapeutics. PMID:26845413

  18. Mathematical modeling of chemical composition modification and etching of polymers under the atomic oxygen influence

    NASA Astrophysics Data System (ADS)

    Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina

    2016-07-01

    Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.

  19. Generation of large-scale structures and vortex systems in numerical experiments for rotating annular channels

    NASA Astrophysics Data System (ADS)

    Gledzer, A. E.

    2016-12-01

    Methods for solving shallow-water equations that describe flows in rotating annular channels are considered and the results of numerical calculations are analyzed for the possible generation of global large-scale flows, narrow jets, and numerous small-scale vortices in laboratory experiments. External effects in fluids are induced using a mass source-sink and the MHD-method of interaction of radial electric current with the magnetic field generated by the field of permanent magnets. A central-upwind scheme modified to suit the specific aspects of geophysical hydrodynamics. Initially, this method was used to solve shallow-water equations only in hydraulic problems, such as for flows in dam breaks, channels, rivers, and lakes. Geophysical hydrodynamics (in addition to free surface and topography) requires a rotation of the system as a whole, which is accompanied by the appearance of a complex system of vortices, jets, and turbulence (these should be taken into account in the formulation of the problem). Accordingly, the basic features of the central-upwind method should be changed. The modifications should ensure that the scheme is well-balanced and choose interpolation methods for desired variables. The main result of this modification is the control over numerical viscosity affecting the fluid motion variety. The active dynamics of a large number of vortices transformed into jets or generating large-scale streams is the general result of modifications suitable for geophysical hydrodynamics. Because there are technical difficulties in the creation of an appropriate laboratory setup for modeling of geophysical flows with the help of numerous source-sinks, it will be appropriate to use numerical experiments for studying the motions generated by this method. Unlike this method, the MHD-method can be rather easily used in laboratory conditions to generate a large variety of flows and vortex currents in the channel by a relatively small number of permanent magnets

  20. 3D geometry and hydrodynamic modifications in fractured and porous rock samples through chemical alterations.

    NASA Astrophysics Data System (ADS)

    Noiriel, C. N.

    2011-12-01

    Fractured and porous rocks are the principal path for water flow and potential contamination. Modification of fracture topology and transmissivity by reactive fluids is an important and complex geological process. In carbonate rocks, fractures and porous media properties may change quickly and strongly due to natural processes (e.g. karstification, salt intrusion) or anthropogenic practice (e.g. CO2 geological sequestration). Recent application of X-ray micro-tomography to the Earth Sciences, which allows the visualization of 3D objects with a micrometre resolution, has considerably increased experimental capability by giving access to a 4D spatio-temporal vision (3D geometry + time) of the physical-chemical processes within the rocks. New information is now accessible, which provides a better understanding of the processes and allows the numerical models to be better constrained. I will present the application of X-ray micro-tomography to study changes of petrophysical properties (e.g. porosity, permeability, mineral surface area, etc.) of fractured and porous rocks in response to fluid-rock interactions (dissolution and precipitation). Experimental results will be discussed in regard to numerical modelling of flow and transport. Keywords: X-ray micro-tomography, fracture, porous media, dissolution, precipitation, carbon dioxide sequestration, limestone, reactive surface, geochemical modelling,