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Sample records for nucleotide-sugar transporters structure

  1. Structure and function of nucleotide sugar transporters: Current progress

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    Barbara Hadley

    2014-06-01

    Full Text Available The proteomes of eukaryotes, bacteria and archaea are highly diverse due, in part, to the complex post-translational modification of protein glycosylation. The diversity of glycosylation in eukaryotes is reliant on nucleotide sugar transporters to translocate specific nucleotide sugars that are synthesised in the cytosol and nucleus, into the endoplasmic reticulum and Golgi apparatus where glycosylation reactions occur. Thirty years of research utilising multidisciplinary approaches has contributed to our current understanding of NST function and structure. In this review, the structure and function, with reference to various disease states, of several NSTs including the UDP-galactose, UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine, GDP-fucose, UDP-N-acetylglucosamine/UDP-glucose/GDP-mannose and CMP-sialic acid transporters will be described. Little is known regarding the exact structure of NSTs due to difficulties associated with crystallising membrane proteins. To date, no three-dimensional structure of any NST has been elucidated. What is known is based on computer predictions, mutagenesis experiments, epitope-tagging studies, in-vitro assays and phylogenetic analysis. In this regard the best-characterised NST to date is the CMP-sialic acid transporter (CST. Therefore in this review we will provide the current state-of-play with respect to the structure–function relationship of the (CST. In particular we have summarised work performed by a number groups detailing the affect of various mutations on CST transport activity, efficiency, and substrate specificity.

  2. Nucleotide-sugar transporters: structure, function and roles in vivo

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    Handford M.

    2006-01-01

    Full Text Available The glycosylation of glycoconjugates and the biosynthesis of polysaccharides depend on nucleotide-sugars which are the substrates for glycosyltransferases. A large proportion of these enzymes are located within the lumen of the Golgi apparatus as well as the endoplasmic reticulum, while many of the nucleotide-sugars are synthesized in the cytosol. Thus, nucleotide-sugars are translocated from the cytosol to the lumen of the Golgi apparatus and endoplasmic reticulum by multiple spanning domain proteins known as nucleotide-sugar transporters (NSTs. These proteins were first identified biochemically and some of them were cloned by complementation of mutants. Genome and expressed sequence tag sequencing allowed the identification of a number of sequences that may encode for NSTs in different organisms. The functional characterization of some of these genes has shown that some of them can be highly specific in their substrate specificity while others can utilize up to three different nucleotide-sugars containing the same nucleotide. Mutations in genes encoding for NSTs can lead to changes in development in Drosophila melanogaster or Caenorhabditis elegans, as well as alterations in the infectivity of Leishmania donovani. In humans, the mutation of a GDP-fucose transporter is responsible for an impaired immune response as well as retarded growth. These results suggest that, even though there appear to be a fair number of genes encoding for NSTs, they are not functionally redundant and seem to play specific roles in glycosylation.

  3. Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases.

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    Wang, Fengbin; Singh, Shanteri; Xu, Weijun; Helmich, Kate E; Miller, Mitchell D; Cao, Hongnan; Bingman, Craig A; Thorson, Jon S; Phillips, George N

    2015-09-18

    Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically L-Glu or L-Gln) to a corresponding ketosugar nucleotide acceptor. Herein we report the strategic structural study of two homologous C4 SATs (Micromonospora echinospora CalS13 and Escherichia coli WecE) that utilize identical substrates but differ in their stereochemistry of aminotransfer. This study reveals for the first time a new mode of SAT sugar nucleotide binding and, in conjunction with previously reported SAT structural studies, provides the basis from which to propose a universal model for SAT stereo- and regiochemical control of amine installation. Specifically, the universal model put forth highlights catalytic divergence to derive solely from distinctions within nucleotide sugar orientation upon binding within a relatively fixed SAT active site where the available ligand bound structures of the three out of four representative C3 and C4 SAT examples provide a basis for the overall model. Importantly, this study presents a new predictive model to support SAT functional annotation, biochemical study and rational engineering.

  4. Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6 before the radiation of Viridiplantae

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    Fredriksson Robert

    2011-05-01

    Full Text Available Abstract Background The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6. We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia. We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions The nucleotide sugar transporters families were formed through differentiation of the

  5. Use of Giardia, which appears to have a single nucleotide-sugar transporter for UDP-GlcNAc, to identify the UDP-Glc transporter of Entamoeba.

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    Banerjee, Sulagna; Cui, Jike; Robbins, Phillips W; Samuelson, John

    2008-05-01

    Nucleotide-sugar transporters (NSTs) transport activated sugars (e.g. UDP-GlcNAc) from the cytosol to the lumen of the endoplasmic reticulum or Golgi apparatus where they are used to make glycoproteins and glycolipids. UDP-Glc is an important component of the N-glycan-dependent quality control (QC) system for protein folding. Because Entamoeba has this QC system while Giardia does not, we hypothesized that transfected Giardia might be used to identify the UDP-Glc transporter of Entamoeba. Here we show Giardia membranes transport UDP-GlcNAc and have apyrases, which hydrolyze nucleoside-diphosphates to make the antiporter nucleoside-monophosphate. The only NST of Giardia (GlNst), which we could identify, transports UDP-GlcNAc in transfected Saccharomyces and is present in perinuclear and peripheral vesicles and increases in expression during encystation. Entamoeba membranes transport three nucleotide-sugars (UDP-Gal, UDP-GlcNAc, and UDP-Glc), and Entamoeba has three NSTs, one of which has been shown previously to transport UDP-Gal (EhNst1). Here we show recombinant EhNst2 transports UDP-Glc in transfected Giardia, while recombinant EhNst3 transports UDP-GlcNAc in transfected Saccharomyces. In summary, all three NSTs of Entamoeba and the single NST of Giardia have been molecularly characterized, and transfected Giardia provides a new system for testing heterologous UDP-Glc transporters.

  6. A dynamic mathematical model for monoclonal antibody N-linked glycosylation and nucleotide sugar donor transport within a maturing Golgi apparatus.

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    Jimenez del Val, Ioscani; Nagy, Judit M; Kontoravdi, Cleo

    2011-01-01

    Monoclonal antibodies (mAbs) are one of the most important products of the biopharmaceutical industry. Their therapeutic efficacy depends on the post-translational process of glycosylation, which is influenced by manufacturing process conditions. Herein, we present a dynamic mathematical model for mAb glycosylation that considers cisternal maturation by approximating the Golgi apparatus to a plug flow reactor and by including recycling of Golgi-resident proteins (glycosylation enzymes and transport proteins [TPs]). The glycosylation reaction rate expressions were derived based on the reported kinetic mechanisms for each enzyme, and transport of nucleotide sugar donors [NSDs] from the cytosol to the Golgi lumen was modeled to serve as a link between glycosylation and cellular metabolism. Optimization-based methodologies were developed for estimating unknown enzyme and TP concentration profile parameters. The resulting model is capable of reproducing glycosylation profiles of commercial mAbs. It can further reproduce the effect gene silencing of the FucT glycosylation enzyme and cytosolic NSD depletion have on the mAb oligosaccharide profile. All novel elements of our model are based on biological evidence and generate more accurate results than previous reports. We therefore believe that the improvements contribute to a more detailed representation of the N-linked glycosylation process. The overall results show the potential of our model toward evaluating cell engineering strategies that yield desired glycosylation profiles. Additionally, when coupled to cellular metabolism, this model could be used to assess the effect of process conditions on glycosylation and aid in the design, control, and optimization of biopharmaceutical manufacturing processes.

  7. Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly

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    Larkin, A.; Olivier, N; Imperiali, B

    2010-01-01

    In recent years, the opportunistic pathogen Pseudomonas aeruginosa has emerged as a major source of hospital-acquired infections. Effective treatment has proven increasingly difficult due to the spread of multidrug resistant strains and thus requires a deeper understanding of the biochemical mechanisms of pathogenicity. The central carbohydrate of the P. aeruginosa PAO1 (O5) B-band O-antigen, ManNAc(3NAc)A, has been shown to be critical for virulence and is produced in a stepwise manner by five enzymes in the Wbp pathway (WbpA, WbpB, WbpE, WbpD, and WbpI). Herein, we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5{prime}-phosphate (PLP) and product UDP-GlcNAc(3NH{sub 2})A as the external aldimine at 1.9 {angstrom} resolution. We also report the structures of WbpE in complex with PMP alone as well as the PLP internal aldimine and show that the dimeric structure of WbpE observed in the crystal structure is confirmed by analytical ultracentrifugation. Analysis of these structures reveals that the active site of the enzyme is composed of residues from both subunits. In particular, we show that a key residue (Arg229), which has previously been implicated in direct interactions with the {alpha}-carboxylate moiety of {alpha}-ketoglutarate, is also uniquely positioned to bestow specificity for the 6{double_prime}-carboxyl group of GlcNAc(3NH2)A through a salt bridge. This finding is intriguing because while an analogous basic residue is present in WbpE homologues that do not process 6{double_prime}-carboxyl-modified saccharides, recent structural studies reveal that this side chain is retracted to accommodate a neutral C6{double_prime} atom. This work represents the first structural analysis of a nucleotide sugar aminotransferase with a bound product modified at the C2{double_prime}, C3{double_prime}, and C6{double_prime} positions and provides insight into a novel target for treatment of P

  8. Molecular cloning of two Arabidopsis UDP-galactose transporters by complementation of a deficient Chinese hamster ovary cell line

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    Bakker, H.; Routier, F.; Oelmann, S.; Jordi, W.J.R.M.; Lommen, A.; Gerardy-Schahn, R.; Bosch, H.J.

    2005-01-01

    Nucleotide-sugar transporters (NSTs) form a family of structurally related transmembrane proteins that transport nucleotide-sugars from the cytoplasm to the endoplasmic reticulum and Golgi lumen. In these organelles, activated sugars are substrates for various glycosyltransferases involved in oligo-

  9. The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development.

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    Rautengarten, Carsten; Ebert, Berit; Liu, Lifeng; Stonebloom, Solomon; Smith-Moritz, Andreia M; Pauly, Markus; Orellana, Ariel; Scheller, Henrik Vibe; Heazlewood, Joshua L

    2016-07-06

    Nucleotide sugar transport across Golgi membranes is essential for the luminal biosynthesis of glycan structures. Here we identify GDP-fucose transporter 1 (GFT1), an Arabidopsis nucleotide sugar transporter that translocates GDP-L-fucose into the Golgi lumen. Using proteo-liposome-based transport assays, we show that GFT preferentially transports GDP-L-fucose over other nucleotide sugars in vitro, while GFT1-silenced plants are almost devoid of L-fucose in cell wall-derived xyloglucan and rhamnogalacturonan II. Furthermore, these lines display reduced L-fucose content in N-glycan structures accompanied by severe developmental growth defects. We conclude that GFT1 is the major nucleotide sugar transporter for import of GDP-L-fucose into the Golgi and is required for proper plant growth and development.

  10. The Arabidopsis Golgi-localized GDP-L-fucose transporter is required for plant development

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    Rautengarten, Carsten; Ebert, Berit; Liu, Lifeng

    2016-01-01

    Nucleotide sugar transport across Golgi membranes is essential for the luminal biosynthesis of glycan structures. Here we identify GDP-fucose transporter 1 (GFT1), an Arabidopsis nucleotide sugar transporter that translocates GDP-L-fucose into the Golgi lumen. Using proteo-liposome-based transport...... assays, we show that GFT preferentially transports GDP-L-fucose over other nucleotide sugars in vitro, while GFT1-silenced plants are almost devoid of L-fucose in cell wall-derived xyloglucan and rhamnogalacturonan II. Furthermore, these lines display reduced L-fucose content in N-glycan structures...... accompanied by severe developmental growth defects. We conclude that GFT1 is the major nucleotide sugar transporter for import of GDP-L-fucose into the Golgi and is required for proper plant growth and development....

  11. Development of a nucleotide sugar purification method using a mixed mode column & mass spectrometry detection.

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    Eastwood, Heather; Xia, Fang; Lo, Mei-Chu; Zhou, Jing; Jordan, John B; McCarter, John; Barnhart, Wesley W; Gahm, Kyung-Hyun

    2015-11-10

    Analysis of nucleotide sugars, nucleoside di- and triphosphates and sugar-phosphates is an essential step in the process of understanding enzymatic pathways. A facile and rapid separation method was developed to analyze these compounds present in an enzymatic reaction mixture utilized to produce nucleotide sugars. The Primesep SB column explored in this study utilizes hydrophobic interactions as well as electrostatic interactions with the phosphoric portion of the nucleotide sugars. Ammonium formate buffer was selected due to its compatibility with mass spectrometry. Negative ion mode mass spectrometry was adopted for detection of the sugar phosphate (fucose-1-phophate), as the compound is not amenable to UV detection. Various mobile phase conditions such as pH, buffer concentration and organic modifier were explored. The semi-preparative separation method was developed to prepare 30mg of the nucleotide sugar. (19)F NMR was utilized to determine purity of the purified fluorinated nucleotide sugar. The collected nucleotide sugar was found to be 99% pure.

  12. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry.

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    Ito, Jun; Herter, Thomas; Baidoo, Edward E K; Lao, Jeemeng; Vega-Sánchez, Miguel E; Michelle Smith-Moritz, A; Adams, Paul D; Keasling, Jay D; Usadel, Björn; Petzold, Christopher J; Heazlewood, Joshua L

    2014-03-01

    Understanding the intricate metabolic processes involved in plant cell wall biosynthesis is limited by difficulties in performing sensitive quantification of many involved compounds. Hydrophilic interaction liquid chromatography is a useful technique for the analysis of hydrophilic metabolites from complex biological extracts and forms the basis of this method to quantify plant cell wall precursors. A zwitterionic silica-based stationary phase has been used to separate hydrophilic nucleotide sugars involved in cell wall biosynthesis from milligram amounts of leaf tissue. A tandem mass spectrometry operating in selected reaction monitoring mode was used to quantify nucleotide sugars. This method was highly repeatable and quantified 12 nucleotide sugars at low femtomole quantities, with linear responses up to four orders of magnitude to several 100pmol. The method was also successfully applied to the analysis of purified leaf extracts from two model plant species with variations in their cell wall sugar compositions and indicated significant differences in the levels of 6 out of 12 nucleotide sugars. The plant nucleotide sugar extraction procedure was demonstrated to have good recovery rates with minimal matrix effects. The approach results in a significant improvement in sensitivity when applied to plant samples over currently employed techniques.

  13. The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis.

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    Rautengarten, Carsten; Ebert, Berit; Moreno, Ignacio; Temple, Henry; Herter, Thomas; Link, Bruce; Doñas-Cofré, Daniela; Moreno, Adrián; Saéz-Aguayo, Susana; Blanco, Francisca; Mortimer, Jennifer C; Schultink, Alex; Reiter, Wolf-Dieter; Dupree, Paul; Pauly, Markus; Heazlewood, Joshua L; Scheller, Henrik V; Orellana, Ariel

    2014-08-05

    Plant cells are surrounded by a cell wall that plays a key role in plant growth, structural integrity, and defense. The cell wall is a complex and diverse structure that is mainly composed of polysaccharides. The majority of noncellulosic cell wall polysaccharides are produced in the Golgi apparatus from nucleotide sugars that are predominantly synthesized in the cytosol. The transport of these nucleotide sugars from the cytosol into the Golgi lumen is a critical process for cell wall biosynthesis and is mediated by a family of nucleotide sugar transporters (NSTs). Numerous studies have sought to characterize substrate-specific transport by NSTs; however, the availability of certain substrates and a lack of robust methods have proven problematic. Consequently, we have developed a novel approach that combines reconstitution of NSTs into liposomes and the subsequent assessment of nucleotide sugar uptake by mass spectrometry. To address the limitation of substrate availability, we also developed a two-step reaction for the enzymatic synthesis of UDP-l-rhamnose (Rha) by expressing the two active domains of the Arabidopsis UDP-l-Rha synthase. The liposome approach and the newly synthesized substrates were used to analyze a clade of Arabidopsis NSTs, resulting in the identification and characterization of six bifunctional UDP-l-Rha/UDP-d-galactose (Gal) transporters (URGTs). Further analysis of loss-of-function and overexpression plants for two of these URGTs supported their roles in the transport of UDP-l-Rha and UDP-d-Gal for matrix polysaccharide biosynthesis.

  14. A theoretical estimate for nucleotide sugar demand towards Chinese Hamster Ovary cellular glycosylation

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    del Val, Ioscani Jimenez; Polizzi, Karen M.; Kontoravdi, Cleo

    2016-01-01

    Glycosylation greatly influences the safety and efficacy of many of the highest-selling recombinant therapeutic proteins (rTPs). In order to define optimal cell culture feeding strategies that control rTP glycosylation, it is necessary to know how nucleotide sugars (NSs) are consumed towards host cell and rTP glycosylation. Here, we present a theoretical framework that integrates the reported glycoproteome of CHO cells, the number of N-linked and O-GalNAc glycosylation sites on individual host cell proteins (HCPs), and the carbohydrate content of CHO glycosphingolipids to estimate the demand of NSs towards CHO cell glycosylation. We have identified the most abundant N-linked and O-GalNAc CHO glycoproteins, obtained the weighted frequency of N-linked and O-GalNAc glycosites across the CHO cell proteome, and have derived stoichiometric coefficients for NS consumption towards CHO cell glycosylation. By combining the obtained stoichiometric coefficients with previously reported data for specific growth and productivity of CHO cells, we observe that the demand of NSs towards glycosylation is significant and, thus, is required to better understand the burden of glycosylation on cellular metabolism. The estimated demand of NSs towards CHO cell glycosylation can be used to rationally design feeding strategies that ensure optimal and consistent rTP glycosylation. PMID:27345611

  15. Disruption of O-GlcNAc cycling in C. elegans perturbs Nucleotide Sugar pools and Complex Glycans

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    Salil K Ghosh

    2014-11-01

    Full Text Available The carbohydrate modification of serine and threonine residues with O-linked beta-N-acetylglucosamine (O-GlcNAc is ubiquitous and governs cellular processes ranging from cell signaling to apoptosis. The O-GlcNAc modification along with other carbohydrate modifications, including N-linked and O-linked glycans, glycolipids, and sugar polymers, all require the use of the nucleotide sugar UDP-GlcNAc, the end product of the hexosamine biosynthetic pathway. In this paper, we describe the biochemical consequences resulting from perturbation of the O-GlcNAc pathway in C. elegans lacking O-GlcNAc transferase and O-GlcNAcase activities. In ogt-1 null animals, steady-state levels of UDP-GlcNAc/UDP-GalNAc and UDP-glucose were substantially elevated. Transcripts of genes encoding for key members in the Hexosamine Biosynthetic Pathway (gfat-2, gna-2, C36A4.4 and trehalose metabolism (tre-1, tre-2, and tps-2 were elevated in ogt-1 null animals. While there is no evidence to suggest changes in the profile of N-linked glycans in the ogt-1 and oga-1 mutants, glycans insensitive to PNGase digestion (including O-linked glycans, glycolipids, and glycopolymers were altered in these strains. Our data supports that changes in O-GlcNAcylation alters nucleotide sugar production, overall glycan composition, and transcription of genes encoding glycan processing enzymes. These data along with our previous findings that disruption in O-GlcNAc cycling alters macronutrient storage underscores the noteworthy influence this posttranslational modification plays in nutrient sensing.

  16. Topology of nucleotide-sugar:dolichyl phosphate glycosyltransferases involved in the dolichol pathway for protein glycosylation in native rat liver microsomes.

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    Bossuyt, X; Blanckaert, N

    1993-01-01

    Activities of nucleotide-sugar:dolichyl phosphate glycosyltransferases (UDP-N-acetylglucosamine:dolichyl phosphate N-acetylglucosaminyl 1-phosphotransferase, UDP-glucose:dolichyl phosphate glucosyltransferase and GDP-mannose:dolichyl phosphate mannosyltransferase) are not fully expressed in native microsomes and can be enhanced by pretreatment of the microsomes with detergent. To examine whether the latency of dolichyl phosphate glycosyltransferases in native microsomes reflects a lumenal orientation of the catalytic centre, we examined the effect of proteinase treatment of native microsomes on enzymic activity and investigated the relationship between enzymic activity and alteration of the permeability of the microsomal membrane barrier. The enzymic activities catalysing transfer of N-acetylglucosamine and glucose to lipid acceptors were proteinase-sensitive in native sealed microsomes. When various detergents were used to disrupt the membrane barrier, we found no relationship between activity of dolichyl phosphate glycosyltransferases and the latency of mannose-6-phosphatase, which is a marker of the permeability properties of the microsomal membrane. Permeabilization of the endoplasmic reticulum membrane by the pore-forming Staphylococcus aureus alpha-toxin did not affect glycosyltransferase activities. These results do not support the hypothesis that latency of the transferase activities is dependent on the permeability properties of the endoplasmic-reticulum membrane. Collectively our findings can best be explained by postulating that the active centres of the transferases are cytoplasmically oriented, while activation by detergent may be conformation-dependent. PMID:8280060

  17. Ballistic transport and electronic structure

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    Schep, Kees M.; Kelly, Paul J.; Bauer, Gerrit E.W.

    1998-01-01

    The role of the electronic structure in determining the transport properties of ballistic point contacts is studied. The conductance in the ballistic regime is related to simple geometrical projections of the Fermi surface. The essential physics is first clarified for simple models. For real

  18. Synergizing metabolic flux analysis and nucleotide sugar metabolism to understand the control of glycosylation of recombinant protein in CHO cells

    LENUS (Irish Health Repository)

    Burleigh, Susan C

    2011-10-18

    Abstract Background The glycosylation of recombinant proteins can be altered by a range of parameters including cellular metabolism, metabolic flux and the efficiency of the glycosylation process. We present an experimental set-up that allows determination of these key processes associated with the control of N-linked glycosylation of recombinant proteins. Results Chinese hamster ovary cells (CHO) were cultivated in shake flasks at 0 mM glutamine and displayed a reduced growth rate, glucose metabolism and a slower decrease in pH, when compared to other glutamine-supplemented cultures. The N-linked glycosylation of recombinant human chorionic gonadotrophin (HCG) was also altered under these conditions; the sialylation, fucosylation and antennarity decreased, while the proportion of neutral structures increased. A continuous culture set-up was subsequently used to understand the control of HCG glycosylation in the presence of varied glutamine concentrations; when glycolytic flux was reduced in the absence of glutamine, the glycosylation changes that were observed in shake flask culture were similarly detected. The intracellular content of UDP-GlcNAc was also reduced, which correlated with a decrease in sialylation and antennarity of the N-linked glycans attached to HCG. Conclusions The use of metabolic flux analysis illustrated a case of steady state multiplicity, where use of the same operating conditions at each steady state resulted in altered flux through glycolysis and the TCA cycle. This study clearly demonstrated that the control of glycoprotein microheterogeneity may be examined by use of a continuous culture system, metabolic flux analysis and assay of intracellular nucleotides. This system advances our knowledge of the relationship between metabolic flux and the glycosylation of biotherapeutics in CHO cells and will be of benefit to the bioprocessing industry.

  19. Synergizing metabolic flux analysis and nucleotide sugar metabolism to understand the control of glycosylation of recombinant protein in CHO cells

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    Rudd Pauline M

    2011-10-01

    Full Text Available Abstract Background The glycosylation of recombinant proteins can be altered by a range of parameters including cellular metabolism, metabolic flux and the efficiency of the glycosylation process. We present an experimental set-up that allows determination of these key processes associated with the control of N-linked glycosylation of recombinant proteins. Results Chinese hamster ovary cells (CHO were cultivated in shake flasks at 0 mM glutamine and displayed a reduced growth rate, glucose metabolism and a slower decrease in pH, when compared to other glutamine-supplemented cultures. The N-linked glycosylation of recombinant human chorionic gonadotrophin (HCG was also altered under these conditions; the sialylation, fucosylation and antennarity decreased, while the proportion of neutral structures increased. A continuous culture set-up was subsequently used to understand the control of HCG glycosylation in the presence of varied glutamine concentrations; when glycolytic flux was reduced in the absence of glutamine, the glycosylation changes that were observed in shake flask culture were similarly detected. The intracellular content of UDP-GlcNAc was also reduced, which correlated with a decrease in sialylation and antennarity of the N-linked glycans attached to HCG. Conclusions The use of metabolic flux analysis illustrated a case of steady state multiplicity, where use of the same operating conditions at each steady state resulted in altered flux through glycolysis and the TCA cycle. This study clearly demonstrated that the control of glycoprotein microheterogeneity may be examined by use of a continuous culture system, metabolic flux analysis and assay of intracellular nucleotides. This system advances our knowledge of the relationship between metabolic flux and the glycosylation of biotherapeutics in CHO cells and will be of benefit to the bioprocessing industry.

  20. Intracellular structure and nucleocytoplasmic transport.

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    Agutter, P S

    1995-01-01

    Intracellular movement of any solute or particle accords with one of two general schemes: either it takes place predominantly in the solution phase or it occurs by dynamic interactions with solid-state structures. If nucleocytoplasmic exchanges of macromolecules and complexes are predominantly solution-phase processes, i.e., if the former ("diffusionist") perspective applies, then the only significant structures in nucleocytoplasmic transport are the pore complexes. However, if such exchanges accord with the latter ("solid-state") perspective, then the roles of the nucleoskeleton and cytoskeleton in nucleocytoplasmic transport are potentially, at least, as important as that of the pore complexes. The role of the nucleoskeleton in mRNA transport is more difficult to evaluate than that of the cytoskeleton because it is less well characterized, and current evidence does not exclude either perspective. However, the balance of evidence favors a solid-state scheme. It is argued that ribosomal subunits are also more likely to migrate by a solid-state rather than a diffusionist mechanism, though the opposite is true of proteins and tRNAs. Moreover, recent data on the effects of viral proteins on intranuclear RNA processing and migration accord with the solid-state perspective. In view of this balance of evidence, three possible solid-state mechanisms for nucleocytoplasmic mRNA transport are described and evaluated. The explanatory advantage of solid-state models is contrasted with the heuristic advantage of diffusion theory, but it is argued that diffusion theory itself, even aided by modern computational techniques and numerical and graphical approaches, cannot account for data describing the movements of materials within the cell. Therefore, the mechanisms envisaged in a diffusionist perspective cannot be confined to diffusion alone, but must include other processes such as bulk fluid flow.

  1. The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis

    DEFF Research Database (Denmark)

    Rautengarten, Carsten; Ebert, Berit; Moreno, Ignacio

    2014-01-01

    Delivery of nucleotide sugar substrates into the Golgi apparatus and endoplasmic reticulum for processes such as cell wall biosynthesis and protein glycosylation is critical for plant growth and development. Plant genomes encode large families of uncharacterized nucleotide sugar transporters......-of-function and overexpression lines for two of these transporters identified biochemical alterations supporting their roles in the biosynthesis of Rha- and Gal-containing polysaccharides. Thus, cell wall polysaccharide biosynthesis in the Golgi apparatus of plants is likely also regulated by substrate transport mechanisms....

  2. IMPROVEMENT OF ORGANIZATIONAL FREIGHT TRANSPORTATION STRUCTURE

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    T. V. Teslenko

    2011-01-01

    Full Text Available The organizational structure of management of railway freight transportations based on product principle is offered that allows functioning of private operator companies and realizing of transportations on competition basis.

  3. A note on transport of algebraic structures

    DEFF Research Database (Denmark)

    Holm, Henrik Granau

    2015-01-01

    We study transport of algebraic structures and prove a theorem which subsumes results of Comfort and Ross on topological group structures on Stone-Cech compactifications, of Chevalley and of Gil de Lamadrid and Jans on topological group and ring structures on universal covering spaces......, and of Gleason on topological group structures on universal locally connected refinements....

  4. Quantum transport through hierarchical structures.

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    Boettcher, S; Varghese, C; Novotny, M A

    2011-04-01

    The transport of quantum electrons through hierarchical lattices is of interest because such lattices have some properties of both regular lattices and random systems. We calculate the electron transmission as a function of energy in the tight-binding approximation for two related Hanoi networks. HN3 is a Hanoi network with every site having three bonds. HN5 has additional bonds added to HN3 to make the average number of bonds per site equal to five. We present a renormalization group approach to solve the matrix equation involved in this quantum transport calculation. We observe band gaps in HN3, while no such band gaps are observed in linear networks or in HN5. We provide a detailed scaling analysis near the edges of these band gaps.

  5. Transport Market and its Structure

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    Teodor Perić

    2002-05-01

    Full Text Available Market is the integrity of relations between supply and demandof traffic or some other service (goods which at a ce11ainplace and location, at a certain time affect the supply and purchaseof certain products, including services, stocks, money,and the set of all institutions, areas, devices and instrumentsthat act on the sale and other transactions realised at that point.It is the main resource allocator (~resource allocation in thesystems of free private ownership economic and transport systems.

  6. Urban structure and sustainable transport

    DEFF Research Database (Denmark)

    Große, Juliane

    . The study achieves a comprehensive understanding of travel behaviour and qualifies the role of urban structure in relation to further determinants. The influence of urban structure is largely limited to daily travel (bounded trips). Beyond urban structure, other determinants such as socio-economic factors......This PhD study explores the relationship between urban structure and travel behaviour and the role of urban planning in promoting more sustainable travel patterns. The study conceptualises the role of urban planning by means of a multiple-case study of the three medium-sized Northern European...... cities, Eskilstuna, Turku and Tartu, that was conducted based on qualitative methods. Further, the study investigates the relationship between the urban structure of people’s living environment and their travel behaviour by integrating daily modality styles (work and leisure), and weekend and holiday...

  7. Structural Stability of Tokamak Equilibrium: Transport Barriers

    Energy Technology Data Exchange (ETDEWEB)

    Solano, E. R.

    2001-07-01

    A generalised theory of structural stability of differential equations is introduced and applied to the Grad-Shafranov equation. It is discussed how the formation and loss of transport barrier could be associated with the appearance/disappearance of equilibria. The equilibrium conjecture is presented: transport barriers are associated with locally diamagnetic regions in the plasma, and affected by the paramagnetism of the bootstrap current. (Author) 18 refs.

  8. Porous media fluid transport and pore structure

    CERN Document Server

    Dullien, F A L

    1992-01-01

    This book examines the relationship between transport properties and pore structure of porous material. Models of pore structure are presented with a discussion of how such models can be used to predict the transport properties of porous media. Portions of the book are devoted to interpretations of experimental results in this area and directions for future research. Practical applications are given where applicable, and are expected to be useful for a large number of different fields, including reservoir engineering, geology, hydrogeology, soil science, chemical process engineering, biomedica

  9. Lagrangian coherent structures and plasma transport processes

    CERN Document Server

    Falessi, M V; Schep, T J

    2015-01-01

    A dynamical system framework is used to describe transport processes in plasmas embedded in a magnetic field. For periodic systems with one degree of freedom the Poincar\\'e map provides a splitting of the phase space into regions where particles have different kinds of motion: periodic, quasi-periodic or chaotic. The boundaries of these regions are transport barriers; i.e., a trajectory cannot cross such boundaries during the whole evolution of the system. Lagrangian Coherent Structure (LCS) generalize this method to systems with the most general time dependence, splitting the phase space into regions with different qualitative behaviours. This leads to the definition of finite-time transport barriers, i.e. trajectories cannot cross the barrier for a finite amount of time. This methodology can be used to identify fast recirculating regions in the dynamical system and to characterize the transport between them.

  10. Transport and coherent structures in wall turbulence

    CERN Document Server

    Tardu, Sedat

    2014-01-01

    Wall bounded turbulent flows are of major importance in industrial and environmental fluid mechanics. The structure of the wall turbulence is intrinsically related to the coherent structures that play a fundamental role in the transport process. The comprehension of their regeneration mechanism is indispensable for the development of efficient strategies in terms of drag control and near wall turbulence management. This book provides an up-to-date overview on the progress made in this specific area in recent years.

  11. Arabidopsis thaliana AtUTr7 Encodes a Golgi-Localized UDP-Glucose/UDP-Galactose Transporter that Affects Lateral Root Emergence

    Institute of Scientific and Technical Information of China (English)

    Michael Handford; Cecilia Rodríguez-Furlán; Lorena Marchant; Marcelo Segura; Daniela Gómez; Elena Alvarez-Buyll; Guang-Yan Xiong; Markus Pauly; Ariel Orellana

    2012-01-01

    Nucleotide sugar transporters (NSTs) are antiporters comprising a gene family that plays a fundamental role in the biosynthesis of complex cell wall polysaccharides and glycoproteins in plants.However,due to the limited number of related mutants that have observable phenotypes,the biological function(s) of most NSTs in cell wall biosynthesis and assembly have remained elusive.Here,we report the characterization of AtUTr7 from Arabidopsis (Arabidopsis thaliana (L.) Heynh.),which is homologous to multi-specific UDP-sugar transporters from Drosophila melanogaster,humans,and Caenorhabditis elegans.We show that AtUTr7 possesses the common structural characteristics conserved among NSTs.Using a green fluorescent protein (GFP) tagged version,we demonstrate that AtUTr7 is localized in the Golgi apparatus.We also show that AtUTr7 is widely expressed,especially in the roots and in specific floral organs.Additionally,the results of an in vitro nucleotide sugar transport assay carried out with a tobacco and a yeast expression system suggest that AtUTr7 is capable of transferring UDP-Gal and UDP-GIc,but not a range of other UDP-and GDP-sugars,into the Golgi lumen.Mutants lacking expression of AtUTr7 exhibited an early proliferation of lateral roots as well as distorted root hairs when cultivated at high sucrose concentrations.Furthermore,the distribution of homogalacturonan with a low degree of methyl esterification differed in lateral root tips of the mutant compared to wild-type plants,although additional analytical procedures revealed no further differences in the composition of the root cell walls.This evidence suggests that the transport of UDP-Gal and UDP-GIc into the Golgi under conditions of high root biomass production plays a role in lateral root and root hair development.

  12. Transport and structure in nanoscale channels

    Science.gov (United States)

    Lakatos, Gregory William

    Driven by the rapidly advancing fields of nano- and biotechnology, there has been an explosion of interest in molecular transport and structure formation on small length scales. A canonical model for the transport of particles along one dimensional pathways in nanoscale channels is the Totally Asymmetric Simple Exclusion Process (TASEP). After introducing the standard TASEP, modifications of the TASEP designed to increase its utility in modeling biological transport processes are described. One variant of the TASEP is particularly suitable for modeling protein translation, and the results of using this variant to investigate the effects of slow-codons on the translation process are discussed. A related topic is the voltage-driven translocation of DNA hairpins through membrane-embedded nanopores. Motivated by recent experiments, a stochastic model is developed that couples the translocation and dehybridization of the DNA hairpin. This model is used to explore the behaviour of the mean translocation time of hairpins as a function of driving voltage, and two translocation mechanisms are identified and discussed. Finally, the adsorption and equilibrium structures of water in the interior of ion-bearing nanoscale pores are considered. The behaviour of water and ions under confinement is critical to the functioning of biological ion channels and nanoporous filters. Here, the adsorption isotherms of water are examined, and the layered structures formed by the confined water are described.

  13. Structure and Transport Anomalies in Soft Colloids

    KAUST Repository

    Srivastava, Samanvaya

    2013-04-01

    Anomalous trends in nanoparticle correlation and motion are reported in soft nanoparticle suspensions using static and dynamic x-ray scattering measurements. Contrary to normal expectations, we find that particle-particle correlations decrease and particle dynamics become faster as volume fraction rises above a critical particle loading associated with overlap. Our observations bear many similarities to the cascade of structural and transport anomalies reported for complex, network forming molecular fluids such as water, and are argued to share similar physical origins. © 2013 American Physical Society.

  14. Epitaxial graphene electronic structure and transport

    Energy Technology Data Exchange (ETDEWEB)

    De Heer, Walt A; Berger, Claire; Wu Xiaosong; Sprinkle, Mike; Hu Yike; Ruan Ming; First, Phillip N [School of Physics, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Stroscio, Joseph A [Center for Nanoscale Science and Technology, NIST, Gaithersburg, MD 20899 (United States); Haddon, Robert [Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical and Environmental Engineering, University of California, Riverside, CA 92521 (United States); Piot, Benjamin; Faugeras, Clement; Potemski, Marek [LNCMI -CNRS, Grenoble, 38042 Cedex 9 (France); Moon, Jeong-Sun, E-mail: walt.deheer@physics.gateh.ed [HRL Laboratories LLC, Malibu, CA 90265 (United States)

    2010-09-22

    Since its inception in 2001, the science and technology of epitaxial graphene on hexagonal silicon carbide has matured into a major international effort and is poised to become the first carbon electronics platform. A historical perspective is presented and the unique electronic properties of single and multilayered epitaxial graphenes on electronics grade silicon carbide are reviewed. Early results on transport and the field effect in Si-face grown graphene monolayers provided proof-of-principle demonstrations. Besides monolayer epitaxial graphene, attention is given to C-face grown multilayer graphene, which consists of electronically decoupled graphene sheets. Production, structure and electronic structure are reviewed. The electronic properties, interrogated using a wide variety of surface, electrical and optical probes, are discussed. An overview is given of recent developments of several device prototypes including resistance standards based on epitaxial graphene quantum Hall devices and new ultrahigh frequency analogue epitaxial graphene amplifiers.

  15. Functional YFP-tagging of the essential GDP-mannose transporter reveals an important role for the secretion related small GTPase SrgC protein in maintenance of Golgi bodies in Aspergillus niger

    NARCIS (Netherlands)

    Carvalho, N.D.S.P.; Arentshorst, M.; Weenink, X.O.; Punt, P.J.; Hondel, C.A.M.J.J. van den; Ram, A.F.J.

    2011-01-01

    The addition of mannose residues to glycoproteins and glycolipids in the Golgi is carried out by mannosyltransferases. Their activity depends on the presence of GDP-mannose in the lumen of the Golgi. The transport of GDP-mannose (mannosyl donor) into the Golgi requires a specific nucleotide sugar tr

  16. Electrical transport engineering of semiconductor superlattice structures

    Science.gov (United States)

    Shokri, Aliasghar

    2014-04-01

    We investigate the influence of doping concentration on band structures of electrons and electrical transmission in a typical aperiodic semiconductor superlattice consisting of quantum well and barrier layers, theoretically. For this purpose, we assume that each unit cell of the superlattice contains alternately two types of material GaAs (as a well) and GaAlAs (as a barrier) with six sublayers of two materials. Our calculations are based on the generalized Kronig-Penny (KP) model and the transfer matrix method within the framework of the parabolic conductance band effective mass approximation in the coherent regime. This model reduces the numerical calculation time and enables us to use the transfer matrix method to investigate transport in the superlattices. We show that by varying the doping concentration and geometrical parameters, one can easily block the transmission of the electrons. The numerical results may be useful in designing of nanoenergy filter devices.

  17. Electrical transport engineering of semiconductor superlattice structures

    Energy Technology Data Exchange (ETDEWEB)

    Shokri, Aliasghar, E-mail: aashokri@tpnu.ac.ir

    2014-04-01

    We investigate the influence of doping concentration on band structures of electrons and electrical transmission in a typical aperiodic semiconductor superlattice consisting of quantum well and barrier layers, theoretically. For this purpose, we assume that each unit cell of the superlattice contains alternately two types of material GaAs (as a well) and GaAlAs (as a barrier) with six sublayers of two materials. Our calculations are based on the generalized Kronig–Penny (KP) model and the transfer matrix method within the framework of the parabolic conductance band effective mass approximation in the coherent regime. This model reduces the numerical calculation time and enables us to use the transfer matrix method to investigate transport in the superlattices. We show that by varying the doping concentration and geometrical parameters, one can easily block the transmission of the electrons. The numerical results may be useful in designing of nanoenergy filter devices.

  18. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis.

    Science.gov (United States)

    Ebert, Berit; Rautengarten, Carsten; Guo, Xiaoyuan; Xiong, Guangyan; Stonebloom, Solomon; Smith-Moritz, Andreia M; Herter, Thomas; Chan, Leanne Jade G; Adams, Paul D; Petzold, Christopher J; Pauly, Markus; Willats, William G T; Heazlewood, Joshua L; Scheller, Henrik Vibe

    2015-04-01

    Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis.

  19. Expression, solubilisation, and purification of a functional CMP-sialic acid transporter in Pichia pastoris.

    Science.gov (United States)

    Maggioni, Andrea; Hadley, Barbara; von Itzstein, Mark; Tiralongo, Joe

    2014-09-01

    Membrane proteins, including solute transporters play crucial roles in cellular function and have been implicated in a variety of important diseases, and as such are considered important targets for drug development. Currently the drug discovery process is heavily reliant on the structural and functional information discerned from high-resolution crystal structures. However, membrane protein structure determination is notoriously difficult, due in part to challenges faced in their expression, solubilisation and purification. The CMP-sialic acid transporter (CST) is considered to be an attractive target for drug discovery. CST inhibition reduces cancer cell sialylation and decreases the metastatic potential of cancer cells and to date, no crystal structure of the CST, or any other nucleotide sugar transporter exists. Here we describe the optimised conditions for expression in Pichia pastoris, solubilisation using n-nonyl β-d-maltopyranoside (NM) and single step purification of a functional CST. Importantly we show that despite being able to solubilise and purify the CST using a number of different detergents, only NM was able to maintain CST functionality.

  20. Characterization of fluid transport in microscale structures

    Energy Technology Data Exchange (ETDEWEB)

    Paul, P.H.

    1998-01-01

    A new tool for imaging both scalar transport and velocity fields in liquid flows through microscale structures is described. The technique employs an ultraviolet laser pulse to write a pattern into the flow by uncaging a fluorescent dye. This is followed, at selected time delays, by flood illumination with a pulse of visible light which excites the uncaged dye. The resulting fluorescence image collected onto a sensitive CCD camera. The instrument is designed as an oil immersion microscope to minimize the beam steering effects. The caged fluorescent dye is seeded in trace quantities throughout the active fluid, thus images with high contrast and minimal distortion due to any molecular diffusion history can be obtained at any point within the microchannel by selectivity activating the dye in the immediate region of interest. The author reports images of pressure- and electrokinetically-driven steady flow within round cross section capillaries having micron scale inner diameters. The author also demonstrates the ability to recover the velocity profile from a time sequence of these scalar images by direct inversion of the conserved scalar advection-convection equation.

  1. Coupled ion Binding and Structural Transitions Along the Transport Cycle of Glutamate Transporters

    Energy Technology Data Exchange (ETDEWEB)

    Verdon, Gregory [Weill Cornell Medical College, New York, NY (United States); Oh, SeCheol [Weill Cornell Medical College, New York, NY (United States); Serio, Ryan N. [Weill Cornell Medical College, New York, NY (United States); Boudker, Olga [Weill Cornell Medical College, New York, NY (United States)

    2014-05-19

    Membrane transporters that clear the neurotransmitter glutamate from synapses are driven by symport of sodium ions and counter-transport of a potassium ion. Previous crystal structures of a homologous archaeal sodium and aspartate symporter showed that a dedicated transport domain carries the substrate and ions across the membrane. We report new crystal structures of this homologue in ligand-free and ions-only bound outward- and inward-facing conformations. We then show that after ligand release, the apo transport domain adopts a compact and occluded conformation that can traverse the membrane, completing the transport cycle. Sodium binding primes the transport domain to accept its substrate and triggers extracellular gate opening, which prevents inward domain translocation until substrate binding takes place. Moreover, we describe a new cation-binding site ideally suited to bind a counter-transported ion. We suggest that potassium binding at this site stabilizes the translocation-competent conformation of the unloaded transport domain in mammalian homologues.

  2. Modelling multicomponent solute transport in structured soils

    NARCIS (Netherlands)

    Beinum, van G.W.

    2007-01-01

    The mobility of contaminants in soil is an important factor in determining their ability to spread into the wider environment. For non-volatile substances, transport within the soil is generally dominated by transport of dissolved fractions in the soil water phase, via either diffusion or convection

  3. Structuring a Sustainable Transportation System in Beijing

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    <正> Since the implementation of the Master Plan of Beijing in 1993, Beijing has acquired economic development continually, and the construction of urban transportation has gained obvious achievements. But with the continually high-speed development of Beijing’s economy, the quickened tenor of urbanization and traffic motorization, the increasing need for transportation and amount of motor

  4. Structural advances for the major facilitator superfamily (MFS) transporters.

    Science.gov (United States)

    Yan, Nieng

    2013-03-01

    The major facilitator superfamily (MFS) is one of the largest groups of secondary active transporters conserved from bacteria to humans. MFS proteins selectively transport a wide spectrum of substrates across biomembranes and play a pivotal role in multiple physiological processes. Despite intense investigation, only seven MFS proteins from six subfamilies have been structurally elucidated. These structures were captured in distinct states during a transport cycle involving alternating access to binding sites from either side of the membrane. This review discusses recent progress in MFS structure analysis and focuses on the molecular basis for substrate binding, co-transport coupling, and alternating access.

  5. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis[OPEN

    Science.gov (United States)

    Ebert, Berit; Rautengarten, Carsten; Guo, Xiaoyuan; Xiong, Guangyan; Stonebloom, Solomon; Smith-Moritz, Andreia M.; Herter, Thomas; Chan, Leanne Jade G.; Adams, Paul D.; Petzold, Christopher J.; Pauly, Markus; Willats, William G.T.; Heazlewood, Joshua L.; Scheller, Henrik Vibe

    2015-01-01

    Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis. PMID:25804536

  6. Membrane transport mechanism 3D structure and beyond

    CERN Document Server

    Ziegler, Christine

    2014-01-01

    This book provides a molecular view of membrane transport by means of numerous biochemical and biophysical techniques. The rapidly growing number of atomic structures of transporters in different conformations and the constant progress in bioinformatics have recently added deeper insights.   The unifying mechanism of energized solute transport across membranes is assumed to consist of the conformational cycling of a carrier protein to provide access to substrate binding sites from either side of a cellular membrane. Due to the central role of active membrane transport there is considerable interest in deciphering the principles of one of the most fundamental processes in nature: the alternating access mechanism.   This book brings together particularly significant structure-function studies on a variety of carrier systems from different transporter families: Glutamate symporters, LeuT-like fold transporters, MFS transporters and SMR (RND) exporters, as well as ABC-type importers.   The selected examples im...

  7. SLC6 Neurotransmitter Transporters: Structure, Function, and Regulation

    DEFF Research Database (Denmark)

    Kristensen, Anders S; Andersen, Jacob; Jørgensen, Trine N

    2011-01-01

    The neurotransmitter transporters (NTTs) belonging to the solute carrier 6 (SLC6) gene family (also referred to as the neurotransmitter-sodium-symporter family or Na(+)/Cl(-)-dependent transporters) comprise a group of nine sodium- and chloride-dependent plasma membrane transporters for the monoa......The neurotransmitter transporters (NTTs) belonging to the solute carrier 6 (SLC6) gene family (also referred to as the neurotransmitter-sodium-symporter family or Na(+)/Cl(-)-dependent transporters) comprise a group of nine sodium- and chloride-dependent plasma membrane transporters....... Furthermore, psychostimulants such as cocaine and amphetamines have the SLC6 NTTs as primary targets. Beginning with the determination of a high-resolution structure of a prokaryotic homolog of the mammalian SLC6 transporters in 2005, the understanding of the molecular structure, function, and pharmacology...

  8. Turbulent transport and structural transition in confined plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Kimitaka; Itoh, Sanae; Fukuyama, Atsushi; Yagi, Masatoshi

    1996-10-01

    Theory of the far-nonequilibrium transport of plasmas is described. Analytic as well as simulation studies are developed. The subcritical nature of turbulence and the mechanism for self-sustaining are discussed. The transport coefficient is obtained. The pressure gradient is introduced as an order parameter, and the bifurcation from the collisional transport to the turbulent one is shown. The generation of the electric field and its influence on the turbulent transport are analyzed. The bifurcation of the radial electric field structure is addressed. The hysteresis appears in the flux-gradient relation. This bifurcation causes the multifold states in the plasma structure, driving the transition in transport coefficient or the self-generating oscillations in the flux. Structural formation and dynamics of plasma profiles are explained. (author)

  9. Structural and functional dynamics of Excitatory Amino Acid Transporters (EAAT

    Directory of Open Access Journals (Sweden)

    Thomas Rauen

    2014-09-01

    Full Text Available Glutamate transporters control the glutamate homeostasis in the central nervous system, and, thus, are not only crucial for physiological excitatory synaptic signaling, but also for the prevention of a large number of neurodegenerative diseases that are associated with excessive and prolonged presence of the neurotransmitter glutamate in the extracellular space. Until now, five subtypes of high-affinity glutamate transporters (excitatory amino acid transporters, EAATs 1–5 have been identified. These 5 high-affinity glutamate transporter subtypes belong to the solute carrier 1 (SLC1 family of transmembrane proteins: EAAT1/GLAST (SLC1A3, EAAT2/GLT1 (SLC1A2, EAAT3/EAAC1 (SLC1A1, EAAT4 (SLC1A6 and EAAT5 (SLC1A7. EAATs are secondary-active transporters, taking up glutamate into the cell against a substantial concentration gradient. The driving force for concentrative uptake is provided by the co-transport of Na+ ions and the counter-transport of one K+ in a step independent of the glutamate translocation step. Due to the electrogenicity of transport, the transmembrane potential can also act as driving force. Glutamate transporters are also able to run in reverse, resulting in glutamate release from cells. Due to these important physiological functions, glutamate transporter expression and, therefore, the transport rate, are tightly regulated. The EAAT protein family are structurally expected to be highly similar, however, these transporters show a functional diversity that ranges from high capacity glutamate uptake systems (EAATs 1–3 to receptor-like glutamate activated anion channels (EAATs 4–5. Here, we provide an update on most recent progress made on EAAT’s molecular transport mechanism, structure-function relationships, pharmacology, and will add recent insights into mechanism of rapid membrane trafficking of glutamate transporters.

  10. Instability of Vertical Current Transport in Layered Structures

    Science.gov (United States)

    Wang, Jiannong

    2000-03-01

    Many interesting phenomena related to interface electronic structure of layered structures have been found, including stable sawtooth-like current-voltage characteristic, unstable current self-oscillations, and chaos in the vertical electron transport. While many studies of current self-oscillation have been focused on the effect of changing the carrier concentration, we show that a transverse magnetic field and the sample temperature can also control the transition from stable to unstable current transport. We show that the unstable current self-oscillation is due to the generation of a limit cycle around an unstable steady state solution which, in turn, is due to the negative differential resistance (NDR) existed at layer interfaces. This new insight both generalizes and unifies our understanding of the instability in current transport through layer structures. We also show that a dynamic dc voltage band emerges in the transition from stable to unstable current transport.

  11. Turbulent transport and structural transition in confined plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Kimitaka [National Inst. for Fusion Science, Nagoya (Japan); Itoh, Sanae-I; Yagi, Masatoshi [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics; Fukuyama, Atsushi [Okayama Univ. (Japan). School of Engineering

    1997-05-01

    The theory of far-nonequilibrium transport of plasmas is described. Analytic as well as simulation studies are developed. The subcritical nature coefficient is obtained. The pressure gradient is introduced as an order parameter, and the bifurcation from collisional to turbulent transport is shown. The generation of the electric field and its influence on the turbulent transport are analysed. The bifurcation of the radial electric field structure is addressed. Hysteresis appears in the flux-gradient relation. This bifurcation causes the multifold states in the plasma structure, driving the transition in the transport coefficient or the self-generating oscillations in the flux. The structural formation and dynamics of plasma profiles are explained. (Author).

  12. Structural Design of Oligopeptides for Intestinal Transport Model.

    Science.gov (United States)

    Hong, Seong-Min; Tanaka, Mitsuru; Koyanagi, Riho; Shen, Weilin; Matsui, Toshiro

    2016-03-16

    Glycyl-sarcosine (Gly-Sar) is a well-known model substrate for the intestinal uptake of dipeptides through peptide transporter 1 (PepT1). However, there are no other model peptides larger than tripeptides to evaluate their intestinal transport ability. In this study, we designed new oligopeptides based on the Gly-Sar structure in terms of protease resistance. Gly-Sar-Sar was found to be an appropriate transport model for tripeptides because it does not degrade during the transport across the rat intestinal membrane, while Gly-Gly-Sar was degraded to Gly-Sar during the 60 min transport. Caco-2 cell transport experiments revealed that the designed oligopeptides based on Gly-Sar-Sar showed a significantly (p transport ability by factors of 1/10-, 1/25-, and 1/40-fold for Gly-Sar-Sar, Gly-Sar-Sar-Sar, and Gly-Sar-Sar-Sar-Sar, respectively, compared to Gly-Sar (apparent permeability coefficient: 38.6 ± 11.4 cm/s). Cell experiments also showed that the designed tripeptide and Gly-Sar were transported across Caco-2 cell via PepT1, whereas the tetra- and pentapeptides were transported through the paracellular tight-junction pathway.

  13. Global Local Structural Optimization of Transportation Aircraft Wings

    NARCIS (Netherlands)

    Ciampa, P.D.; Nagel, B.; Van Tooren, M.J.L.

    2010-01-01

    The study presents a multilevel optimization methodology for the preliminary structural design of transportation aircraft wings. A global level is defined by taking into account the primary wing structural components (i.e., ribs, spars and skin) which are explicitly modeled by shell layered finite e

  14. Structure of a Eurkaryotic CLC Transporter Defines an Intermediate State in the Transport Cycle

    Energy Technology Data Exchange (ETDEWEB)

    L Feng; E Campbell; Y Hsiung; R MacKinnon

    2011-12-31

    CLC proteins transport chloride (Cl{sup -}) ions across cell membranes to control the electrical potential of muscle cells, transfer electrolytes across epithelia, and control the pH and electrolyte composition of intracellular organelles. Some members of this protein family are Cl{sup -} ion channels, whereas others are secondary active transporters that exchange Cl{sup -} ions and protons (H{sup +}) with a 2:1 stoichiometry. We have determined the structure of a eukaryotic CLC transporter at 3.5 angstrom resolution. Cytoplasmic cystathionine beta-synthase (CBS) domains are strategically positioned to regulate the ion-transport pathway, and many disease-causing mutations in human CLCs reside on the CBS-transmembrane interface. Comparison with prokaryotic CLC shows that a gating glutamate residue changes conformation and suggests a basis for 2:1 Cl{sup -}/H{sup +} exchange and a simple mechanistic connection between CLC channels and transporters.

  15. On structural inelasticity of modal substitution in freight transport

    DEFF Research Database (Denmark)

    Rich, Jeppe; Kveiborg, Ole; Overgård, Christian Hansen

    2011-01-01

    At the European level there is an increasing focus on how freight transport can be moved from trucks on roads to more environmentally friendly modes such as rail and ship. A large proportion of the transport services between OD pairs, however, cannot be substituted since there is only one...... alternative available. The paper investigates the magnitude of this ‘‘structural inelasticity” of modal substitution in freight transport due to a sparser layout of rail and ship-based freight networks compared to road. In the analysis we use a recent Scandinavian freight demand model covering more than 800...... zones. We find that the structural inelasticity is very significant – in particular for transportation over less than 500 km. Moreover, the inelasticity varies greatly with commodity groups and between OD pairs, and it depends strongly on the port and rail infrastructure. The results suggest that pure...

  16. Correlating atomic structure and transport in suspended graphene nanoribbons.

    Science.gov (United States)

    Qi, Zhengqing John; Rodríguez-Manzo, Julio A; Botello-Méndez, Andrés R; Hong, Sung Ju; Stach, Eric A; Park, Yung Woo; Charlier, Jean-Christophe; Drndić, Marija; Johnson, A T Charlie

    2014-08-13

    Graphene nanoribbons (GNRs) are promising candidates for next generation integrated circuit (IC) components; this fact motivates exploration of the relationship between crystallographic structure and transport of graphene patterned at IC-relevant length scales (edges after current annealing, presenting a pathway for the controlled fabrication of semiconducting GNRs with known edge geometry. Finally, we report on simulations of quantum transport in GNRs that are in qualitative agreement with the observations.

  17. Structural controls on anomalous transport in fractured porous rock

    Science.gov (United States)

    Edery, Yaniv; Geiger, Sebastian; Berkowitz, Brian

    2016-07-01

    Anomalous transport is ubiquitous in a wide range of disordered systems, notably in fractured porous formations. We quantitatively identify the structural controls on anomalous tracer transport in a model of a real fractured geological formation that was mapped in an outcrop. The transport, determined by a continuum scale mathematical model, is characterized by breakthrough curves (BTCs) that document anomalous (or "non-Fickian") transport, which is accounted for by a power law distribution of local transition times ψ>(t>) within the framework of a continuous time random walk (CTRW). We show that the determination of ψ>(t>) is related to fractures aligned approximately with the macroscopic direction of flow. We establish the dominant role of fracture alignment and assess the statistics of these fractures by determining a concentration-visitation weighted residence time histogram. We then convert the histogram to a probability density function (pdf) that coincides with the CTRW ψ>(t>) and hence anomalous transport. We show that the permeability of the geological formation hosting the fracture network has a limited effect on the anomalous nature of the transport; rather, it is the fractures transverse to the flow direction that play the major role in forming the long BTC tail associated with anomalous transport. This is a remarkable result, given the complexity of the flow field statistics as captured by concentration transitions.

  18. Structure of a Type-1 Secretion System ABC Transporter.

    Science.gov (United States)

    Morgan, Jacob L W; Acheson, Justin F; Zimmer, Jochen

    2017-03-07

    Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membrane porin. These three components assemble into a complex spanning both membranes and providing a conduit for the translocation of unfolded polypeptides. We show that ATP hydrolysis and assembly of the entire T1SS complex is necessary for protein secretion. Furthermore, we present a 3.15-Å crystal structure of AaPrtD, the ABC transporter found in the Aquifex aeolicus T1SS. The structure suggests a substrate entry window just above the transporter's nucleotide binding domains. In addition, highly kinked transmembrane helices, which frame a narrow channel not observed in canonical peptide transporters, are likely involved in substrate translocation. Overall, the AaPrtD structure supports a polypeptide transport mechanism distinct from alternating access.

  19. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  20. Structure-function relationships in sapwood water transport and storage.

    Science.gov (United States)

    Barbara L. Gartner; Frederick C. Meinzer

    2005-01-01

    Primary production by plants requires the loss of substantial quantities of water when the stomata are open for carbon assimilation. The delivery of that water to the leaves occurs through the xylem. The structure, condition, and quantity of the xylem control not only the transport efficiency but also the release of water from storage. For example, if there is high...

  1. Phase Structure and Transport Properties of Dense Quark Matter

    CERN Document Server

    Schaefer, Thomas

    2010-01-01

    We provide a summary of our current knowledge of the phase structure of very dense quark matter. We concentrate on the question how the ground state at asymptotically high density -- color-flavor-locked (CFL) matter -- is modified as the density is lowered. We discuss the nature of the quasi-particle excitations, and present work on the transport properties of dense QCD matter.

  2. The structural basis of calcium transport by the calcium pump

    DEFF Research Database (Denmark)

    Olesen, Claus; Picard, Martin; Winther, Anne-Marie Lund;

    2007-01-01

    , Ca2+ translocation and dephosphorylation, that are based on complexes with a functional ATP analogue, beryllium fluoride and aluminium fluoride, respectively. The structures complete the cycle of nucleotide binding and cation transport of Ca2+-ATPase. Phosphorylation of the enzyme triggers the onset...

  3. Cosmic-Ray Transport in Heliospheric Magnetic Structures. II. Modeling Particle Transport through Corotating Interaction Regions

    Science.gov (United States)

    Kopp, Andreas; Wiengarten, Tobias; Fichtner, Horst; Effenberger, Frederic; Kühl, Patrick; Heber, Bernd; Raath, Jan-Louis; Potgieter, Marius S.

    2017-03-01

    The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework Cronos (Wiengarten et al., referred as Paper I), and the results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with Cronos, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, and study the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.

  4. Segregation of the Qb-SNAREs GS27 and GS28 into Golgi vesicles regulates intra-Golgi transport.

    Science.gov (United States)

    Fusella, Aurora; Micaroni, Massimo; Di Giandomenico, Daniele; Mironov, Alexandre A; Beznoussenko, Galina V

    2013-05-01

    The Golgi apparatus is the main glycosylation and sorting station along the secretory pathway. Its structure includes the Golgi vesicles, which are depleted of anterograde cargo, and also of at least some Golgi-resident proteins. The role of Golgi vesicles remains unclear. Here, we show that Golgi vesicles are enriched in the Qb-SNAREs GS27 (membrin) and GS28 (GOS-28), and depleted of nucleotide sugar transporters. A block of intra-Golgi transport leads to accumulation of Golgi vesicles and partitioning of GS27 and GS28 into these vesicles. Conversely, active intra-Golgi transport induces fusion of these vesicles with the Golgi cisternae, delivering GS27 and GS28 to these cisternae. In an in vitro assay based on a donor compartment that lacks UDP-galactose translocase (a sugar transporter), the segregation of Golgi vesicles from isolated Golgi membranes inhibits intra-Golgi transport; re-addition of isolated Golgi vesicles devoid of UDP-galactose translocase obtained from normal cells restores intra-Golgi transport. We conclude that this activity is due to the presence of GS27 and GS28 in the Golgi vesicles, rather than the sugar transporter. Furthermore, there is an inverse correlation between the number of Golgi vesicles and the number of inter-cisternal connections under different experimental conditions. Finally, a rapid block of the formation of vesicles via COPI through degradation of ϵCOP accelerates the cis-to-trans delivery of VSVG. These data suggest that Golgi vesicles, presumably with COPI, serve to inhibit intra-Golgi transport by the extraction of GS27 and GS28 from the Golgi cisternae, which blocks the formation of inter-cisternal connections.

  5. Crystal structure of the human glucose transporter GLUT1

    Science.gov (United States)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  6. Structure and localisation of drug binding sites on neurotransmitter transporters.

    Science.gov (United States)

    Ravna, Aina W; Sylte, Ingebrigt; Dahl, Svein G

    2009-10-01

    The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in each transporter were identified. Cocaine was docked into binding pocket 1 of DAT, corresponding to the leucine binding site in LeuT(Aa), which involved transmembrane helices (TMHs) 1, 3, 6 and 8. Clomipramine was docked into binding pocket 2 of DAT, involving TMHs 1, 3, 6, 10 and 11, and extracellular loops 4 and 6, corresponding to the clomipramine binding site in a crystal structure of a LeuT(Aa)-clomipramine complex. The structures of the proposed cocaine- and tricyclic antidepressant-binding sites may be of particular interest for the design of novel DAT interacting ligands.

  7. Comparative Traffic Performance Analysis of Urban Transportation Network Structures

    CERN Document Server

    Amini, Behnam; Mojarradi, Morteza; Derrible, Sybil

    2015-01-01

    The network structure of an urban transportation system has a significant impact on its traffic performance. This study uses network indicators along with several traffic performance measures including speed, trip length, travel time, and traffic volume, to compare a selection of seven transportation networks with a variety of structures and under different travel demand conditions. The selected network structures are: modified linear, branch, grid, 3-directional grid, 1-ring web, 2-ring web, and radial. For the analysis, a base origin-destination matrix is chosen, to which different growth factors are applied in order to simulate various travel demand conditions. Results show that overall the 2-ring web network offers the most efficient traffic performance, followed by the grid and the 1-ring networks. A policy application of this study is that the branch, 3-directional grid, and radial networks are mostly suited for small cities with uncongested traffic conditions. In contrast, the 2-ring web, grid, and 1-r...

  8. Quantum-walk transport properties on graphene structures

    Science.gov (United States)

    Bougroura, Hamza; Aissaoui, Habib; Chancellor, Nicholas; Kendon, Viv

    2016-12-01

    We present numerical studies of quantum walks on C60 and related graphene structures to investigate their transport properties. Also known as a honeycomb lattice, the lattice formed by carbon atoms in the graphene phase can be rolled up to form nanotubes of various dimensions. Graphene nanotubes have many important applications, some of which rely on their unusual electrical conductivity and related properties. Quantum walks on graphs provide an abstract setting in which to study such transport properties independent of the other chemical and physical properties of a physical substance. They can thus be used to further the understanding of mechanisms behind such properties. We find that nanotube structures are significantly more efficient in transporting a quantum walk than cycles of equivalent size, provided the symmetry of the structure is respected in how they are used. We find faster transport on zigzag nanotubes compared to armchair nanotubes, which is unexpected given that for the actual materials the armchair nanotube is metallic, while the zigzag is semiconducting.

  9. Electronic structure and thermoelectric transport of black phosphorus

    Science.gov (United States)

    Craco, L.; Pereira, T. A. da Silva; Leoni, S.

    2017-08-01

    We investigate anisotropic electronic structure and thermal transport properties of bulk black phosphorus (BP). Using density functional dynamical mean-field theory we first derive a correlation-induced electronic reconstruction, showing band-selective Kondoesque physics in this elemental p -band material. The resulting correlated picture is expected to shed light onto the temperature and doping dependent evolution of resistivity, Seebeck coefficient, and thermal conductivity, as seen in experiments on bulk single crystal BP. Therein, large anisotropic particle-hole excitations are key to consistently understand thermoelectric transport responses of pure and doped BP.

  10. 3D Shape and Indirect Appearance by Structured Light Transport.

    Science.gov (United States)

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture.

  11. Connections between transport in events and transport at landscape-structuring timescales

    Science.gov (United States)

    Harman, C. J.; Lohse, K. A.; Troch, P. A.; Sivapalan, M.

    2012-12-01

    Complex spatial and temporal variability can arise in the critical zone when feedbacks occur at multiple time scales between transported materials and the landscape and soils through which it is transported. This is clearly illustrated where geomorphic transport processes, soil development, and vegetation interact in semi-arid shrublands. Here we use soil and terrain data and a numerical model of overland flow on semi-arid hillslopes to show that microtopography can generate spatial variations in the dominance of transport processes operating at different timescales, with consequences for the direction of resource redistribution between functional units within these ecosystems. Conceptual and numerical models of the redistribution of mineral, organic and water have mostly been developed on low-gradient alluvial fans and pediments. These have focused on the fluvial transport of resources from the inter-spaces between shrub canopies to the areas below the canopy in those few storm events that generate significant run-off. These processes are believed to produce a mosaic of resource islands in which biota are concentrated. We investigated the spatial distribution of soil properties (including organic matter and soil hydraulic properties), vegetation, and microtopography on two steeper hillslopes of contrasting lithology (one granite, one schist) in the Sonoran desert foothills of the Catalina Mountains. Three hypotheses were developed through iteration between fieldwork and data analysis. These tested whether there were significant differences in soil composition and hydraulic properties below- and between-canopy, whether the surface soil organic matter was directly associated with above-ground biomass, and whether soil organic matter distributions measured along transects below shrubs showed downslope asymmetries indicative of the processes that create them. Data from these sites were used in a numerical model to investigate how these structures could be related to

  12. TonB-dependent transporters: regulation, structure, and function.

    Science.gov (United States)

    Noinaj, Nicholas; Guillier, Maude; Barnard, Travis J; Buchanan, Susan K

    2010-01-01

    TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that bind and transport ferric chelates, called siderophores, as well as vitamin B(12), nickel complexes, and carbohydrates. The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. The siderophore substrates range in complexity from simple small molecules such as citrate to large proteins such as serum transferrin and hemoglobin. Because iron uptake is vital for almost all bacteria, expression of TBDTs is regulated in a number of ways that include metal-dependent regulators, σ/anti-σ factor systems, small RNAs, and even a riboswitch. In recent years, many new structures of TBDTs have been solved in various states, resulting in a more complete understanding of siderophore selectivity and binding, signal transduction across the outer membrane, and interaction with the TonB-ExbB-ExbD complex. However, the transport mechanism is still unclear. In this review, we summarize recent progress in understanding regulation, structure, and function in TBDTs and questions remaining to be answered.

  13. Coherent structures and anomalous transport in reversed field pinch plasmas

    Science.gov (United States)

    Antoni, V.; Drake, J. R.; Spada, E.; Spolaore, M.; Vianello, N.; Bergsåker, H.; Cavazzana, R.; Cecconello, M.; Martines, E.; Serianni, G.

    2006-02-01

    The results leading to the identification of coherent structures emerging from the background turbulence in the edge region of the reversed field pinch experiments EXTRAP-T2R and RFX are reviewed. These structures have traits of vortices in velocity field and blobs in density, and the reconstruction of their spatial structure and of their time evolution is discussed focusing on the analysis tools applied. The role of these structures in the particle anomalous transport is addressed, showing that their collisions can contribute up to 50% the total particle losses.This process is shown to be responsible for bursts in particle flux and it is found to set a characteristic collision time, which is in agreement with the statistical properties of laminar times for particle flux bursts.

  14. Crystal structure of the CorA Mg2+ transporter.

    Science.gov (United States)

    Lunin, Vladimir V; Dobrovetsky, Elena; Khutoreskaya, Galina; Zhang, Rongguang; Joachimiak, Andrzej; Doyle, Declan A; Bochkarev, Alexey; Maguire, Michael E; Edwards, Aled M; Koth, Christopher M

    2006-04-06

    The magnesium ion, Mg2+, is essential for myriad biochemical processes and remains the only major biological ion whose transport mechanisms remain unknown. The CorA family of magnesium transporters is the primary Mg2+ uptake system of most prokaryotes and a functional homologue of the eukaryotic mitochondrial magnesium transporter. Here we determine crystal structures of the full-length Thermotoga maritima CorA in an apparent closed state and its isolated cytoplasmic domain at 3.9 A and 1.85 A resolution, respectively. The transporter is a funnel-shaped homopentamer with two transmembrane helices per monomer. The channel is formed by an inner group of five helices and putatively gated by bulky hydrophobic residues. The large cytoplasmic domain forms a funnel whose wide mouth points into the cell and whose walls are formed by five long helices that are extensions of the transmembrane helices. The cytoplasmic neck of the pore is surrounded, on the outside of the funnel, by a ring of highly conserved positively charged residues. Two negatively charged helices in the cytoplasmic domain extend back towards the membrane on the outside of the funnel and abut the ring of positive charge. An apparent Mg2+ ion was bound between monomers at a conserved site in the cytoplasmic domain, suggesting a mechanism to link gating of the pore to the intracellular concentration of Mg2+.

  15. Structure and Water Transport in Nafion Nanocomposite Membranes

    Science.gov (United States)

    Davis, Eric; Page, Kirt

    2014-03-01

    Perfluorinated ionomers, specifically Nafion, are the most widely used ion exchange membranes for vanadium redox flow battery applications, where an understanding of the relationship between membrane structure and transport of water/ions is critical to battery performance. In this study, the structure of Nafion/SiO2 nanocomposite membranes, synthesized using sol-gel chemistry, as well as cast directly from Nafion/SiO2 nanoparticle dispersions, was measured using both small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS). Through contrast match studies of the SiO2 nanoparticles, direct information on the change in the structure of the Nafion membranes and the ion-transport channels within was obtained, where differences in membrane structure was observed between the solution-cast membranes and the membranes synthesized using sol-gel chemistry. Additionally, water sorption and diffusion in these Nafion/SiO2 nanocomposite membranes were measured using in situ time-resolved Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy and dynamic vapor sorption (DVS).

  16. FLOW STRUCTURE AND SEDIMENT TRANSPORT WITH IMPACTS OF AQUATIC VEGETATION

    Institute of Scientific and Technical Information of China (English)

    LIU Cheng; SHEN Yong-ming

    2008-01-01

    Aquatic vegetation plays an important role in the flow structure of open channels and thus changes the fate and the transport of sediment. This article proposes a three-dimensional turbulence model by introducing vegetation density and drag force into the control equations of water flow in the presence of vegetation. The model was used to calculate the impacts of submerged vegetation on the vertical profiles of longitudinal flow velocities, the changes of the depth-averaged flow velocities in a compound channel with emergent vegetation in the floodplain, the removal of suspended sediment from the channels by emergent vegetation, and the bed changes around and in a vegetated island. Numerical investigations show that aquatic vegetation retards flow in the vegetation zone, reduces the sediment transport capacity, and contributes to erosion on both sides of the vegetated island. Calculated results agree well with experimental results.

  17. Structural and robustness properties of smart-city transportation networks

    Science.gov (United States)

    Zhang, Zhen-Gang; Ding, Zhuo; Fan, Jing-Fang; Meng, Jun; Ding, Yi-Min; Ye, Fang-Fu; Chen, Xiao-Song

    2015-09-01

    The concept of smart city gives an excellent resolution to construct and develop modern cities, and also demands infrastructure construction. How to build a safe, stable, and highly efficient public transportation system becomes an important topic in the process of city construction. In this work, we study the structural and robustness properties of transportation networks and their sub-networks. We introduce a complementary network model to study the relevance and complementarity between bus network and subway network. Our numerical results show that the mutual supplement of networks can improve the network robustness. This conclusion provides a theoretical basis for the construction of public traffic networks, and it also supports reasonable operation of managing smart cities. Project supported by the Major Projects of the China National Social Science Fund (Grant No. 11 & ZD154).

  18. Structural influences on quantum transport in InAs nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Frielinghaus, Robert; Sladek, Kamil; Trellenkamp, Stefan; Hardtdegen, Hilde; Schneider, Claus M.; Meyer, Carola [Peter Gruenberg Institut, Forschungszentrum Juelich (Germany); JARA - Fundamentals of Future Information Technology (Germany); Floehr, Kilian [II. Physikalisches Institut, RWTH Aachen University, 52074 Aachen (Germany); JARA - Fundamentals of Future Information Technology (Germany); Weirich, Thomas E. [Central Facility for Electron Microscopy GFE, RWTH Aachen University, 52074 Aachen (Germany); JARA - Fundamentals of Future Information Technology (Germany); Schaepers, Thomas [Peter Gruenberg Institut, Forschungszentrum Juelich (Germany); II. Physikalisches Institut, RWTH Aachen University, 52074 Aachen (Germany); JARA - Fundamentals of Future Information Technology (Germany)

    2012-07-01

    Self-assembled nanostructures such as InAs nanowires are candidates for future semiconductor nanoscale devices. However their atomic arrangement usually differs from device to device leading to fluctuations in the electrical properties as e.g. the electron phase coherence length. Using a special sample design we present quantum transport measurements together with transmission electron micrographs (TEM) taken from the same individual InAs nanowires. The as-grown nanowires are selectively placed on holes patterned in a TEM membrane. Low-temperature magnetotransport measurements of these suspended nanowires reveal universal conductance fluctuations that allow for the determination of the phase coherence length without any influence of the substrate. Variations in the transport behavior are correlated to the atomically resolved structure observed in TEM.

  19. Charge carrier transport properties in layer structured hexagonal boron nitride

    Directory of Open Access Journals (Sweden)

    T. C. Doan

    2014-10-01

    Full Text Available Due to its large in-plane thermal conductivity, high temperature and chemical stability, large energy band gap (˜ 6.4 eV, hexagonal boron nitride (hBN has emerged as an important material for applications in deep ultraviolet photonic devices. Among the members of the III-nitride material system, hBN is the least studied and understood. The study of the electrical transport properties of hBN is of utmost importance with a view to realizing practical device applications. Wafer-scale hBN epilayers have been successfully synthesized by metal organic chemical deposition and their electrical transport properties have been probed by variable temperature Hall effect measurements. The results demonstrate that undoped hBN is a semiconductor exhibiting weak p-type at high temperatures (> 700 °K. The measured acceptor energy level is about 0.68 eV above the valence band. In contrast to the electrical transport properties of traditional III-nitride wide bandgap semiconductors, the temperature dependence of the hole mobility in hBN can be described by the form of μ ∝ (T/T0−α with α = 3.02, satisfying the two-dimensional (2D carrier transport limit dominated by the polar optical phonon scattering. This behavior is a direct consequence of the fact that hBN is a layer structured material. The optical phonon energy deduced from the temperature dependence of the hole mobility is ħω = 192 meV (or 1546 cm-1, which is consistent with values previously obtained using other techniques. The present results extend our understanding of the charge carrier transport properties beyond the traditional III-nitride semiconductors.

  20. Structures, profile consistency, and transport scaling in electrostatic convection

    DEFF Research Database (Denmark)

    Bian, N.H.; Garcia, O.E.

    2005-01-01

    that for interchange modes, profile consistency is in fact due to mixing by persistent large-scale convective cells. This mechanism is not a turbulent diffusion, cannot occur in collisionless systems, and is the analog of the well-known laminar "magnetic flux expulsion" in magneiohydrodynamics. This expulsion process...... involves a "pinch" across closed streamlines and further results in the formation of pressure fingers along the-separatrix of the convective cells. By nature, these coherent structures are dissipative because the mixing process that leads to their formation relies on a finite amount of collisional...... diffusion. Numerical simulations of two-dimensional interchange modes confirm the role of laminar expulsion by convective cells, for profile consistency and structure formation. They also show that the fingerlike pressure structures ultimately control the rate of heat transport across the plasma layer...

  1. Basic materials and structures aspects for hypersonic transport vehicles (HTV)

    Science.gov (United States)

    Steinheil, E.; Uhse, W.

    A Mach 5 transport design is used to illustrate structural concepts and criteria for materials selections and also key technologies that must be followed in the areas of computational methods, materials and construction methods. Aside from the primary criteria of low weight, low costs, and conceivable risks, a number of additional requirements must be met, including stiffness and strength, corrosion resistance, durability, and a construction adequate for inspection, maintenance and repair. Current aircraft construction requirements are significantly extended for hypersonic vehicles. Additional consideration is given to long-duration temperature resistance of the airframe structure, the integration of large-volume cryogenic fuel tanks, computational tools, structural design, polymer matrix composites, and advanced manufacturing technologies.

  2. Structure of a eukaryotic SWEET transporter in a homotrimeric complex.

    Science.gov (United States)

    Tao, Yuyong; Cheung, Lily S; Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B; Feng, Liang

    2015-11-12

    Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as the dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter family (SSF; only in the animal kingdom), and SWEETs. SWEETs carry mono- and disaccharides across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion, phloem loading for long distance translocation, pollen nutrition, and seed filling. Plant SWEETs cause pathogen susceptibility possibly by sugar leakage from infected cells. The vacuolar Arabidopsis thaliana AtSWEET2 sequesters sugars in root vacuoles; loss-of-function mutants show increased susceptibility to Pythium infection. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice (Oryza sativa), consists of an asymmetrical pair of triple-helix bundles, connected by an inversion linker transmembrane helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first triple-helix bundle within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs are valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux.

  3. Atomistic modeling of phonon transport in turbostratic graphitic structures

    Science.gov (United States)

    Mao, Rui; Chen, Yifeng; Kim, Ki Wook

    2016-05-01

    Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated at the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10-10 K m2/W to 116 × 10-10 K m2/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.

  4. Evidence for a Homodimeric Structure of Human Monocarboxylate Transporter 8

    Science.gov (United States)

    Visser, W. Edward; Philp, Nancy J.; van Dijk, Thamar B.; Klootwijk, Wim; Friesema, Edith C. H.; Jansen, Jurgen; Beesley, Philip W.; Ianculescu, Alexandra G.; Visser, Theo J.

    2009-01-01

    The human monocarboxylate transporter 8 (hMCT8) protein mediates transport of thyroid hormone across the plasma membrane. Association of hMCT8 mutations with severe psychomotor retardation and disturbed thyroid hormone levels has established its physiological relevance, but little is still known about the basic properties of hMCT8. In this study we present evidence that hMCT8 does not form heterodimers with the ancillary proteins basigin, embigin, or neuroplastin, unlike other MCTs. In contrast, it is suggested that MCT8 exists as monomer and homodimer in transiently and stably transfected cells. Apparently hMCT8 forms stable dimers because the complex is resistant to denaturing conditions and dithiothreitol. Cotransfection of wild-type hMCT8 with a mutant lacking amino acids 267–360 resulted in formation of homo-and heterodimers of the variants, indicating that transmembrane domains 4–6 are not involved in the dimerization process. Furthermore, we explored the structural and functional role of the 10 Cys residues in hMCT8. All possible Cys>Ala mutants did not behave differently from wild-type hMCT8 in protein expression, cross-linking experiments with HgCl2 and transport function. Our findings indicate that individual Cys residues are not important for the function of hMCT8 or suggest that hMCT8 has other yet-undiscovered functions in which cysteines play an essential role. PMID:19797118

  5. Uncovering hierarchical data structure in single molecule transport

    Science.gov (United States)

    Wu, Ben H.; Ivie, Jeffrey A.; Johnson, Tyler K.; Monti, Oliver L. A.

    2017-03-01

    Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

  6. Transport in low-dimensional superconductor-semiconductor structures; Transport in niederdimensionalen Supraleiter-Halbleiter-Strukturen

    Energy Technology Data Exchange (ETDEWEB)

    Eroms, J.

    2003-07-01

    Transport in periodic superconductor-semiconductor structures was investigated in magnetic fields up to several Tesla. The experiments were made on highly mobile InAs/AlGaSb quantum pots in contact with dots or strips of sputtered Nb. The high contact quality permitted observations of the ballistic motion of Andreev-reflected particles. In Nb-filled antidote lattices, commensurability effects were observed to be suppressed. This can be explained in the context of a classic Kubo transport theory in which the trajectories of the charge carriers are chaotic but have no influence on the transport variables because of the Andreev reflection. Experiments provided several hints to induced superconductivity in InAs. This explains the magnetic field dependence of the Andreev reflection in dot and strip lattices; also, peaks were observed in differential characteristics of SNS contacts which cannot be explained alone by the energy gap in Nb. Measurement son strip lattices at high magnetic fields showed that transport in the quantum Hall regime takes place in boundary channels with electrons and Andreev-reflected holes. In case of very small magnetic fields, flux-periodic oscillations and reproducible resistance fluctuations occurred. (orig.) [German] Diese Arbeit befasst sich mit dem Transport in periodischen Supraleiter-Halbleiter-Strukturen bei Magnetfeldern bis zu mehreren Tesla. Die Experimente wurden an hochbeweglichen InAs/AlGaSb-Quantentoepfen in Kontakt mit Dots oder Streifen aus gesputtertem Niob durchgefuehrt. Die hohe Kontaktqualitaet erlaubte es, die ballistische Bewegung Andreev-reflektierter Teilchen zu studieren. In Niob-gefuellten Antidotgittern wurde eine Unterdrueckung von Kommensurabilitaetseffekten beobachtet. Sie laesst sich im Rahmen einer klassischen Kubo-Transporttheorie erklaeren. Die Trajektorien der Ladungstraeger sind dann zwar chaotisch, das hat wegen der Andreev-Reflexion aber keinen Einfluss auf die Transportgroessen. Die Experimente ergaben

  7. Coherent quantum transport features in carbon superlattice structures

    Science.gov (United States)

    McIntosh, R.; Henley, S. J.; Silva, S. R. P.; Bhattacharyya, S.

    2016-10-01

    Whilst resonant transmission is well understood and can be fully harnessed for crystalline superlattices, a complete picture has not yet emerged for disordered superlattices. It has proven difficult to tune resonant transmission in disordered diamond-like carbon (DLC) superlattices as conventional models are not equipped to incorporate significant structural disorder. In this work, we present concurrent experimental and theoretical analysis which addresses resonant transmission in DLC superlattices. Devices were fabricated by growing alternate layers of DLC with different percentages of sp3 hybridized carbon.Coherent quantum transport effects were demonstrated in these structurally disordered DLC superlattices through distinct current modulation with negative differential resistance (NDR) in the current-voltage (I-V) measurements. A model was developed using tight-binding calculations assuming a random variation of the hopping integral to simulate structural (bond-length) disorder. Calculations of the I-V characteristics compliment the interpretation of the measurements and illustrate that while DLC superlattice structures are unlike their classical counterparts, the near-field structural order will help with the confinement of quantised states. The present model provides an empirical guide for tailoring the properties of future devices, giving rise to much hope that carbon electronics operating at high frequencies over large areas can now be developed.

  8. Structure and permeation mechanism of a mammalian urea transporter

    Energy Technology Data Exchange (ETDEWEB)

    Levin, Elena J.; Cao, Yu; Enkavi, Giray; Quick, Matthias; Pan, Yaping; Tajkhorshid, Emad; Zhou, Ming (UIUC); (Columbia)

    2012-09-17

    As an adaptation to infrequent access to water, terrestrial mammals produce urine that is hyperosmotic to plasma. To prevent osmotic diuresis by the large quantity of urea generated by protein catabolism, the kidney epithelia contain facilitative urea transporters (UTs) that allow rapid equilibration between the urinary space and the hyperosmotic interstitium. Here we report the first X-ray crystal structure of a mammalian UT, UT-B, at a resolution of 2.36 {angstrom}. UT-B is a homotrimer and each protomer contains a urea conduction pore with a narrow selectivity filter. Structural analyses and molecular dynamics simulations showed that the selectivity filter has two urea binding sites separated by an approximately 5.0 kcal/mol energy barrier. Functional studies showed that the rate of urea conduction in UT-B is increased by hypoosmotic stress, and that the site of osmoregulation coincides with the location of the energy barrier.

  9. The structural basis of calcium transport by the calcium pump

    DEFF Research Database (Denmark)

    Olesen, Claus; Picard, Martin; Winther, Anne-Marie Lund

    2007-01-01

    The sarcoplasmic reticulum Ca2+-ATPase, a P-type ATPase, has a critical role in muscle function and metabolism. Here we present functional studies and three new crystal structures of the rabbit skeletal muscle Ca2+-ATPase, representing the phosphoenzyme intermediates associated with Ca2+ binding......, Ca2+ translocation and dephosphorylation, that are based on complexes with a functional ATP analogue, beryllium fluoride and aluminium fluoride, respectively. The structures complete the cycle of nucleotide binding and cation transport of Ca2+-ATPase. Phosphorylation of the enzyme triggers the onset...... of a conformational change that leads to the opening of a luminal exit pathway defined by the transmembrane segments M1 through M6, which represent the canonical membrane domain of P-type pumps. Ca2+ release is promoted by translocation of the M4 helix, exposing Glu 309, Glu 771 and Asn 796 to the lumen...

  10. Structural basis of transport of lysophospholipids by human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Shihui; Shi, Xiaoli; Yang, Feng; Chen, Liqing; Meehan, Edward J.; Bian, Chuanbing; Huang, Mingdong; (UAH); (Chinese Aca. Sci.)

    2010-10-08

    Lysophospholipids play important roles in cellular signal transduction and are implicated in many biological processes, including tumorigenesis, angiogenesis, immunity, atherosclerosis, arteriosclerosis, cancer and neuronal survival. The intracellular transport of lysophospholipids is through FA (fatty acid)-binding protein. Lysophospholipids are also found in the extracellular space. However, the transport mechanism of lysophospholipids in the extracellular space is unknown. HSA (human serum albumin) is the most abundant carrier protein in blood plasma and plays an important role in determining the absorption, distribution, metabolism and excretion of drugs. In the present study, LPE (lysophosphatidylethanolamine) was used as the ligand to analyse the interaction of lysophospholipids with HSA by fluorescence quenching and crystallography. Fluorescence measurement showed that LPE binds to HSA with a K{sub d} (dissociation constant) of 5.6 {micro}M. The presence of FA (myristate) decreases this binding affinity (K{sub d} of 12.9 {micro}M). Moreover, we determined the crystal structure of HSA in complex with both myristate and LPE and showed that LPE binds at Sudlow site I located in subdomain IIA. LPE occupies two of the three subsites in Sudlow site I, with the LPE acyl chain occupying the hydrophobic bottom of Sudlow site I and the polar head group located at Sudlow site I entrance region pointing to the solvent. This orientation of LPE in HSA suggests that HSA is capable of accommodating other lysophospholipids and phospholipids. The study provides structural information on HSA-lysophospholipid interaction and may facilitate our understanding of the transport and distribution of lysophospholipids.

  11. Structure, Ion Transport, and Rheology of Nanoparticle Salts

    KAUST Repository

    Wen, Yu Ho

    2014-07-08

    Above a critical surface chemistry-dependent particle loading associated with nanoscale interparticle spacing, ligand-ligand interactions-both electrostatic and steric-come into play and govern the structure and dynamics of charged oligomer-functionalized nanoparticle suspensions. We report in particular on the structure, ion transport, and rheology of suspensions of nanoparticle salts created by cofunctionalization of silica particles with tethered sulfonate salts and oligomers. Dispersion of the hairy ionic particles into medium and high dielectric constant liquids yields electrolytes with unique structure and transport properties. We find that electrostatic repulsion imparted by ion dissociation can be tuned to control the dispersion state and rheology through counterion size (i.e., Li+, Na+, and K+) and dielectric properties of the dispersing medium. Analysis of small-angle X-ray scattering (SAXS) structure factors and the mechanical modulus shows that when the interparticle spacing approaches nanometer dimensions, weakly entangled anchored ligands experience strong and long-lived topological constraints analogous to those normally found in well-entangled polymeric fluids. This finding provides insight into the molecular origins of the surprisingly similar rubbery plateau moduli observed in hairy nanoparticle suspensions and entangled polymers of the same chemistry as the tethered ligands. Additionally, we find that a time-composition superposition (TCS) principle exists for the suspensions, which can be used to substantially extend the observation time over which dynamics are observed in jammed, soft glassy suspensions. Application of TCS reveals dynamical similarities between the suspensions and entangled solutions of linear polymer chains; i.e., a hairy particle trapped in a cage appears to exhibit analogous dynamics to a long polymer chain confined to a tube. © 2014 American Chemical Society.

  12. Aging Evaluation Programs for Jet Transport Aircraft Structural Integrity

    Directory of Open Access Journals (Sweden)

    Borivoj Galović

    2012-10-01

    Full Text Available The paper deals with criteria and procedures in evaluationof timely preventive maintenance recommendations that willsupport continued safe operation of aging jet transports untiltheir retirement from service. The active service life of commercialaircraft has increased in recent years as a result of low fuelcost, and increasing costs and delivery times for fleet replacements.Air transport industry consensus is that older jet transportswill continue in service despite anticipated substantial increasesin required maintenance. Design concepts, supportedby testing, have worked well due to the system that is used to ensureflying safety. Continuing structural integrity by inspectionand overhaul recommendation above the level contained inmaintenance and service bulletins is additional requirement, insuch cases. Airplane structural safety depends on the performanceof all participants in the system and the responsibility forsafety cannot be delegated to a single participant. This systemhas three major participants: the manufacturers who design,build and support airplanes in service, the airlines who operate,inspect and mantain airplanes and the airworthiness authoritieswho establish rules and regulations, approve the design andpromote airline maintenance performance.

  13. Features of transport in ultrathin gold nanowire structures.

    Science.gov (United States)

    Pud, Sergii; Kisner, Alexandre; Heggen, Marc; Belaineh, Dagmawi; Temirov, Ruslan; Simon, Ulrich; Offenhäusser, Andreas; Mourzina, Yulia; Vitusevich, Svetlana

    2013-03-25

    The origin of the interface formation appearing due to the realization of contacts to ultrathin gold nanowire devices is revealed. Such interfaces play an important role in transport mechanisms in nanowire structures and can determine the electrical and operating parameters of a nanodevice. Based on experimental results, the specific electrical properties of bundles of ultrathin gold nanowires fabricated by wet chemical synthesis and subsequently assembled and contacted with gold electrodes are reported. It is demonstrated that these properties are strongly affected by the monolayers of organic molecules inevitably present on the surface of the nanowires due to synthetic conditions. In particular, such layers form a potential barrier to tunneling of the electrons from contacts to the nanowires. The electric transport behavior of the investigated nanowire structures in the temperature range from 500 mK to 300 K obeys the model of thermal fluctuation-induced tunneling conduction through the nanowire-metal electrode molecular junction. Application of this model allows calculation of the parameters of the molecular potential barrier. The formation of such a molecular barrier is verified by scanning tunneling microscope (STM) and transmission electron microscope (TEM) measurements performed using a supporting graphene layer. These findings are important for designing novel nanodevices for molecular electronics on the basis of ultrathin nanowires.

  14. The structure of glutamate transporters shows channel-like features

    NARCIS (Netherlands)

    Slotboom, DJ; Konings, WN; Lolkema, JS

    2001-01-01

    Neuronal and glial glutamate transporters remove the excitatory neurotransmitter glutamate from the synaptic cleft and thus prevent neurotoxicity, The proteins belong to a large family of secondary transporters, which includes transporters from a variety of bacterial, archaeal and eukaryotic organis

  15. Understanding transport by the major facilitator superfamily (MFS): structures pave the way.

    Science.gov (United States)

    Quistgaard, Esben M; Löw, Christian; Guettou, Fatma; Nordlund, Pär

    2016-02-01

    Members of the major facilitator superfamily (MFS) of transport proteins are essential for the movement of a wide range of substrates across biomembranes. As this transport requires a series of conformational changes, structures of MFS transporters captured in different conformational states are needed to decipher the transport mechanism. Recently, a large number of MFS transporter structures have been determined, which has provided us with an unprecedented opportunity to understand general aspects of the transport mechanism. We propose an updated model for the conformational cycle of MFS transporters, the 'clamp-and-switch model', and discuss the role of so-called 'gating residues' and the substrate in modulating these conformational changes.

  16. Structural and mechanistic insights into prokaryotic energy-coupling factor transporters

    NARCIS (Netherlands)

    Slotboom, Dirk J.

    2014-01-01

    Energy-coupling factor (ECF) transporters belong to the ATP-binding cassette (ABC)-transporter family and mediate the uptake of essential micronutrients in many prokaryotic species. Two crystal structures of bacterial ECF transporters have recently been obtained and suggest that transport involves

  17. Quaternary Structure and Functional Unit of Energy Coupling Factor (ECF)-type Transporters

    NARCIS (Netherlands)

    Beek, Josy ter; Duurkens, Ria H.; Erkens, Guus B.; Slotboom, Dirk Jan

    2011-01-01

    ATP-binding cassette (ABC) transporters mediate transport of diverse substrates across membranes. We have determined the quaternary structure and functional unit of the recently discovered ECF-type (energy coupling factor) of ABC transporters, which is widespread among prokaryotes. ECF transporters

  18. Electronic structure and transport in the low-temperature thermoelectric CsBi4Te6: Semiclassical transport equations

    DEFF Research Database (Denmark)

    Lykke, Lars; Iversen, Bo Brummerstedt; Madsen, Georg

    2006-01-01

    The band structure of the low-temperature thermoelectric material, CsBi4Te6, is calculated and analyzed using the semiclassic transport equations. It is shown that to obtain a quantitative agreement with measured transport properties, a band gap of 0.08 eV must be enforced. A gap in reasonable...

  19. Fluid transport due to nonlinear fluid-structure interaction

    Energy Technology Data Exchange (ETDEWEB)

    Soendergaard Jensen, J.

    1996-08-01

    This work considers nonlinear fluid-structure interaction for a vibrating pipe containing fluid. Transverse pipe vibrations will force the fluid to move relative to the pipe creating uni-directional fluid flow towards the pipe end. The fluid flow induced affects the damping and the stiffness of the pipe. The behavior of the system in response to lateral resonant base excitation is analyzed numerically mode of vibration seems to be most effective for high mean fluid speed, whereas higher modes of vibration can be used to transport fluid with the same fluid speed but with smaller magnitude of pipe vibrations. The effect of the nonlinear geometrical terms is analyzed and these terms are shown to affect the response for higher modes of vibration. Experimental investigations show good agreement with theoretical predictions. (au) 16 refs.

  20. Subgap transport in silicene-based superconducting hybrid structures

    Science.gov (United States)

    Li, Hai

    2016-08-01

    We investigate the influences of exchange field and perpendicular electric field on the subgap transport in silicene-based ferromagnetic/superconducting (FS) and ferromagnetic/superconducting/ferromagnetic (FSF) junctions. Owing to the unique buckling structure of silicene, the Andreev reflection and subgap conductance can be effectively modulated by a perpendicular electric field. It is revealed that the subgap conductance in the FS junction can be distinctly enhanced by an exchange field. Remarkably, resorting to the tunable band gap of silicene, an exclusive crossed Andreev reflection (CAR) process in the FSF junction can be realized within a wide range of related parameters. Moreover, in the FSF junction the exclusive CAR and exclusive elastic cotunneling processes can be switched by reversing the magnetization direction in one of the ferromagnetic regions.

  1. Fluid transport due to nonlinear fluid-structure interaction

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard

    1997-01-01

    This work considers nonlinear fluid-structure interaction for a vibrating pipe containing fluid. Transverse pipe vibrations will force the fluid to move relative to the pipe creating unidirectional fluid flow towards the pipe end. The fluid flow induced affects the damping and the stiffness...... of the pipe. The behavior of the system in response to lateral resonant base excitation is analysed numerically and by the use of a perturbation method (multiple scales). Exciting the pipe in the fundamental mode of vibration seems to be most effective for transferring energy from the shaker to the fluid......, whereas higher modes of vibration can be used to transport fluid with pipe vibrations of smaller amplitude. The effect of the nonlinear geometrical terms is analysed and these terms are shown to affect the response for higher modes of vibration. Experimental investigations show good agreement...

  2. Atomistic modeling of electronic structure and transport in disordered nanostructures

    Science.gov (United States)

    Kharche, Neerav

    As the Si-CMOS technology approaches the end of the International Technology Roadmap for Semiconductors (ITRS), the semiconductor industry faces a formidable challenge to continue the transistor scaling according to Moore's law. To continue the scaling of classical devices, alternative channel materials such as SiGe, carbon nanotubes, nanowires, and III-V based materials are being investigated along with novel 3D device geometries. Researchers are also investigating radically new quantum computing devices, which are expected to perform calculations faster than the existing classical Si-CMOS based structures. Atomic scale disorders such as interface roughness, alloy randomness, non-uniform strain, and dopant fluctuations are routinely present in the experimental realization of such devices. These disorders now play an increasingly important role in determining the electronic structure and transport properties as device sizes enter the nanometer regime. This work employs the atomistic tight-binding technique, which is ideally suited for modeling systems with local disorders on an atomic scale. High-precision multi-million atom electronic structure calculations of (111) Si surface quantum wells and (100) SiGe/Si/SiGe heterostructure quantum wells are performed to investigate the modulation of valley splitting induced by atomic scale disorders. The calculations presented here resolve the existing discrepancies between theoretically predicted and experimentally measured valley splitting, which is an important design parameter in quantum computing devices. Supercell calculations and the zone-unfolding method are used to compute the bandstructures of inhomogeneous nanowires made of AlGaAs and SiGe and their connection with the transmission coefficients computed using non-equilibrium Green's function method is established. A unified picture of alloy nanowires emerges, in which the nanodevice (transmission) and nanomaterials (bandstructure) viewpoints complement each other

  3. Multidrug transporters from bacteria to man : similarities in structure and function

    NARCIS (Netherlands)

    van Veen, HW; Konings, WN

    1997-01-01

    Organisms ranging from bacteria to man possess transmembrane transporters which confer resistance to toxic corn pounds. Underlining their biological significance, prokaryotic and eukaryotic multidrug transport proteins are very similar in structure and function. Therefore, a study of the factors whi

  4. Multidrug transporters from bacteria to man : similarities in structure and function

    NARCIS (Netherlands)

    van Veen, HW; Konings, WN

    Organisms ranging from bacteria to man possess transmembrane transporters which confer resistance to toxic corn pounds. Underlining their biological significance, prokaryotic and eukaryotic multidrug transport proteins are very similar in structure and function. Therefore, a study of the factors

  5. COMPARISON OF SUSTAINABILITY BETWEEN PRIVATE AND PUBLIC TRANSPORT CONSIDERING URBAN STRUCTURE

    Directory of Open Access Journals (Sweden)

    Masanobu KII

    2003-01-01

    In this paper, we present the interaction between urban structure and transport using a simple urban-transport model. We also examine the sustain ability, measured by economic efficiency and environmental impact, of private and public transport in a hypothetical urban space. In this regard, it is specially focused on the path dependence of urban-transport interactions, and showed the possibility of multiple urban and transport situations. Several policy implications are proposed for utilizing the results of the models.

  6. Inventory theory, mode choice and network structure in freight transport

    NARCIS (Netherlands)

    Combes, F.; Tavasszy, L.A.

    2016-01-01

    In passenger transport, hub-and-spoke networks allow the transportation of small passenger flows with competitive frequencies, in a way that direct line networks cannot. Equivalently, in freight transport, it can be expected that small shipper-receiver flows of high added value commodities transit t

  7. Light transport and lasing in complex photonic structures

    Science.gov (United States)

    Liew, Seng Fatt

    theoretical modeling and analysis explains why single scattering of light is dominant over multiple scattering in similar biological structures and is responsible for color generation. In collaboration with evolutionary biologists, we examine how closely-related species and populations of butterflies have evolved their structural color. We have used artificial selection on a lab model butterfly to evolve violet color from an ultra-violet brown color. The same coloration mechanism is found in other blue/violet species that have evolved their color in nature, which implies the same evolution path for their nanostructure. While the absorption of light is ubiquitous in nature and in applications, the question remains how absorption modifies the transmission in random media. Therefore, we numerically study the effects of optical absorption on the highest transmission states in a two-dimensional disordered waveguide. Our results show that strong absorption turns the highest transmission channel in random media from diffusive to ballistic-like transport. Finally, we have demonstrated lasing mode selection in a nearly circular semiconductor microdisk laser by shaping the spatial profile of the pump beam. Despite of strong mode overlap, selective pumping suppresses the competing lasing modes by either increasing their thresholds or reducing their power slopes. As a result, we can switch both the lasing frequency and the output direction. This powerful technique can have potential application as an on-chip tunable light source.

  8. BOOK REVIEW: Transport and Structural Formation in Plasmas

    Science.gov (United States)

    Thyagaraja, A.

    1999-06-01

    The book under review is one of a series of monographs on plasma physics published by the Institute of Physics under the editorship of Peter Stott and Hans Wilhelmsson. It is nicely produced and is aimed at research workers and advanced students of both laboratory (i.e. tokamak plasmas) and astrophysical plasma physics. The authors are prolific contributors to the subject of plasma turbulence and transport with a well-defined message: ``The authors' view is that the plasma structure, fluctuations and turbulent transport are continually regulating each other and, in addition, that the structural formation and structural transition of plasmas are typical of the physics of far from equilibrium systems. The book presents and explains why the plasma inhomogeneity is the ordering parameter governing transport and how self-sustained fluctuations can be driven through subcritical excitation even beyond linear instability''. This point of view is expounded in 24 chapters, including topics such as transport phenomena in toroidal plasmas (Chapters 2-4), low frequency modes and instabilities of confined systems (Chapters 5-7), renormalization (Chapter 8), self-sustained turbulence due to the current diffusive mode and resistive effects (Chapters 9-11), subcritical turbulence and numerical simulations (Chapters 12-14), scale invariance arguments (Chapter 15), electric field effects (Chapters 17-21) and self-organized dynamics (Chapter 22). The material is essentially drawn from the authors' many and varied original contributions to the plasma turbulence and transport literature. Whatever view one might have about the merits of this work, there is little doubt in this reviewer's mind that it is indeed thought-provoking and presents a worthy intellectual challenge to plasma theorists and experimentalists alike. The authors take a consistent stance and discuss the issues from their own standpoint. They observe that the plasmas one encounters in practice (for definiteness, the

  9. Crystal Structure of a Potassium Ion Transporter TrkH

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; H Huang; M Getahun Derebe; E Levin; V Kabaleeswaran; Y Pan; M Punta; J Love; et al.

    2011-12-31

    The TrkH/TrkG/KtrB proteins mediate K{sup +} uptake in bacteria and probably evolved from simple K{sup +} channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K{sup +} channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K{sup +} and Rb{sup +} over smaller ions such as Na{sup +} or Li{sup +}. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K{sup +} flux. These results reveal the molecular basis of K{sup +} selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

  10. Structure and transport studies on nanometer YBCO/PBCGO multilayers

    Institute of Scientific and Technical Information of China (English)

    CHEN Tar-Pin; WU Ke; LI Qi; CHEN Ben; WANG ShonZeng; KANDEL Hom; SOO YuChong; TIPPARACH Udom; CUI JingBiao; SEO HyeWon; CHEN ChiJen

    2009-01-01

    We have fabricated M doped (M = Al,Co,Fe,Ga,Ni and Zn) PrBa2Cu3O7(PBCO),i.e.PrBa2(CU1-xMx)3O7.The doping levels×are 0.05,0.10,0.15,and 0.20.X-ray data indicated no significant second phase for substituting Cu by Al,Co,Fe and Ga up to 20%.However impurity phases were detected for Ni and Zn substituted samples with doping levels equal to and higher than 15%.At 77 K the electrical resistivity of these compounds is orders in magnitude higher than that of PBCO.We also found that although the lattice parameters in the doped samples differ from PBCO,all samples remain orthorhombic.The lattice parameters of the doped sample are very close to those of YBa2Cu3O7-δ (YBCO) and PBCO.For this reason these compounds are better materials to be used as the I-layer for YBCO SiS junctions.Results of structural and transport studies on 2000 (A) thick PrBa2[Cu0.80G0.2]3O7 (PBCGO) and YBCO/PBCGO muItilayers are presented in this paper.

  11. An Improved Racetrack Structure for Transporting a Skyrmion

    Science.gov (United States)

    Lai, P.; Zhao, G. P.; Tang, H.; Ran, N.; Wu, S. Q.; Xia, J.; Zhang, X.; Zhou, Y.

    2017-03-01

    Magnetic skyrmions are promising building blocks for next generation data storage due to their stability, small size and extremely low currents to drive them, which can be used instead of traditional magnetic domain walls to store information as data bits in metalic racetrack memories. However, skyrmions can drift from the direction of electron flow due to the Magnus force and thus may annihilate at the racetrack edges, resulting in the loss of information. Here we propose a new skyrmion-based racetrack structure by adding high-K materials (materials with high magnetic crystalline anisotropy) at the edges, which confines the skyrmions in the center region of the metalic racetrack efficiently. This design can overcome both the clogging and annihilation of skyrmions according to our micromagnetic simulation, which occur normally for skyrmions moving on a racetrack under small and large driving currents, respectively. Phase diagrams for skyrmion motion on the proposed racetrack with various values of current density and racetrack edge width have been calculated and given, showing that skyrmions can be driven at a high speed (about 300 m/s) in the racetrack under relatively smaller driving currents. This design offers the possiblity of building an ultrafast and energy-efficient skyrmion transport device.

  12. An Improved Racetrack Structure for Transporting a Skyrmion

    Science.gov (United States)

    Lai, P.; Zhao, G. P.; Tang, H.; Ran, N.; Wu, S. Q.; Xia, J.; Zhang, X.; Zhou, Y.

    2017-01-01

    Magnetic skyrmions are promising building blocks for next generation data storage due to their stability, small size and extremely low currents to drive them, which can be used instead of traditional magnetic domain walls to store information as data bits in metalic racetrack memories. However, skyrmions can drift from the direction of electron flow due to the Magnus force and thus may annihilate at the racetrack edges, resulting in the loss of information. Here we propose a new skyrmion-based racetrack structure by adding high-K materials (materials with high magnetic crystalline anisotropy) at the edges, which confines the skyrmions in the center region of the metalic racetrack efficiently. This design can overcome both the clogging and annihilation of skyrmions according to our micromagnetic simulation, which occur normally for skyrmions moving on a racetrack under small and large driving currents, respectively. Phase diagrams for skyrmion motion on the proposed racetrack with various values of current density and racetrack edge width have been calculated and given, showing that skyrmions can be driven at a high speed (about 300 m/s) in the racetrack under relatively smaller driving currents. This design offers the possiblity of building an ultrafast and energy-efficient skyrmion transport device. PMID:28358009

  13. Structural and transport properties of directly assembled nanowires

    Science.gov (United States)

    Ozturk, Birol

    Scope and method of study. In this work, we present a systematic study on the assembly and characterization of nanostructures. We employed self and directed assembly methods in order to organize nanostructures. Quantitative film balance studies of self-assembled semiconductor nanoparticles enabled the determination of their effective interparticle potential. As a directed-assembly method, dielectrophoresis was used in the fabrication of interconnects from dispersions of nanostructures between targeted points in external circuitry. Directed electrochemical nanowire assembly (DENA) was developed and used in the fabrication of metallic nanowires from simple salt solutions. The structural and charge transport properties of the assembled nanostructures and the DENA-grown nanowires were characterized. Findings and conclusions. The CdSe nanoparticles of a given diameter were found to behave like hard-disks with significantly smaller diameters. This behavior was attributed to an attractive contribution to the interparticle potential, such as the dipolar potential. We found that nanoparticulate CdS converts to bulk CdS during dielectrophoretic interconnect fabrication. We demonstrated that the dielectrophoretic interconnects fabricated from gold nanorods are nanostructured, limiting their conductivity. DENA technique enabled the single-step growth and low-resistance interconnecting of crystalline diameter-tunable metallic nanowires. The preliminary results of the diameter-dependent resistivity studies with the DENA-grown gold nanowires were consistent with the predicted behavior.

  14. The dominant role of structure for solute transport in soil: experimental evidence and modelling of structure and transport in a field experiment

    Directory of Open Access Journals (Sweden)

    H.-J. Vogel

    2006-01-01

    Full Text Available A classical transport experiment was performed in a field plot of 2.5 m2 using the dye tracer brilliant blue. The measured tracer distribution demonstrates the dominant role of the heterogeneous soil structure for solute transport. As with many other published experiments, this evidences the need of considering the macroscopic structure of soil to predict flow and transport. We combine three different approaches to represent the relevant structure of the specific situation of our experiment: i direct measurement, ii statistical description of heterogeneities and iii a conceptual model of structure formation. The structure of soil layers was directly obtained from serial sections in the field. The sub-scale heterogeneity within the soil horizons was modelled through correlated random fields with estimated correlation lengths and anisotropy. Earthworm burrows played a dominant role at the transition between the upper soil horizon and the subsoil. A model based on percolation theory is introduced that mimics the geometry of earthworm burrow systems. The hydraulic material properties of the different structural units were obtained by direct measurements where available and by a best estimate otherwise. From the hydraulic structure, the 3-dimensional velocity field of water was calculated by solving Richards' Equation and solute transport was simulated. The simulated tracer distribution compares reasonably well with the experimental data. We conclude that a rough representation of the structure and a rough representation of the hydraulic properties might be sufficient to predict flow and transport, but both elements are definitely required.

  15. Spin transport in lateral structures with semiconducting channel

    Science.gov (United States)

    Zainuddin, Abu Naser

    Spintronics is an emerging field of electronics with the potential to be used in future integrated circuits. Spintronic devices are already making their mark in storage technologies in recent times and there are proposals for using spintronic effects in logic technologies as well. So far, major improvement in spintronic effects, for example, the `spin-valve' effect, is being achieved in metals or insulators as channel materials. But not much progress is made in semiconductors owing to the difficulty in injecting spins into them, which has only very recently been overcome with the combined efforts of many research groups around the world. The key motivations for semiconductor spintronics are their ease in integration with the existing semiconductor technology along with the gate controllability. At present semiconductor based spintronic devices are mostly lateral and are showing a very poor performance compared to their metal or insulator based vertical counterparts. The objective of this thesis is to analyze these devices based on spin-transport models and simulations. At first a lateral spin-valve device is modeled with the spin-diffusion equation based semiclassical approach. Identifying the important issues regarding the device performance, a compact circuit equivalent model is presented which would help to improve the device design. It is found that the regions outside the current path also have a significant influence on the device performance under certain conditions, which is ordinarily neglected when only charge transport is considered. Next, a modified spin-valve structure is studied where the spin signal is controlled with a gate in between the injecting and detecting contacts. The gate is used to modulate the rashba spin-orbit coupling of the channel which, in turn, modulates the spin-valve signal. The idea of gate controlled spin manipulation was originally proposed by Datta and Das back in 1990 and is called 'Datta-Das' effect. In this thesis, we have

  16. Structure-function analysis of multidrug transporters in Lactococcus lactis

    NARCIS (Netherlands)

    van Veen, HW; Putman, M; Margolles, A; Sakamoto, K; Konings, WN

    1999-01-01

    The active extrusion of cytotoxic compounds from the cell by multidrug transporters is one of the major causes of failure of chemotherapeutic treatment of tumor cells and of infections by pathogenic microorganisms. A multidrug transporter in Lactococcus lactis, LmrA, is a member of the ATP-binding c

  17. High Energy Density Nastic Structures Using Biological Transport Mechanisms

    Science.gov (United States)

    2007-02-28

    occur at the cell wall and membranes of inter-cellular organelles to transport nutrients in the plant. The concentration of ions from the active and...pp. 459–467. [6] dos Santos, A. C., da Silva, W. S., de Meis, L., and Galina, A., “Proton Transport in Maize Tonoplasts Supported by Fructose-1,6

  18. Structural Properties of the Brazilian Air Transportation Network.

    Science.gov (United States)

    Couto, Guilherme S; da Silva, Ana Paula Couto; Ruiz, Linnyer B; Benevenuto, Fabrício

    2015-09-01

    The air transportation network in a country has a great impact on the local, national and global economy. In this paper, we analyze the air transportation network in Brazil with complex network features to better understand its characteristics. In our analysis, we built networks composed either by national or by international flights. We also consider the network when both types of flights are put together. Interesting conclusions emerge from our analysis. For instance, Viracopos Airport (Campinas City) is the most central and connected airport on the national flights network. Any operational problem in this airport separates the Brazilian national network into six distinct subnetworks. Moreover, the Brazilian air transportation network exhibits small world characteristics and national connections network follows a power law distribution. Therefore, our analysis sheds light on the current Brazilian air transportation infrastructure, bringing a novel understanding that may help face the recent fast growth in the usage of the Brazilian transport network.

  19. Structure and mechanism of a Na+-independent amino acid transporter.

    Science.gov (United States)

    Shaffer, Paul L; Goehring, April; Shankaranarayanan, Aruna; Gouaux, Eric

    2009-08-21

    Amino acid, polyamine, and organocation (APC) transporters are secondary transporters that play essential roles in nutrient uptake, neurotransmitter recycling, ionic homeostasis, and regulation of cell volume. Here, we present the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 angstrom resolution. The structure contains 12 transmembrane helices, with the first 10 consisting of an inverted structural repeat of 5 transmembrane helices like the leucine transporter LeuT. The ApcT structure reveals an inward-facing, apo state and an amine moiety of lysine-158 located in a position equivalent to the sodium ion site Na2 of LeuT. We propose that lysine-158 is central to proton-coupled transport and that the amine group serves the same functional role as the Na2 ion in LeuT, thus demonstrating common principles among proton- and sodium-coupled transporters.

  20. VvGONST-A and VvGONST-B are Golgi-localised GDP-sugar transporters in grapevine (Vitis vinifera L.).

    Science.gov (United States)

    Utz, Daniella; Handford, Michael

    2015-02-01

    Plant nucleotide-sugar transporters (NSTs) are responsible for the import of nucleotide-sugar substrates into the Golgi lumen, for subsequent use in glycosylation reactions. NSTs are specific for either GDP- or UDP-sugars, and almost all transporters studied to date have been isolated from Arabidopsis thaliana L. In order to determine the conservation of the import mechanism in other higher plant species, here we report the identification and characterisation of VvGONST-A and VvGONST-B from grapevine (Vitis vinifera L. cv. Thompson Seedless), which are the orthologues of the GDP-sugar transporters GONST3 and GONST4 in Arabidopsis. Both grapevine NSTs possess the molecular features characteristic of GDP-sugar transporters, including a GDP-binding domain (GXL/VNK) towards the C-terminal. VvGONST-A and VvGONST-B expression is highest at berry setting and decreases throughout berry development and ripening. Moreover, we show using green fluorescent protein (GFP) tagged versions and brefeldin A treatments, that both are localised in the Golgi apparatus. Additionally, in vitro transport assays after expression of both NSTs in tobacco leaves indicate that VvGONST-A and VvGONST-B are capable of transporting GDP-mannose and GDP-glucose, respectively, but not a range of other UDP- and GDP-sugars. The possible functions of these NSTs in glucomannan synthesis and/or glycosylation of sphingolipids are discussed. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters

    DEFF Research Database (Denmark)

    Lyons, Joseph A.; Parker, Joanne L.; Solcan, Nicolae

    2014-01-01

    An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di‐ and tripeptide‐bound complexes of a bacterial homologue of PepT1, which reveal at leas...

  2. Opportunity Structure for Gambling and Problem Gambling among Employees in the Transport Industry

    Science.gov (United States)

    Revheim, Tevje; Buvik, Kristin

    2009-01-01

    Working conditions for employees in the transport sector might present an opportunity structure for gambling by providing access to gambling during the workday. This study investigates connections between opportunity structure, gambling during the workday, and gambling problems among employees in the transport sector. Data has been collected from…

  3. Structure and function of thyroid hormone plasma membrane transporters.

    Science.gov (United States)

    Schweizer, Ulrich; Johannes, Jörg; Bayer, Dorothea; Braun, Doreen

    2014-09-01

    Thyroid hormones (TH) cross the plasma membrane with the help of transporter proteins. As charged amino acid derivatives, TH cannot simply diffuse across a lipid bilayer membrane, despite their notorious hydrophobicity. The identification of monocarboxylate transporter 8 (MCT8, SLC16A2) as a specific and very active TH transporter paved the way to the finding that mutations in the MCT8 gene cause a syndrome of psychomotor retardation in humans. The purpose of this review is to introduce the current model of transmembrane transport and highlight the diversity of TH transmembrane transporters. The interactions of TH with plasma transfer proteins, T3 receptors, and deiodinase are summarized. It is shown that proteins may bind TH owing to their hydrophobic character in hydrophobic cavities and/or by specific polar interaction with the phenolic hydroxyl, the aminopropionic acid moiety, and by weak polar interactions with the iodine atoms. These findings are compared with our understanding of how TH transporters interact with substrate. The presumed effects of mutations in MCT8 on protein folding and transport function are explained in light of the available homology model.

  4. Transportation of Floating Structures by Using Newly Built Heavy Lifting Semi Vessel HYSY278

    Institute of Scientific and Technical Information of China (English)

    SUN Wei-ying; ZHANG Da-gang; FAN Zhi-xia

    2013-01-01

    Transportation of floating structures for long distance has always been associated with the use of heavy semi transport vessel.The requirements of this type of vessel are always special,and its availability is limited.To prepare for the future development of the South China Sea deepwater projects,COOEC has recently built a heavy lift transport vessel-Hai Yang Shi You 278 (HYSY278).This semi-submersible vessel has displacement capacity of 50k DWT,and a breath of 42 m.Understanding the vessel's applicability and preparing its use for future deepwater projects are becoming imminent need.This paper reviews the critical issues associated with the floating structure transportation and performs detailed analysis of two designed floating structures during transportation.The newly built COOEC transportation vessel HYSY278 will be used to dry transport the floating structures from COOEC fabrication yard in Qingdao to the oil field in the South China Sea.The entire process will start with load-out/float-offthe floating structures from the construction sites,offload the platform from the vessel if needed,dry transport floating structures through a long distance,and finally offload the platform.Both hydrodynamic and structural analyses are performed to evaluate transport vessel and floating structures.Critical issues associated with the transportation and offloading of platform from the vessel will be studied in detail.Detailed study is performed to evaluate the response of the system during this phase and additional work needed to make the vessel feasible for use of this purpose.The results demonstrate that with proper modifications,HYSY278 can effectively be used for transporting structures with proper arrangement and well-prepared operation.The procedure and details are presented on the basis of study results.Special attentions associated with future use will also be discussed based on the results from analysis.

  5. Density-Based and Transport-Based Core-Periphery Structures in Networks

    CERN Document Server

    Lee, Sang Hoon; Porter, Mason A

    2013-01-01

    Networks often possess mesoscale structures, and studying them can yield insights into both structure and function. It is most common to study community structure, but numerous other types of mesoscale structures also exist. In this paper, we examine core-periphery structures based on both density and transportation. In such structures, core network components are well-connected both among themselves and to peripheral components, which are not well-connected to anything. We examine core-periphery structures in a wide range of examples of transportation, social, and financial networks---including road networks in large urban areas, a rabbit warren, a dolphin social network, a European interbank network, and a migration network between counties in the United States. We illustrate that a recently developed transport-based notion of node coreness is very useful for characterizing transportation networks. We also generalize this notion to examine core versus peripheral edges, and we show that this new diagnostic i...

  6. Intracellular transport proteins: classification, structure and function of kinesins

    Directory of Open Access Journals (Sweden)

    Agnieszka Chudy

    2011-09-01

    Full Text Available Correct cell functioning, division and morphogenesis rely on efficient intracellular transport. Apart from dyneins and myosins, kinesins are the main proteins responsible for intracellular movement. Kinesins are a large, diverse group of motor proteins, which based on phylogenetic similarity were classified into fourteen families. Among these families, due to the location of their motor domains, three groups have been characterized: N-, C- and M-kinesin. As molecular motors, kinesins transport various molecules and vesicles mainly towards the microtubule plus end (from the cell body participating in anterograde transport, although there are also kinesins involved in retrograde transport (C-kinesins. Kinesins are also involved in spindle formation, chromosome segregation, and spermatogenesis. Because of their great importance for the correct functioning of cells, mutations in kinesin coding genes may lead to such neurodegenerative diseases as dominant hereditary spastic paraplegia or Charcot-Marie-Tooth disease.

  7. Structure and mechanism of ATP-dependent phospholipid transporters

    DEFF Research Database (Denmark)

    Lopez Marques, Rosa Laura; Poulsen, Lisbeth Rosager; Bailly, Aurélien

    2015-01-01

    Background ATP-binding cassette (ABC) transporters and P4-ATPases are two large and seemingly unrelated families of primary active pumps involved in moving phospholipids from one leaflet of a biological membrane to the other. Scope of review This review aims to identify common mechanistic features...... in the way phospholipid flipping is carried out by two evolutionarily unrelated families of transporters. Major conclusions Both protein families hydrolyze ATP, although they employ different mechanisms to use it, and have a comparable size with twelve transmembrane segments in the functional unit. Further......, despite differences in overall architecture, both appear to operate by an alternating access mechanism and during transport they might allow access of phospholipids to the internal part of the transmembrane domain. The latter feature is obvious for ABC transporters, but phospholipids and other hydrophobic...

  8. Structural and Thermal Safety Analysis Report for the Type B Radioactive Waste Transport Package

    Energy Technology Data Exchange (ETDEWEB)

    Kim, D. H.; Seo, K. S.; Lee, J. C.; Bang, K. S

    2007-09-15

    We carried out structural safety evaluation for the type B radioactive waste transport package. Requirements for type B packages according to the related regulations such as IAEA Safety Standard Series No. TS-R-1, Korea Most Act. 2001-23 and US 10 CFR Part 71 were evaluated. General requirements for packages such as those for a lifting attachment, a tie-down attachment and pressure condition were considered. For the type B radioactive waste transport package, the structural, thermal and containment analyses were carried out under the normal transport conditions. Also the safety analysis were conducted under the accidental transport conditions. The 9 m drop test, 1 m puncture test, fire test and water immersion test under the accidental transport conditions were consecutively done. The type B radioactive waste transport packages were maintained the structural and thermal integrities.

  9. Magnetic resonance imaging of mass transport and structure inside a phototrophic biofilm.

    Science.gov (United States)

    Ramanan, Baheerathan; Holmes, William M; Sloan, William T; Phoenix, Vernon R

    2013-05-01

    The aim of this study was to utilize magnetic resonance imaging (MRI) to image structural heterogeneity and mass transport inside a biofilm which was too thick for photon based imaging. MRI was used to map water diffusion and image the transport of the paramagnetically tagged macromolecule, Gd-DTPA, inside a 2.5 mm thick cyanobacterial biofilm. The structural heterogeneity of the biofilm was imaged at resolutions down to 22 × 22 μm, enabling the impact of biofilm architecture on the mass transport of both water and Gd-DTPA to be investigated. Higher density areas of the biofilm correlated with areas exhibiting lower relative water diffusion coefficients and slower transport of Gd-DTPA, highlighting the impact of biofilm structure on mass transport phenomena. This approach has potential for shedding light on heterogeneous mass transport of a range of molecular mass molecules in biofilms.

  10. Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4;#8201;Å

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Zachary Lee; Cheong, Cheom-Gil; Lee, Seok-Yong (Duke)

    2012-07-11

    Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes. A wide range of nucleoside-derived drugs, including anticancer drugs (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 {angstrom}. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.

  11. The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.

    Science.gov (United States)

    McCoy, Jason G; Ren, Zhenning; Stanevich, Vitali; Lee, Jumin; Mitra, Sharmistha; Levin, Elena J; Poget, Sebastien; Quick, Matthias; Im, Wonpil; Zhou, Ming

    2016-06-07

    The phosphoenolpyruvate:carbohydrate phosphotransferase systems are found in bacteria, where they play central roles in sugar uptake and regulation of cellular uptake processes. Little is known about how the membrane-embedded components (EIICs) selectively mediate the passage of carbohydrates across the membrane. Here we report the functional characterization and 2.55-Å resolution structure of a maltose transporter, bcMalT, belonging to the glucose superfamily of EIIC transporters. bcMalT crystallized in an outward-facing occluded conformation, in contrast to the structure of another glucose superfamily EIIC, bcChbC, which crystallized in an inward-facing occluded conformation. The structures differ in the position of a structurally conserved substrate-binding domain that is suggested to play a central role in sugar transport. In addition, molecular dynamics simulations suggest a potential pathway for substrate entry from the periplasm into the bcMalT substrate-binding site. These results provide a mechanistic framework for understanding substrate recognition and translocation for the glucose superfamily EIIC transporters.

  12. Structure-dependent water transport across nanopores of carbon nanotubes: toward selective gating upon temperature regulation.

    Science.gov (United States)

    Zhao, Kuiwen; Wu, Huiying

    2015-04-28

    Determining water structure in nanopores and its influence on water transport behaviour is of great importance for understanding and regulating the transport across nanopores. Here we report an ultrafast-slow flow transition phenomenon for water transport across nanopores of carbon nanotubes owing to the change in water structure in nanopores induced by temperature. By performing extensive molecular dynamics simulations, we show the dependence of water transport behaviours on water structures. Our results indicate that owing to the change in water structure in nanopores, water flux across nanopores with certain pore sizes decreases sharply (nearly 3 orders of magnitude) with the decreasing temperature. This phenomenon is very sensitive to the pore size. The threshold temperatures for the occurrence of the ultrafast-slow flow transition for water transport are also determined for various pore sizes. These findings suggest a novel protocol for selective gating of water and proton conduction across nanopores and temperature-controlled drug release.

  13. Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus.

    Science.gov (United States)

    Manjula, M; Pampa, K J; Kumar, S M; Mukherjee, S; Kunishima, N; Rangappa, K S; Lokanath, N K

    2015-03-27

    The ATP binding cassette (ABC) transporters, represent one of the largest superfamilies of primary transporters, which are very essential for various biological functions. The crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus has been determined at 1.77 Å resolution. The crystal structure revealed that the protomer has two thick arms, (arm I and II), which resemble 'L' shape. The ATP-binding pocket is located close to the end of arm I. ATP molecule is docked into the active site of the protein. The dimeric crystal structure of ATP-binding subunit of ABC transporter from G. kaustophilus has been compared with the previously reported crystal structure of ATP-binding subunit of ABC transporter from Salmonella typhimurium.

  14. Short- and Long- Time Transport Structures in a Three Dimensional Time Dependent Flow

    CERN Document Server

    Chabreyrie, Rodolphe

    2014-01-01

    Lagrangian transport structures for three-dimensional and time-dependent fluid flows are of great interest in numerous applications, particularly for geophysical or oceanic flows. In such flows, chaotic transport and mixing can play important environmental and ecological roles, for examples in pollution spills or plankton migration. In such flows, where simulations or observations are typically available only over a short time, understanding the difference between short-time and long-time transport structures is critical. In this paper, we use a set of classical (i.e. Poincar\\'e section, Lyapunov exponent) and alternative (i.e. finite time Lyapunov exponent, Lagrangian coherent structures) tools from dynamical systems theory that analyze chaotic transport both qualitatively and quantitatively. With this set of tools we are able to reveal, identify and highlight differences between short- and long-time transport structures inside a flow composed of a primary horizontal contra-rotating vortex chain, small later...

  15. Gulf Stream density structure and transport during the past millennium

    OpenAIRE

    Lund, David C.; Lynch-Stieglitz, Jean; Curry, William B.

    2006-01-01

    The Gulf Stream transports approximately 31 Sv (1 Sv = 10^6 m^3 s^(-1)) of water and 1.3 10^(15) W of heat into the North Atlantic ocean. The possibility of abrupt changes in Gulf Stream heat transport is one of the key uncertainties in predictions of climate change for the coming centuries. Given the limited length of the instrumental record, our knowledge of Gulf Stream behaviour on long timescales must rely heavily on information from geologic archives. Here we use foraminifera from a su...

  16. Spatiotemporal Structure of Aeolian Particle Transport on Flat Surface

    Science.gov (United States)

    Niiya, Hirofumi; Nishimura, Kouichi

    2017-05-01

    We conduct numerical simulations based on a model of blowing snow to reveal the long-term properties and equilibrium state of aeolian particle transport from 10-5 to 10 m above the flat surface. The numerical results are as follows. (i) Time-series data of particle transport are divided into development, relaxation, and equilibrium phases, which are formed by rapid wind response below 10 cm and gradual wind response above 10 cm. (ii) The particle transport rate at equilibrium is expressed as a power function of friction velocity, and the index of 2.35 implies that most particles are transported by saltation. (iii) The friction velocity below 100 µm remains roughly constant and lower than the fluid threshold at equilibrium. (iv) The mean particle speed above 300 µm is less than the wind speed, whereas that below 300 µm exceeds the wind speed because of descending particles. (v) The particle diameter increases with height in the saltation layer, and the relationship is expressed as a power function. Through comparisons with the previously reported random-flight model, we find a crucial problem that empirical splash functions cannot reproduce particle dynamics at a relatively high wind speed.

  17. Spatiotemporal Structure of Aeolian Particle Transport on Flat Surface

    CERN Document Server

    Niiya, Hirofumi

    2016-01-01

    We conduct numerical simulations based on a model of blowing snow to reveal the long-term properties and equilibrium state of aeolian particle transport from $10^{-5} \\hspace{0.5 ex} \\mathrm{m}$ to $10 \\hspace{0.5 ex} \\mathrm{m}$ above the flat surface. The numerical results are s follows. (i) Time-series data of particle transport are divided into development, relaxation, and equilibrium phases, which are formed by rapid wind response below $10 \\hspace{0.5 ex} \\mathrm{cm}$ and gradual wind response above $10 \\hspace{0.5 ex} \\mathrm{cm}$. (ii) The particle transport rate at equilibrium is expressed as a power function of friction velocity, and the index of 2.35 implies that most particles are transported by saltation. (iii) The friction velocity below $100 \\hspace{0.5 ex} \\mu\\mathrm{m}$ remains roughly constant and lower than the fluid threshold at equilibrium. (iv) The mean particle speed above $300 \\hspace{0.5 ex} \\mu\\mathrm{m}$ is less than the wind speed, whereas that below $300 \\hspace{0.5 ex} \\mu\\mathrm...

  18. Gulf Stream density structure and transport during the past millennium.

    Science.gov (United States)

    Lund, David C; Lynch-Stieglitz, Jean; Curry, William B

    2006-11-30

    The Gulf Stream transports approximately 31 Sv (1 Sv = 10(6) m(3) s(-1)) of water and 1.3 x 10(15) W of heat into the North Atlantic ocean. The possibility of abrupt changes in Gulf Stream heat transport is one of the key uncertainties in predictions of climate change for the coming centuries. Given the limited length of the instrumental record, our knowledge of Gulf Stream behaviour on long timescales must rely heavily on information from geologic archives. Here we use foraminifera from a suite of high-resolution sediment cores in the Florida Straits to show that the cross-current density gradient and vertical current shear of the Gulf Stream were systematically lower during the Little Ice Age (ad approximately 1200 to 1850). We also estimate that Little Ice Age volume transport was ten per cent weaker than today's. The timing of reduced flow is consistent with temperature minima in several palaeoclimate records, implying that diminished oceanic heat transport may have contributed to Little Ice Age cooling in the North Atlantic. The interval of low flow also coincides with anomalously high Gulf Stream surface salinity, suggesting a tight linkage between the Atlantic Ocean circulation and hydrologic cycle during the past millennium.

  19. Structure of a cation-bound multidrug and toxic compound extrusion transporter

    Energy Technology Data Exchange (ETDEWEB)

    He, Xiao; Szewczyk, Paul; Karyakin, Andrey; Evin, Mariah; Hong, Wen-Xu; Zhang, Qinghai; Chang, Geoffrey (Scripps)

    2010-10-26

    Transporter proteins from the MATE (multidrug and toxic compound extrusion) family are vital in metabolite transport in plants, directly affecting crop yields worldwide. MATE transporters also mediate multiple-drug resistance (MDR) in bacteria and mammals, modulating the efficacy of many pharmaceutical drugs used in the treatment of a variety of diseases. MATE transporters couple substrate transport to electrochemical gradients and are the only remaining class of MDR transporters whose structure has not been determined. Here we report the X-ray structure of the MATE transporter NorM from Vibrio cholerae determined to 3.65 {angstrom}, revealing an outward-facing conformation with two portals open to the outer leaflet of the membrane and a unique topology of the predicted 12 transmembrane helices distinct from any other known MDR transporter. We also report a cation-binding site in close proximity to residues previously deemed critical for transport. This conformation probably represents a stage of the transport cycle with high affinity for monovalent cations and low affinity for substrates.

  20. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    Science.gov (United States)

    Owens, Jonathan R.

    In this work, we first present two powerful methods for understanding the electronic, structural, conducting, and energetic properties of nano-materials: density functional theory (DFT) and quantum transport. The basics of the theory and background of both methods are discussed thoroughly. After establishing a firm foundation, we turn our attention to using these tools to solve practical problems, often in collaboration with experimental colleagues. The first two projects pertain to nitrogen doping in graphene nanoribbons (GNRs). We study nitrogen doping in two different schema: concentration-based (N_x-doped) and structural based (N_2. {AA}-doped). Concentration based doping is explored in the context of experimental measurements of IV curves on GNRs with differing dopant concentrations. These results show a shift towards semi-conducting behavior with an increase in dopant concentration. We combine first principles calculations (DFT) and transport calculations in the Landauer formalism to compute the density-of-states (DOS) and transport curves for various dopant concentrations (0.46%, 1.39%, 1.89%, and 2.31%), which corroborate the experimental observations. The N_2. {AA}-doped GNR study was inspired by experimental observation of an atomically precise nitrogen doping scheme in bulk graphene. Experimental STM images, combined with simulated STM images, revealed that the majority (80%) of doping sites consist of nitrogen atoms on neighboring sites of the same sublattice (A) in graphene, hence N_2. {AA} doping. We examine this doping scheme applied to zigzag and armchair GNRs under different orientations of the dopants. We present spin-resolved charge densities, energetics, transport, DOS, and simulated STM images for all four systems studied. Our results show the possibility of spin-filtered devices and the STM images provide an aid in helping experimentalist identify the dopant patterns, if these GNRs are fabricated. We next venture to explain different observed

  1. Structure and Mechanism of the S Component of a Bacterial ECF Transporter

    Energy Technology Data Exchange (ETDEWEB)

    P Zhang; J Wang; Y Shi

    2011-12-31

    The energy-coupling factor (ECF) transporters, responsible for vitamin uptake in prokaryotes, are a unique family of membrane transporters. Each ECF transporter contains a membrane-embedded, substrate-binding protein (known as the S component), an energy-coupling module that comprises two ATP-binding proteins (known as the A and A' components) and a transmembrane protein (known as the T component). The structure and transport mechanism of the ECF family remain unknown. Here we report the crystal structure of RibU, the S component of the ECF-type riboflavin transporter from Staphylococcus aureus at 3.6-{angstrom} resolution. RibU contains six transmembrane segments, adopts a previously unreported transporter fold and contains a riboflavin molecule bound to the L1 loop and the periplasmic portion of transmembrane segments 4-6. Structural analysis reveals the essential ligand-binding residues, identifies the putative transport path and, with sequence alignment, uncovers conserved structural features and suggests potential mechanisms of action among the ECF transporters.

  2. An Activity-Based Multimodal Model Structure to assess Transportation Management Strategies for Urban Emergencies

    NARCIS (Netherlands)

    Van der Gun, J.P.T.; Pel, A.J.; Van Arem, B.

    2014-01-01

    There are many kinds of disasters that can severely impact the transportation system of an urbanized region. Transportation authorities therefore need to develop management strategies to adequately deal with such emergencies. In this paper, we discuss the structure of a simulation model that can be

  3. An Activity-Based Multimodal Model Structure to assess Transportation Management Strategies for Urban Emergencies

    NARCIS (Netherlands)

    Van der Gun, J.P.T.; Pel, A.J.; Van Arem, B.

    2014-01-01

    There are many kinds of disasters that can severely impact the transportation system of an urbanized region. Transportation authorities therefore need to develop management strategies to adequately deal with such emergencies. In this paper, we discuss the structure of a simulation model that can be

  4. Structure of Bor1 supports an elevator transport mechanism for SLC4 anion exchangers.

    Science.gov (United States)

    Thurtle-Schmidt, Bryan H; Stroud, Robert M

    2016-09-20

    Boron is essential for plant growth because of its incorporation into plant cell walls; however, in excess it is toxic to plants. Boron transport and homeostasis in plants is regulated in part by the borate efflux transporter Bor1, a member of the solute carrier (SLC) 4 transporter family with homology to the human bicarbonate transporter Band 3. Here, we present the 4.1-Å resolution crystal structure of Arabidopsis thaliana Bor1. The structure displays a dimeric architecture in which dimerization is mediated by centralized Gate domains. Comparisons with a structure of Band 3 in an outward-open state reveal that the Core domains of Bor1 have rotated inwards to achieve an occluded state. Further structural comparisons with UapA, a xanthine transporter from the nucleobase-ascorbate transporter family, show that the downward pivoting of the Core domains relative to the Gate domains may access an inward-open state. These results suggest that the SLC4, SLC26, and nucleobase-ascorbate transporter families all share an elevator transport mechanism in which alternating access is provided by Core domains that carry substrates across a membrane.

  5. Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter

    DEFF Research Database (Denmark)

    Weyand, Simone; Shimamura, Tatsuro; Yajima, Shunsuke

    2008-01-01

    The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 trans...

  6. Model of coherent transport in metal-insulator-midband gap semiconductor-insulator-semiconductor structure

    Science.gov (United States)

    Abramov, I. I.; Danilyuk, A. L.

    1997-08-01

    A kinetic model of coherent transport with self-organized carrier transfer via midband gap semiconductor states in metal-insulator-midband gap semiconductor-insulator-semiconductor structure at room temperature is proposed. The coherent transport at room temperature can be a result of continuous oscillations of charge carriers at midband gap semiconductor states.

  7. Domain structure and pore loops in the 2-hydroxycarboxylate transporter family

    NARCIS (Netherlands)

    Lolkema, Juke S.

    2006-01-01

    The 2-hydroxycarboxylate transporter (2HCT) family is a family of bacterial secondary transporters for substrates like citrate, malate and lactate. The family is in class ST[3] of the MemGen classification system that groups membrane proteins in structural classes based on hydropathy profile analysi

  8. Coherent structures and transport in drift wave plasma turbulence

    DEFF Research Database (Denmark)

    Korsholm, Søren Bang

    for optimization. The present work is a part of the puzzle to understand the basic physics of transport induced by drift wave turbulence in the edge region of a plasma. The basis for the study is the Hasegawa- Wakatani model. Simulation results for 3D periodic and nonperiodic geometries are presented. The Hasegawa......-Wakatani model is further expanded to include ion temperature effects. Another expansion of the model is derived from the Braginskii electron temperature equation. The result is a self-consistent set of equations describing the dynamical evolution of the drift wave fluctuations of the electron density, electron......Fusion energy research aims at developing fusion power plants providing safe and clean energy with abundant fuels. Plasma turbulence induced transport of energy and particles is a performance limiting factor for fusion devices. Hence the understanding of plasma turbulence is important...

  9. Modular structure of sodium-coupled bicarbonate transporters

    Science.gov (United States)

    Boron, Walter F.; Chen, Liming; Parker, Mark D.

    2009-01-01

    Summary Mammalian genomes contain 10 SLC4 genes that, between them, encode three Cl–HCO3 exchangers, five Na+-coupled HCO3 transporters (NCBTs), one reported borate transporter, and what is reported to be a fourth Cl–HCO3 exchanger. The NCBTs are expressed throughout the body and play important roles in maintaining intracellular and whole-body pH, as well as contributing to transepithelial transport processes. The importance of NCBTs is underscored by the genetic association of dysfunctional NCBT genes with blindness, deafness, epilepsy, hypertension and metal retardation. Key to understanding the action and regulation of NCBTs is an appreciation of the diversity of NCBT gene products. The transmembrane domains of human NCBT paralogs are 50–84% identical to each other at the amino acid level, and are capable of a diverse range of actions, including electrogenic Na/HCO3 cotransport (i.e. NBCe1 and NBCe2) and electroneutral Na/HCO3 cotransport (i.e. NBCn1 and NBCn2), as well as Na+-dependent Cl–HCO3 exchange (i.e. NDCBE). Furthermore, by the use of alternative promoters and alternative-splicing events, individual SLC4 genes have the potential to generate multiple splice variants (as many as 16 in the case of NBCn1), each of which could have unique temporal and spatial patterns of distribution, unitary transporter activity (i.e. flux mediated by one molecule), array of protein-binding partners, and complement of regulatory stimuli. In the first section of this review, we summarize our present knowledge of the function and distribution of mammalian NCBTs and their multiple variants. In the second section of this review we consider the molecular consequences of NCBT variation. PMID:19448079

  10. INVESTIGATION OF TURBULENCE STRUCTURES AND TURBULENT COUNTER-GRADIENT TRANSPORT PROPERTIES IN STRATIFIED FLOWS

    Institute of Scientific and Technical Information of China (English)

    QIU Xiang

    2006-01-01

    Turbulence structures and turbulent Counter-Gradient Transport(CGT) properties in the stratified flows with a sharp temperature interface are investigated by experimental measurements using LIF and PIV, by LES and by correlation analysis.

  11. Pathogenic mutations causing glucose transport defects in GLUT1 transporter: The role of intermolecular forces in protein structure-function.

    Science.gov (United States)

    Raja, Mobeen; Kinne, Rolf K H

    2015-01-01

    Two families of glucose transporter - the Na(+)-dependent glucose cotransporter-1 (SGLT family) and the facilitated diffusion glucose transporter family (GLUT family) - play a crucial role in the translocation of glucose across the epithelial cell membrane. How genetic mutations cause life-threatening diseases like GLUT1-deficiency syndrome (GLUT1-DS) is not well understood. In this review, we have combined previous functional data with our in silico analyses of the bacterial homologue of GLUT members, XylE (an outward-facing, partly occluded conformation) and previously proposed GLUT1 homology model (an inward-facing conformation). A variety of native and mutant side chain interactions were modeled to highlight the potential roles of mutations in destabilizing protein-protein interaction hence triggering structural and functional defects. This study sets the stage for future studies of the structural properties that mediate GLUT1 dysfunction and further suggests that both SGLT and GLUT families share conserved domains that stabilize the transporter structure/function via a similar mechanism.

  12. Structure of Quantum Chaotic Wavefunctions Ergodicity, Localization, and Transport

    CERN Document Server

    Kaplan, L

    1999-01-01

    We discuss recent developments in the study of quantum wavefunctions and transport in classically ergodic systems. Surprisingly, short-time classical dynamics leaves permanent imprints on long-time and stationary quantum behavior, which are absent from the long-time classical motion. These imprints can lead to quantum behavior on single-wavelength or single-channel scales which are very different from random matrix theory expectations. Robust and quantitative predictions are obtained using semiclassical methods. Applications to wavefunction intensity statistics and to resonances in open systems are discussed.

  13. Protective structure for storage and transport of explosive materials

    Energy Technology Data Exchange (ETDEWEB)

    Elshafey, M.; El Halim, Abd [Carleton Univ., Ottawa, ON (Canada). Dept. of Civil and Environmental Engineering; Contestabile, E. [Natural Resources Canada, CANMET Canadian Explosives Research Laboratory, Ottawa, ON (Canada)

    2007-07-01

    A blast attenuation concept using leaky barriers as suppressive shields was presented. The technology was designed for use in the storage, transport and processing of explosives, and can also be used to protect targets and infrastructure vulnerable to explosive attacks. Experimental studies were conducted in which various configurations of commercially-available steel modules were assembled as barrier walls. A finite element analysis was then conducted to model the blast attenuations from different explosive charges interacting with the barrier walls. Results of the study showed that the barrier walls attenuated blast pressure by 30 per cent.

  14. Fluid transport due to nonlinear fluid-structure interaction

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard

    1997-01-01

    of the pipe. The behavior of the system in response to lateral resonant base excitation is analysed numerically and by the use of a perturbation method (multiple scales). Exciting the pipe in the fundamental mode of vibration seems to be most effective for transferring energy from the shaker to the fluid......, whereas higher modes of vibration can be used to transport fluid with pipe vibrations of smaller amplitude. The effect of the nonlinear geometrical terms is analysed and these terms are shown to affect the response for higher modes of vibration. Experimental investigations show good agreement...

  15. Behavioral Logistics - Analysis of behavioral routines and governance structures in the interorganizational maritime transport chain

    Directory of Open Access Journals (Sweden)

    2010-09-01

    Full Text Available The strong improvements in information and communication systems as well as better transshipment technologies provide the platform for more efficient transport within interorganizational transport chains. Nevertheless these technologies do not automatically optimize systems based on routines and behavioral patterns, established over the last decades. Logisticians - in theory and practice - have to consider the field of behavioral science to describe and analyse transport problems regarding to involved actors' strategic behavior and social embeddedness, too. The objective of this paper is to illustrate behavioral aspects of supposed technical problems in interorganizational transport chains. Therefore, this paper analyses behavioral routines and governance structures in the interorganizational maritime transport chain using a case study, dealing with the generation and circulation of transport information at the earliest point available, so called "estimated time of arrival" (ETA.

  16. Density functional theory calculations of charge transport properties of ‘plate-like’ coronene topological structures

    Indian Academy of Sciences (India)

    ZIRAN CHEN; ZHANRONG HE; YOUHUI XU; WENHAO YU

    2017-09-01

    Charge transport rate is one of the key parameters determining the performance of organic electronic devices. In this paper, we used density functional theory (DFT) at the M06-2X/6−31+G(d) level to compute the charge transport rates of nine coronene topological structures. The results show that the energy gap of these nine coronene derivatives is in the range 2.90–3.30 eV, falling into the organic semiconductor category. The size of the conjugate ring has a large influence on the charge transport properties. Incorporation of methyl groupson the rigid core of tetrabenzocoronene and hexabenzocoronene is more conducive to the hole transport of the molecule than incorporating methoxyl groups. The derivatisation of a ‘long plate-like’ coronene with methoxylgroups facilitates both hole and electron transport. This class of molecules can thus be used in the design of ambipolar transport semiconductor materials.

  17. Coherent structures and transport in drift wave plasma turbulence

    Energy Technology Data Exchange (ETDEWEB)

    Bang Korsholm, S.

    2011-12-15

    Fusion energy research aims at developing fusion power plants providing safe and clean energy with abundant fuels. Plasma turbulence induced transport of energy and particles is a performance limiting factor for fusion devices. Hence the understanding of plasma turbulence is important for optimization. The present work is a part of the puzzle to understand the basic physics of transport induced by drift wave turbulence in the edge region of a plasma. The basis for the study is the Hasegawa-Wakatani model. Simulation results for 3D periodic and nonperiodic geometries are presented. The Hasegawa-Wakatani model is further expanded to include ion temperature effects. Another expansion of the model is derived from the Braginskii electron temperature equation. The result is a self-consistent set of equations describing the dynamical evolution of the drift wave fluctuations of the electron density, electron temperature and the potential in the presence of density and temperature gradients. 3D simulation results of the models are presented. Finally, the construction and first results from the MAST fluctuation reflectometer is described. The results demonstrate how L- to H-mode transitions as well as edge-localized-modes can be detected by the relatively simple diagnostic system. The present Risoe report is a slightly updated version of my original PhD report which was submitted in April 2002 and defended in August 2002. (Author)

  18. Charge Transport in Polyaniline and Vapour Induced Structural Changes

    Science.gov (United States)

    Minto, C. D. G.; Vaughan, A. S.

    1996-03-01

    Camphor sulphonic acid protonation renders polyaniline soluble in both m-cresol and chloroform. Films cast from these solvents exhibit vastly differing transport properties. m-cresol cast films are metallic or lie on the metal/insulator transition, whereas those cast from chloroform are insulators. Similarly pellets of pressed doped polyaniline powder exhibit insulating characteristics. We present an investigation of such effects in polyaniline obtained from both insulating conditions (films and powders). We find that m-cresol -- vapour treatment of these materials causes a rapid increase both in the conductivity and the type of conduction, changing from an insulator to a material approaching the metal/insulator transition. Chloroform films actually take on characteristics of those cast from m-cresol, including a positive temperature coefficient of resistivity. Both starting materials exhibit similar X-ray scattering patterns, after exposure to vapour, the pattern becomes more similar to that which is found in m-cresol cast films. Conformational changes resulting from a strong polymer--interaction are discussed as the motivation for the improvements in transport properties.

  19. Structure and function of SemiSWEET and SWEET sugar transporters.

    Science.gov (United States)

    Feng, Liang; Frommer, Wolf B

    2015-08-01

    SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure-function relations in this new class of transporters. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    Science.gov (United States)

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport.

  1. Low Resolution Structure of a Bacterial SLC26 Transporter Reveals Dimeric Stoichiometry and Mobile Intracellular Domains*

    Science.gov (United States)

    Compton, Emma L. R.; Karinou, Eleni; Naismith, James H.; Gabel, Frank; Javelle, Arnaud

    2011-01-01

    The SLC26/SulP (solute carrier/sulfate transporter) proteins are a superfamily of anion transporters conserved from bacteria to man, of which four have been identified in human diseases. Proteins within the SLC26/SulP family exhibit a wide variety of functions, transporting anions from halides to carboxylic acids. The proteins comprise a transmembrane domain containing between 10–12 transmembrane helices followed a by C-terminal cytoplasmic sulfate transporter and anti-sigma factor antagonist (STAS) domain. These proteins are expected to undergo conformational changes during the transport cycle; however, structural information for this family remains sparse, particularly for the full-length proteins. To address this issue, we conducted an expression and detergent screen on bacterial Slc26 proteins. The screen identified a Yersinia enterocolitica Slc26A protein as the ideal candidate for further structural studies as it can be purified to homogeneity. Partial proteolysis, co-purification, and analytical size exclusion chromatography demonstrate that the protein purifies as stable oligomers. Using small angle neutron scattering combined with contrast variation, we have determined the first low resolution structure of a bacterial Slc26 protein without spectral contribution from the detergent. The structure confirms that the protein forms a dimer stabilized via its transmembrane core; the cytoplasmic STAS domain projects away from the transmembrane domain and is not involved in dimerization. Supported by additional biochemical data, the structure suggests that large movements of the STAS domain underlie the conformational changes that occur during transport. PMID:21659513

  2. Structure dependent spin selectivity in electron transport through oligopeptides

    Science.gov (United States)

    Kiran, Vankayala; Cohen, Sidney R.; Naaman, Ron

    2017-03-01

    The chiral-induced spin selectivity (CISS) effect entails spin-selective electron transmission through chiral molecules. In the present study, the spin filtering ability of chiral, helical oligopeptide monolayers of two different lengths is demonstrated using magnetic conductive probe atomic force microscopy. Spin-specific nanoscale electron transport studies elucidate that the spin polarization is higher for 14-mer oligopeptides than that of the 10-mer. We also show that the spin filtering ability can be tuned by changing the tip-loading force applied on the molecules. The spin selectivity decreases with increasing applied force, an effect attributed to the increased ratio of radius to pitch of the helix upon compression and increased tilt angles between the molecular axis and the surface normal. The method applied here provides new insights into the parameters controlling the CISS effect.

  3. Structure and transport properties of atomic chains and molecules

    DEFF Research Database (Denmark)

    Strange, Mikkel

    2008-01-01

    conductance properties are explained in terms of a resonating-chain model, which takes the reflection probability and phase-shift of a single bulk-chain interface as the only input. The stability of silver-oxygen chains was studied with a thermodynamic model. This model has been developed in this work...... to describe tip-suspended atomically thin chains between macroscopic size electrodes. It has been tested with the use of DFT calculations on metal chains for which good agreement with experiments was obtained. To ensure the correctness of the DFT based transport calculations presented here, and in more...... tilted bridge configuration is found, with a conductance of 0.5G0 over a wide range of electrode displacements. This is in agreement with the observed peak at 0.5G0 in the experimentally obtained conductance histogram for Pt/CO [4]. Also, for homogenous Pt point contacts and short chains good agreement...

  4. Transport de paires EPR dans des structures mesoscopiques

    Science.gov (United States)

    Dupont, Emilie

    Dans cette these, nous nous sommes particulierement interesses a la propagation de paires EPR1 delocalisees et localisees, et a l'influence d'un supraconducteur sur le transport de ces paires. Apres une introduction de cette etude, ainsi que du cadre scientifique qu'est l'informatique quantique dans lequel elle s'inscrit, nous allons dans le chapitre 1 faire un rappel sur le systeme constitue de deux points quantiques normaux entoures de deux fils supraconducteurs. Cela nous permettra d'introduire une methode de calcul qui sera reutilisee par la suite, et de trouver egalement le courant Josephson produit par ce systeme transforme en SQUID-dc par l'ajout d'une jonction auxiliaire. Le SQUID permet de mesurer l'etat de spin (singulet ou triplet), et peut etre forme a partir d'autres systemes que nous etudierons ensuite. Dans le chapitre 2, nous rappellerons l'etude detaillee d'un intricateur d'Andreev faite par un groupe de Bale. La matrice T, permettant d'obtenir le courant dans les cas ou les electrons sont separes spatialement ou non, sera etudiee en detail afin d'en faire usage au chapitre suivant. Le chapitre 3 est consacre a l'etude de l'influence du bruit sur le fonctionnement de l'intricateur d'Andreev. Ce bruit modifie la forme du courant jusqu'a aboutir a d'autres conditions de fonctionnement de l'intricateur. En effet, le bruit present sur les points quantiques peut perturber le transport des paires EPR par l'intermediaire des degres de liberte. Nous montrerons que, du fait de l'"intrication" entre la charge de la paire et le bruit, la paire est detruite pour des temps longs. Cependant, le resultat le plus important sera que le bruit perturbe plus le transport des paires delocalisees, qui implique une resonance de Breit-Wigner a deux particules. Le transport parasite n'implique pour sa part qu'une resonance de Breit-Wigner a une particule. Dans le chapitre 4, nous reviendrons au systeme constitue de deux points quantiques entoures de deux fils

  5. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhongshan [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom); College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Xiang, Quanju [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Department of Microbiology, College of Resource and Environment Science, Sichuan Agriculture University, Yaan 625000 (China); Zhu, Xiaofeng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Dong, Haohao [Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); He, Chuan [School of Electronics and Information, Wuhan Technical College of Communications, No. 6 Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065 (China); Wang, Haiyan; Zhang, Yizheng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Wang, Wenjian, E-mail: Wenjian166@gmail.com [Laboratory of Department of Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080 (China); Dong, Changjiang, E-mail: C.Dong@uea.ac.uk [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom)

    2014-09-26

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  6. Managing Transportation Megaproject Schedule Risks Using Structural Equation Modelling: A Case Study of Shanghai Hongqiao Integrated Transport Hub in China

    Directory of Open Access Journals (Sweden)

    Peng Wei

    2016-01-01

    Full Text Available Tight schedules, multifunctional scopes, and colossal sizes usually characterize transportation megaprojects as challenging tasks for completion. In order to address these situations, a schedule risk management method was developed in this paper based on the structural equation model. In the proposed method, risk identification, evaluation and response were arranged as a sequence, and the expert elicitation technique was adopted in order to quantify the schedule risk status. To demonstrate the applicability of the proposed model, a megaproject case in China, the Shanghai Hongqiao Integrated Transport Hub (SHITH, was chosen. Information within the expanded risk register was collected including the probability and consequence of risk events, the complexity of risk responsible owners, the reaction time, and the time lasting for risk countermeasures. Final risk control results showed that the method could not only address the schedule risks correlations effectively, but also maintained the simplicity for construction management practices.

  7. Photon-assisted Andreev transport and sub-gap structures

    DEFF Research Database (Denmark)

    Wildt, M; Kutchinsky, Jonatan; Taboryski, Rafael Jozef;

    2000-01-01

    We report new measurements of microwave-induced perturbations of the sub-harmonic energy gap structures in the current-voltage characteristics of superconductor-semiconductor-superconductor junctions. Around the sub-gap bias voltages associated with the enhanced quasi-particle transfer mediated b...

  8. A spatial analysis of hierarchical waste transport structures under growing demand.

    Science.gov (United States)

    Tanguy, Audrey; Glaus, Mathias; Laforest, Valérie; Villot, Jonathan; Hausler, Robert

    2016-10-01

    The design of waste management systems rarely accounts for the spatio-temporal evolution of the demand. However, recent studies suggest that this evolution affects the planning of waste management activities like the choice and location of treatment facilities. As a result, the transport structure could also be affected by these changes. The objective of this paper is to study the influence of the spatio-temporal evolution of the demand on the strategic planning of a waste transport structure. More particularly this study aims at evaluating the effect of varying spatial parameters on the economic performance of hierarchical structures (with one transfer station). To this end, three consecutive generations of three different spatial distributions were tested for hierarchical and non-hierarchical transport structures based on costs minimization. Results showed that a hierarchical structure is economically viable for large and clustered spatial distributions. The distance parameter was decisive but the loading ratio of trucks and the formation of clusters of sources also impacted the attractiveness of the transfer station. Thus the territories' morphology should influence strategies as regards to the installation of transfer stations. The use of spatial-explicit tools such as the transport model presented in this work that take into account the territory's evolution are needed to help waste managers in the strategic planning of waste transport structures.

  9. Structural basis for amino acid export by DMT superfamily transporter YddG.

    Science.gov (United States)

    Tsuchiya, Hirotoshi; Doki, Shintaro; Takemoto, Mizuki; Ikuta, Tatsuya; Higuchi, Takashi; Fukui, Keita; Usuda, Yoshihiro; Tabuchi, Eri; Nagatoishi, Satoru; Tsumoto, Kouhei; Nishizawa, Tomohiro; Ito, Koichi; Dohmae, Naoshi; Ishitani, Ryuichiro; Nureki, Osamu

    2016-05-30

    The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.

  10. Structural basis of transport function in major facilitator superfamily protein from Trichoderma harzianum.

    Science.gov (United States)

    Chaudhary, Nitika; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

    2017-02-01

    Trichothecenes are the sesquiterpenes secreted by Trichoderma spp. residing in the rhizosphere. These compounds have been reported to act as plant growth promoters and bio-control agents. The structural knowledge for the transporter proteins of their efflux remained limited. In this study, three-dimensional structure of Thmfs1 protein, a trichothecene transporter from Trichoderma harzianum, was homology modelled and further Molecular Dynamics (MD) simulations were used to decipher its mechanism. Fourteen transmembrane helices of Thmfs1 protein are observed contributing to an inward-open conformation. The transport channel and ligand binding sites in Thmfs1 are identified based on heuristic, iterative algorithm and structural alignment with homologous proteins. MD simulations were performed to reveal the differential structural behaviour occurring in the ligand free and ligand bound forms. We found that two discrete trichothecene binding sites are located on either side of the central transport tunnel running from the cytoplasmic side to the extracellular side across the Thmfs1 protein. Detailed analysis of the MD trajectories showed an alternative access mechanism between N and C-terminal domains contributing to its function. These results also demonstrate that the transport of trichodermin occurs via hopping mechanism in which the substrate molecule jumps from one binding site to another lining the transport tunnel. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Electron transport in n-doped Si/SiGe quantum cascade structures

    NARCIS (Netherlands)

    Lazic, I.; Ikonic, Z.; Milanovic, V.; Kelsall, R.W.; Indjin, D.; Harrison, P.

    2007-01-01

    An electron transport model in n-Si/SiGe quantum cascade or superlattice structures is described. The model uses the electronic structure calculated within the effective-mass complex-energy framework, separately for perpendicular (Xz) and in-plane (Xxy) valleys, the degeneracy of which is lifted by

  12. Electron transport in n-doped Si/SiGe quantum cascade structures

    NARCIS (Netherlands)

    Lazic, I.; Ikonic, Z.; Milanovic, V.; Kelsall, R.W.; Indjin, D.; Harrison, P.

    2007-01-01

    An electron transport model in n-Si/SiGe quantum cascade or superlattice structures is described. The model uses the electronic structure calculated within the effective-mass complex-energy framework, separately for perpendicular (Xz) and in-plane (Xxy) valleys, the degeneracy of which is lifted by

  13. Structure and elevator mechanism of the Na(+)-citrate transporter CitS

    NARCIS (Netherlands)

    Lolkema, Juke S; Slotboom, Dirk Jan

    2016-01-01

    The recently determined crystal structure of the bacterial Na(+)-citrate symporter CitS provides unexpected structural and mechanistic insights. The protein has a fold that has not been seen in other proteins, but the oligomeric state, domain organization and proposed transport mechanism strongly re

  14. Spin-related transport phenomena in HgTe-based quantum well structures

    Energy Technology Data Exchange (ETDEWEB)

    Koenig, Markus

    2007-12-15

    Within the scope of this thesis, spin related transport phenomena have been investigated in HgTe/Hg{sub 0.3}Cd{sub 0.7}Te quantum well structures. In our experiments, the existence of the quantum spin Hall (QSH) state was successfully demonstrated for the first time and the presented results provide clear evidence for the charge transport properties of the QSH state. Our experiments provide the first direct observation of the Aharonov-Casher (AC) effect in semiconductor structures. In conclusion, HgTe quantum well structures have proven to be an excellent template for studying spin-related transport phenomena: The QSH relies on the peculiar band structure of the material and the existence of both the spin Hall effect and the AC effect is a consequence of the substantial spin-orbit interaction. (orig.)

  15. Correlation of Crystalline Structure with Magnetic and Transport Properties of Glass-Coated Microwires

    Directory of Open Access Journals (Sweden)

    Arcady Zhukov

    2017-02-01

    Full Text Available We overviewed the correlation between the structure, magnetic and transport properties of magnetic microwires prepared by the Taylor-Ulitovsky method involving rapid quenching from the melt and drawing of the composite (metallic core, glass coated wire. We showed that this method can be useful for the preparation of different families of magnetic microwires: soft magnetic microwires displaying Giant magnetoimpedance (GMI effect, semi-hard magnetic microwires, microwires with granular structure exhibiting Giant Magnetoresistance (GMR effect and Heusler-type microwires. Magnetic and transport properties of magnetic microwires depend on the chemical composition of metallic nucleus and on the structural features (grain size, precipitating phases of prepared microwires. In all families of crystalline microwires, their structure, magnetic and transport properties are affected by internal stresses induced by the glass coating, depending on the quenching rate. Therefore, properties of glass-coated microwires are considerably different from conventional bulk crystalline alloys.

  16. Emergence of Macroscopic Transport Barriers from Staircase Structures

    Science.gov (United States)

    Ashourvan, Arash; Diamond, Patrick H.

    2016-10-01

    A theory is presented for the formation and evolution of coupled density staircases (SC) and zonal shear profiles in a simple model of drift-wave turbulence. Density, vorticity and fluctuation potential enstrophy are the fields evolved for this system. Formation of SC structures is due to inhomogeneous mixing of generalized potential vorticity (PV), resulting in the sharpening of density and vorticity gradients in some regions and weakening them in others. The positive feedback which drives SC formation is implemented via a Rhines scale dependent mixing length. When PV gradients steepen, the density SC structure develops into a lattice of mesoscale `jumps', and `steps', which are respectively, regions of local gradient steepening and flattening. The jumps merge and migrate in radius, leading to the development of macroscale profile structures from mesoscale elements. Furthermore, depending on the sources and boundary conditions, either a region of enhanced confinement, or a region with strong turbulence can form at the edge. We present extensive studies of bifurcation physics of the global state, including results on the flux-gradient landscapes. This model is the first to demonstrate how mesoscale condensation of SCs leads to global states of enhanced confinement. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, under Award Numbers DE-FG02-04ER54738 and DE-SC0008378.

  17. Outer membrane active transport: structure of the BtuB:TonB complex.

    Science.gov (United States)

    Shultis, David D; Purdy, Michael D; Banchs, Christian N; Wiener, Michael C

    2006-06-02

    In Gram-negative bacteria, the import of essential micronutrients across the outer membrane requires a transporter, an electrochemical gradient of protons across the inner membrane, and an inner membrane protein complex (ExbB, ExbD, TonB) that couples the proton-motive force to the outer membrane transporter. The inner membrane protein TonB binds directly to a conserved region, called the Ton-box, of the transporter. We solved the structure of the cobalamin transporter BtuB in complex with the C-terminal domain of TonB. In contrast to its conformations in the absence of TonB, the Ton-box forms a beta strand that is recruited to the existing beta sheet of TonB, which is consistent with a mechanical pulling model of transport.

  18. Structural basis of the alternating-access mechanism in a bile acid transporter

    Science.gov (United States)

    Zhou, Xiaoming; Levin, Elena J.; Pan, Yaping; McCoy, Jason G.; Sharma, Ruchika; Kloss, Brian; Bruni, Renato; Quick, Matthias; Zhou, Ming

    2014-01-01

    Bile acids are synthesized from cholesterol in hepatocytes and secreted through the biliary tract into the small intestine, where they aid in absorption of lipids and fat-soluble vitamins. Through a process known as enterohepatic recirculation, more than 90% of secreted bile acids are then retrieved from the intestine and returned to the liver for resecretion. In humans, there are two Na+-dependent bile acid transporters involved in enterohepatic recirculation, the Na+-taurocholate co-transporting polypeptide (NTCP; also known as SLC10A1) expressed in hepatocytes, and the apical sodium-dependent bile acid transporter (ASBT; also known as SLC10A2) expressed on enterocytes in the terminal ileum. In recent years, ASBT has attracted much interest as a potential drug target for treatment of hypercholesterolaemia, because inhibition of ASBT reduces reabsorption of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption. However, a lack of three-dimensional structures of bile acid transporters hampers our ability to understand the molecular mechanisms of substrate selectivity and transport, and to interpret the wealth of existing functional data. The crystal structure of an ASBT homologue from Neisseria meningitidis (ASBTNM) in detergent was reported recently, showing the protein in an inward-open conformation bound to two Na+ and a taurocholic acid. However, the structural changes that bring bile acid and Na+ across the membrane are difficult to infer from a single structure. To understand the structural changes associated with the coupled transport of Na+ and bile acids, here we solved two structures of an ASBT homologue from Yersinia frederiksenii (ASBTYf) in a lipid environment, which reveal that a large rigid-body rotation of a substrate-binding domain gives the conserved `crossover' region, where two discontinuous helices cross each other, alternating accessibility from either side of the cell membrane. This result has implications

  19. Development of an Acoustic Levitation Linear Transportation System Based on a Ring-Type Structure.

    Science.gov (United States)

    Thomas, Gilles P L; Andrade, Marco A B; Adamowski, Julio Cezar; Silva, Emilio Carlos Nelli

    2017-05-01

    A linear acoustic levitation transportation system based on a ring-type vibrator is presented. The system is composed by two 21-kHz Langevin transducers connected to a ring-shaped structure formed by two semicircular sections and two flat plates. In this system, a flexural standing wave is generated along the ring structure, producing an acoustic standing wave between the vibrating ring and a plane reflector located at a distance of approximately a half wavelength from the ring. The acoustic standing wave in air has a series of pressure nodes, where small particles can be levitated and transported. The ring-type transportation system was designed and analyzed by using the finite element method. Additionally, a prototype was built and the acoustic levitation and transport of a small polystyrene particle was demonstrated.

  20. Structural Basis for a Ribofuranosyl Binding Protein: Insights into the Furanose Specific Transport

    Energy Technology Data Exchange (ETDEWEB)

    Bagaria, A.; Swaminathan, S.; Kumaran, D.; Burley, S. K.

    2011-04-01

    The ATP-binding cassette transporters (ABC-transporters) are members of one of the largest protein superfamilies, with representatives in all extant phyla. These integral membrane proteins utilize the energy of ATP hydrolysis to carry out certain biological processes, including translocation of various substrates across membranes and non-transport related processes such as translation of RNA and DNA repair. Typically, such transport systems in bacteria consist of an ATP binding component, a transmembrane permease, and a periplasmic receptor or binding protein. Soluble proteins found in the periplasm of gram-negative bacteria serve as the primary receptors for transport of many compounds, such as sugars, small peptides, and some ions. Ligand binding activates these periplasmic components, permitting recognition by the membrane spanning domain, which supports for transport and, in some cases, chemotaxis. Transport and chemotaxis processes appear to be independent of one another, and a few mutants of bifunctional periplasmic components reveal the absence of one or the other function. Previously published high-resolution X-ray structures of various periplasmic ligand binding proteins include Arabinose binding protein (ABP), Allose binding protein (ALBP), Glucose-galactose binding protein (GBP) and Ribose binding protein (RBP). Each of these proteins consists of two structurally similar domains connected by a three-stranded hinge region, with ligand buried between the domains. Upon ligand binding and release, various conformational changes have been observed. For RBP, open (apo) and closed (ligand bound) conformations have been reported and so for MBP. The closed/active form of the protein interacts with the integral membrane component of the system in both transport and chemotaxis. Herein, we report 1.9{angstrom} resolution X-ray structure of the R{sub f}BP periplasmic component of an ABC-type sugar transport system from Hahella chejuensis (UniProt Id Q2S7D2) bound to

  1. Atomistic Simulation and Electronic Structure of Lithium Doped Ionic Liquids: Structure, Transport, and Electrochemical Stability

    Science.gov (United States)

    Haskins, Justin B.; Bauschlicher, Charles W.; Lawson, John W.

    2015-01-01

    Zero-temperature density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Lithium ion on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N--methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N--methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3--methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Lithium ion solvation shell through zero-temperature DFT simulations of [Li(Anion)sub n](exp n-1) -clusters, DFT-MD simulations of isolated lithium ions in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having 2-3 anions are seen in both [pyr14][TFSI] and [pyr13][FSI], while solvation shells with 4 anions dominate in [EMIM][BF sub 4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of 4 anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion) sub n](exp n -1) - clusters shows that our proposed structures are consistent with experiment. We estimate the ion diffusion coefficients and quantify both size and simulation time effects. We find estimates of lithium ion diffusion are a reasonable order of magnitude and can be corrected for simulation time effects. Simulation size, on the other hand, is also important, with diffusion coefficients from long PFF-MD simulations of small cells having 20-40% error compared to large-cell values. Finally, we compute the electrochemical window using differences in electronic energy levels of both isolated cation/anion pairs and small ionic liquid systems with Li-salt doping. The single pair and liquid

  2. Random lasing in structures with multi-scale transport properties

    CERN Document Server

    Leonetti, Marco

    2013-01-01

    In a random laser (RL), a system possessing in itself both resonator and amplifying medium while lacking of a macroscopic cavity, the feedback is provided by the scattering, which forces light to travel across very long random paths. Here we demonstrate that RL properties may be tuned by the topology of the scattering system retaining unchanged scattering strength and gain efficiency. This is possible in a system based on sparse clusters, possessing two relevant structural lengths: the macroscopic inter cluster separation and the mesoscopic intra-cluster mean free path.

  3. Direct measurement of chiral structure and transport in single- and multi-walled carbon nanotubes

    Science.gov (United States)

    Cui, Taoran; Lin, Letian; Qin, Lu-Chang; Washburn, Sean

    2016-11-01

    Electrical devices based on suspended multi-wall carbon nanotubes were constructed and studied. The chiral structure of each shell in a particular nanotube was determined using nanobeam electron diffraction in a transmission electron microscope. The transport properties of the carbon nanotube were also measured. The nanotube device length was short enough that the transport was nearly ballistic, and multiple subbands contributed to the conductance. Thermal excitation of carriers significantly affected nanotube resistance at room temperature.

  4. Anomalous plasma transport and induced electric field in a stochastic magnetic field structure

    Energy Technology Data Exchange (ETDEWEB)

    Kubota, Tetsuyuki; Itoh, Sanae-I.; Toda, Shinichiro; Yamaguchi, Hiroki [Kyushu Univ., Fukuoka (Japan); Fukuyama, Atsushi [Okayama Univ. (Japan)

    1995-04-01

    The plasma transport matrix is formulated using the kinetic equation for the particles in the stochastic magnetic field. The radial electric field generation is analyzed using this transport matrix. This thermoelectric field is dictated by the difference between the electron heat flux and the ion heat flux. We calculate the spatial structures of the radial electric field and the temperature in the stochastic field region. 7 refs., 3 figs.

  5. COMPARISON OF SUSTAINABILITY BETWEEN PRIVATE AND PUBLIC TRANSPORT CONSIDERING URBAN STRUCTURE

    OpenAIRE

    Masanobu KII

    2003-01-01

    It is said that the car is convenient but consumes high-energy per passenger, while public transport is an environmentally friendly mode but needs high cost of investment and management. However, this view does not take account of urban structure such as population size and density. For instance, higher population density would cause congestion and consequent inconvenience for car usage. This may shift demand to public transport use. On the other hand, in a lower density of urban area, public...

  6. Band structure and transport studies of copper selenide: An efficient thermoelectric material

    Science.gov (United States)

    Tyagi, Kriti; Gahtori, Bhasker; Bathula, Sivaiah; Auluck, S.; Dhar, Ajay

    2014-10-01

    We report the band structure calculations for high temperature cubic phase of copper selenide (Cu2Se) employing Hartree-Fock approximation using density functional theory within the generalized gradient approximation. These calculations were further extended to theoretically estimate the electrical transport coefficients of Cu2Se employing Boltzmann transport theory, which show a reasonable agreement with the corresponding experimentally measured values. The calculated transport coefficients are discussed in terms of the thermoelectric (TE) performance of this material, which suggests that Cu2Se can be a potential p-type TE material with an optimum TE performance at a carrier concentration of ˜ 4 - 6 × 10 21 cm - 3 .

  7. Structure and transport investigations on lithium-iron-phosphate glasses

    Science.gov (United States)

    Banday, Azeem; Sharma, Monika; Murugavel, Sevi

    2016-05-01

    Cathode materials for Lithium Ion Batteries (LIB's) are being constantly studied and reviewed especially in the past few decades. LiFePO4 (LFP) is one of the most potential candidates in the pedigree of cathode materials and has been under extensive study ever since. In this work, we report the synthesis of amorphous analogs of crystallite LFP by conventional melt quenching method. Thermal study by using differential scanning calorimetry (DSC) was used to determine the glass transition Tg and crystallization Tc temperatures on the obtained glass sample Fourier transform infrared (FTIR) absorption spectroscopy is being used to investigate the structural properties of the glass sample. The intrinsic electrical conductivity measurements were done using broad-band impedance spectroscopy with wide different temperature ranges. The conduction mechanism is described by non-adiabatic small polaron hopping between nearest neighbors. Based on the obtained results, we suggest that the glassy LFP is more suitable cathode material as compared to its crystalline counterpart.

  8. Structural mechanism of nuclear transport mediated by importin β and flexible amphiphilic proteins.

    Science.gov (United States)

    Yoshimura, Shige H; Kumeta, Masahiro; Takeyasu, Kunio

    2014-12-02

    Karyopherin β family proteins mediate the nuclear/cytoplasmic transport of various proteins through the nuclear pore complex (NPC), although they are substantially larger than the size limit of the NPC.To elucidate the molecular mechanism underlying this paradoxical function, we focused on the unique structures called HEAT repeats, which consist of repetitive amphiphilic α helices. An in vitro transport assay and FRAP analyses demonstrated that not only karyopherin β family proteins but also other proteins with HEAT repeats could pass through the NPC by themselves, and serve as transport mediators for their binding partners. Biochemical and spectroscopic analyses and molecular dynamics simulations of purified HEAT-rich proteins revealed that they interact with hydrophobic groups, including phenyl and alkyl groups, and undergo reversible conformational changes in tertiary structures, but not in secondary structures. These results show that conformational changes in the flexible amphiphilic motifs play a critical role in translocation through the NPC.

  9. Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter

    Science.gov (United States)

    Pak, John Edward; Ekendé, Elisabeth Ngonlong; Kifle, Efrem G.; O’Connell, Joseph Daniel; De Angelis, Fabien; Tessema, Meseret B.; Derfoufi, Kheiro-Mouna; Robles-Colmenares, Yaneth; Robbins, Rebecca A.; Goormaghtigh, Erik; Vandenbussche, Guy; Stroud, Robert M.

    2013-01-01

    Efflux pumps belonging to the ubiquitous resistance–nodulation–cell division (RND) superfamily transport substrates out of cells by coupling proton conduction across the membrane to a conformationally driven pumping cycle. The heavy metal-resistant bacteria Cupriavidus metallidurans CH34 relies notably on as many as 12 heavy metal efflux pumps of the RND superfamily. Here we show that C. metallidurans CH34 ZneA is a proton driven efflux pump specific for Zn(II), and that transport of substrates through the transmembrane domain may be electrogenic. We report two X-ray crystal structures of ZneA in intermediate transport conformations, at 3.0 and 3.7 Å resolution. The trimeric ZneA structures capture protomer conformations that differ in the spatial arrangement and Zn(II) occupancies at a proximal and a distal substrate binding site. Structural comparison shows that transport of substrates through a tunnel that links the two binding sites, toward an exit portal, is mediated by the conformation of a short 14-aa loop. Taken together, the ZneA structures presented here provide mechanistic insights into the conformational changes required for substrate efflux by RND superfamily transporters. PMID:24173033

  10. Short- and Long- Time Transport Structures in a Three Dimensional Time Dependent Flow

    Science.gov (United States)

    Chabreyrie, Rodolphe; Llewellyn Smith, Stefan

    2012-11-01

    Lagrangian transport structures for three-dimensional and time-dependent fluid flows are of great interest in numerous applications, particularly for geophysical or oceanic flows. In such flows, chaotic transport and mixing can play important environmental and ecological roles, for examples in pollution spills or plankton migration. In such flows, where simulations or observations are typically available only over a short time, understanding the difference between short-time and long-time transport structures is critical. In this talk, we use a set of classical (i.e. Poincaré section, Lyapunov exponent) and alternative (i.e. finite time Lyapunov exponent, Lagrangian coherent structures) tools from dynamical systems theory that analyze chaotic transport both qualitatively and quantitatively. With this set of tools we are able to reveal, identify and highlight differences between short- and long-time transport structures inside a flow composed of a primary horizontal contra-rotating vortex chain, small lateral oscillations and a weak Ekman pumping. The difference is mainly the existence of regular or extremely slowly developing chaotic regions that are only present at short time. This research was funded by the ONR MURI Dynamical Systems Theory and Lagrangian Data Assimilation in 3D+1 Geophysical Fluid Dynamics.

  11. Structure and transport properties of ethylcellulose membranes with different types and granulation of magnetic powder

    Science.gov (United States)

    Krasowska, Monika; Strzelewicz, Anna; Rybak, Aleksandra; Dudek, Gabriela; Cieśla, Michał

    2016-06-01

    Structure and transport properties of ethylcellulose membranes with dispersed magnetic powder were investigated. The study mainly focused on diffusion, which is one of the transport mechanisms. The transport properties depend on many parameters like: polymeric matrix used, type of powder, its amount and granulation. The structure of the pattern formed by magnetic particles in the membrane matrix was studied. Description of the system was based on the phenomenological and molecular (random walk on a fractal lattice) approaches. Two parameters were calculated: the fractal dimension of random walk dw, and the fractal dimension of membrane structure df. The knowledge of both parameters made it possible to use the generalized equation of diffusion on the fractal structure obtained by Metzler et al. The research was carried out to determine the influence of magnetic powder granulation on the transport properties. The results showed that the random walk within the membranes of the smallest magnetic powder granulation was of the most subdiffusive character. Detailed investigation and quantitative description of gas transport through the membranes enables designing the membranes to be used in air oxygen enrichment.

  12. Structural Basis for a Ribofuranosyl Binding Protein: Insights into the Furanose Specific Transport

    Energy Technology Data Exchange (ETDEWEB)

    A Bagaria; D Kumaran; S Burley; S Swaminathan

    2011-12-31

    The APT-binding cassette transporters (ABC-transporters) are members of one of the largest protein superfamilies, with representatives in all extant phyla. These integral membrane proteins utilize the energy of ATP hydrolysis to carry out certain biological processes, including translocation of various substrates across membranes and nontransport related processes such as translation of RNA and DNA repair. typically, such transport systems in bacteria consist of an ATP binding component, a transmembrane permease, and a periplasmic receptor or binding protein. Soluble proteins found in the periplasm of gram-negative bacteria serve as the primary receptors for transport of many compounds, such as sugars, small peptides, and some ions. Ligand binding activates these periplasmic components, permitting recognition by the membrane spanning domain, which supports for transport, and, in some cases, chemotaxis. Transport and chemotaxis processes appear to be independent of one another, and a few mutants of bifunctional periplasmic components reveal the absence of one or the other function. Previously published high-resolution X-ray structures of various periplasmic ligand binding proteins include Arabinose binding protein (ABP), Allose binding protein (ALBP), Glucose-galactose binding protein (GBP), and Ribose binding protein (RBP). Each of these proteins consits of two structurally similar domains connected by a three-stranded hinge region, with ligand buried between the domains. Upon ligand binding and release, various conformational changes have been observed. For RBP, open (apo) and closed (ligand bound) conformations hafve been reported and so for MBP. The closed/active form of the protein interacts with the ingral membrane component of the system in both transport and chemotaxis. Herein, they report 1.9 {angstrom} resolution X-ray structure of the R{sub f}BP periplasmic component of an ABC-type sugar transport system from Hahella chejuensis (UniProt Id Q2S7D2) bound

  13. Flow structure and vorticity transport on a plunging wing

    Science.gov (United States)

    Eslam Panah, Azar

    The structure and dynamics of the flow field created by a plunging flat plate airfoil are investigated at a chord Reynolds number of 10,000 while varying plunge amplitude and Strouhal number. Digital particle image velocimetry measurements are used to characterize the shedding patterns and the interactions between the leading and trailing edge vortex structures (LEV and TEV), resulting in the development of a wake classification system based on the nature and timing of interactions between the leading- and trailing-edge vortices. The convection speed of the LEV and its resulting interaction with the TEV is primarily dependent on reduced frequency; however, at Strouhal numbers above approximately 0.4, a significant influence of Strouhal number (or plunge amplitude) is observed in which LEV convection is retarded, and the contribution of the LEV to the wake is diminished. It is shown that this effect is caused by an enhanced interaction between the LEV and the airfoil surface, due to a significant increase in the strength of the vortices in this Strouhal number range, for all plunge amplitudes investigated. Comparison with low-Reynolds-number studies of plunging airfoil aerodynamics reveals a high degree of consistency and suggests applicability of the classification system beyond the range examined in the present work. Some important differences are also observed. The three-dimensional flow field was characterized for a plunging two-dimensional flat-plate airfoil using three-dimensional reconstructions of planar PIV data. Whereas the phase-averaged description of the flow field shows the secondary vortex penetrating the leading-edge shear layer to terminate LEV formation on the airfoil, time-resolved, instantaneous PIV measurements show a continuous and growing entrainment of secondary vorticity into the shear layer and LEV. A planar control volume analysis on the airfoil indicated that the generation of secondary vorticity produced approximately one half the

  14. Structure and transport properties of polymer grafted nanoparticles

    KAUST Repository

    Goyal, Sushmit

    2011-01-01

    We perform molecular dynamics simulations on a bead-spring model of pure polymer grafted nanoparticles (PGNs) and of a blend of PGNs with a polymer melt to investigate the correlation between PGN design parameters (such as particle core concentration, polymer grafting density, and polymer length) and properties, such as microstructure, particle mobility, and viscous response. Constant strain-rate simulations were carried out to calculate viscosities and a constant-stress ensemble was used to calculate yield stresses. The PGN systems are found to have less structural order, lower viscosity, and faster diffusivity with increasing length of the grafted chains for a given core concentration or grafting density. Decreasing grafting density causes depletion effects associated with the chains leading to close contacts between some particle cores. All systems were found to shear thin, with the pure PGN systems shear thinning more than the blend; also, the pure systems exhibited a clear yielding behavior that was absent in the blend. Regarding the mechanism of shear thinning at the high shear rates examined, it was found that the shear-induced decrease of Brownian stresses and increase in chain alignment, both correlate with the reduction of viscosity in the system with the latter being more dominant. A coupling between Brownian stresses and chain alignment was also observed wherein the non-equilibrium particle distribution itself promotes chain alignment in the direction of shear. © 2011 American Institute of Physics.

  15. Structure and transport investigations on lithium-iron-phosphate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Banday, Azeem; Sharma, Monika; Murugavel, Sevi, E-mail: murug@physics.du.ac.in [Department of Physics and Astrophysics, University of Delhi, Delhi-110007 (India)

    2016-05-23

    Cathode materials for Lithium Ion Batteries (LIB’s) are being constantly studied and reviewed especially in the past few decades. LiFePO{sub 4} (LFP) is one of the most potential candidates in the pedigree of cathode materials and has been under extensive study ever since. In this work, we report the synthesis of amorphous analogs of crystallite LFP by conventional melt quenching method. Thermal study by using differential scanning calorimetry (DSC) was used to determine the glass transition T{sub g} and crystallization T{sub c} temperatures on the obtained glass sample Fourier transform infrared (FTIR) absorption spectroscopy is being used to investigate the structural properties of the glass sample. The intrinsic electrical conductivity measurements were done using broad-band impedance spectroscopy with wide different temperature ranges. The conduction mechanism is described by non-adiabatic small polaron hopping between nearest neighbors. Based on the obtained results, we suggest that the glassy LFP is more suitable cathode material as compared to its crystalline counterpart.

  16. Structure and mechanism of Zn2+-transporting P-type ATPases

    DEFF Research Database (Denmark)

    Wang, Kaituo; Sitsel, Oleg; Meloni, Gabriele

    2014-01-01

    Zinc is an essential micronutrient for all living organisms. It is required for signalling and proper functioning of a range of proteins involved in, for example, DNA binding and enzymatic catalysis1. In prokaryotes and photosynthetic eukaryotes, Zn2+-transporting P-type ATPases of class IB (Znt....... The structures reveal a similar fold to Cu+-ATPases, with an amphipathic helix at the membrane interface. A conserved electronegative funnel connects this region to the intramembranous high-affinity ion-binding site and may promote specific uptake of cellular Zn2+ ions by the transporter. The E2P structure...

  17. Linking phloem function to structure: analysis with a coupled xylem-phloem transport model.

    Science.gov (United States)

    Hölttä, T; Mencuccini, M; Nikinmaa, E

    2009-07-21

    We carried out a theoretical analysis of phloem transport based on Münch hypothesis by developing a coupled xylem-phloem transport model. Results showed that the maximum sugar transport rate of the phloem was limited by solution viscosity and that transport requirements were strongly affected by prevailing xylem water potential. The minimum number of xylem and phloem conduits required to sustain transpiration and assimilation, respectively, were calculated. At its maximum sugar transport rate, the phloem functioned with a high turgor pressure difference between the sugar sources and sinks but the turgor pressure difference was reduced if additional parallel conduits were added or solute relays were introduced. Solute relays were shown to decrease the number of parallel sieve tubes needed for phloem transport, leading to a more uniform turgor pressure and allowing faster information transmission within the phloem. Because xylem water potential affected both xylem and phloem transport, the conductance of the two systems was found to be coupled such that large structural investments in the xylem reduced the need for investment in the phloem and vice versa.

  18. Crystal structure of the human sterol transporter ABCG5/ABCG8.

    Science.gov (United States)

    Lee, Jyh-Yeuan; Kinch, Lisa N; Borek, Dominika M; Wang, Jin; Wang, Junmei; Urbatsch, Ina L; Xie, Xiao-Song; Grishin, Nikolai V; Cohen, Jonathan C; Otwinowski, Zbyszek; Hobbs, Helen H; Rosenbaum, Daniel M

    2016-05-26

    ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral sterols in liver and intestines. Mutations disrupting G5G8 cause sitosterolaemia, a disorder characterized by sterol accumulation and premature atherosclerosis. Here we use crystallization in lipid bilayers to determine the X-ray structure of human G5G8 in a nucleotide-free state at 3.9 Å resolution, generating the first atomic model of an ABC sterol transporter. The structure reveals a new transmembrane fold that is present in a large and functionally diverse superfamily of ABC transporters. The transmembrane domains are coupled to the nucleotide-binding sites by networks of interactions that differ between the active and inactive ATPases, reflecting the catalytic asymmetry of the transporter. The G5G8 structure provides a mechanistic framework for understanding sterol transport and the disruptive effects of mutations causing sitosterolaemia.

  19. Structural Studies on Cytosolic Domain of Magnesium Transporter MgtE from Enterococcus faecalis

    Energy Technology Data Exchange (ETDEWEB)

    Ragumani, S.; Sauder, J; Burley, S; Swaminathan, S

    2009-01-01

    Magnesium (Mg{sup 2+}) is an essential element for growth and maintenance of living cells. It acts as a cofactor for many enzymes and is also essential for stability of the plasma membrane. There are two distinct classes of magnesium transporters identified in bacteria that convey Mg{sup 2+} from periplasm to cytoplasm [ATPase-dependent (MgtA and MgtB) and constitutively active (CorA and MgtE)]. Previously published work on Mg{sup 2+} transporters yielded structures of full length MgtE from Thermus thermophilus, determined at 3.5 {angstrom} resolution, and its cytoplasmic domain with and without bond Mg{sup 2+} determined at 2.3 and 3.9 {angstrom} resolution, respectively. Here, they report the crystal structure of the Mg{sup 2+} bound form of the cytosolic portion of MgtE (residues 6-262) from Enterococcus faecalis at 2.2 {angstrom} resolution. The present structure and magnesium bound cytosolic domain structure from T. thermophilus (PDB ID: 2YVY) are structurally similar. Three magnesium binding sites are common to both MgtE full length and the present structure. Their work revealed an additional Mg{sup 2+} binding site in the E. faecalis structure. In this report, they discuss the functional significance of Mg{sup 2+} binding sites in the cytosolic domains of MgtE transporters.

  20. Nanoscale quantification of charge injection and transportation process in Si-nanocrystal based sandwiched structure.

    Science.gov (United States)

    Xu, Jie; Xu, Jun; Zhang, Pengzhan; Li, Wei; Chen, Kunji

    2013-10-21

    Si nanocrystals are formed by using KrF pulsed laser crystallization of an amorphous SiC/ultrathin amorphous Si/amorphous SiC sandwiched structure. Electrons and holes are injected into Si nanocrystals via a biased conductive AFM tip and the carrier decay and transportation behaviours at the nanoscale are studied by joint characterization techniques of Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy (CAFM). Quantification of the surface charge density is realized by solving the Poisson equation based on KPFM measurements. Besides, the asymmetric barrier height for electrons and holes is considered to play a dominant role in controlling the charge retention and transportation characteristics. The methodology developed in this work is promising for studying the charge injection and transportation process in other materials and structures at the nanoscale.

  1. Modeling of the electrical carrier transport in III-V on silicon tandem solar cell structures

    Science.gov (United States)

    Maiti, T. K.; Cheong, Dan; Yang, Jingfeng; Kleiman, R. N.

    2011-08-01

    The electrical carrier transport of a tandem cell structure was evaluated by investigating the band alignment of and carrier transport through a tunnel junction. The modeling structure of a tandem cell consists of a III-V (or II-VI) top cell layer, a Si bottom cell layer and tunnel junction layers in-between which connect the top and the bottom cells. The values of energy bandgap and electron affinity of each layer were varied to investigate their effect on the energy barrier height at the interface between Si and compound semiconductors of interest. The contour plots of barrier heights for majority and minority carriers at the hetero-interface are used as a starting point to define the successful regions for electrical carrier transport through the tunnel junctions.

  2. Vertical charge-carrier transport in Si nanocrystal/SiO2 multilayer structures.

    Science.gov (United States)

    Osinniy, V; Lysgaard, S; Kolkovsky, Vl; Pankratov, V; Nylandsted Larsen, A

    2009-05-13

    Charge-carrier transport in multilayer structures of Si nanocrystals (NCs) embedded in a SiO(2) matrix grown by magnetron sputtering has been investigated. The presence of two types of Si NCs with different diameters after post-growth annealing is concluded from transmission-electron microscopy and photoluminescence measurements. Based on the electric field and temperature dependences of capacitance and resistivity, it is established that the carrier transport is best described by a combination of phonon-assisted and direct tunneling mechanisms. Poole-Frenkel tunneling seems to be a less suitable mechanism to explain the vertical carrier transport due to the very high values of refractive indices obtained within this model. The possibility to more effectively collect charge carriers generated by light in structures having Si NCs of different size is discussed.

  3. Crystal structure and electrical transport properties of single layered perovskite LaSrCoO4

    Science.gov (United States)

    Ahad, Abdul; Shukla, D. K.; Rahman, F.; Majid, S.; Tarachand; Okram, G. S.; Phase, D. M.

    2016-10-01

    We present here investigations on the influence of structure on electrical transport properties of polycrystalline LaSrCoO4 that is single layered perovskite with K2NiF4 type structure synthesized using solid state reaction route. Using Reitveld refinement of X-ray diffraction (XRD) data, it is found that the sample is in single phase with tetragonal structure (space group I4/mmm). Electrical resistivity performed in the temperature range 140-300K shows semiconducting character of the sample. Considerable contrasts in the Co-O bond length is associated with the intermediate spin (IS) state of Co ion that correlates the structural and transport properties. Detailed analysis indicates that the temperature dependent electrical resistivity follows the three-dimensional variable range hopping (VRH) model in low temperature region below 225K. The high temperature (225-300K) resistivity data has been found to follow the thermally activated behaviour.

  4. Combined Structural and Compositional Evolution of Planetary Rings Due to Micrometeoroid Impacts and Ballistic Transport

    Science.gov (United States)

    Estrada, Paul R.; Durisen, Richard H.; Cuzzi, Jeffrey N.; Morgan, Demitri A.

    2015-01-01

    We introduce improved numerical techniques for simulating the structural and compositional evolution of planetary rings due to micrometeoroid bombardment and subsequent ballistic transport of impact ejecta. Our current, robust code is capable of modeling structural changes and pollution transport simultaneously over long times on both local and global scales. In this paper, we describe the methodology based on the original structural code of Durisen et al. (1989, Icarus 80, 136-166) and on the pollution transport code of Cuzzi and Estrada (1998, Icarus 132, 1-35). We provide demonstrative simulations to compare with, and extend upon previous work, as well as examples of how ballistic transport can maintain the observed structure in Saturn's rings using available Cassini occultation optical depth data. In particular, we explicitly verify the claim that the inner B (and presumably A) ring edge can be maintained over long periods of time due to an ejecta distribution that is heavily biased in the prograde direction through a balance between the sharpening effects of ballistic transport and the broadening effects of viscosity. We also see that a "ramp"-like feature forms over time just inside that edge. However, it does not remain linear for the duration of the runs presented here unless a less steep ejecta velocity distribution is adopted. We also model the C ring plateaus and find that their outer edges can be maintained at their observed sharpness for long periods due to ballistic transport. We hypothesize that the addition of a significant component of a retrograde-biased ejecta distribution may help explain the linearity of the ramp and is probably essential for maintaining the sharpness of C ring plateau inner edges. This component would arise for the subset of micrometeoroid impacts which are destructive rather than merely cratering. Such a distribution will be introduced in future work.

  5. Structure and Morphology Control in Thin Films of Conjugated Polymers for an Improved Charge Transport

    OpenAIRE

    Haiyang Wang; Yaozhuo Xu; Xinhong Yu; Rubo Xing; Jiangang Liu; Yanchun Han

    2013-01-01

    The morphological and structural features of the conjugated polymer films play an important role in the charge transport and the final performance of organic optoelectronics devices [such as organic thin-film transistor (OTFT) and organic photovoltaic cell (OPV), etc.] in terms of crystallinity, packing of polymer chains and connection between crystal domains. This review will discuss how the conjugated polymer solidify into, for instance, thin-film structures, and how to control the molecula...

  6. Structure and Morphology Control in Thin Films of Conjugated Polymers for an Improved Charge Transport

    OpenAIRE

    Haiyang Wang; Yaozhuo Xu; Xinhong Yu; Rubo Xing; Jiangang Liu; Yanchun Han

    2013-01-01

    The morphological and structural features of the conjugated polymer films play an important role in the charge transport and the final performance of organic optoelectronics devices [such as organic thin-film transistor (OTFT) and organic photovoltaic cell (OPV), etc.] in terms of crystallinity, packing of polymer chains and connection between crystal domains. This review will discuss how the conjugated polymer solidify into, for instance, thin-film structures, and how to control the molecula...

  7. Structural optimization and its interaction with aerodynamic optimization for a high speed civil transport wing

    OpenAIRE

    Huang, Ximing

    1994-01-01

    A variable-complexity design strategy with combined aerodynamic and structural optimization procedures is presented for the high speed civil transport design (HSCT). Variable-complexity analysis methods are used to reduce the computational expense. A finite element-model based structural optimization procedure with flexible loads is implemented to evaluate the wing bending material weight. Static aeroelastic effects, evaluated through the comparison of rigid and flexible win...

  8. Electronic properties of mesoscopic graphene structures: Charge confinement and control of spin and charge transport

    Energy Technology Data Exchange (ETDEWEB)

    Rozhkov, A.V., E-mail: arozhkov@gmail.co [Advanced Science Institute, RIKEN, Wako-shi, Saitama, 351-0198 (Japan); Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, 125412, Moscow (Russian Federation); Giavaras, G. [Advanced Science Institute, RIKEN, Wako-shi, Saitama, 351-0198 (Japan); Bliokh, Yury P. [Advanced Science Institute, RIKEN, Wako-shi, Saitama, 351-0198 (Japan); Department of Physics, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Freilikher, Valentin [Advanced Science Institute, RIKEN, Wako-shi, Saitama, 351-0198 (Japan); Department of Physics, Bar-Ilan University, Ramat-Gan 52900 (Israel); Nori, Franco [Advanced Science Institute, RIKEN, Wako-shi, Saitama, 351-0198 (Japan); Department of Physics, University of Michigan, Ann Arbor, MI 48109-1040 (United States)

    2011-06-15

    This brief review discusses electronic properties of mesoscopic graphene-based structures. These allow controlling the confinement and transport of charge and spin; thus, they are of interest not only for fundamental research, but also for applications. The graphene-related topics covered here are: edges, nanoribbons, quantum dots, pn-junctions, pnp-structures, and quantum barriers and waveguides. This review is partly intended as a short introduction to graphene mesoscopics.

  9. Model for ballistic spin-transport in ferromagnet/two-dimensional electron gas/ferromagnet structures

    NARCIS (Netherlands)

    Schapers, T; Nitta, J; Heersche, HB; Takayanagi, H

    2002-01-01

    The spin dependent conductance of a ferromagnet/two-dimensional electron gas ferromagnet structure is theoretically examined in the ballistic transport regime. It is shown that the spin signal can be improved considerably by making use of the spin filtering effect of a barrier at the ferromagnet two

  10. Insights into molecular properties of the human monocarboxylate transporter 8 by combining functional with structural information

    Directory of Open Access Journals (Sweden)

    Kleinau Gunnar

    2011-08-01

    Full Text Available Abstract Background The monocarboxylate transporter 8 (MCT8 is a member of the major facilitator superfamily (MFS and transports specificly iodothyronines. MCT8 mutations are the underlying cause of a syndrome of severe X-linked psychomotor retardation known as the Allan-Herndon-Dudley syndrome. This syndrome is characterized by abnormally high T3, low/normal T4 serum levels and slightly elevated serum TSH. To date, more than 25 pathogenic mutations in hMCT8 are known and they are valuable indicators of important regions for structural and functional MCT8 properties. Methods We designed a structural human MCT8 model and studied reported pathogenic missense mutations with focus on the estimation of those amino acid positions which are probably sensitive for substrate transport. Furthermore, assuming similarities between determinants of T3 binding observed in the published crystal structure of the thyroid hormone receptor beta occupied by its ligand T3 and the structural MCT8 model, we explore potential T3 binding sites in the MCT8 substrate channel cavity. Results We found that all known pathogenic missense mutations are located exclusively in the transmembrane helices and to a high degree at conserved residues among the MCT family. Furthermore, mutations either of or to prolines/glycines are located mainly at helices 9-12 and are expected to cause steric clashes or structural misfolding. In contrast, several other mutations are close to the potential substrate channel and affected amino acids are likely involved in the switching mechanism between different transporter conformations. Finally, three potential substrate binding sites are predicted for MCT8. Conclusions Naturally occurring mutations of MCT8 provide molecular insights into protein regions important for protein folding, substrate binding and the switching mechanism during substrate transport. Future studies guided by this information should help to clarify structure

  11. Photoluminescence Imaging of Polyfluorene Surface Structures on Semiconducting Carbon Nanotubes: Implications for Thin Film Exciton Transport.

    Science.gov (United States)

    Hartmann, Nicolai F; Pramanik, Rajib; Dowgiallo, Anne-Marie; Ihly, Rachelle; Blackburn, Jeffrey L; Doorn, Stephen K

    2016-12-27

    Single-walled carbon nanotubes (SWCNTs) have potential to act as light-harvesting elements in thin film photovoltaic devices, but performance is in part limited by the efficiency of exciton diffusion processes within the films. Factors contributing to exciton transport can include film morphology encompassing nanotube orientation, connectivity, and interaction geometry. Such factors are often defined by nanotube surface structures that are not yet well understood. Here, we present the results of a combined pump-probe and photoluminescence imaging study of polyfluorene (PFO)-wrapped (6,5) and (7,5) SWCNTs that provide additional insight into the role played by polymer structures in defining exciton transport. Pump-probe measurements suggest exciton transport occurs over larger length scales in films composed of PFO-wrapped (7,5) SWCNTs, compared to those prepared from PFO-bpy-wrapped (6,5) SWCNTs. To explore the role the difference in polymer structure may play as a possible origin of differing transport behaviors, we performed a photoluminescence imaging study of individual polymer-wrapped (6,5) and (7,5) SWCNTs. The PFO-bpy-wrapped (6,5) SWCNTs showed more uniform intensity distributions along their lengths, in contrast to the PFO-wrapped (7,5) SWCNTs, which showed irregular, discontinuous intensity distributions. These differences likely originate from differences in surface coverage and suggest the PFO wrapping on (7,5) nanotubes produces a more open surface structure than is available with the PFO-bpy wrapping of (6,5) nanotubes. The open structure likely leads to improved intertube coupling that enhances exciton transport within the (7,5) films, consistent with the results of our pump-probe measurements.

  12. Photoluminescence Imaging of Polyfluorene Surface Structures on Semiconducting Carbon Nanotubes: Implications for Thin Film Exciton Transport

    Energy Technology Data Exchange (ETDEWEB)

    Hartmann, Nicolai F.; Pramanik, Rajib; Dowgiallo, Anne-Marie; Ihly, Rachelle; Blackburn, Jeffrey L.; Doorn, Stephen K.

    2016-12-27

    Single-walled carbon nanotubes (SWCNTs) have potential to act as light-harvesting elements in thin film photovoltaic devices, but performance is in part limited by the efficiency of exciton diffusion processes within the films. Factors contributing to exciton transport can include film morphology encompassing nanotube orientation, connectivity, and interaction geometry. Such factors are often defined by nanotube surface structures that are not yet well understood. Here, we present the results of a combined pump-probe and photoluminescence imaging study of polyfluorene (PFO)-wrapped (6,5) and (7,5) SWCNTs that provide additional insight into the role played by polymer structures in defining exciton transport. Pump-probe measurements suggest exciton transport occurs over larger length scales in films composed of PFO-wrapped (7,5) SWCNTs, compared to those prepared from PFO-bpy-wrapped (6,5) SWCNTs. To explore the role the difference in polymer structure may play as a possible origin of differing transport behaviors, we performed a photoluminescence imaging study of individual polymer-wrapped (6,5) and (7,5) SWCNTs. The PFO-bpy-wrapped (6,5) SWCNTs showed more uniform intensity distributions along their lengths, in contrast to the PFO-wrapped (7,5) SWCNTs, which showed irregular, discontinuous intensity distributions. These differences likely originate from differences in surface coverage and suggest the PFO wrapping on (7,5) nanotubes produces a more open surface structure than is available with the PFO-bpy wrapping of (6,5) nanotubes. The open structure likely leads to improved intertube coupling that enhances exciton transport within the (7,5) films, consistent with the results of our pump-probe measurements.

  13. Development of a structural health monitoring system for the life assessment of critical transportation infrastructure.

    Energy Technology Data Exchange (ETDEWEB)

    Roach, Dennis Patrick; Jauregui, David Villegas (New Mexico State University, Las Cruces, NM); Daumueller, Andrew Nicholas (New Mexico State University, Las Cruces, NM)

    2012-02-01

    Recent structural failures such as the I-35W Mississippi River Bridge in Minnesota have underscored the urgent need for improved methods and procedures for evaluating our aging transportation infrastructure. This research seeks to develop a basis for a Structural Health Monitoring (SHM) system to provide quantitative information related to the structural integrity of metallic structures to make appropriate management decisions and ensuring public safety. This research employs advanced structural analysis and nondestructive testing (NDT) methods for an accurate fatigue analysis. Metal railroad bridges in New Mexico will be the focus since many of these structures are over 100 years old and classified as fracture-critical. The term fracture-critical indicates that failure of a single component may result in complete collapse of the structure such as the one experienced by the I-35W Bridge. Failure may originate from sources such as loss of section due to corrosion or cracking caused by fatigue loading. Because standard inspection practice is primarily visual, these types of defects can go undetected due to oversight, lack of access to critical areas, or, in riveted members, hidden defects that are beneath fasteners or connection angles. Another issue is that it is difficult to determine the fatigue damage that a structure has experienced and the rate at which damage is accumulating due to uncertain history and load distribution in supporting members. A SHM system has several advantages that can overcome these limitations. SHM allows critical areas of the structure to be monitored more quantitatively under actual loading. The research needed to apply SHM to metallic structures was performed and a case study was carried out to show the potential of SHM-driven fatigue evaluation to assess the condition of critical transportation infrastructure and to guide inspectors to potential problem areas. This project combines the expertise in transportation infrastructure at New

  14. Integrated analysis of residue coevolution and protein structure in ABC transporters.

    Directory of Open Access Journals (Sweden)

    Attila Gulyás-Kovács

    Full Text Available Intraprotein side chain contacts can couple the evolutionary process of amino acid substitution at one position to that at another. This coupling, known as residue coevolution, may vary in strength. Conserved contacts thus not only define 3-dimensional protein structure, but also indicate which residue-residue interactions are crucial to a protein's function. Therefore, prediction of strongly coevolving residue-pairs helps clarify molecular mechanisms underlying function. Previously, various coevolution detectors have been employed separately to predict these pairs purely from multiple sequence alignments, while disregarding available structural information. This study introduces an integrative framework that improves the accuracy of such predictions, relative to previous approaches, by combining multiple coevolution detectors and incorporating structural contact information. This framework is applied to the ABC-B and ABC-C transporter families, which include the drug exporter P-glycoprotein involved in multidrug resistance of cancer cells, as well as the CFTR chloride channel linked to cystic fibrosis disease. The predicted coevolving pairs are further analyzed based on conformational changes inferred from outward- and inward-facing transporter structures. The analysis suggests that some pairs coevolved to directly regulate conformational changes of the alternating-access transport mechanism, while others to stabilize rigid-body-like components of the protein structure. Moreover, some identified pairs correspond to residues previously implicated in cystic fibrosis.

  15. Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family.

    Science.gov (United States)

    Geertsma, Eric R; Chang, Yung-Ning; Shaik, Farooque R; Neldner, Yvonne; Pardon, Els; Steyaert, Jan; Dutzler, Raimund

    2015-10-01

    The SLC26 family of membrane proteins combines a variety of functions within a conserved molecular scaffold. Its members, besides coupled anion transporters and channels, include the motor protein Prestin, which confers electromotility to cochlear outer hair cells. To gain insight into the architecture of this protein family, we characterized the structure and function of SLC26Dg, a facilitator of proton-coupled fumarate symport, from the bacterium Deinococcus geothermalis. Its modular structure combines a transmembrane unit and a cytoplasmic STAS domain. The membrane-inserted domain consists of two intertwined inverted repeats of seven transmembrane segments each and resembles the fold of the unrelated transporter UraA. It shows an inward-facing, ligand-free conformation with a potential substrate-binding site at the interface between two helix termini at the center of the membrane. This structure defines the common framework for the diverse functional behavior of the SLC26 family.

  16. Electron transport in n-doped Si/SiGe quantum cascade structures

    Science.gov (United States)

    Lazic, I.; Ikonic, Z.; Milanovic, V.; Kelsall, R. W.; Indjin, D.; Harrison, P.

    2007-05-01

    An electron transport model in n-Si/SiGe quantum cascade or superlattice structures is described. The model uses the electronic structure calculated within the effective-mass complex-energy framework, separately for perpendicular (Xz) and in-plane (Xxy) valleys, the degeneracy of which is lifted by strain, and additionally by size quantization. The transport is then described via scattering between quantized states, using a rate equations approach and tight-binding expansion, taking the coupling with two nearest-neighbor periods. Acoustic phonon, optical phonon, alloy disorder, and interface roughness scattering are taken into account. The calculated current/voltage dependence and gain profiles are presented for two simple superlattice structures.

  17. Electronic structure and transport properties of the Heusler compound Co{sub 2}TiAl

    Energy Technology Data Exchange (ETDEWEB)

    Graf, Tanja; Fecher, Gerhard H; Barth, Joachim; Winterlik, Juergen; Felser, Claudia, E-mail: fecher@uni-mainz.d [Johannes Gutenberg Universitaet, Institut fuer Analytische und Anorganische Chemie, 55099 Mainz (Germany)

    2009-04-21

    The properties of the Heusler compound Co{sub 2}TiAl were investigated in detail by experimental techniques and theoretical methods. X-ray diffraction measurements indicate that as-cast samples of the compound exhibit the L2{sub 1} structure with a small amount of B2-type disorder. This leads to a reduced saturation magnetization per formula unit of 0.747 {mu}{sub B}. The Curie temperature is approximately 120 K. The transport properties are influenced by the change in the electronic structure at the Curie temperature, as revealed experimentally by conductivity, thermal transport and specific heat measurements. Different theoretical models based on ab initio calculations of the electronic structure are used to explain the experimental observations.

  18. Quantum transport model for zigzag molybdenum disulfide nanoribbon structures : A full quantum framework

    Directory of Open Access Journals (Sweden)

    Chun-Nan Chen

    2016-08-01

    Full Text Available Mainly based on non-equilibrium Green’s function technique in combination with the three-band model, a full atomistic-scale and full quantum method for solving quantum transport problems of a zigzag-edge molybdenum disulfide nanoribbon (zMoSNR structure is proposed here. For transport calculations, the relational expressions of a zMoSNR crystalline solid and its whole device structure are derived in detail and in its integrity. By adopting the complex-band structure method, the boundary treatment of this open boundary system within the non-equilibrium Green’s function framework is so straightforward and quite sophisticated. The transmission function, conductance, and density of states of zMoSNR devices are calculated using the proposed method. The important findings in zMoSNR devices such as conductance quantization, van Hove singularities in the density of states, and contact interaction on channel are presented and explored in detail.

  19. Coherent thermoelectric transport in single, double, and U-bend structures

    Energy Technology Data Exchange (ETDEWEB)

    Pye, A. J.; Faux, D. A.; Kearney, M. J. [Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom)

    2015-02-14

    Coherent, i.e., ballistic, thermoelectric transport in electron waveguide structures containing right-angle bends in single, double, and U-bend configurations is investigated. A theory based on Green's functions is used to derive the transmission function (and from that the transport coefficients) and allows for the inclusion of realistic models of spatially distributed imperfections. The results for the single and double-bend structures are presented in more detail than elsewhere in the literature. In the U-bend structure, sharp resonances in the stop-band region of the transmission function lead to large-magnitude peaks in the thermopower and consequently a large thermoelectric figure of merit (of order ten in some instances). These properties are still readily apparent even in the presence of moderate edge roughness or Anderson disorder.

  20. Energy-filtered Electron Transport Structures for Low-power Low-noise 2-D Electronics.

    Science.gov (United States)

    Pan, Xuan; Qiu, Wanzhi; Skafidas, Efstratios

    2016-10-31

    In addition to cryogenic techniques, energy filtering has the potential to achieve high-performance low-noise 2-D electronic systems. Assemblies based on graphene quantum dots (GQDs) have been demonstrated to exhibit interesting transport properties, including resonant tunnelling. In this paper, we investigate GQDs based structures with the goal of producing energy filters for next generation lower-power lower-noise 2-D electronic systems. We evaluate the electron transport properties of the proposed GQD device structures to demonstrate electron energy filtering and the ability to control the position and magnitude of the energy passband by appropriate device dimensioning. We also show that the signal-to-thermal noise ratio performance of the proposed nanoscale device can be modified according to device geometry. The tunability of two-dimensional GQD structures indicates a promising route for the design of electron energy filters to produce low-power and low-noise electronics.

  1. Interfacial Structure, Dynamics, and Transport of Polyelectrolyte Membrane Materials for Fuel Cells

    Science.gov (United States)

    Soles, Christopher; Page, K.; Eastman, S.; Kim, S.; Kang, S.; Dura, J.; National Institute of Standards; Technology; Polymers Divison Team; NIST Collaboration

    2011-03-01

    Polymer electrolyte membranes (PEM) fuel cells show promise for a wide range of applications both in the transportation sector and for stationary power production due to their high charge density and low operating temperatures. While the structure and transport of bulk PEMs have been studied extensively, little is known about these materials at interfaces and under confinement, as they exist within the membrane electrode assembly (MEA). Using neutron/ x-ray reflectivity and polarization-modulation infrared reflection-absorption spectroscopy, we have studied the polymer-substrate interfacial structure, swelling, and water transport as function of humidity, surface chemistry, and film thickness. The interfacial structure is highly dependent upon the substrate surface chemistry and the swelling/water diffusivity are suppressed when the PEM is confined to a thin film. This new information will enable researchers to more accurately model the performance of the MEA as current simulations typically rely on bulk property values to predict water and proton transport under these conditions.

  2. Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA.

    Science.gov (United States)

    Guskov, Albert; Nordin, Nurhuda; Reynaud, Aline; Engman, Henrik; Lundbäck, Anna-Karin; Jong, Agnes Jin Oi; Cornvik, Tobias; Phua, Terri; Eshaghi, Said

    2012-11-06

    Despite the importance of Mg(2+) for numerous cellular activities, the mechanisms underlying its import and homeostasis are poorly understood. The CorA family is ubiquitous and is primarily responsible for Mg(2+) transport. However, the key questions-such as, the ion selectivity, the transport pathway, and the gating mechanism-have remained unanswered for this protein family. We present a 3.2 Å resolution structure of the archaeal CorA from Methanocaldococcus jannaschii, which is a unique complete structure of a CorA protein and reveals the organization of the selectivity filter, which is composed of the signature motif of this family. The structure reveals that polar residues facing the channel coordinate a partially hydrated Mg(2+) during the transport. Based on these findings, we propose a unique gating mechanism involving a helical turn upon the binding of Mg(2+) to the regulatory intracellular binding sites, and thus converting a polar ion passage into a narrow hydrophobic pore. Because the amino acids involved in the uptake, transport, and gating are all conserved within the entire CorA family, we believe this mechanism is general for the whole family including the eukaryotic homologs.

  3. Electrical transport properties of graphene on SiO2 with specific surface structures

    OpenAIRE

    Nagashio, K.; Yamashita, T; Nishimura, T.; K. Kita; Toriumi, A.

    2011-01-01

    The mobility of graphene transferred on a SiO2/Si substrate is limited to ~10,000 cm2/Vs. Without understanding the graphene/SiO2 interaction, it is difficult to improve the electrical transport properties. Although surface structures on SiO2 such as silanol and siloxane groups are recognized, the relation between the surface treatment of SiO2 and graphene characteristics has not yet been elucidated. This paper discusses the electrical transport properties of graphene on specific surface stru...

  4. Development of pressure containment and damage tolerance technology for composite fuselage structures in large transport aircraft

    Science.gov (United States)

    Smith, P. J.; Thomson, L. W.; Wilson, R. D.

    1986-01-01

    NASA sponsored composites research and development programs were set in place to develop the critical engineering technologies in large transport aircraft structures. This NASA-Boeing program focused on the critical issues of damage tolerance and pressure containment generic to the fuselage structure of large pressurized aircraft. Skin-stringer and honeycomb sandwich composite fuselage shell designs were evaluated to resolve these issues. Analyses were developed to model the structural response of the fuselage shell designs, and a development test program evaluated the selected design configurations to appropriate load conditions.

  5. IMPROVEMENT OF THE SUPPORTING STRUCTURE OF PLATFORM CAR FOR HIGHER EFFICIENCY OF CONTAINER TRANSPORTATIONS

    Directory of Open Access Journals (Sweden)

    A. O. Lovska

    2017-02-01

    Full Text Available Purpose. The article is aimed to improve supporting structures of the platform car to increase the efficiency of container transportations. Methodology. In order to achieve the objective, the strength investigations of the universal platform car of the model 13-401 were conducted, strength reserves of the supporting elements were defined, and more optimal profiles of basic longitudinal beams of the frame in terms of the minimum material capacity were proposed. Decision correctness was confirmed by the strength calculation of the platform car supporting structure at basic loading operational modes and fatigue taking into account the research database of 107 cycles. It has been proposed to equip a platform car with swing fitting stops for fastening containers on the frame, which allows transportation of 20ft and 40ft containers. In order to improve container transportation efficiency along international transport corridors running through Ukraine, a platform car of articulated type has been designed on the base of the improved platform car structure. The mathematical simulation of dynamic loads of the platform car with containers (two 1CC containers at operational loading modes has been carried out, the maximum accelerations influencing the support structure have been defined, and their multiple values have been considered in computer simulation of the strength of the platform car of articulated type. Findings. The support structure of the platform car of articulated type on the basis of the standard platform car has been developed. Refined values of dynamic loads influencing supporting structure the platform car of articulated type with containers at operational loading modes have been obtained; the maximum equivalent stresses in the platform car support structure have been defined. Originality and practical value. A mathematical model of displacements for a platform car of articulated type with containers at operational loading modes of

  6. Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport

    Energy Technology Data Exchange (ETDEWEB)

    Long, Feng; Su, Chih-Chia; Zimmermann, Michael T.; Boyken, Scott E.; Rajashankar, Kanagalaghatta R.; Jernigan, Robert L.; Yu, Edward W. (Cornell); (Iowa State)

    2010-09-23

    Gram-negative bacteria, such as Escherichia coli, frequently use tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel various toxic compounds from the cell. The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. No previous structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner-membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide new structural information about the HME subfamily of RND efflux pumps. The structures suggest that the metal-binding sites, formed by a three-methionine cluster, are located within the cleft region of the periplasmic domain. This cleft is closed in the apo-CusA form but open in the CusA-Cu(I) and CusA-Ag(I) structures, which directly suggests a plausible pathway for ion export. Binding of Cu(I) and Ag(I) triggers significant conformational changes in both the periplasmic and transmembrane domains. The crystal structure indicates that CusA has, in addition to the three-methionine metal-binding site, four methionine pairs - three located in the transmembrane region and one in the periplasmic domain. Genetic analysis and transport assays suggest that CusA is capable of actively picking up metal ions from the cytosol, using these methionine pairs or clusters to bind and export metal ions. These structures suggest a stepwise shuttle mechanism for transport between these sites.

  7. Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding

    NARCIS (Netherlands)

    Soysa, R.; Venselaar, H.; Poston, J.; Ullman, B.; Hasne, M.P.

    2013-01-01

    The TcPOT1.1 gene from Trypanosoma cruzi encodes a high affinity putrescine-cadaverine transporter belonging to the APC (amino acid/polyamine/organocation) transporter superfamily. No experimental three-dimensional structure exists for any eukaryotic member of the APC family, and thus the structural

  8. Transport Properties of Two-Dimensional Electron Gases in Antiparallel Magnetic-Electric Barrier Structures

    Institute of Scientific and Technical Information of China (English)

    PING Yun-Xia; CHENG Ze

    2006-01-01

    We study theoretically transport properties of two-dimensional electron gases through antiparallel magnetic electric barrier structures. Two kinds of magnetic barrier configurations are employed: one is that the strength of the double δ-function in opposite directions is equal and the other is that the strength is unequal. Similarities and differences of electronic transports are presented. It is found that the transmission and the conductance depend strongly on the shape of the magnetic barrier and the height of the electric barrier. The results indicate that this system does not possess any spin filtering and spin polarization and electron gases can realize perfect resonant tunneling and wave-vector filtering properties. Moreover, the strength of the effect of the inhomogeneous magnetic field on the transport properties is discussed.

  9. Theoretical study on charge injection and transport properties of six emitters with push-pull structure

    Science.gov (United States)

    Lin, Tao; Liu, Xiaojun; Lou, Zhidong; Hou, Yanbing; Teng, Feng

    2014-08-01

    The charge injection and transport properties of six organic light-emitting molecules with push-pull structures were studied by theoretical calculations. The ground-state geometries for the neutral, cationic and anionic states were optimized using density functional theory. Subsequently, the ionization potentials and electron affinities were calculated. We computed the reorganization energies and the transfer integrals based on the Marcus electron transfer theory. It was found that in addition to being emitters the six compounds are multifunctional materials being capable of transport for both holes and electrons. Moreover, the double-branched compound DCDPC2 was found to have higher charge injection ability and better balanced charge transport properties than single-branched compounds.

  10. [Structure and function of heavy metal transporter P(1B)-ATPase in plant: a review].

    Science.gov (United States)

    Zhang, Yuxiu; Zhang, Yuanya; Sun, Tao; Chai, Tuanyao

    2010-06-01

    The regulation of the heavy-metal accumulation in vivo for plant survival is very complex. The metal cation transporter plays key roles in the metabolic process. P(1B)-ATPases are the only subgroup of P-ATPases that contribute to heavy metal homeostasis presented in most organisms. Arabidopsis thaliana contains eight genes encoding P(1B)-ATPases. The current reports show that the functions of P(1B)-ATPases are involved in maintaining metal homeostasis, transporting and detoxification in plants. P(1B)-ATPases not only mediated metal ion mobilization and uptake in roots, but also contribute to the metal transport, storage and tolerance in shoots, especially in heavy metal hyperaccumulators. In this paper, we reviewed and discussed the evolution, classification, structure and function of P(1B)-ATPases in plants. HMAs-transgenic manipulation could be a feasible approach for phytoremediation and mineral nutrition fortification.

  11. Electronic transport on the spatial structure of the protein: Three-dimensional lattice model

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Ciências Biológicas, Universidade Federal do Piauí, 64800-000 Floriano, PI (Brazil); Frazão, N.F. [Centro de Educação e Saúde, Universidade Federal de Campina Grande, 581750-000 Cuité, PB (Brazil); Macedo-Filho, A., E-mail: amfilho@gmail.com [Campus Prof. Antonio Geovanne Alves de Sousa, Universidade Estadual do Piauí, 64260-000 Piripiri, PI (Brazil)

    2017-01-30

    Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.

  12. LeuT: a prokaryotic stepping stone on the way to a eukaryotic neurotransmitter transporter structure.

    Science.gov (United States)

    Singh, Satinder K

    2008-01-01

    Ion-coupled secondary transport is utilized by a broad range of integral membrane proteins to catalyze the energetically unfavorable movement of solute molecules across a lipid bilayer. Members of the solute carrier 6 (SLC6) family, present in both prokaryotes and eukaryotes, are sodium-coupled symporters that play crucial roles in processes as diverse as nutrient uptake and neurotransmitter clearance. The crystal structure of LeuT, a bacterial member of this family, provided the first atomic-level glimpse into overall architecture, pinpointed the substrate and sodium binding sites and implicated candidate helices and residues in the "gating" conformational changes that accompany ion binding and release. The structure is consistent with a wealth of elegant biochemical data on the eukaryotic counterparts and has for the first time permitted the construction of accurate homology models that can be directly tested experimentally. Sequence identity is especially high near the substrate and sodium binding sites and, thus, molecular insights within these regions have been substantial. However, there are several topics relevant to transport mechanism, inhibition and regulation that structure/function studies of LeuT cannot adequately address, suggesting the need for a eukaryotic transporter crystal structure.

  13. Atomic resolution structure of the E. coli YajR transporter YAM domain

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Daohua [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Zhao, Yan [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); Zhang, Xuejun C., E-mail: zhangc@ibp.ac.cn [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China)

    2014-07-25

    Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration.

  14. Mathematical structure of ocean container transport systems; Kaiyo container yuso system no suriteki kozo ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Shinkai, A. [Kyushu University, Fukuoka (Japan). Faculty of Engineering; Chikushi, Y. [Nippon Telegraph and Telephone Corp., Tokyo (Japan)

    1997-10-01

    Mathematical structure of a vessel arrangement program was discussed in order to learn roles of container ships in ocean transport systems among China, NIES/ASEAN countries and Japan. Formulation is possible on a mathematical handling method for sailing route connection diagrams between ports, a transport network to indicate container movements, a service network to indicate sailing routes, and a network generalizing them. This paper describes an analysis made on the container transport system between Japan and China, taken as an example. Four ports were selected each from Japan and China, and the statistical database for fiscals 1996 and 1994 was utilized to set models for: (a) the liner network system with transshipment at the port of Shanghai and (b) the cruising route system going through the ports of Yokohama, Nagoya and Kobe. A hypothesis was set that a consortium (coordinated ship allocation) can be implemented ideally and completely. The transport network (a) is lower by 10% in total cost than the transport network (b), resulting in 1.6 times greater productivity. Actual service network is closer to the network (b), but the system can be utilized for discussing guidelines on vessel arrangement programs with which shipping companies pursue better management efficiency under a condition that the consortium can be formed. 10 refs., 6 figs., 2 tabs.

  15. Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family

    Science.gov (United States)

    Ehrnstorfer, Ines A.; Manatschal, Cristina; Arnold, Fabian M.; Laederach, Juerg; Dutzler, Raimund

    2017-01-01

    Secondary active transporters of the SLC11/NRAMP family catalyse the uptake of iron and manganese into cells. These proteins are highly conserved across all kingdoms of life and thus likely share a common transport mechanism. Here we describe the structural and functional properties of the prokaryotic SLC11 transporter EcoDMT. Its crystal structure reveals a previously unknown outward-facing state of the protein family. In proteoliposomes EcoDMT mediates proton-coupled uptake of manganese at low micromolar concentrations. Mutants of residues in the transition-metal ion-binding site severely affect transport, whereas a mutation of a conserved histidine located near this site results in metal ion transport that appears uncoupled to proton transport. Combined with previous results, our study defines the conformational changes underlying transition-metal ion transport in the SLC11 family and it provides molecular insight to its coupling to protons. PMID:28059071

  16. Structure and Morphology Control in Thin Films of Conjugated Polymers for an Improved Charge Transport

    Directory of Open Access Journals (Sweden)

    Haiyang Wang

    2013-11-01

    Full Text Available The morphological and structural features of the conjugated polymer films play an important role in the charge transport and the final performance of organic optoelectronics devices [such as organic thin-film transistor (OTFT and organic photovoltaic cell (OPV, etc.] in terms of crystallinity, packing of polymer chains and connection between crystal domains. This review will discuss how the conjugated polymer solidify into, for instance, thin-film structures, and how to control the molecular arrangement of such functional polymer architectures by controlling the polymer chain rigidity, polymer solution aggregation, suitable processing procedures, etc. These basic elements in intrinsic properties and processing strategy described here would be helpful to understand the correlation between morphology and charge transport properties and guide the preparation of efficient functional conjugated polymer films correspondingly.

  17. Charge transport in graphene and light propagation in periodic dielectric structures with metamaterials: a comparative study

    CERN Document Server

    Bliokh, Yury; Nori, Franco

    2013-01-01

    We explore the optical properties of periodic layered media containing left-handed metamaterials. This study is facilitated by several analogies between the propagation of light in such media and charge transport in graphene. We derive conditions when these two problems become equivalent, i.e., the equations and the boundary conditions for the corresponding wave functions coincide. It is shown that the photonic band-gap structure of a periodic system built of alternating left- and right-handed dielectrics contains conical singularities similar to the Dirac points in the energy spectrum of charged quasiparticles in graphene. Such singularities in the zone structure of the infinite systems give rise to rather unusual properties of the light transport in finite samples. In a single numerical experiment (propagation of a Gaussian beam through a mixed stack of normal and meta-dielectrics) we demonstrate simultaneously four Dirac point-induced anomalies: (i) diffusion-like decay of the intensity at forbidden freque...

  18. Urban structure and transport-related climate impact. An overview of knowledge; Stadsstruktur och transportrelaterad klimatpaaverkan. En kunskapsoeversikt

    Energy Technology Data Exchange (ETDEWEB)

    Tornberg, Patrik; Eriksson, Inga-Maj

    2012-07-01

    There is considerable interest, both in Sweden and at the EU level, in what urban and spatial planning can contribute with to reduce the need for motorized transports in cities.This report highlights what recent research findings and other sources of knowledge say about the importance of urban density, mixed functions, regional structure and the scope and design of transport infrastructure, for the transportation patterns of society, with particular focus on passenger transport. Essential to reducing the need for motorized transport (car travel) in cities is that accessibility to various functions and destinations in the city is better by walking, cycling and public transport than by car. An assessment of proposed measures for physical changes in a particular city requires an in depth understanding of how the transport system functions and its vulnerability, capacity problems, etc., as well as how existing and new built environments can contribute to conditions for walking, cycling and public transport, in each particular context.

  19. Logistics real estate markets: indicators of structural change, linking land use and freight transport

    OpenAIRE

    Hesse, Markus

    2002-01-01

    The system of physical distribution that comprises transport and logistics, warehousing and wholesale, is an ideal indicator of structural change. Distribution and logistics have developed dynamically, with respect to new technologies, corporate restructuring, and a changing market environment. Whereas traditional logistics were characterized primarily by the demand of manufacturing customers for the shipment of bulk-commodities, modern production and service systems require frequent deliveri...

  20. On Theory of Dispersive Transport in a Two-Layer Polymer Structure

    Science.gov (United States)

    Sibatov, R. T.; Morozova, E. V.

    2016-09-01

    Dispersive transport of charge carriers in a two-layer polymer structure is modeled on the basis of the integrodifferential equation of hereditary diffusion. The model of multiple trapping in a bilayer is generalized to the case of an arbitrary density of localized states. With the help of an efficient Monte Carlo algorithm, curves of the transient current are calculated and their features are explained within the framework of a stochastic interpretation of the process.

  1. The water mass structure and transports in the Atlantic Subpolar Gyre

    Science.gov (United States)

    García-Ibáñez, Maribel I.; Pardo, Paula C.; Carracedo, Lidia I.; Mercier, Herlé; Lherminier, Pascale; Ríos, Aida F.; Pérez, Fiz F.

    2014-05-01

    The water mass structure, mixing and spreading in the North Atlantic Subpolar Gyre (SPG) were analyzed by means of an extended Optimum MultiParameter (eOMP) approach over the six repeats of the WOCE A25 hydrographic line located at the southern boundary of this gyre. The data includes the Fourex (4x) line taken in 1997 and the five repeat sections of the OVIDE line taken every other year from 2002 to 2010. We proposed 10 water masses, defined by their thermohaline properties (potential temperature and salinity), oxygen and nutrients (nitrate, phosphate and silicate), to resolve the water mass structure of the SPG. The eOMP enables to decompose the transports by water mass quantitatively. Our model provides water mass distributions that are able to reproduce the input data of potential temperature, salinity and silicate with r2>0.997 and of oxygen, nitrate and phosphate with r2>0.96. By combining the velocity field and the water mass structure across each section we provide the relative contribution of each water mass to the Meridional Overturning Circulation (MOC) and we evaluate the water mass transformation in the North Atlantic. The MOC upper limb during OVIDE (2002-2010) is constituted by the northward transports of the central waters (9.4 Sv; 1 Sv = 106 m3 s-1), the Subarctic Intermediate Water (SAIW, 2.8 Sv) and the Subpolar Mode Water (SPMW) of the Iceland Basin (2.1 Sv). The MOC lower limb is constituted by the southward transports of the Iceland-Scotland Overflow Water (ISOW, 2.9 Sv), the Denmark Strait Overflow Water (DSOW, 2.5 Sv), the Polar Intermediate Water (PIW, 0.8 Sv), the Labrador Sea Water (LSW, 3.6 Sv) and the SPMW of the Irminger Sea (4.7 Sv). These results contrast with those obtained for the 1997, cruise developed after a period of high NAO index. The greater MOC strength in 1997 resulted in greater northward transports of central waters (17.5 Sv), while the SAIW transports remained approximately unchanged. The increase of the northward

  2. Research Update: Structural and transport properties of (Ca,LaFeAs2 single crystal

    Directory of Open Access Journals (Sweden)

    F. Caglieris

    2016-02-01

    Full Text Available Structural and transport properties in the normal and superconducting states are investigated in a Ca0.8La0.2FeAs2 single crystal with Tc = 27 K, belonging to the newly discovered 112 family of iron based superconductors. The transport critical current density Jc for both field directions measured in a focused ion beam patterned microbridge reveals a weakly field dependent and low anisotropic behaviour with a low temperature value as high as Jc(B = 0 ∼ 105 A/cm2. This demonstrates not only bulk superconductivity but also the potential of 112 superconductors towards applications. Interestingly, this superconducting compound undergoes a structural transition below 100 K which is evidenced by temperature-dependent X-ray diffraction measurements. Data analysis of Hall resistance and magnetoresistivity indicate that magnetotransport properties are largely dominated by an electron band, with a change of regime observed in correspondence of the onset of a structural transition. In the low temperature regime, the contribution of a hole band to transport is suggested, possibly playing a role in determining the superconducting state.

  3. Research Update: Structural and transport properties of (Ca,La)FeAs{sub 2} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Caglieris, F.; Pallecchi, I.; Lamura, G.; Putti, M. [CNR-SPIN and Università di Genova, Via Dodecaneso 33, I-16146 Genova (Italy); Sala, A. [CNR-SPIN and Università di Genova, Via Dodecaneso 33, I-16146 Genova (Italy); Department of Applied Chemistry, The University of Tokyo, Bunkyo, Tokyo 113-8656 (Japan); National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565 (Japan); Fujioka, M. [National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0047 (Japan); Hokkaido University, Sapporo, Hokkaido 001-0020 (Japan); Hummel, F.; Johrendt, D. [Ludwig-Maximilians-Universität München, Department Chemie, Butenandtstr. 5-13, 81377 München (Germany); Takano, Y. [National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0047 (Japan); Ishida, S.; Iyo, A.; Eisaki, H. [National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565 (Japan); Ogino, H.; Yakita, H. [Department of Applied Chemistry, The University of Tokyo, Bunkyo, Tokyo 113-8656 (Japan); Shimoyama, J. [Department of Applied Chemistry, The University of Tokyo, Bunkyo, Tokyo 113-8656 (Japan); Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258 (Japan)

    2016-02-01

    Structural and transport properties in the normal and superconducting states are investigated in a Ca{sub 0.8}La{sub 0.2}FeAs{sub 2} single crystal with T{sub c} = 27 K, belonging to the newly discovered 112 family of iron based superconductors. The transport critical current density J{sub c} for both field directions measured in a focused ion beam patterned microbridge reveals a weakly field dependent and low anisotropic behaviour with a low temperature value as high as J{sub c}(B = 0) ∼ 10{sup 5} A/cm{sup 2}. This demonstrates not only bulk superconductivity but also the potential of 112 superconductors towards applications. Interestingly, this superconducting compound undergoes a structural transition below 100 K which is evidenced by temperature-dependent X-ray diffraction measurements. Data analysis of Hall resistance and magnetoresistivity indicate that magnetotransport properties are largely dominated by an electron band, with a change of regime observed in correspondence of the onset of a structural transition. In the low temperature regime, the contribution of a hole band to transport is suggested, possibly playing a role in determining the superconducting state.

  4. Research Update: Structural and transport properties of (Ca,La)FeAs2 single crystal

    Science.gov (United States)

    Caglieris, F.; Sala, A.; Fujioka, M.; Hummel, F.; Pallecchi, I.; Lamura, G.; Johrendt, D.; Takano, Y.; Ishida, S.; Iyo, A.; Eisaki, H.; Ogino, H.; Yakita, H.; Shimoyama, J.; Putti, M.

    2016-02-01

    Structural and transport properties in the normal and superconducting states are investigated in a Ca0.8La0.2FeAs2 single crystal with Tc = 27 K, belonging to the newly discovered 112 family of iron based superconductors. The transport critical current density Jc for both field directions measured in a focused ion beam patterned microbridge reveals a weakly field dependent and low anisotropic behaviour with a low temperature value as high as Jc(B = 0) ˜ 105 A/cm2. This demonstrates not only bulk superconductivity but also the potential of 112 superconductors towards applications. Interestingly, this superconducting compound undergoes a structural transition below 100 K which is evidenced by temperature-dependent X-ray diffraction measurements. Data analysis of Hall resistance and magnetoresistivity indicate that magnetotransport properties are largely dominated by an electron band, with a change of regime observed in correspondence of the onset of a structural transition. In the low temperature regime, the contribution of a hole band to transport is suggested, possibly playing a role in determining the superconducting state.

  5. Scaling of phloem structure and optimality of photoassimilate transport in conifer needles.

    Science.gov (United States)

    Ronellenfitsch, Henrik; Liesche, Johannes; Jensen, Kaare H; Holbrook, N Michele; Schulz, Alexander; Katifori, Eleni

    2015-02-22

    The phloem vascular system facilitates transport of energy-rich sugar and signalling molecules in plants, thus permitting long-range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in the simplest possible geometry: a linear leaf, found, for example, in the needles of conifer trees. We measure the phloem structure in four tree species representing a diverse set of habitats and needle sizes, from 1 (Picea omorika) to 35 cm (Pinus palustris). We show that the phloem shares common traits across these four species and find that the size of its conductive elements obeys a power law. We present a minimal model that accounts for these common traits and takes into account the transport strategy and natural constraints. This minimal model predicts a power law phloem distribution consistent with transport energy minimization, suggesting that energetics are more important than translocation speed at the leaf level.

  6. Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.

    Science.gov (United States)

    Bozzi, Aaron T; Bane, Lukas B; Weihofen, Wilhelm A; Singharoy, Abhishek; Guillen, Eduardo R; Ploegh, Hidde L; Schulten, Klaus; Gaudet, Rachelle

    2016-12-06

    The widely conserved natural resistance-associated macrophage protein (Nramp) family of divalent metal transporters enables manganese import in bacteria and dietary iron uptake in mammals. We determined the crystal structure of the Deinococcus radiodurans Nramp homolog (DraNramp) in an inward-facing apo state, including the complete transmembrane (TM) segment 1a (absent from a previous Nramp structure). Mapping our cysteine accessibility scanning results onto this structure, we identified the metal-permeation pathway in the alternate outward-open conformation. We investigated the functional impact of two natural anemia-causing glycine-to-arginine mutations that impaired transition metal transport in both human Nramp2 and DraNramp. The TM4 G153R mutation perturbs the closing of the outward metal-permeation pathway and alters the selectivity of the conserved metal-binding site. In contrast, the TM1a G45R mutation prevents conformational change by sterically blocking the essential movement of that helix, thus locking the transporter in an inward-facing state.

  7. Extended Hückel theory for carbon nanotubes: band structure and transport properties.

    Science.gov (United States)

    Zienert, Andreas; Schuster, Jörg; Gessner, Thomas

    2013-05-02

    Extended Hückel theory (EHT) is a well established method for the description of the electronic structure of molecules and solids. In this article, we present a set of extended Hückel parameters for carbon nanotubes (CNTs), obtained by fitting the ab initio band structure of the (6,0) CNT. The new parameters are highly transferable to different types of CNTs. To demonstrate the versatility of the approach, we perform self-consistent EHT-based electron transport calculations for finite length CNTs with metal electrodes.

  8. Structural and transport properties of orthorhombic GdMnO3

    Science.gov (United States)

    Modi, Anchit; Thakur, Rajesh K.; Thakur, Rasna; Gaur, N. K.; Kaurav, N.; Okram, G. S.

    2013-06-01

    We report structural and transport properties of the polycrystalline orthorhombic GdMnO3 compound synthesized by using conventional solid state reaction method. The XRD pattern reveals the single phase formation of the reported compound in orthorhombic crystal structure with space group Pbnm (JCPDS: 25-0337). The temperature dependent resistivity study indicates the highly resistive nature of the compound especially in the low temperature region. The effect of low temperature magnetic ordering can be clearly understood from the resistivity versus temperature plot. The calculated activation energy by using Arrhenius equation fitting are found slightly lesser than the reported value which indicates the lesser dense nature of the prepared compound.

  9. System data communication structures for active-control transport aircraft, volume 2

    Science.gov (United States)

    Hopkins, A. L.; Martin, J. H.; Brock, L. D.; Jansson, D. G.; Serben, S.; Smith, T. B.; Hanley, L. D.

    1981-01-01

    The application of communication structures to advanced transport aircraft are addressed. First, a set of avionic functional requirements is established, and a baseline set of avionics equipment is defined that will meet the requirements. Three alternative configurations for this equipment are then identified that represent the evolution toward more dispersed systems. Candidate communication structures are proposed for each system configuration, and these are compared using trade off analyses; these analyses emphasize reliability but also address complexity. Multiplex buses are recognized as the likely near term choice with mesh networks being desirable for advanced, highly dispersed systems.

  10. Multi-process herbicide transport in structured soil columns: experiments and model analysis.

    Science.gov (United States)

    Köhne, J Maximilian; Köhne, Sigrid; Simůnek, Jirka

    2006-05-01

    Model predictions of pesticide transport in structured soils are complicated by multiple processes acting concurrently. In this study, the hydraulic, physical, and chemical nonequilibrium (HNE, PNE, and CNE, respectively) processes governing herbicide transport under variably saturated flow conditions were studied. Bromide (Br-), isoproturon (IPU, 3-(4-isoprpylphenyl)-1,1-dimethylurea) and terbuthylazine (TER, N2-tert-butyl-6-chloro-N4-ethyl-1,3,5-triazine-2,4-diamine) were applied to two soil columns. An aggregated Ap soil column and a macroporous, aggregated Ah soil column were irrigated at a rate of 1 cm h(-1) for 3 h. Two more irrigations at the same rate and duration followed in weekly intervals. Nonlinear (Freundlich) equilibrium and two-site kinetic sorption parameters were determined for IPU and TER using batch experiments. The observed water flow and Br- transport were inversely simulated using mobile-immobile (MIM), dual-permeability (DPM), and combined triple-porosity (DP-MIM) numerical models implemented in HYDRUS-1D, with improving correspondence between empirical data and model results. Using the estimated HNE and PNE parameters together with batch-test derived equilibrium sorption parameters, the preferential breakthrough of the weakly adsorbed IPU in the Ah soil could be reasonably well predicted with the DPM approach, whereas leaching of the strongly adsorbed TER was predicted less well. The transport of IPU and TER through the aggregated Ap soil could be described consistently only when HNE, PNE, and CNE were simultaneously accounted for using the DPM. Inverse parameter estimation suggested that two-site kinetic sorption in inter-aggregate flow paths was reduced as compared to within aggregates, and that large values for the first-order degradation rate were an artifact caused by irreversible sorption. Overall, our results should be helpful to enhance the understanding and modeling of multi-process pesticide transport through structured soils

  11. Structural determinants of NH3 and NH4+ transport by mouse Rhbg, a renal Rh glycoprotein.

    Science.gov (United States)

    Abdulnour-Nakhoul, Solange; Le, Trang; Rabon, Edd; Hamm, L Lee; Nakhoul, Nazih L

    2016-12-01

    Renal Rhbg is localized to the basolateral membrane of intercalated cells and is involved in NH3/NH4(+) transport. The structure of Rhbg is not yet resolved; however, a high-resolution crystal structure of AmtB, a bacterial homolog of Rh, has been determined. We aligned the sequence of Rhbg to that of AmtB and identified important sites of Rhbg that may affect transport. Our analysis positioned three conserved amino acids, histidine 183 (H183), histidine 342 (H342), and tryptophan 230 (W230), within the hydrophobic pore where they presumably serve to control NH3 transport. A fourth residue, phenylalanine 128 (F128) was positioned at the upper vestibule, presumably contributing to recruitment of NH4(+) We generated three mutations each of H183, H342, W230, and F128 and expressed them in frog oocytes. Immunolabeling showed that W230 and F128 mutants were localized to the cell membrane, whereas H183 and H342 staining was diffuse and mostly intracellular. To determine function, we compared measurements of NH3/NH4(+) and methyl amine (MA)/methyl ammonium (MA(+))-induced currents, intracellular pH, and surface pH (pHs) among oocytes expressing the mutants, Rhbg, or injected with H2O. In H183 and W230 mutants, NH4(+)-induced current and intracellular acidification were inhibited compared with that of Rhbg, and MA-induced intracellular alkalinization was completely absent. Expression of H183A or W230A mutants inhibited NH3/NH4(+)- and MA/MA(+)-induced decrease in pHs to the level observed in H2O-injected oocytes. Mutations of F128 did not significantly affect transport of NH3 or NH4(+) These data demonstrated that mutating H183 or W230 caused loss of function but not F128. H183 and H342 may affect membrane expression of the transporter.

  12. Ionic structures and transport properties of hot dense W and U plasmas

    Science.gov (United States)

    Hou, Yong; Yuan, Jianmin

    2016-10-01

    We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

  13. Structural and electrical transport studies on CrN(001) thin films

    Energy Technology Data Exchange (ETDEWEB)

    Swamy, G. Venkat, E-mail: swamygv@nplindia.org; Rakshit, R. K.; Basheed, G. A.; Maurya, K. K.; Gupta, Anurag [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Road, New Delhi-110012 (India); Academy of Scientific and Innovative Research (AcSIR), CSIR-NPL Campus, Dr. K. S. Krishnan Road, New Delhi - 110012 (India); Kumar, Dinesh; Singh, Manju [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Road, New Delhi-110012 (India)

    2016-05-23

    We report the structural and electrical transport studies on CrN{sub 1-x} (CrN) thin films with varying of N{sub 2} flow (5 – 25 SCCM) in an Argon environment of 25 SCCM. CrN thin films were grown at 600°C, in a multi chamber vacuum system at working pressure of 1×10{sup −2} Torr, under the base pressure of 1×10{sup −7} Torr. Structural and electrical transport measurements were carried out using X-ray diffraction (XRD), atomic force microscopy (AFM) and SQUID magnetometer, respectively. XRD (θ-2θ, ω-2θ, and ω) patterns on CrN thin films revealed a structural phase transition which is associated with the lattice parameter variation from 4.136 to 4.168 Å. The temperature dependent resistivity measurements on CrN/MgO(001) showed a clear change in slope at ≈280 K which confirms the magneto-structural transition of CrN from paramagnetic rock salt face-centered-cubic (FCC) to antiferromagnetic orthorhombic structure.

  14. Structure-dependent optical and electrical transport properties of nanostructured Al-doped ZnO.

    Science.gov (United States)

    Gondoni, P; Ghidelli, M; Di Fonzo, F; Carminati, M; Russo, V; Li Bassi, A; Casari, C S

    2012-09-14

    The structure-property relation of nanostructured Al-doped ZnO thin films has been investigated in detail through a systematic variation of structure and morphology, with particular emphasis on how they affect optical and electrical properties. A variety of structures, ranging from compact polycrystalline films to mesoporous, hierarchically organized cluster assemblies, are grown by pulsed laser deposition at room temperature at different oxygen pressures. We investigate the dependence of functional properties on structure and morphology and show how the correlation between electrical and optical properties can be studied to evaluate energy gap, conduction band effective mass and transport mechanisms. Understanding these properties opens up opportunities for specific applications in photovoltaic devices, where optimized combinations of conductivity, transparency and light scattering are required.

  15. Variable-complexity aerodynamic-structural design of a high-speed civil transport wing

    Science.gov (United States)

    Hutchison, M. G.; Huang, X.; Mason, W. H.; Haftka, R. T.; Grossman, B.

    1992-01-01

    A variable-complexity strategy of combining simple and detailed analysis methods is presented for the design optimization of a high-speed civil transport (HSCT) wing. Two sets of results are shown: the aerodynamic design of the wing using algebraic weight equations for structural considerations, and optimization results of the internal wing structure for a fixed wing configuration. We show example results indicating that using simple analysis methods alone for the calculation of a critical constraint can allow an optimizer to exploit weaknesses in the analysis. The structural optimization results provide a valuable check for the weight equations used in the aerodynamic design. In addition, these results confirm the need for using simple, algebraic models in conjunction with more detailed analysis methods. A strategy of interlaced aerodynanic-structural design is proposed.

  16. Quantum transport in graphene normal-metal superconductor- normal-metal structures

    Directory of Open Access Journals (Sweden)

    H. Mohammadpour

    2008-06-01

    Full Text Available  We study the transport of electrons in a graphene NSN structure in which two normal regions are connected by a superconducting strip of thickness d. Within Dirac-Bogoliubov-de Gennes equations we describe the transmission through the contact in terms of different scattering processes consisting of quasiparticle cotunneling, local and crossed Andreev reflections. Compared to a fully normal structure we show that the angular dependence of the transmission probability is significantly modified by the presence of superconducting correlations. This modifation can be explained in terms of the interplay between Andreev reflection and Klein tunneling of chiral quasiparticles. We further analyze the energy dependence of the resulting differential conductance of the structure. The subgap differential conductance shows features of Andreev reflection and cotunelling processes, which tends to the values of an NS structure for large ds. Above the gap, the differential conductance shows an oscillatory behavior with energy even at very large ds.

  17. Urban structure and transport behaviour. Results from the survey of transport habits; Bystruktur og transportadfaerd. Hvad siger transportvaneundersoegelsen?

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, L.

    2001-12-01

    The purpose of this report is to analyse the effects on private transport and environmental impact from urban size and structure, and the localisation. In this analysis, the CO{sub 2}-emission is used as the indicator of the environmental impact of the transport i.e. as a result of the energy consumption. The report is organised in 3 main chapters concerning localisation of residential areas, workplace, and centre functions. One of the important results from the analyses is the environmental benefit of avoiding residential development in smaller towns and villages. It is especially important to avoid urban sprawl around the big cities. Concentration in the big cities or in the neighbouring cities is environmentally much more promising. On the other hand it might be expedient to promote a slow development with workplaces in smaller towns to get a good balance between inhabitants and workplaces but it is important to give priority to non-specialised workplaces. Residential or business development in whichever size of the cities above 10,000 inhabitants makes no difference. On the other hand an expansion of centre activities has substantial effect on the CO{sub 2}-emission especially in cities with more than 22,000 inhabitants. Variation in localization inside the cities influences the CO{sub 2}-emission much more than the variability between cities. Residential areas as well as workplace intensive business ought to be promoted at central places near the stations. Upon deciding whether to give priority to residential areas or business at an actual area, more aspects need to be considered. One problem is that a residence and a workplace generate different person kilometres and the areas they occupy vary. It seems to be best to give priority to residential areas in the central areas and to business development around the stations. But this depends on the actual conditions and more detailed analyses might also be revealed. A planning policy promoting a development with

  18. Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.

    Science.gov (United States)

    Giménez-Mascarell, Paula; Oyenarte, Iker; Hardy, Serge; Breiderhoff, Tilman; Stuiver, Marchel; Kostantin, Elie; Diercks, Tammo; Pey, Angel L; Ereño-Orbea, June; Martínez-Chantar, María Luz; Khalaf-Nazzal, Reham; Claverie-Martin, Felix; Müller, Dominik; Tremblay, Michel L; Martínez-Cruz, Luis Alfonso

    2017-01-20

    Phosphatases of regenerating liver (PRLs), the most oncogenic of all protein-tyrosine phosphatases (PTPs), play a critical role in metastatic progression of cancers. Recent findings established a new paradigm by uncovering that their association with magnesium transporters of the cyclin M (CNNM) family causes a rise in intracellular magnesium levels that promote oncogenic transformation. Recently, however, essential roles for regulation of the circadian rhythm and reproduction of the CNNM family have been highlighted. Here, we describe the crystal structure of PRL-1 in complex with the Bateman module of CNNM2 (CNNM2BAT), which consists of two cystathionine β-synthase (CBS) domains (IPR000664) and represents an intracellular regulatory module of the transporter. The structure reveals a heterotetrameric association, consisting of a disc-like homodimer of CNNM2BAT bound to two independent PRL-1 molecules, each one located at opposite tips of the disc. The structure highlights the key role played by Asp-558 at the extended loop of the CBS2 motif of CNNM2 in maintaining the association between the two proteins and proves that the interaction between CNNM2 and PRL-1 occurs via the catalytic domain of the phosphatase. Our data shed new light on the structural basis underlying the interaction between PRL phosphatases and CNNM transporters and provides a hypothesis about the molecular mechanism by which PRL-1, upon binding to CNNM2, might increase the intracellular concentration of Mg(2+) thereby contributing to tumor progression and metastasis. The availability of this structure sets the basis for the rational design of compounds modulating PRL-1 and CNNM2 activities.

  19. Transport of magnetic flux and the vertical structure of accretion discs - I. Uniform diffusion coefficients

    Science.gov (United States)

    Guilet, Jérôme; Ogilvie, Gordon I.

    2012-08-01

    Standard models of accretion discs study the transport of mass on a viscous time-scale but do not consider the transport of magnetic flux. The evolution of a large-scale poloidal magnetic field is, however, an important problem because of its role in the launching of jets and winds and in determining the intensity of turbulence. As a consequence, the transport of poloidal magnetic flux should be considered on an equal basis to the transport of mass. In this paper, we develop a formalism to study such a transport of mass and magnetic flux in a thin accretion disc. The governing equations are derived by performing an asymptotic expansion in the limit of a thin disc, in the regime where the magnetic field is dominated by its vertical component. Turbulent viscosity and resistivity are included, with an arbitrary vertical profile that can be adjusted to mimic the vertical structure of the turbulence. At a given radius and time, the rates of transport of mass and magnetic flux are determined by a one-dimensional problem in the vertical direction, in which the radial gradients of various quantities appear as source terms. We solve this problem to obtain the transport rates and the vertical structure of the disc. This paper is then restricted to the idealized case of uniform diffusion coefficients, while a companion paper will study more realistic vertical profiles of these coefficients. We show the advection of weak magnetic fields to be significantly faster than the advection of mass, contrary to what a crude vertical averaging might suggest. This results from the larger radial velocities away from the mid-plane, which barely affect the mass accretion owing to the low density in these regions but do affect the advection of magnetic flux. Possible consequences of this larger accretion velocity include a potentially interesting time dependence with the magnetic flux distribution evolving faster than the mass distribution. If the disc is not too thin, this fast advection

  20. Experimental investigation of internal structure of open-channel flow with intense transport of sediment

    Directory of Open Access Journals (Sweden)

    Matoušek Václav

    2015-12-01

    Full Text Available Gravity-driven open-channel flows carrying coarse sediment over an erodible granular deposit are studied. Results of laboratory experiments with artificial sediments in a rectangular tilting flume are described and analyzed. Besides integral quantities such as flow rate of mixture, transport concentration of sediment and hydraulic gradient, the experiments include measurements of the one-dimensional velocity distribution across the flow. A vertical profile of the longitudinal component of local velocity is measured across the vertical axis of symmetry of a flume cross section using three independent measuring methods. Due to strong flow stratification, the velocity profile covers regions of very different local concentrations of sediment from virtually zero concentration to the maximum concentration of bed packing. The layered character of the flow results in a velocity distribution which tends to be different in the transport layer above the bed and in the sediment-free region between the top of the transport layer and the water surface. Velocity profiles and integral flow quantities are analyzed with the aim of evaluating the layered structure of the flow and identifying interfaces in the flow with a developed transport layer above the upper plane bed.

  1. Electrical Transport and Network Percolation in Graphene and Boron Nitride Mixed-Platelet Structures.

    Science.gov (United States)

    Debbarma, Rousan; Behura, Sanjay; Nguyen, Phong; Sreeprasad, T S; Berry, Vikas

    2016-04-06

    Percolating network of mixed 2D nanomaterials (2DNs) can leverage the unique electronic structures of different 2DNs, their interfacial doping, manipulable conduction pathways, and local traps. Here, we report on the percolation mechanism and electro-capacitive transport pathways of mixed-platelet network of hexagonal boron nitride (hBN) and reduced graphene oxide (rGO), two isostructural and isoelectronic 2DNs. The transport mechanism is explained in terms of electron hopping through isolated hBN defect traps between rGO (possibly via electron tunneling/hopping through "funneling" points). With optical bandgaps of 4.57 and 4.08 eV for the hBN-domains and 2.18 eV for the rGO domains, the network of hBN with rGO exhibits Poole-Frenkel emission-based transport with mean hopping gap of 1.12 nm (∼hBN trilayer) and an activation barrier of ∼15 ± 0.7 meV. Further, hBN (1.7 pF) has a 6-fold lower capacitance than 1:1 hBN:rGO, which has a resistance 2 orders of magnitude higher than that of rGO (1.46 MΩ). These carrier transport results can be applied to other multi-2DN networks for development of next-generation functional 2D-devices.

  2. Antidepressant Specificity of Serotonin Transporter Suggested by Three LeuT-SSRI Structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Z.; Zhen, J; Karpowich, N; Law, C; Reith, M; Wang, D

    2009-01-01

    Sertraline and fluoxetine are selective serotonin re-uptake inhibitors (SSRIs) that are widely prescribed to treat depression. They exert their effects by inhibiting the presynaptic plasma membrane serotonin transporter (SERT). All SSRIs possess halogen atoms at specific positions, which are key determinants for the drugs' specificity for SERT. For the SERT protein, however, the structural basis of its specificity for SSRIs is poorly understood. Here we report the crystal structures of LeuT, a bacterial SERT homolog, in complex with sertraline, R-fluoxetine or S-fluoxetine. The SSRI halogens all bind to exactly the same pocket within LeuT. Mutation at this halogen-binding pocket (HBP) in SERT markedly reduces the transporter's affinity for SSRIs but not for tricyclic antidepressants. Conversely, when the only nonconserved HBP residue in both norepinephrine and dopamine transporters is mutated into that found in SERT, their affinities for all the three SSRIs increase uniformly. Thus, the specificity of SERT for SSRIs is dependent largely on interaction of the drug halogens with the protein's HBP.

  3. Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

    2012-05-25

    Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).

  4. Antidepressant specificity of serotonin transporter suggested by three LeuT-SSRI structures.

    Science.gov (United States)

    Zhou, Zheng; Zhen, Juan; Karpowich, Nathan K; Law, Christopher J; Reith, Maarten E A; Wang, Da-Neng

    2009-06-01

    Sertraline and fluoxetine are selective serotonin re-uptake inhibitors (SSRIs) that are widely prescribed to treat depression. They exert their effects by inhibiting the presynaptic plasma membrane serotonin transporter (SERT). All SSRIs possess halogen atoms at specific positions, which are key determinants for the drugs' specificity for SERT. For the SERT protein, however, the structural basis of its specificity for SSRIs is poorly understood. Here we report the crystal structures of LeuT, a bacterial SERT homolog, in complex with sertraline, R-fluoxetine or S-fluoxetine. The SSRI halogens all bind to exactly the same pocket within LeuT. Mutation at this halogen-binding pocket (HBP) in SERT markedly reduces the transporter's affinity for SSRIs but not for tricyclic antidepressants. Conversely, when the only nonconserved HBP residue in both norepinephrine and dopamine transporters is mutated into that found in SERT, their affinities for all the three SSRIs increase uniformly. Thus, the specificity of SERT for SSRIs is dependent largely on interaction of the drug halogens with the protein's HBP.

  5. Ion Transport and Structural Properties of Polymeric Electrolytes and Ionic Liquids from Molecular Dynamics Simulations

    Science.gov (United States)

    Borodin, Oleg

    2010-03-01

    Molecular dynamics simulations are well suited for exploring electrolyte structure and ion transport mechanisms on the nanometer length scale and the nanosecond time scales. In this presentation we will describe how MD simulations assist in answering fundamental questions about the lithium transport mechanisms in polymeric electrolytes and ionic liquids. In particular, in the first part of the presentation the extent of ion aggregation, the structure of ion aggregates and the lithium cation diffusion in binary polymeric electrolytes will be compared with that of single-ion conducting polymers. In the second part of the talk, the lithium transport in polymeric electrolytes will be compared with that of three ionic liquids ( [emim][FSI] doped with LiFSI , [pyr13][FSI] doped with LiFSI, [emim][BF4] doped with LiBF4). The relation between ionic liquid self-diffusion, conductivity and thermodynamic properties will be discussed in details. A number of correlations between heat of vaporization Hvap, cation-anion binding energy (E+/-), molar volume (Vm), self-diffusion coefficient (D) and ionic conductivity for 29 ionic liquids have been investigated using MD simulations. A significant correlation between D and Hvap has been found, while best correlation was found for -log((D Vm)) vs. Hvap+0.28E+/-. A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids.

  6. Structural insights into nonvesicular lipid transport by the oxysterol binding protein homologue family.

    Science.gov (United States)

    Tong, Junsen; Manik, Mohammad Kawsar; Yang, Huiseon; Im, Young Jun

    2016-08-01

    Sterols such as cholesterol in mammals and ergosterol in fungi are essential membrane components and play a key role in membrane function and in cell signaling. The intracellular distribution and processing of sterols and other phospholipids are in part carried out by oxysterol binding protein-related proteins (ORPs) in eukaryotes. Seven ORPs (Osh1-Osh7 proteins) in yeast have distinct functions in maintaining distribution, metabolism and signaling of intracellular lipids but they share at least one essential function. Significant progress has been made in understanding the ligand specificity and mechanism of non-vesicular lipid transport by ORPs. The unique structural features of Osh proteins explain the diversity and specificity of functions in PI(4)P-coupled lipid transport optimized in membrane contact sites. This review discusses the current advances in structural biology regarding this protein family and its potential functions, introducing them as the key players in the novel pathways of phosphoinositide-coupled directional transport of various lipids. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.

  7. Investigations on structural disorder-induced modifications in the transport behaviour of rare-earth manganites

    Indian Academy of Sciences (India)

    ZALAK JOSHI; D D PANDYA; DAVIT DHRUV; KEVAL GADANI; HETAL BORICHA; SANJAY KANSARA; J H MARKNA; P S SOLANKI; N A SHAH

    2016-08-01

    The results of the studies on structural disorder-induced modifications in the transport behaviour of La$_{0.5}$Pr$_{0.2}$Ca$_{0.3−x}$Ba$_x$MnO$_3$ (LPCBMO) ($0.05 ≤ x ≤ 0.30$) manganites were reported. Structural studies using X-ray diffraction (XRD) measurements confirmed the single phasic nature of all the samples without any detectable impurities. The A-site size disorder ($σ_2$ A) increased from $3.81 \\times 10^{−5} (x = 0.05)$ to $14.9 \\times 10−5 (x = 0.30)$. With the increase in structural disorder in LPCBMO system, the transport improved for the range: $0.15 ≤ x ≤ 0.30$, which can be ascribed to the enhancement in one electron bandwidth which dominates over the structural disorder effect, while for lower values of $x$, strong competition existed between size disorder and one electron bandwidth. Below 50 K, all $\\rho–T$ plots showed resistivity minimum behaviour, which modified with disorder. This behaviour wasdiscussed in detail on the basis of electron–electron interaction having the form: $\\rho = [1/(\\rho_0 + BT^{1/2})] + \\rho_nT_n$. Variation in temperature sensitivity with disorder was also discussed in context of granular morphology and phasesegregation scenario.

  8. Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

    Science.gov (United States)

    Zhang, Tuo; Sui, Dexin; Hu, Jian

    2016-06-01

    The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins.

  9. Structured triglyceride vehicles for oral delivery of halofantrine: examination of intestinal lymphatic transport and bioavailability in conscious rats

    DEFF Research Database (Denmark)

    Holm, René; Porter, Christopher J H; Müllertz, Anette

    2002-01-01

    animals, and this was most pronounced for the animals dosed with the structured triglycerides. CONCLUSIONS: Using MLM as vehicle increases the portal absorption of halofantrine and results in similar lymphatic transport levels when compared to sunflower oil. Total absorption when assessed as absorption...... in the blood plus lymphatic transport for halofantrine after administration in the MLM triglyceride was higher than after administration in sunflower oil.......PURPOSE: To compare the influence of triglyceride vehicle intramolecular structure on the intestinal lymphatic transport and systemic absorption of halofantrine in conscious rats. METHODS: Conscious, lymph cannulated and nonlymph cannulated rats were dosed orally with three structurally different...

  10. The structure and function of the dopamine transporter and its role in CNS diseases.

    Science.gov (United States)

    McHugh, Patrick C; Buckley, David A

    2015-01-01

    In this chapter, we explore the basic science of the dopamine transporter (DAT), an integral component of a system that regulates dopamine homeostasis. Dopamine is a key neurotransmitter for several brain functions including locomotor control and reward systems. The transporter structure, function, mechanism of action, localization, and distribution, in addition to gene regulation, are discussed. Over many years, a wealth of information concerning the DAT has been accrued and has led to increased interest in the role of the DAT in a plethora of central nervous system diseases. These DAT characteristics are explored in relation to a range of neurological and neuropsychiatric diseases, with a particular focus on the genetics of the DAT. In addition, we discuss the pharmacology of the DAT and how this relates to disease and addiction. © 2015 Elsevier Inc. All rights reserved.

  11. How historical copper contamination affects soil structure and mobilization and transport of colloids

    DEFF Research Database (Denmark)

    Paradelo, Marcos; Møldrup, Per; Holmstrup, Martin;

    between 0.01 to 0.43 pore volumes, with longer times for the most contaminated point, likely related with its higher soil density and lower air permeability. The copper pollution affected colloid and tracer transport in the soil columns. The release of colloids especially in the most contaminated points......Copper is accumulated in soils due to human activities such as mining industry, agriculture practises, or waste deposals. High concentrations of copper can affect plants and soil organisms, and subsequently the soil structure and its inner space architecture. In this work we investigated the effect...... of copper concentration on the movement of an inert tracer, tritium, and the mobilization and transport of colloid particles in undisturbed soil cores (10 cm diameter and 8 cm height). The cores were sampled along a copper gradient of 21 to 3837 mg Cu kg-1 soil on an abandoned arable soil polluted by copper...

  12. Structural correlates of the creatine transporter function regulation: the undiscovered country.

    Science.gov (United States)

    Santacruz, Lucia; Jacobs, Danny O

    2016-08-01

    Creatine (Cr) and phosphocreatine constitute an energy shuttle that links ATP production in mitochondria to subcellular locations of ATP consumption. Cells in tissues that are reliant on this energy shuttle, such as myocytes and neurons, appear to have very limited ability to synthesize creatine. Therefore, these cells depend on Cr uptake across the cell membrane by a specialized creatine transporter (CrT solute carrier SLC6A8) in order to maintain intracellular creatine levels. Cr supplementation has been shown to have a beneficial effect in numerous in vitro and in vivo models, particularly in cases of oxidative stress, and is also widely used by athletes as a performance enhancement nutraceutical. Intracellular creatine content is maintained within narrow limits. However, the physiological and cellular mechanisms that mediate Cr transport during health and disease (such as cardiac failure) are not understood. In this narrative mini-review, we summarize the last three decades of research on CrT structure, function and regulation.

  13. Ratchet transport of an active-passive mixture chain in confined structures

    Science.gov (United States)

    Lu, Shi-cai; Ou, Ya-li; Ai, Bao-quan

    2017-09-01

    Rectified transport of the active-passive mixture chain is numerically investigated in periodic confined structures. Due to the out-of-equilibrium property of active particles in the chain, the whole chain can be rectified. It is found that the interaction between particles can significantly affect the rectified transport. When all particles in the chain are active, the directed velocity decreases monotonously with increasing the interaction strength. When the particles are mixture, on increasing the interaction strength, the directed velocity firstly decreases to its minimal value, then increases to its maximal value, and finally decreases to zero. In addition, there exist optimal parameters (self-propelled velocity, the natural length of the spring) at which the average velocity is maximal.

  14. Membrane transporters for the special amino acid glutamine: Structure/function relationships and relevance to human health.

    Directory of Open Access Journals (Sweden)

    Lorena ePochini

    2014-08-01

    Full Text Available Glutamine together with glucose is essential for body’s homeostasis. It is the most abundant amino acid and is involved in many biosynthetic, regulatory and energy production processes. Several membrane transporters which differ in transport modes, ensure glutamine homeostasis by coordinating its absorption, reabsorption and delivery to tissues. These transporters belong to different protein families, are redundant and ubiquitous. Their classification, originally based on functional properties, has recently been associated with the SLC nomenclature. Function of glutamine transporters is studied in cells over-expressing the transporters or, more recently in proteoliposomes harboring the proteins extracted from animal tissues or over-expressed in microorganisms. The role of the glutamine transporters is linked to their transport modes and coupling with Na+ and H+. Most transporters share specificity for other neutral or cationic amino acids. Na+-dependent co-transporters efficiently accumulate glutamine while antiporters regulate the pools of glutamine and other amino acids. The most acknowledged glutamine transporters belong to the SLC1, 6, 7 and 38 families. The members involved in the homeostasis are the co-transporters B0AT1 and the SNAT members 1, 2, 3, 5 and 7; the antiporters ASCT2, LAT1 and 2. The last two are associated to the ancillary CD98 protein. Some information on regulation of the glutamine transporters exist, which, however, need to be deepened. No information at all is available on structures, besides some homology models obtained using similar bacterial transporters as templates. Some models of rat and human glutamine transporters highlight very similar structures between the orthologues. Moreover the presence of glycosylation and/or phosphorylation sites located at the extracellular or intracellular faces has been predicted. ASCT2 and LAT1 are over-expressed in several cancers, thus representing potential targets for

  15. Membrane transporters for the special amino acid glutamine: Structure/function relationships and relevance to human health.

    Science.gov (United States)

    Pochini, Lorena; Scalise, Mariafrancesca; Galluccio, Michele; Indiveri, Cesare

    2014-08-01

    Glutamine together with glucose is essential for body’s homeostasis. It is the most abundant amino acid and is involved in many biosynthetic, regulatory and energy production processes. Several membrane transporters which differ in transport modes, ensure glutamine homeostasis by coordinating its absorption, reabsorption and delivery to tissues. These transporters belong to different protein families, are redundant and ubiquitous. Their classification, originally based on functional properties, has recently been associated with the SLC nomenclature. Function of glutamine transporters is studied in cells over-expressing the transporters or, more recently in proteoliposomes harboring the proteins extracted from animal tissues or over-expressed in microorganisms. The role of the glutamine transporters is linked to their transport modes and coupling with Na+ and H+. Most transporters share specificity for other neutral or cationic amino acids. Na+-dependent co-transporters efficiently accumulate glutamine while antiporters regulate the pools of glutamine and other amino acids. The most acknowledged glutamine transporters belong to the SLC1, 6, 7 and 38 families. The members involved in the homeostasis are the co-transporters B0AT1 and the SNAT members 1, 2, 3, 5 and 7; the antiporters ASCT2, LAT1 and 2. The last two are associated to the ancillary CD98 protein. Some information on regulation of the glutamine transporters exist, which, however, need to be deepened. No information at all is available on structures, besides some homology models obtained using similar bacterial transporters as templates. Some models of rat and human glutamine transporters highlight very similar structures between the orthologues. Moreover the presence of glycosylation and/or phosphorylation sites located at the extracellular or intracellular faces has been predicted. ASCT2 and LAT1 are over-expressed in several cancers, thus representing potential targets for pharmacological intervention.

  16. Peptides actively transported across the tympanic membrane: Functional and structural properties

    Science.gov (United States)

    Kurabi, Arwa; Beasley, Kerry A.; Chang, Lisa; McCann, James; Pak, Kwang; Ryan, Allen F.

    2017-01-01

    Otitis media (OM) is the most common infectious disease of children under six, causing more antibiotic prescriptions and surgical procedures than any other pediatric condition. By screening a bacteriophage (phage) library genetically engineered to express random peptides on their surfaces, we discovered unique peptides that actively transport phage particles across the intact tympanic membrane (TM) and into the middle ear (ME). Herein our goals were to characterize the physiochemical peptide features that may underlie trans-TM phage transport; assess morphological and functional effects of phage peptides on the ME and inner ear (IE); and determine whether peptide-bearing phage transmigrate from the ME into the IE. Incubation of five peptide-bearing phage on the TM for over 4hrs resulted in demonstrably superior transport of one peptide, in level and in exponential increase over time. This suggests a preferred peptide motif for TM active transport. Functional and structural comparisons revealed unique features of this peptide: These include a central lysine residue, isoelectric point of 0.0 at physiological pH and a hydrophobic C-terminus. When the optimal peptide was applied to the TM independent of phage, similar transport was observed, indicating that integration into phage is not required. When 109 particles of the four different trans-TM phage were applied directly into the ME, no morphological effects were detected in the ME or IE when compared to saline or wild-type (WT) phage controls. Comparable, reversible hearing loss was observed for saline controls, WT phage and trans-TM peptide phage, suggesting a mild conductive hearing loss due to ME fluid. Perilymph titers after ME incubation established that few copies of trans-TM peptide phage crossed into the IE. The results suggest that, within the parameters tested, trans-TM peptides are safe and could be used as potential agents for noninvasive delivery of drugs, particles and gene therapy vectors to the ME

  17. Structural basis for action by diverse antidepressants on biogenic amine transporters.

    Science.gov (United States)

    Wang, Hui; Goehring, April; Wang, Kevin H; Penmatsa, Aravind; Ressler, Ryan; Gouaux, Eric

    2013-11-07

    The biogenic amine transporters (BATs) regulate endogenous neurotransmitter concentrations and are targets for a broad range of therapeutic agents including selective serotonin reuptake inhibitors (SSRIs), serotonin-noradrenaline reuptake inhibitors (SNRIs) and tricyclic antidepressants (TCAs). Because eukaryotic BATs are recalcitrant to crystallographic analysis, our understanding of the mechanism of these inhibitors and antidepressants is limited. LeuT is a bacterial homologue of BATs and has proven to be a valuable paradigm for understanding relationships between their structure and function. However, because only approximately 25% of the amino acid sequence of LeuT is in common with that of BATs, and as LeuT is a promiscuous amino acid transporter, it does not recapitulate the pharmacological properties of BATs. Indeed, SSRIs and TCAs bind in the extracellular vestibule of LeuT and act as non-competitive inhibitors of transport. By contrast, multiple studies demonstrate that both TCAs and SSRIs are competitive inhibitors for eukaryotic BATs and bind to the primary binding pocket. Here we engineered LeuT to harbour human BAT-like pharmacology by mutating key residues around the primary binding pocket. The final LeuBAT mutant binds the SSRI sertraline with a binding constant of 18 nM and displays high-affinity binding to a range of SSRIs, SNRIs and a TCA. We determined 12 crystal structures of LeuBAT in complex with four classes of antidepressants. The chemically diverse inhibitors have a remarkably similar mode of binding in which they straddle transmembrane helix (TM) 3, wedge between TM3/TM8 and TM1/TM6, and lock the transporter in a sodium- and chloride-bound outward-facing open conformation. Together, these studies define common and simple principles for the action of SSRIs, SNRIs and TCAs on BATs.

  18. Effect of counter- and co-ions on the structural transport parameters of sulfoacid cationite membranes

    Science.gov (United States)

    Demina, O. A.; Falina, I. V.; Kononenko, N. A.; Demin, A. V.

    2016-08-01

    The diffusion permeability and specific electroconductivity of MK-40 sulfoacid cationite and Nafion 425 membranes are studied experimentally in NaOH, NaCl, and HCl solutions with various concentrations. The resulting concentration dependences of the electrodiffusion characteristics and data on the nonexchange sorption of the electrolytes are used to calculate the structural transport parameters of the membranes in terms of a two-phase conduction model. Analysis of a set of parameters, including the electroconductivity and diffusion permeability of the membrane gel phase, the volume fractions of the conductive phases, and a parameter that reflects their relative positions, the Donnan constant, and the diffusion coefficients of counter and co-ions in the membrane gel phase reveals the effect the nature of counter- and co-ions has on the electrodiffusion, structural, and sorption characteristics of sulfoacid cationite membranes with different types of structure.

  19. Finite-time Partitions for Lagrangian Structure Identification in Gulf Stream Eddy Transport

    CERN Document Server

    Fabregat, Alexandre; Poje, Andrew C

    2016-01-01

    We develop a methodology to identify finite-time Lagrangian structures from data and models using an extension of the Koopman operator-theoretic methods developed for velocity fields with simple (periodic, quasi-periodic) time-dependence. To achieve this, the notion of the Finite Time Ergodic (FiTER) partition is developed and rigorously justified. In combination with a clustering-based approach, the methodology enables identification of the temporal evolution of Lagrangian structures in a classic, benchmark, oceanographic transport problem, namely the cross-stream flux induced by the interaction of a meso- scale Gulf Stream Ring eddy with the main jet. We focus on a single mixing event driven by the interaction between an energetic cold core ring (a cyclone), the strong jet, and a number of smaller scale cyclones and anticyclones. The new methodology enab les reconstruction of Lagrangian structures in three dimensions and analysis of their time-evolution.

  20. Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog

    NARCIS (Netherlands)

    Jähme, Michael; Guskov, Albert; Slotboom, Dirk Jan

    2014-01-01

    PnuC transporters catalyze cellular uptake of the NAD(+) precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3 + 1 + 3 membrane topology

  1. Membrane topology screen of secondary transport proteins in structural class ST[3] of the MemGen classification. Confirmation and structural diversity

    NARCIS (Netherlands)

    ter Horst, Ramon; Lolkema, Juke S.

    2012-01-01

    The MemGen structural classification of membrane proteins groups families of proteins by hydropathy profile alignment. Class ST[3] of the MemGen classification contains 32 families of transporter proteins including the IT superfamily. Transporters from 19 different families in class ST[3] were evalu

  2. Transforming growth factor β signaling upregulates the expression of human GDP-fucose transporter by activating transcription factor Sp1.

    Science.gov (United States)

    Xu, Yu-Xin; Ma, Anna; Liu, Li

    2013-01-01

    GDP-fucose transporter plays a crucial role in fucosylation of glycoproteins by providing activated fucose donor, GDP-fucose, for fucosyltransferases in the lumen of the Golgi apparatus. Fucose-containing glycans are involved in many biological processes, which are essential for growth and development. Mutations in the GDP-fucose transporter gene cause leukocyte adhesion deficiency syndrome II, a disease characterized by slow growth, mental retardation and immunodeficiency. However, no information is available regarding its transcriptional regulation. Here, by using human cells, we show that TGF-β1 specifically induces the GDP-fucose transporter expression, but not other transporters tested such as CMP-sialic acid transporter, suggesting a diversity of regulatory pathways for the expression of these transporters. The regulatory elements that are responsive to the TGF-β1 stimulation are present in the region between bp -330 and -268 in the GDP-fucose transporter promoter. We found that this region contains two identical octamer GC-rich motifs (GGGGCGTG) that were demonstrated to be essential for the transporter expression. We also show that the transcription factor Sp1 specifically binds to the GC-rich motifs in vitro and Sp1 coupled with phospho-Smad2 is associated with the promoter region covering the Sp1-binding motifs in vivo using chromatin immunoprecipitation (ChIP) assays. In addition, we further confirmed that Sp1 is essential for the GDP-fucose transporter expression stimulated by TGF-β1 using a luciferase reporter system. These results highlight the role of TGF-β signaling in regulation of the GDP-fucose transporter expression via activating Sp1. This is the first transcriptional study for any nucleotide sugar transporters that have been identified so far. Notably, TGF-β1 receptor itself is known to be modified by fucosylation. Given the essential role of GDP-fucose transporter in fucosylation, the finding that TGF-β1 stimulates the expression of

  3. Structure, biosynthesis, and function of bacterial capsular polysaccharides synthesized by ABC transporter-dependent pathways.

    Science.gov (United States)

    Willis, Lisa M; Whitfield, Chris

    2013-08-30

    Bacterial capsules are formed primarily from long-chain polysaccharides with repeat-unit structures. A given bacterial species can produce a range of capsular polysaccharides (CPSs) with different structures and these help distinguish isolates by serotyping, as is the case with Escherichia coli K antigens. Capsules are important virulence factors for many pathogens and this review focuses on CPSs synthesized via ATP-binding cassette (ABC) transporter-dependent processes in Gram-negative bacteria. Bacteria utilizing this pathway are often associated with urinary tract infections, septicemia, and meningitis, and E. coli and Neisseria meningitidis provide well-studied examples. CPSs from ABC transporter-dependent pathways are synthesized at the cytoplasmic face of the inner membrane through the concerted action of glycosyltransferases before being exported across the inner membrane and translocated to the cell surface. A hallmark of these CPSs is a conserved reducing terminal glycolipid composed of phosphatidylglycerol and a poly-3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) linker. Recent discovery of the structure of this conserved lipid terminus provides new insights into the early steps in CPS biosynthesis.

  4. Magnetic, transport and structural properties of Co/Ir multilayers grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Colis, S.; Dinia, A.; Ulhaq-Bouillet, C.; Panissod, P.; Meny, C.; Schmerber, G.; Arabski, J. [IPCMS-GEMME (UMR 7504 du CNRS), 23 rue du Loess, BP 34, F-67034 Strasbourg Cedex 2 (France)

    2003-09-01

    We report on the structural properties of a [Co{sub 30}/Ir{sub 10}]{sub 10} {sub x} (A) superlattice, as well as on the magnetic and transport properties of a Co{sub 15}/Ir{sub 5}/Co{sub 30} (A) artificial ferrimagnetic system. The samples were grown by molecular beam epitaxy (MBE) on MgO(001) substrates covered with a Ir{sub 130} (A) buffer layer. High resolution cross section and plan view transmission electron microscopy (TEM) images present a high quality epitaxial stack [100]MgO(001) parallel [100]Ir(001) parallel [100]Co(001), with a tetragonalization of the Co fcc structure, due to strains induced by the Ir buffer. TEM images also show that the Co/Ir interfaces are flat, while the layers are continuous and free of bridges. These observations are consistent with zero field nuclear magnetic resonance measurements which indicate an fcc structure of the Co layers, and an interface mixing between Co and Ir limited to one atomic layer. As a consequence the antiferromagnetically coupled Co/Ir/Co sandwich presents large saturation and coercive fields which exceed 20 kOe and 220 Oe, respectively. Annealing made on the same sandwich indicate that the magnetic and transport properties are stable up to 300 C. (copyright 2003 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  5. Specific features of quasineutral carrier transport modes in semiconductors and semiconductor structures

    Science.gov (United States)

    Mnatsakanov, T. T.; Tandoev, A. G.; Yurkov, S. N.; Levinshtein, M. E.

    2009-07-01

    It has been demonstrated that the field dependence of the electron and hole mobility strongly affects the carrier distribution in semiconductor structures under quasineutral conditions. Taking into account this phenomenon, a new equation for quasineutral carrier transport in semiconductors and semiconductor structures has been suggested. The concept of the critical current density jcr has been introduced and validated. At j Lt jcr, the suggested equation transforms to the well-known 'classical' equation of quasineutral transport. By contrast, at j > jcr, novel solutions become apparent from the suggested equation. The performed analysis gives insight into what happens in regions in which the quasineutral drift and DSQD (diffusion stimulated by quasineutral drift) modes predominate. Analytical expressions have been derived for the dependences of the voltage drops across the quasineutral drift and DQSD regions on current. It has been shown that, at high current densities, the voltage drop across the DSQD region tends to decrease as the current density increases. The results obtained enable a qualitative interpretation of the negative differential conductivity region in the current-voltage characteristic of forward-biased semiconductor structures, which arises at high current densities.

  6. A comparative study of structures and structural transitions of secondary transporters with the LeuT fold.

    Science.gov (United States)

    Jeschke, Gunnar

    2013-03-01

    Secondary active transporters from several protein families share a core of two five-helix inverted repeats that has become known as the LeuT fold. The known high-resolution protein structures with this fold were analyzed by structural superposition of the core transmembrane domains (TMDs). Three angle parameters derived from the mean TMD axes correlate with accessibility of the central binding site from the outside or inside. Structural transitions between distinct conformations were analyzed for four proteins in terms of changes in relative TMD arrangement and in internal conformation of TMDs. Collectively moving groups of TMDs were found to be correlated in the covariance matrix of elastic network models. The main features of the structural transitions can be reproduced with the 5 % slowest normal modes of anisotropic elastic network models. These results support the rocking bundle model for the major conformational change between the outward- and inward-facing states of the protein and point to an important role for the independently moving last TMDs of each repeat in occluding access to the central binding site. Occlusion is also supported by flexing of some individual TMDs in the collectively moving bundle and hash motifs.

  7. Study of structural and electronic transport properties of Ce-doped LaMnO3

    Indian Academy of Sciences (India)

    Shahid Husain; R J Choudhary; Ravi Kumar; S I Patil; J P Srivastava

    2002-05-01

    The structural and electronic transport properties of La1-CeMnO3 (=0.0-1.0) have been studied. All the samples exhibit orthorhombic crystal symmetry and the unit cell volume decreases with Ce doping. They also make a metal–insulator transition (MIT) and transition temperature increases with increase in Ce concentration up to 50% doping. The system La0.5Ce0.5MnO3 also exhibits MIT instead of charge-ordered state as observed in the hole doped systems of the same composition.

  8. Trim and Structural Optimization of Subsonic Transport Wings Using Nonconventional Aeroelastic Tailoring

    Science.gov (United States)

    Stanford, Bret K.; Jutte, Christine V.

    2014-01-01

    Several minimum-mass aeroelastic optimization problems are solved to evaluate the effectiveness of a variety of novel tailoring schemes for subsonic transport wings. Aeroelastic strength and panel buckling constraints are imposed across a variety of trimmed maneuver loads. Tailoring with metallic thickness variations, functionally graded materials, composite laminates, tow steering, and distributed trailing edge control effectors are all found to provide reductions in structural wing mass with varying degrees of success. The question as to whether this wing mass reduction will offset the increased manufacturing cost is left unresolved for each case.

  9. Analysis of the possibilities of adapting the DMS-65 structure for modern transportation infrastructure requirements

    Directory of Open Access Journals (Sweden)

    Jan Marszałek

    2016-09-01

    Full Text Available The paper presents the possibility of applying the DMS-65 structure for temporary reconstruction of a bridge infrastructure. These constructions can be widely applied for restoration or repairing a transport infrastructure, damaged by natural disasters or other cata-strophes. The article includes the problems of applicability of this design in variety of mounting ar-rangements. The authors attempt to assess the possibility of applying the DMS-65 road folding bridge in the current service conditions, including the already completed modernization.[b]Keywords[/b]: folding bridges, operation of bridges, special conditions, modernization of constructions

  10. Structural, magnetic and transport properties of discontinuous granular multi-layers

    Energy Technology Data Exchange (ETDEWEB)

    Denardin, J.C. [Instituto de Fisica Gleb Wataghin (IFGW), Universidade Estadual de Campinas (UNICAMP), C.P. 6165, Campinas SP (Brazil); Knobel, M. [Instituto de Fisica Gleb Wataghin (IFGW), Universidade Estadual de Campinas (UNICAMP), C.P. 6165, Campinas SP (Brazil)]. E-mail: knobel@ifi.unicamp.br; Dorneles, L.S. [Departamento de Fisica, CCNE, UFSM 97105-900, Santa Maria RS (Brazil); Schelp, L.F. [Departamento de Fisica, CCNE, UFSM 97105-900, Santa Maria RS (Brazil)

    2005-07-15

    Results of structural, magnetic and transport properties of magnetic Co/SiO{sub 2} discontinuous multi-layers produced by sequential deposition are presented. Transmission electron microscopy (TEM) images show that the samples that are close to metal-insulation transition are composed by a connected network of metallic paths, and display an enhanced Hall Effect. The granular samples are composed by an almost periodic array of Co nanoparticles, and after annealing these samples show a clear evolution in the nanostructure, with increasing average Co grain sizes and decreasing size dispersion. Relationships between the nanostructure and magnetotransport properties are discussed and compared with previous results obtained in cosputtered films.

  11. Synthesis, transport properties, and electronic structure of Cu{sub 2}CdSnTe{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Yongkwan; Khabibullin, Artem R.; Wei, Kaya; Ge, Zhen-Hua; Woods, Lilia M., E-mail: lmwoods@usf.edu; Nolas, George S., E-mail: gnolas@usf.edu [Department of Physics, University of South Florida, Tampa, Florida 33620 (United States); Martin, Joshua [Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States); Salvador, James R. [Chemical and Materials Systems Laboratory, GM R and D Center, Warren, Michigan 48090 (United States)

    2014-06-23

    A new stannite phase was synthesized and its temperature dependent transport properties were investigated. Cu{sub 2}CdSnTe{sub 4} possesses strong p-type conduction, while the temperature dependence of the thermal conductivity exhibits typical dielectric behavior. Electronic structure calculations allowed for a description of the transport characteristics in terms the energy band structure, density of states, and Fermi surface. The potential for thermoelectric applications is also discussed.

  12. The effects of surface functionalization on rheology, structure and transport properties of nanocomposites

    Science.gov (United States)

    Ranka, Moulik A.

    In this thesis, the effects of surface functionalization using hydrophobic silanes on properties of nanocomposites comprising 42 nm silica particles suspended in a melt of polyethylene-glycol (PEG) are studied using rheological, static and dynamic x-ray scattering studies. The nanocomposites are studied in the low molecular weight unentangled (PEG-400) and high molecular weight entangled (PEG-20000) regimes. We find no differences in the properties of the bare and silanized particles in the low volume fraction regime up to where the interparticle separation distance h > 6Rg. In the region of 6Rg > h > 3Rg (5Rg > h > 3Rg, in case of entangled melts), we find substantial differences in the rheological, structure and transport properties when comparing the bare and silanized particles. In the unentangled melts, we observe up to four orders of magnitude drop in the viscosity of the composites at the highest levels of silanization and observe shear thinning behavior that is unlike what is universally seen for hard spheres. For the entangled melts, a yield stress is observed for the silanized particles that is absent in the case of the bare particles and there is a divergence in the elastic modulus in comparison to bare particles. We observe an anomalous speed up in the density relaxations and an associated maxima in structure properties in the case of unentangled melts which has been reported previously for particles experiencing soft repulsive potentials. A clear reentrant behavior in structure and transport properties is observed for bare particles in the entangled melts that have been previously reported for particles interacting with soft repulsive potentials such as square shoulder and ramp potentials. In the silanized systems, the density relaxation times although lower than bare particles, is ii unaffected by increasing volume fraction up to h ~ 3Rg and is decoupled from the structure properties which are non-monotonic similar to bare particles. In the region of

  13. Efficiency Enhancement of Inverted Structure Perovskite Solar Cells via Oleamide Doping of PCBM Electron Transport Layer.

    Science.gov (United States)

    Xia, Fei; Wu, Qiliang; Zhou, Pengcheng; Li, Yi; Chen, Xiang; Liu, Qing; Zhu, Jun; Dai, Songyuan; Lu, Yalin; Yang, Shangfeng

    2015-06-24

    An amphiphilic surfactant, oleamide, was applied to dope the PCBM electron transport layer (ETL) of inverted structure perovskite solar cells (ISPSCs), resulting in a dramatic efficiency enhancement. Under the optimized oleamide doping ratio of 5.0 wt %, the power conversion efficiency of the CH3NH3PbIxCl(3-x) perovskite-based ISPSC device is enhanced from 10.05% to 12.69%, and this is primarily due to the increases of both fill factor and short-circuit current. According to the surface morphology study of the perovskite/PCBM bilayer film, oleamide doping improves the coverage of PCBM ETL onto the perovskite layer, and this is beneficial for the interfacial contact between the perovskite layer and the Ag cathode and consequently the electron transport from perovskite to the Ag cathode. Such an improved electron transport induced by oleamide doping is further evidenced by the impedance spectroscopic study, revealing the prohibited electron-hole recombination at the interface between the perovskite layer and the Ag cathode.

  14. Investigation of Terminal Group Effect on Electron Transport Through Open Molecular Structures

    Institute of Scientific and Technical Information of China (English)

    C.Preferencial Kala; P.Aruna Priya; D.John Thiruvadigal

    2013-01-01

    The effect of terminal groups on the electron transport through metal-molecule-metal system has been investigated using nonequilibrium Green's function (NEGF) formalism combined with extended Huckel theory (EHT).Au-molecule-Au junctions are constructed with borazine and BCN unit structure as core molecule and sulphur (S),oxygen (O),selenium (Se) and cyano-group (CN) as terminal groups.The electron transport characteristics of the borazine and BCN molecular systems are analyzed through the transmission spectra and the current-voltage curve.The results demonstrate that the terminal groups modifying the transport behaviors of these systems in a controlled way.Our result shows that,selenium is the best linker to couple borazine to Au electrode and oxygen is the best one to couple BCN to Au electrode.Furthermore,the results of borazine systems are compared with that of BCN molecular systems and are discussed.Simulation results show that the conductance through BCN molecular systems is four times larger than the borazine molecular systems.Negative differential resistance behavior is observed with borazine-CN system and the saturation feature appears in BCN systems.

  15. GENERAL: Mean-field Theory for Some Bus Transport Networks with Random Overlapping Clique Structure

    Science.gov (United States)

    Yang, Xu-Hua; Sun, Bao; Wang, Bo; Sun, You-Xian

    2010-04-01

    Transport networks, such as railway networks and airport networks, are a kind of random network with complex topology. Recently, more and more scholars paid attention to various kinds of transport networks and try to explore their inherent characteristics. Here we study the exponential properties of a recently introduced Bus Transport Networks (BTNs) evolution model with random overlapping clique structure, which gives a possible explanation for the observed exponential distribution of the connectivities of some BTNs of three major cities in China. Applying mean-field theory, we analyze the BTNs model and prove that this model has the character of exponential distribution of the connectivities, and develop a method to predict the growth dynamics of the individual vertices, and use this to calculate analytically the connectivity distribution and the exponents. By comparing mean-field based theoretic results with the statistical data of real BTNs, we observe that, as a whole, both of their data show similar character of exponential distribution of the connectivities, and their exponents have same order of magnitude, which show the availability of the analytical result of this paper.

  16. Structures and transport dynamics of a Campylobacter jejuni multidrug efflux pump

    Energy Technology Data Exchange (ETDEWEB)

    Su, Chih-Chia; Yin, Linxiang; Kumar, Nitin; Dai, Lei; Radhakrishnan, Abhijith; Bolla, Jani Reddy; Lei, Hsiang-Ting; Chou, Tsung-Han; Delmar, Jared A.; Rajashankar, Kanagalaghatta R.; Zhang, Qijing; Shin, Yeon-Kyun; Yu, Edward W. (Cornell); (Iowa State)

    2017-08-01

    Resistance-nodulation-cell division efflux pumps are integral membrane proteins that catalyze the export of substrates across cell membranes. Within the hydrophobe-amphiphile efflux subfamily, these resistance-nodulation-cell division proteins largely form trimeric efflux pumps. The drug efflux process has been proposed to entail a synchronized motion between subunits of the trimer to advance the transport cycle, leading to the extrusion of drug molecules. Here we use X-ray crystallography and single-molecule fluorescence resonance energy transfer imaging to elucidate the structures and functional dynamics of the Campylobacter jejuni CmeB multidrug efflux pump. We find that the CmeB trimer displays a very unique conformation. A direct observation of transport dynamics in individual CmeB trimers embedded in membrane vesicles indicates that each CmeB subunit undergoes conformational transitions uncoordinated and independent of each other. On the basis of our findings and analyses, we propose a model for transport mechanism where CmeB protomers function independently within the trimer.

  17. The Factors Influencing Satisfaction with Public City Transport: A Structural Equation Modelling Approach

    Directory of Open Access Journals (Sweden)

    Pawlasova Pavlina

    2015-12-01

    Full Text Available Satisfaction is one of the key factors which influences customer loyalty. We assume that the satisfied customer will be willing to use the ssame service provider again. The overall passengers´ satisfaction with public city transport may be affected by the overall service quality. Frequency, punctuality, cleanliness in the vehicle, proximity, speed, fare, accessibility and safety of transport, information and other factors can influence passengers´ satisfaction. The aim of this paper is to quantify factors and identify the most important factors influencing customer satisfaction with public city transport within conditions of the Czech Republic. Two methods of analysis are applied in order to fulfil the aim. The method of factor analysis and the method Varimax were used in order to categorize variables according to their mutual relations. The method of structural equation modelling was used to evaluate the factors and validate the model. Then, the optimal model was found. The logistic parameters, including service continuity and frequency, and service, including information rate, station proximity and vehicle cleanliness, are the factors influencing passengers´ satisfaction on a large scale.

  18. ANALYSIS OF TRANSPORT STRUCTURE OF ROAD CONSTRUCTION COMPANIES IN SOUTH RUSSIA

    Directory of Open Access Journals (Sweden)

    Senkevich A. A.

    2015-05-01

    Full Text Available The modern state of the territorial road system in South Russia is analyzed in the article. It considers some districts of the Rostov region, the Krasnodar region and the Stavropol region, which have roads with inappropriate technical parameters, and some districts, which don’t have paved roads for transport connection localities. Road service is a function of road construction companies. Numbers of vehicles in companies participating in the technological process of prepare, delivery and asphalting don’t match the amount of work. Therefore, the article analyzes the transport structure of road construction companies in the most problem districts of the Krasnodar region, the Stavropol region and the Rostov region. On basis of data on providing the companies with vehicles and length of roads the closeness of the relationship is defined which is estimated with the correlation coefficient. The road construction company with the best coordination of the delivery power, the number of vehicles for preparation, transportation and asphalting, and the length of roads is identified. The optimal coefficient of providing every hundred kilometers with rolling stock for service is defined as the analysis result

  19. Structural control of mixed ionic and electronic transport in conducting polymers

    Science.gov (United States)

    Rivnay, Jonathan; Inal, Sahika; Collins, Brian A.; Sessolo, Michele; Stavrinidou, Eleni; Strakosas, Xenofon; Tassone, Christopher; Delongchamp, Dean M.; Malliaras, George G.

    2016-04-01

    Poly(3,4-ethylenedioxythiophene) doped with poly(styrenesulfonate), PEDOT:PSS, has been utilized for over two decades as a stable, solution-processable hole conductor. While its hole transport properties have been the subject of intense investigation, recent work has turned to PEDOT:PSS as a mixed ionic/electronic conductor in applications including bioelectronics, energy storage and management, and soft robotics. Conducting polymers can efficiently transport both holes and ions when sufficiently hydrated, however, little is known about the role of morphology on mixed conduction. Here, we show that bulk ionic and electronic mobilities are simultaneously affected by processing-induced changes in nano- and meso-scale structure in PEDOT:PSS films. We quantify domain composition, and find that domain purification on addition of dispersion co-solvents limits ion mobility, even while electronic conductivity improves. We show that an optimal morphology allows for the balanced ionic and electronic transport that is critical for prototypical mixed conductor devices. These findings may pave the way for the rational design of polymeric materials and processing routes to enhance devices reliant on mixed conduction.

  20. Structural basis of water-specific transport through the AQP1 water channel

    Science.gov (United States)

    Sui, Haixin; Han, Bong-Gyoon; Lee, John K.; Walian, Peter; Jap, Bing K.

    2001-12-01

    Water channels facilitate the rapid transport of water across cell membranes in response to osmotic gradients. These channels are believed to be involved in many physiological processes that include renal water conservation, neuro-homeostasis, digestion, regulation of body temperature and reproduction. Members of the water channel superfamily have been found in a range of cell types from bacteria to human. In mammals, there are currently 10 families of water channels, referred to as aquaporins (AQP): AQP0-AQP9. Here we report the structure of the aquaporin 1 (AQP1) water channel to 2.2Å resolution. The channel consists of three topological elements, an extracellular and a cytoplasmic vestibule connected by an extended narrow pore or selectivity filter. Within the selectivity filter, four bound waters are localized along three hydrophilic nodes, which punctuate an otherwise extremely hydrophobic pore segment. This unusual combination of a long hydrophobic pore and a minimal number of solute binding sites facilitates rapid water transport. Residues of the constriction region, in particular histidine 182, which is conserved among all known water-specific channels, are critical in establishing water specificity. Our analysis of the AQP1 pore also indicates that the transport of protons through this channel is highly energetically unfavourable.

  1. Tailoring the water structure and transport in nanotubes with tunable interiors

    Science.gov (United States)

    Ruiz, Luis; Wu, Yuanqiao; Keten, Sinan

    2014-11-01

    Self-assembly of cyclic peptide nanotubes (CPNs) in polymer thin films has opened up the possibility of creating separation membranes with tunable nanopores that can differentiate molecules at the sub-nanometer level. While it has been demonstrated that the interior chemistry of the CPNs can be tailored by inserting functional groups in the nanopore lumen (mCPNs), a design strategy for picking the chemical modifications that lead to particular transport properties has not been established. Drawing from the knowledgebase of functional groups in natural amino acids, here we use molecular dynamics simulations to elucidate how bioinspired mutations influence the transport of water through mCPNs. We show that, at the nanoscale, factors besides the pore size, such as electrostatic interactions and steric effects, can dramatically change the transport properties. We recognize a novel asymmetric structure of water under nanoconfinement inside the chemically functionalized nanotubes and identify that the small non-polar glycine-mimic groups that minimize the steric constraints and confer a hydrophobic character to the nanotube interior are the fastest transporters of water. Our computationally developed experiments on a realistic material system circumvent synthetic challenges, and lay the foundation for bioinspired principles to tailor artificial nanochannels for separation applications such as desalination, ion-exchange and carbon capture.Self-assembly of cyclic peptide nanotubes (CPNs) in polymer thin films has opened up the possibility of creating separation membranes with tunable nanopores that can differentiate molecules at the sub-nanometer level. While it has been demonstrated that the interior chemistry of the CPNs can be tailored by inserting functional groups in the nanopore lumen (mCPNs), a design strategy for picking the chemical modifications that lead to particular transport properties has not been established. Drawing from the knowledgebase of functional

  2. Influence of structure disorders and temperaturesof systems on the bio-energy transport in proteinmolecules (Ⅱ)

    Institute of Scientific and Technical Information of China (English)

    Xiao-feng PANG

    2008-01-01

    The influence of molecular structure disor-ders and physiological temperature on the states and properties of solitons as transporters of bio-energy are numerically studied through the fourth-order Runge-Kutta method and a new theory based on my paper [Front. Phys. China, 2007, 2(4): 469]. The structure dis-orders include fluctuations in the characteristic parame-ters of the spring constant, dipole-dipole interaction con-stant and exciton-phonon coupling constant, as well as the chain-chain interaction coefficient among the three channels and ground state energy resulting from the dis-order distributions of masses of amino acid residues and impurities. In this paper, we investigate the behav-iors and states of solitons in a single protein molecu-lar chain, and in α-Helix protein molecules with three channels. In the former we prove first that the new soli-tons can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. In this case of structure disorder, the fluctu-ations of the spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant, as well as the ground state energy and the disorder distribu-tions of masses of amino acid residues of the proteins influence the states and properties of motion of solitons. However, they are still quite stable and are very robust against these structure disorders, even in the presence of larger disorders in the sequence of masses, spring con-stants and coupling constants. Still, the solitons may disperse or be destroyed when the disorder distribution of the masses and fluctuations of structure parameters are quite great. If the effect of thermal perturbation of the environment on the soliton in nonuniform proteins is considered again, it is still thermally stable at the biolog-ical temperature of 300 K, and at the longer time period of 300 ps and larger spacing of 400 amino acids. The new soliton is also thermally stable in the case of motion

  3. The influence of small intestinal mucus structure on particle transport ex vivo.

    Science.gov (United States)

    Bajka, Balázs H; Rigby, Neil M; Cross, Kathryn L; Macierzanka, Adam; Mackie, Alan R

    2015-11-01

    Mucus provides a barrier to bacteria and toxins while allowing nutrient absorption and waste transport. Unlike colonic mucus, small intestinal mucus structure is poorly understood. This study aimed to provide evidence for a continuous, structured mucus layer and assess the diffusion of different sized particles through it. Mucus structure was assessed by histology and immunohistochemistry. Ultra-structure was assessed by scanning electron microscopy. Tracking of 100 nm and 500 nm latex beads was conducted using ex vivo porcine mucus. The porcine jejunum and ileum were filled with mucus. Layered MUC2 staining was visible throughout the small intestine, covering villus tips. Scanning electron microscopy showed net-like mucin sheets covering villi (211 ± 7 nm pore diameter). Particle tracking of 100 nm latex beads, showed no inhibition of diffusion through mucus while 500 nm beads displayed limited diffusion. These results suggest a continuous mucus layer exists throughout the small intestine, which is highly stratified adjacent to the epithelium. The network observed is consistent with previous observations and correlates with stratified MUC2 staining. Mucin pore size is consistent with free diffusion of 100 nm and limited diffusion of 500 nm particles. Small Intestinal mucus structure has important implications for drug delivery systems and prevention and treatment of conditions like mucositis and inflammatory bowel disease.

  4. Structural features of ion transport and allosteric regulation in sodium-calcium exchanger (NCX proteins

    Directory of Open Access Journals (Sweden)

    Moshe eGiladi

    2016-02-01

    Full Text Available Na+/Ca2+ exchanger (NCX proteins extrude Ca2+ from the cell to maintain cellular homeostasis. Since NCX proteins contribute to numerous physiological and pathophysiological events, their pharmacological targeting has been desired for a long time. This intervention remains challenging owing to our poor understanding of the underlying structure-dynamic mechanisms. Recent structural studies have shed light on the structure-function relationships underlying the ion-transport and allosteric regulation of NCX. The crystal structure of an archaeal NCX (NCX_Mj along with molecular dynamic simulations and ion flux analyses, have assigned the ion binding sites for 3Na+ and 1Ca2+, which are being transported in separate steps. In contrast with NCX_Mj, eukaryotic NCXs contain the regulatory Ca2+-binding domains, CBD1 and CBD2, which affect the membrane embedded ion-transport domains over a distance of ~80 Å. The Ca2+-dependent regulation is ortholog, isoform and splice-variant dependent to meet physiological requirements, exhibiting either a positive, negative or no response to regulatory Ca2+. The crystal structures of the two-domain (CBD12 tandem have revealed a common mechanism involving a Ca2+-driven tethering of CBDs in diverse NCX variants. However, dissociation kinetics of occluded Ca2+ (entrapped at the two-domain interface depends on the alternative-splicing segment (at CBD2, thereby representing splicing-dependent dynamic coupling of CBDs. The HDX-MS, SAXS, NMR, FRET, equilibrium 45Ca2+ binding and stopped-flow techniques provided insights into the dynamic mechanisms of CBDs. Ca2+ binding to CBD1 results in a population shift, where more constraint conformational states become highly populated without global conformational changes in the alignment of CBDs. This mechanism is common among NCXs. Recent HDX-MS studies have demonstrated that the apo CBD1 and CBD2 are stabilized by interacting with each other, while Ca2+ binding to CBD1 rigidifies

  5. Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

    Energy Technology Data Exchange (ETDEWEB)

    Chinthavali, Supriya [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-04-01

    Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) and the criticality index is found to be effective for one test network to identify the vulnerable nodes.

  6. Effect of biochar on soil structural characteristics: water retention and gas transport

    DEFF Research Database (Denmark)

    Sun, Zhencai; Møldrup, Per; Vendelboe, Anders Lindblad

    Biochar addition to agricultural soil has been reported to reduce climate gas emission, as well as improve soil fertility and crop productivity. Little, however, is known about biochar effects on soil structural characteristics. This study investigates if biochar-application changes soil structural...... characteristics, as indicated from water retention and gas transport measurements on intact soil samples. Soil was sampled from a field experiment on a sandy loam with four control plots (C) without biochar and four plots (B) with incorporated biochar at a rate of 20 tons per hectare (plot size, 6 x 8 m). The C......-gas diffusivity on intact 100cm3 soil samples (5 replicates in each plot). We found that biochar application significantly decreased soil bulk density, hereby creating higher porosity. At the same soil-water matric potential, all the soil-gas phase parameters (air-filled porosity, air permeability and gas...

  7. Spin transport and spin-flip scattering in magnetic multilayer structures

    Science.gov (United States)

    Garzon, Samir

    2006-03-01

    The existence of spin-flip scattering at the interface between ferromagnetic (F) and nonmagnetic (N) layers of magnetoresistive F/N/F structures can significantly reduce the size of the magnetoresistance, limiting the sensitivity and increasing the power consumption of F/N/F devices such as GMR magnetic field sensors, magnetic read heads, and MRAM's [1]. Detecting and measuring the degree of spin flip scattering in F/N/F structures can allow further optimization in such devices as well as increase the understanding of interfacial spin transport. Our nonlocal spin injection and detection experiments on mesoscopic Co-Al2O3-Cu-Al2O3-Co spin valves provide evidence for the existence of interfacial spin-flip scattering in magnetoresistive devices [2]. By extending the conventional picture of spin-dependent interfacial resistances (R, R) to include two additional spin-flip scattering channels (R,R) [3] we have shown that the nonlocal resistance contains information about both the degree of spin polarization and the degree of spin-flip scattering at the F/N interface. The magnitudes of R and R depend on the relative orientation of the detector magnetization and the nonequilibrium magnetization in the normal metal. We have observed that the difference in spin-flip scattering between up and down channels vanishes at low temperatures, but for T>100K it increases nonlinearly with temperature. Further evidence for the presence of interfacial spin-flip scattering can be obtained from noise measurements, which are extremely sensitive to the microscopic transport details. [1] Spin Dependent Transport in Magnetic Nanostructures, edited by S. Maekawa and T. Shinjo (Taylor & Francis, New York, 2002). [2] S. Garzon, I. Zuti'c, and R. A. Webb, Phys. Rev. Lett. 94, 176601 (2005). [3] E. I. Rashba, Eur. Phys. J. B 29, 513 (2002).

  8. Structural and fast ion transport properties of glassy and amorphous materials

    Energy Technology Data Exchange (ETDEWEB)

    Whitmore, D.H.; Georgopoulos, P.

    1989-11-01

    This research has dealt with ionic conductivity in two classes of electrolytes. Solid inorganic, as well as polymer. In the former case, a structural characterization study of the fast Ag{sup +} ion conducting glassy electrolyte Ag{sub 0.25}Ge{sub 0.19}Se{sub 0.56} was undertaken by means of differential anomalous x-ray scattering techniques. The Ag{sup +} ion transport behavior was probed with the aid of complex impedance spectroscopy and pulsed field gradient NMR measurements of the Ag{sup +} ion diffusivity. We found evidence suggesting that short (3.1--3.5 A) Ag-Ag distances are present. The observed prefactor for conductivity suggests that the number of mobile Ag{sup +} ions in this glass is significantly less than expected from its stoichiometry. The transport property results were examined in the light of our structural findings and analyses were attempted in terms of some reasonable microscopic models. The other major aspect of this research, dealing with amorphous poly(ethylene glycol)-LiCF{sub 3}SO{sub 3} electrolytes, involved measurements, via the pulsed field gradient NMR method, of the diffusivity of the polymer host, the cation (Li{sup +}) and the anion (CF{sub 3}SO{sub 3}{sup -}) in these complexes and the ionic conductivity, via complex impedance spectroscopy. Based on the conductivity prefactors, it appears that these amorphous polymer electrolytes exhibit classical Meyer-Nelder behavior; moreover, our ion transport results could be rationalized in terms of an ion association model (involving ion pairs and higher order aggregates).

  9. Strategies for tuning phonon transport in multilayered structures using a mismatch-based particle model

    Science.gov (United States)

    Le, Nam Q.; Duda, John C.; English, Timothy S.; Hopkins, Patrick E.; Beechem, Thomas E.; Norris, Pamela M.

    2012-04-01

    The performance of many micro- and nanoscale devices depends on the ability to control interfacial thermal transport, which is predominantly mediated by phonons in semiconductor systems. The phonon transmissivity at an interface is therefore a quantity of interest. In this work, an empirical model, termed the thermal mismatch model, is developed to predict transmissivity at ideal interfaces between semiconductor materials, producing an excellent agreement with molecular dynamics simulations of wave packets. To investigate propagation through multilayered structures, this thermal mismatch model is then incorporated into a simulation scheme that represents wave packets as particles, showing a good agreement with a similar scheme that used molecular dynamics simulations as input [P. K. Schelling and S. R. Phillpot, J. Appl. Phys. 93, 5377 (2003)]. With these techniques validated for both single interfaces and superlattices, they are further used to identify ways to tune the transmissivity of multilayered structures. It is shown that by introducing intermediate layers of certain atomic masses, the total transmissivity can either be systematically enhanced or reduced compared to that of a single interface. Thus, this model can serve as a computationally inexpensive means of developing strategies to control phonon transmissivity in applications that may benefit from either enhancement (e.g., microelectronics) or reduction (e.g., thermoelectrics) in thermal transport.

  10. Tourism sector, Travel agencies, and Transport Suppliers: Comparison of Different Estimators in the Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Kovačić Nataša

    2015-11-01

    Full Text Available The paper addresses the effect of external integration (EI with transport suppliers on the efficiency of travel agencies in the tourism sector supply chains. The main aim is the comparison of different estimation methods used in the structural equation modeling (SEM, applied to discover possible relationships between EIs and efficiencies. The latter are calculated by the means of data envelopment analysis (DEA. While designing the structural equation model, the exploratory and confirmatory factor analyses are also used as preliminary statistical procedures. For the estimation of parameters of SEM model, three different methods are explained, analyzed and compared: maximum likelihood (ML method, Bayesian Markov Chain Monte Carlo (BMCMC method, and unweighted least squares (ULS method. The study reveals that all estimation methods calculate comparable estimated parameters. The results also give an evidence of good model fit performance. Besides, the research confirms that the amplified external integration with transport providers leads to increased efficiency of travel agencies, which might be a very interesting finding for the operational management.

  11. The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na[superscript +]/sugar symport

    Energy Technology Data Exchange (ETDEWEB)

    Faham, S.; Watanabe, A.; Besserer, G.M.; Cascio, D.; Specht, A.; Hirayama, B.A.; Wright, E.M.; Abramson, J. (CNRS-UMR); (UCLA)

    2009-08-27

    Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The -3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.

  12. Microscopic observation of carrier-transport dynamics in quantum-structure solar cells using a time-of-flight technique

    Energy Technology Data Exchange (ETDEWEB)

    Toprasertpong, Kasidit; Fujii, Hiromasa; Sugiyama, Masakazu; Nakano, Yoshiaki [School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032 (Japan); Kasamatsu, Naofumi; Kada, Tomoyuki; Asahi, Shigeo; Kita, Takashi [Graduate School of Engineering, Kobe University, Nada-ku, Kobe 657-8501 (Japan); Wang, Yunpeng; Watanabe, Kentaroh [Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904 (Japan)

    2015-07-27

    In this study, we propose a carrier time-of-flight technique to evaluate the carrier transport time across a quantum structure in an active region of solar cells. By observing the time-resolved photoluminescence signal with a quantum-well probe inserted under the quantum structure at forward bias, the carrier transport time can be efficiently determined at room temperature. The averaged drift velocity shows linear dependence on the internal field, allowing us to estimate the quantum structure as a quasi-bulk material with low effective mobility containing the information of carrier dynamics. We show that this direct and real-time observation is more sensitive to carrier transport than other conventional techniques, providing better insights into microscopic carrier transport dynamics to overcome a device design difficulty.

  13. Integration of XAS and NMR techniques for the structure determination of metalloproteins. Examples from the study of copper transport proteins.

    Science.gov (United States)

    Banci, Lucia; Bertini, Ivano; Mangani, Stefano

    2005-01-01

    Nuclear magnetic resonance (NMR) is a powerful technique for protein structure determination in solution. However, when dealing with metalloproteins, NMR methods are unable to directly determine the structure of the metal site and its coordination geometry. The capability of X-ray absorption spectroscopy (XAS) to provide the structure of a metal ion bound to a protein is then perfectly suited to complement the process of the structure determination. This aspect is particularly relevant in structural genomic projects where high throughput of structural results is the main goal. The synergism of the two techniques has been exploited in the structure determination of bacterial copper transport proteins.

  14. Pavement-Transportation Computer Assisted Structural Engineering (PCASE) Implementation of the Modified Berggren (ModBerg) Equation for Computing the Frost Penetration Depth within Pavement Structures

    Science.gov (United States)

    2012-04-01

    effects of soil freezing and thawing cycles when designing any structure, in particular pavement structures. Pavements , either rigid or flexible...ER D C/ G SL T R -1 2 -1 5 Pavement -Transportation Computer Assisted Structural Engineering (PCASE) Implementation of the Modified...Berggren (ModBerg) Equation for Computing the Frost Penetration Depth within Pavement Structures G eo te ch n ic al a n d S tr u ct u re s La b or at

  15. Vertical structure of aeolian turbulence in a boundary layer with sand transport

    Science.gov (United States)

    Lee, Zoe S.; Baas, Andreas C. W.

    2016-04-01

    Recently we have found that Reynolds shear stress shows a significant variability with measurement height (Lee and Baas, 2016), and so an alternative parameter for boundary layer turbulence may help to explain the relationship between wind forcing and sediment transport. We present data that were collected during a field study of boundary layer turbulence conducted on a North Atlantic beach. High-frequency (50 Hz) 3D wind velocity measurements were collected using ultrasonic anemometry at thirteen different measurement heights in a tight vertical array between 0.11 and 1.62 metres above the surface. Thanks to the high density installation of sensors a detailed analysis of the boundary layer flow can be conducted using methods more typically used in studies where data is only available from one or just a few measurement heights. We use quadrant analysis to explore the vertical structure of turbulence and track the changes in quadrant signatures with measurement elevation and over time. Results of quadrant analysis, at the 'raw' 50 Hz timescale, demonstrates the tendency for event clustering across all four quadrants, which implies that at-a-point quadrant events are part of larger-scale turbulent structures. Using an HSV colour model, applied to the quadrant analysis data and plotted in series, we create colour maps of turbulence, which can provide a clear visualisation of the clustering of event activity at each height and illustrate the shape of the larger coherent flow structures that are present within the boundary layer. By including a saturation component to the colour model, the most significant stress producing sections of the data are emphasised. This results in a 'banded' colour map, which relates to clustering of quadrant I (Outward Interaction) and quadrant IV (Sweep) activity, separate from clustering of quadrant II (Burst) and quadrant III (Inward Interaction). Both 'sweep-type' and 'burst-type' sequences are shown to have a diagonal structure

  16. Helical Shell Structures of Ni-Al Alloy Nanowires and Their Electronic Transport Properties

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xue-Qing; LI Hui; LIEW Kim-Meow; LI Yun-Fang; SUN Feng-Wei

    2007-01-01

    Six kinds of Ni-Al alloy nanowires are optimized by means of simulated annealing. The optimized structures show that the Ni-Al alloy nanowires are helical shell structures that are wound by three atomic strands, which is very similar to the case with pure metallic nanowires. The densities of states (DOS), transmission function T(E), current-voltage (Ⅰ-Ⅴ) curves, and the conductance spectra of these alloy nanowires are also investigated. Our results indicate that the conductance spectra depend on the geometric structure properties and the ingredients of the alloy nanowires. We observe and study the nonlinear contribution to the Ⅰ-Ⅴ characteristics that are due to the quantum size effect and the impurity effect. The addition of Ni atoms decreases the conductance of the Ni-Al alloy nanowire because the doping atom Ni change the electronic band structures and the charge density distribution. The interesting statistical results shed light on the physics of quantum transport at the nano-scale.

  17. Crystal structure of a copper-transporting PIB-type ATPase

    DEFF Research Database (Denmark)

    Gourdon, Pontus; Liu, Xiang-Yu; Skjørringe, Tina

    2011-01-01

    Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, ......Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu......(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 Å resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative...... copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B...

  18. Structure-transport correlation for the diffusive tortuosity of bulk, monodisperse, random sphere packings.

    Science.gov (United States)

    Khirevich, Siarhei; Höltzel, Alexandra; Daneyko, Anton; Seidel-Morgenstern, Andreas; Tallarek, Ulrich

    2011-09-16

    The mass transport properties of bulk random sphere packings depend primarily on the bed (external) porosity ε, but also on the packing microstructure. We investigate the influence of the packing microstructure on the diffusive tortuosity τ=D(m)/D(eff), which relates the bulk diffusion coefficient (D(m)) to the effective (asymptotic) diffusion coefficient in a porous medium (D(eff)), by numerical simulations of diffusion in a set of computer-generated, monodisperse, hard-sphere packings. Variation of packing generation algorithm and protocol yielded four Jodrey-Tory and two Monte Carlo packing types with systematically varied degrees of microstructural heterogeneity in the range between the random-close and the random-loose packing limit (ε=0.366-0.46). The distinctive tortuosity-porosity scaling of the packing types is influenced by the extent to which the structural environment of individual pores varies in a packing, and to quantify this influence we propose a measure based on Delaunay tessellation. We demonstrate that the ratio of the minimum to the maximum void face area of a Delaunay tetrahedron around a pore between four adjacent spheres, (A(min)/A(max))(D), is a measure for the structural heterogeneity in the direct environment of this pore, and that the standard deviation σ of the (A(min)/A(max))(D)-distribution considering all pores in a packing mimics the tortuosity-porosity scaling of the generated packing types. Thus, σ(A(min)/A(max))(D) provides a structure-transport correlation for diffusion in bulk, monodisperse, random sphere packings. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. Theory of valley-dependent transport in graphene-based lateral quantum structures

    Science.gov (United States)

    Chen, Feng-Wu; Chou, Mei-Yin; Chen, Yiing-Rei; Wu, Yu-Shu

    2016-08-01

    Modulation of electronic states in two-dimensional materials can be achieved by using in-plane variations of the band gap or the average potential in lateral quantum structures. In the atomic configurations with hexagonal symmetry, this approach makes it possible to tailor the valleytronic properties for potential device applications. In this work, we present a multiband theory to calculate the valley-dependent electron transport in graphene-based lateral quantum structures. As an example, we consider the structures with a single interface that exhibits an energy gap or potential discontinuity. The theoretical formalism proceeds within the tight-binding description, by first deriving the local bulk complex band structures in the regions of a constant gap or potential and, next, joining the local wave functions across the interface via a cell-averaged current operator to ensure the current continuity. The theory is applied to the study of electron reflection off and transmission through an interface. Both reflection and transmission are found to exhibit valley-contrast behavior that can be used to generate valley-polarized electron sources. The results vary with the type of interfaces, as well as between monolayer and bilayer graphene-based structures. In the monolayer case, the valley contrast originates from the band warping and only becomes sizable for incident carriers of high energy, whereas in AB-stacked bilayer graphene, the vertical interlayer coupling emerges as an additional important cause for valley contrast, and the favorable carrier energy is also found to be drastically lower. Our numerical results clearly demonstrate the propitious valleytronic properties of bilayer graphene structures.

  20. Current structure and volume transport across 12 degrees N in the Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Murty, V.S.N.; Suryanarayana, A.; Rao, D.P.

    of 85 degrees E from September to November. Total geostrophic transport in the upper 100 m is comparable in magnitude to that of Ekman transport across 12 degrees N. Total transport (sum of geostrophic and Ekman transports) in the upper 1000 m...

  1. Petrophysical and transport parameters evolution during acid percolation through structurally different limestones

    Science.gov (United States)

    Martinez Perez, Laura; Luquot, Linda

    2017-04-01

    Processes affecting geological media often show complex and unpredictable behavior due to the presence of heterogeneities. This remains problematic when facing contaminant transport problems, in the CO2 storage industry or dealing with the mechanisms underneath natural processes where chemical reactions can be observed during the percolation of rock non-equilibrated fluid (e.g. karst formation, seawater intrusion). To understand the mechanisms taking place in a porous medium as a result of this water-rock interaction, we need to know the flow parameters that control them, and how they evolve with time as a result of that concurrence. This is fundamental to ensure realistic predictions of the behavior of natural systems in response of reactive transport processes. We investigate the coupled influence of structural and hydrodynamic heterogeneities in limestone rock samples tracking its variations during chemical reactions. To do so we use laboratory petrophysical techniques such as helium porosimetry, gas permeability, centrifugue, electrical resistivity and sonic waves measurements to obtain the parameters that characterize flow within rock matrix (porosity, permeability, retention curve and pore size distribution, electrical conductivity, formation factor, cementation index and tortuosity) before and after percolation experiments. We built an experimental setup that allows injection of acid brine into core samples under well controlled conditions, monitor changes in hydrodynamic properties and obtain the chemical composition of the injected solution at different stages. 3D rock images were also acquired before and after the experiments using a micro-CT to locate the alteration processes and perform an acurate analysis of the structural changes. Two limestones with distinct textural classification and thus contrasting transport properties have been used in the laboratory experiments: a crinoid limestone and an oolithic limestone. Core samples dimensions were 1 inch

  2. Moisture harvesting and water transport through specialized micro-structures on the integument of lizards

    Directory of Open Access Journals (Sweden)

    Philipp Comanns

    2011-04-01

    Full Text Available Several lizard species that live in arid areas have developed special abilities to collect water with their bodies' surfaces and to ingest the so collected moisture. This is called rain- or moisture-harvesting. The water can originate from air humidity, fog, dew, rain or even from humid soil. The integument (i.e., the skin plus skin derivatives such as scales has developed features so that the water spreads and is soaked into a capillary system in between the reptiles' scales. Within this capillary system the water is transported to the mouth where it is ingested. We have investigated three different lizard species which have developed the ability for moisture harvesting independently, viz. the Australian thorny devil (Moloch horridus, the Arabian toadhead agama (Phrynocephalus arabicus and the Texas horned lizard (Phrynosoma cornutum. All three lizards have a honeycomb like micro ornamentation on the outer surface of the scales and a complex capillary system in between the scales. By investigation of individual scales and by producing and characterising polymer replicas of the reptiles' integuments, we found that the honeycomb like structures render the surface superhydrophilic, most likely by holding a water film physically stable. Furthermore, the condensation of air humidity is improved on this surface by about 100% in comparison to unstructured surfaces. This allows the animals to collect moisture with their entire body surface. The collected water is transported into the capillary system. For Phrynosoma cornutum we found the interesting effect that, in contrast to the other two investigated species, the water flow in the capillary system is not uniform but directed to the mouth. Taken together we found that the micro ornamentation yields a superhydrophilic surface, and the semi-tubular capillaries allow for an efficient passive – and for Phrynosoma directed – transport of water.

  3. The electronic and transport properties of monolayer transition metal dichalcogenides: a complex band structure analysis

    Science.gov (United States)

    Szczesniak, Dominik

    Recently, monolayer transition metal dichalcogenides have attracted much attention due to their potential use in both nano- and opto-electronics. In such applications, the electronic and transport properties of group-VIB transition metal dichalcogenides (MX2 , where M=Mo, W; X=S, Se, Te) are particularly important. Herein, new insight into these properties is presented by studying the complex band structures (CBS's) of MX2 monolayers while accounting for spin-orbit coupling effects. By using the symmetry-based tight-binding model a nonlinear generalized eigenvalue problem for CBS's is obtained. An efficient method for solving such class of problems is presented and gives a complete set of physically relevant solutions. Next, these solutions are characterized and classified into propagating and evanescent states, where the latter states present not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gaps, which describe the tunneling currents in the MX2 materials. The importance of CBS's and tunneling currents is demonstrated by the analysis of the quantum transport across MX2 monolayers within phase field matching theory. Present work has been prepared within the Qatar Energy and Environment Research Institute (QEERI) grand challenge ATHLOC project (Project No. QEERI- GC-3008).

  4. The turbulent structure and transport in fog layers observed over the Tianjin area

    Science.gov (United States)

    Ye, Xinxin; Wu, Bingui; Zhang, Hongsheng

    2015-02-01

    This paper investigates the vertical structure and turbulence activities in fog events. Three fog cases that occurred in the winter of 2010 over Tianjin, China were selected, including two advection-radiation fog events and an advection fog event. Field observations collected at a 255-m tall meteorological tower in Tianjin were analyzed, including turbulence measurements using the eddy covariance systems installed at three levels, measurements of temperature, horizontal wind and humidity collected at 15 levels, surface radiation fluxes and horizontal visibility. The results suggest that the advection fog was more enduring and thicker than the advection-radiation fog. The fog events were characterized by low wind speed throughout the fog layer. A temperature inversion and low-level jet were observed above the advection-radiation fog layer. The surface net radiation reflected some differences among the fog events. The collapse of turbulence was a necessity for the formation fog, and moderate turbulence was favorable to the development and maintenance. The heat and water vapor fluxes in the advection-radiation fog were weaker than those in the advection fog, in which the stratification was slightly unstable. The relationships among the turbulent transport efficiencies of water vapor, temperature and momentum were examined. The results suggest the applicability of local similarity in the fog layer for the momentum transport efficiency.

  5. Turbulent rotating plane Couette flow: Reynolds and rotation number dependency of flow structure and momentum transport

    Science.gov (United States)

    Kawata, Takuya; Alfredsson, P. Henrik

    2016-07-01

    Plane Couette flow under spanwise, anticyclonic system rotation [rotating plane Couette flow (RPCF)] is studied experimentally using stereoscopic particle image velocimetry for different Reynolds and rotation numbers in the fully turbulent regime. Similar to the laminar regime, the turbulent flow in RPCF is characterized by roll cells, however both instantaneous snapshots of the velocity field and space correlations show that the roll cell structure varies with the rotation number. All three velocity components are measured and both the mean flow and all four nonzero Reynolds stresses are obtained across the central parts of the channel. This also allows us to determine the wall shear stress from the viscous stress and the Reynolds stress in the center of the channel, and for low rotation rates the wall shear stress increases with increasing rotation rate as expected. The results show that zero absolute vorticity is established in the central parts of the channel of turbulent RPCF for high enough rotation rates, but also that the mean velocity profile for certain parameter ranges shows an S shape giving rise to a negative velocity gradient in the center of the channel. We find that from an analysis of the Reynolds stress transport equation using the present data there is a transport of the Reynolds shear stress towards the center of the channel, which may then result in a negative mean velocity gradient there.

  6. Transmission and transport properties in Cantor graphene structures: The case of magnetoelectric modulation

    Science.gov (United States)

    Rodríguez-González, R.; Rodríguez-Vargas, I.

    2017-04-01

    We discuss theoretically the transmission and transport properties of Dirac electrons in a Cantor graphene system under magnetoelectric effects. The transfer matrix method and the Landauer-Büttiker formalism have been implemented to compute the transmittance and the linear-regime conductance, respectively. The fractal order of Cantor type together with the magnetic and electric field are used to distribute and generate the magnetoelectric barriers. This system give us the possibility of compare the mentioned physical properties for magnetic and magnetoelectric barriers. We found a bifurcation process in the transmission spectra which is observable when the generation increases. Also, an asymmetrical and symmetrical behavior is presented for magnetic and magnetoelectric barriers, respectively. In general, an oscillatory behavior is manifested in the conductance. Moreover, we can describe the peaks (form and location) that give rise to the oscillations through the contour plots of the transmittance in the (E ,ky) space. Likewise, by increasing the generation of the system the conductance is enhanced, the oscillations reduced and less pronounced. In short, the magnetoelectric modulation along with the fractal order can be used to control the transmission and transport properties in graphene-based structures.

  7. Molecular cloning and structural analysis of human norepinephrine transporter gene(NETHG)

    Institute of Scientific and Technical Information of China (English)

    GUOLIHE; LIHUAZHU; 等

    1995-01-01

    A cDNA molecule encoding a major part of the human Norepinephrine transporter(hNET) was synthesized by means of Polymerase Chain Reaction(PCR) technique and used as a probe for selecting the human genomic NET gene.A positive clone harbouring the whole gene was obtained from a human lymphocyte genomic library through utilizing the “genomic walking” technique.The clone,designated as phNET,harbours a DNA fragment of about 59 kd in length inserted into BamH I site in cosmid pWE15.The genomic clone contains 14 exons encoding all amino acid residues in the protein.A single exon encodes a distinct transmembrane domain,except for transmembrane domain 10 and 11,which are encoded by part of two exons respectively,and exon 12,which encodes part of domain 11 and all of domain 12.These results imply that there is a close relationship between exon splicing of a gene and structureal domains of the protein,as is the case for the human γ-aminobutyric acid transporter(hGAT) and a number of other membrane proteins.

  8. Electronic and transport properties of Ge nanoparticle pellets structured by focused ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Gondorf, Andreas; Geller, Martin; Lorke, Axel [Universitaet Duisburg-Essen, Duisburg (Germany)

    2010-07-01

    Semiconductor nanoparticles are of interest for future electronic and optoelectronic devices, especially low cost, flexible, printable electronics. We investigate here the transport properties (charge carrier concentration and mobility) of Ge nanoparticles, which were synthesized in the gas-phase and pressed into pellets. The nanoparticles inside these pellets sinter into a sponge-like structure, that may exhibit unusual magneto-transport properties similar to the strong magnetoresistance observed in nanoporous gold [Fujita, PRL 101, 166601 (2008)]. The measurements are made on directly contacted macroscopic pellets and on Hall-bar microstructures fabricated by a focused ion beam (FIB). In the FIB fabrication process, a lamella is cut out of a pellet and positioned onto a prestructured substrate with metal contacts. The sample is connected with the contacts by deposition of platinum. Finally the disk is etched by FIB into a Hallbar shape. We use I-V and Hall-measurements and find a very weak but measurable Hall-effect and a negative magnetoresistance of about 0.01% at 2.5 T. At room temperature, Ge nanoparticles show a charge carrier concentration of about 4.10{sup 14} cm{sup -3}, comparable to the intrinsic charge carrier concentration in bulk germanium. Ge nanoparticles have a very low mobility of 0.1 cm{sup 2}/Vs at 25 C, which is comparable to the mobility of organic semiconductors, so that Ge nanoparticles may be suitable in some applications which are presently based on organic semiconductors.

  9. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    Energy Technology Data Exchange (ETDEWEB)

    Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

  10. Investigations of structure and transport in lithium and silver borophosphate glasses

    Science.gov (United States)

    Kumar, Sundeep; Vinatier, Philippe; Levasseur, Alain; Rao, K. J.

    2004-04-01

    Glasses in the system xLi 2O·(1- x)[0.5B 2O 3·0.5P 2O 5] and xAg 2O·(1- x)[0.5B 2O 3·0.5P 2O 5] have been prepared from melt quenching method. Glasses have been characterized for their densities, molar volumes, glass transition temperatures and heat capacities. Structural studies have been done using infrared and high resolution magic angle spinning nuclear magnetic resonance (HR MAS NMR) of 31P, 11B and 7Li nuclei. Boron is present only in tetrahedral coordination except in Li 2O-rich glasses. Transport properties have been investigated over a wide range of frequency and temperature. Silver containing glasses are found to possess higher conductivities and lower barriers than lithium containing glasses. A structural model has been proposed in which pure B 2O 3-P 2O 5 compositions are assumed to be constituted of BPO 4 units and modification occurs selectively on the phosphate moiety. Tetrahedral boron units are thus expected to be retained in the glass structure.

  11. Production of functional human vitamin A transporter/RBP receptor (STRA6 for structure determination.

    Directory of Open Access Journals (Sweden)

    Conor J Breen

    Full Text Available STRA6 is a plasma membrane protein that mediates the transport of vitamin A, or retinol, from plasma retinol binding protein (RBP into the cell. Mutations in human STRA6 are associated with Matthew-Wood syndrome, which is characterized by severe developmental defects. Despite the obvious importance of this protein to human health, little is known about its structure and mechanism of action. To overcome the difficulties frequently encountered with the production of membrane proteins for structural determination, STRA6 has been expressed in Pichia pastoris as a fusion to green fluorescent protein (GFP, a strategy which has been a critical first step in solving the crystal structures of several membrane proteins. STRA6-GFP was correctly targeted to the cell surface where it bound RBP. Here we report the large-scale expression, purification and characterisation of STRA6-GFP. One litre of culture, corresponding to 175 g cells, yielded about 1.5 mg of pure protein. The interaction between purified STRA6 and its ligand RBP was studied by surface plasmon resonance-based binding analysis. The interaction between STRA6 and RBP was not retinol-dependent and the binding data were consistent with a transient interaction of 1 mole RBP/mole STRA6.

  12. Scaling of phloem structure and optimality of photoassimilate transport in conifer needles

    CERN Document Server

    Ronellenfitsch, Henrik; Jensen, Kaare H; Holbrook, N Michele; Schulz, Alexander; Katifori, Eleni

    2014-01-01

    The phloem vascular system facilitates transport of energy-rich sugar and signaling molecules in plants, thus permitting long range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated by differences in sugar concentration between distal parts of the plant. The phloem is an intricate distribution system, and many questions about its regulation and structural diversity remain unanswered. Here, we investigate the phloem structure in the simplest possible geometry: a linear leaf, found, for example, in the needles of conifer trees. We measure the phloem structure in four tree species representing a diverse set of habitats and needle sizes, from 1 cm (\\textit{Picea omorika}) to 35 cm (\\textit{Pinus palustris}). We show that the phloem shares common traits across these four species and find that the size of its conductive elements obeys a power law. We present a minimal model that accounts for these common traits an...

  13. The Impact of Structural Vibration on Flying Qualities of a Supersonic Transport

    Science.gov (United States)

    Raney, David L.; Jackson, E. Bruce; Buttrill, Carey S.; Adams, William M.

    2001-01-01

    A piloted simulation experiment has been conducted in the NASA Langley Visual/Motion Simulator facility to address the impact of dynamic aeroelastic effects on flying qualities of a supersonic transport. The intent of this experiment was to determine the effectiveness of several measures that may be taken to reduce the impact of aircraft flexibility on piloting tasks. Potential solutions that were examined included structural stiffening, active vibration suppression, and elimination of visual cues associated with the elastic modes. A series of parametric configurations was evaluated by six test pilots for several types of maneuver tasks. During the investigation, several incidents were encountered in which cockpit vibrations due to elastic modes fed back into the control stick through involuntary motions of the pilot's upper body and arm. The phenomenon, referred to as biodynamic coupling, is evidenced by a resonant peak in the power spectrum of the pilot's stick inputs at a structural mode frequency. The results of the investigation indicate that structural stiffening and compensation of the visual display were of little benefit in alleviating the impact of elastic dynamics on the piloting tasks, while increased damping and elimination of control-effector excitation of the lowest frequency modes offered great improvements when applied in sufficient degree.

  14. Enhanced tunnel transport in disordered carbon superlattice structures incorporated with nitrogen

    Science.gov (United States)

    Katkov, Mikhail V.; Bhattacharyya, Somnath

    2012-06-01

    The possibility for enhanced tunnel transport through the incorporation of nitrogen in a quasi-one dimensional superlattice structure of amorphous carbon (a -C) made of sp2-C and sp3-C rich phases is shown by using a tight-binding model. The proposed superstructure can be described by a set of disordered graphite-like carbon clusters (acting as quantum wells) separated by a thin layer of diamond-like carbon (barriers) where the variation of the width and depth of the carbon clusters significantly control the electron transmission peaks. A large structural disorder in the pure carbon system, introduced through the variation of the bond length and associated deformation potential for respective carbon phases, was found to suppress the sharp features of the transmission coefficients. A small percentage of nitrogen addition to the carbon clusters can produce a distinct transmission peak at the low energy; however, it can be practically destroyed due to increase of the level of disorder of carbon sites. Whereas pronounced resonance peaks, both for C and N sites can be achieved through controlling the arrangement of the nitrogen sites of increased concentration within the disordered sp2-C clusters. The interplay of disorder associated with N and C sites illustrated the tunable nature of resistance of the structures as well as their characteristic times.

  15. Effects of anisotropy and Coulomb interactions on quantum transport in a quadruple quantum-dot structure

    Science.gov (United States)

    Kagan, M. Yu.; Val'kov, V. V.; Aksenov, S. V.

    2017-01-01

    We present an analytical and numerical investigation of the spectral and transport properties of a quadruple quantum-dot (QQD) structure which is one of the popular low-dimensional systems in the context of fundamental quantum physics study, future electronic applications, and quantum calculations. The density of states, occupation numbers, and conductance of the structure were analyzed using the nonequilibrium Green's functions in the tight-binding approach and the equation-of-motion method. In particular the anisotropy of hopping integrals and on-site electron energies as well as the effects of the finite intra- and interdot Coulomb interactions were investigated. It was found out that the anisotropy of the kinetic processes in the system leads to the Fano-Feshbach asymmetrical peak. We demonstrated that the conductance of the QQD device has a wide insulating band with steep edges separating triple-peak structures if the intradot Coulomb interactions are taken into account. The interdot Coulomb correlations between the central QDs result in the broadening of this band and the occurrence of an additional band with low conductance due to the Fano antiresonances. It was shown that in this case the conductance of the anisotropic QQD device can be dramatically changed by tuning the anisotropy of on-site electron energies.

  16. Modeling structure-function relationships for diffusive drug transport in inert porous geopolymer matrices.

    Science.gov (United States)

    Jämstorp, Erik; Strømme, Maria; Frenning, Göran

    2011-10-01

    A unique structure-function relationship investigation of mechanically strong geopolymer drug delivery vehicles for sustained release of potent substances is presented. The effect of in-synthesis water content on geopolymer pore structure and diffusive drug transport is investigated. Scanning electron microscopy, N2 gas adsorption, mercury intrusion porosimetry, compression strength test, drug permeation, and release experiments are performed. Effective diffusion coefficients are measured and compared with corresponding theoretical values as derived from pore size distribution and connectivity via pore-network modeling. By solely varying the in-synthesis water content, mesoporous and mechanically strong geopolymers with porosities of 8%-45% are obtained. Effective diffusion coefficients of the model drugs Saccharin and Zolpidem are observed to span two orders of magnitude (∼1.6-120 × 10(-8) cm(2) /s), comparing very well to theoretical estimations. The ability to predict drug permeation and release from geopolymers, and materials alike, allows future formulations to be tailored on a structural and chemical level for specific applications such as controlled drug delivery of highly potent substances.

  17. Crystal structure of a copper-transporting PIB-type ATPase.

    Science.gov (United States)

    Gourdon, Pontus; Liu, Xiang-Yu; Skjørringe, Tina; Morth, J Preben; Møller, Lisbeth Birk; Pedersen, Bjørn Panyella; Nissen, Poul

    2011-07-01

    Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 Å resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B proteins associated with Menkes' and Wilson's diseases.

  18. Theoretical investigation of the electronic structures and carrier transport of hybrid graphene and boron nitride nanostructure

    Directory of Open Access Journals (Sweden)

    Jia-Tao Sun

    2012-09-01

    graphene and hexagonal boron nitride (C-BN nanostructures receive much research interest due to the complementary electronic properties. Graphene is a zero-gap semiconductor, while hexagonal boron nitride (h-BN is a wide gap semiconductor. Here we studied the electronic structures and carrier transport of hybrid C-BN nanostructures by using first principles calculations and deformation potential theory. We have found that the physical quantities in these systems under study, band gap, effective mass, deformation potential, and carrier mobility, can be categorised into three different families depending on the width of graphene nanoribbon. This family behavior is similar to pristine armchair graphene nanoribbon, but with slight difference from the individual component. New opportunities of designing nanoelectric devices are discussed by utilizing the quantum confinement effect based on such kind of hybrid nanostructures.

  19. Fabrication and transport property of artificial structure of CNTs using SPM nano-manipulation

    Science.gov (United States)

    Maejima, K.; Kida, M.; Yaguchi, Y.; Sudo, K.; Kawamura, T.; Morimoto, T.; Aoki, N.; Ochiai, Y.

    2007-04-01

    We have established a novel manipulation technique using a glass-micro capillary under a high-resolution CCD microscope so far. Two isolated multi-wall carbon nanotubes (MWNTs) are settled to form a well-aligned cross structure. Recently, we have tried to develop a fine manipulation system using a scanning probe microscope with a silicon cantilever. Therefore, thinner high-quality MWNTs (˜10 nm in diameter) can be utilized in this system. At the junction, we have observed weak localization and Fano-like-effect, zero bias anomaly whose traces were visible even at room temperature with thick MWNTs (˜100 nm in diameter). On the other hand, with thinner high-quality MWNTs (˜10 nm in diameter), we have observed also anomalous I-V characteristic and Altshuler-Aronov-Spivak-like magneto-oscillations at low temperature in the nano-space transport.

  20. Magnetic structure and magnetic transport properties of graphene nanoribbons with sawtooth zigzag edges.

    Science.gov (United States)

    Wang, D; Zhang, Z; Zhu, Z; Liang, B

    2014-12-23

    The magnetic structure and magnetic transport properties of hydrogen-passivated sawtooth zigzag-edge graphene nanoribbons (STGNRs) are investigated theoretically. It is found that all-sized ground-state STGNRs are ferromagnetic and always feature magnetic semiconductor properties, whose spin splitting energy gap E(g) changes periodically with the width of STGNRs. More importantly, for the STGNR based device, the dual spin-filtering effect with the perfect (100%) spin polarization and high-performance dual spin diode effect with a rectification ratio about 10(10) can be predicted. Particularly, a highly effective spin-valve device is likely to be realized, which displays a giant magnetoresistace (MR) approaching 10(10)%, which is three orders magnitude higher than the value predicted based on the zigzag graphene nanoribbons and six orders magnitude higher than previously reported experimental values for the MgO tunnel junction. Our findings suggest that STGNRs might hold a significant promise for developing spintronic devices.

  1. Model of Optimal Cargo Transport Structure by Full Container Ship on Predefined Sailing Route

    Directory of Open Access Journals (Sweden)

    Serđo Kos

    2004-01-01

    Full Text Available This paper presents the mathematical model for solving theproblem of defining optimal cargo transport structure, occurringwhen, on a predefined sailing route, adequate number ofcontainers of various types, masses and sizes, possibly includingRO!RO cargo, is to be selected, i.e., a "container lot" is to beestablished in loading ports with the aim of gaining maximumship profit and, at the same time, of exploiting useful load andtransport capacity of container ship as much as possible. Theimplementation of the proposed model enables considerableincrease in the efficiency of container ship operations. Themodel was tested using a numerical example with real data.The applied post-optimal analysis examines the influence ofchange in some values of the mathematical model on the resultingoptimal program.

  2. Some aspects of cellulose ethers influence on water transport and porous structure of cement-based materials

    OpenAIRE

    Pourchez, Jérémie; Ruot, Bertrand; Debayle, Johan; Rouèche-Pourchez, Emilie; Grosseau, Philippe

    2010-01-01

    International audience; This paper evaluates and compares the impact of cellulose ethers (CE) on water transport and porous structure of cement-based materials in both fresh and hardened state. Investigations of the porous network (mercury intrusion porosimetry, apparent density, 2D and 3D observations) emphasize an air-entrained stabilisation depending on CE chemistry. We also highlight that CE chemistry leads to a gradual effect on characteristics of the water transport. The global tendenci...

  3. One-hundred-nm-scale electronic structure and transport calculations of organic polymers on the K computer

    Science.gov (United States)

    Imachi, Hiroto; Yokoyama, Seiya; Kaji, Takami; Abe, Yukiya; Tada, Tomofumi; Hoshi, Takeo

    2016-12-01

    One-hundred-nm-scale electronic structure calculations were carried out on the K supercomputer by our original simulation code ELSES (http://www.elses.jp/) The present paper reports preliminary results of transport calculations for condensed organic polymers. Large-scale calculations are realized by novel massively parallel order-N algorithms. The transport calculations were carried out as a theoretical extension for the quantum wavepacket dynamics simulation. The method was applied to a single polymer chain and condensed polymers.

  4. Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog.

    Science.gov (United States)

    Jaehme, Michael; Guskov, Albert; Slotboom, Dirk Jan

    2014-11-01

    PnuC transporters catalyze cellular uptake of the NAD+ precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3+1+3 membrane topology not previously observed in any protein. The high symmetry of PnuC with a single NR bound in the center suggests a simple alternating-access translocation mechanism.

  5. Gene Structure and Expression of the High-affinity Nitrate Transport System in Rice Roots

    Institute of Scientific and Technical Information of China (English)

    Chao Cai; Jun-Yi Wang; Yong-Guan Zhu; Qi-Rong Shen; Bin Li; Yi-Ping Tong; Zhen-Sheng Li

    2008-01-01

    Rice has a preference for uptake of ammonium over nitrate and can use ammonium-N efficiently. Consequently, transporters mediating ammonium uptake have been extensively studied, but nitrate transporters have been largely ignored. Recently,some reports have shown that rice also has high capacity to acquire nitrate from growth medium, so understanding the nitrate transport system in rice roots is very important for improving N use efficiency in rice. The present study identified four putative NRT2 and two putative NAR2 genes that encode components of the high-affinity nitrate transport system (HATS) in the rice (Oryza sativa L. subsp, japonica cv. Nipponbare) genome. OsNRT2.1 and OsNRT2.2 share an identical coding region sequence, and their deduced proteins are closely related to those from monocotyledonous plants. The two NAR2 proteins are closely related to those from mono-cotyledonous plants as well. However, OsNRT2.3 and OsNRT2.4 are more closely related to Arabidopsis NRT2 proteins. Relative quantitative reverse tranecdption-polymerase chain reaction analysis showed that all of the six genes were rapidly upregulated and then downregulated in the roots of N-starved rice plants after they were re-supplied with 0.2 mM nitrate, but the response to nitrate differed among gene members.The results from phylogenetic tree, gene structure and expression analysis implied the divergent roles for the individual members of the rice NRT2 and NAR2 families. High-affinity nitrate influx rates associated with nitrate induction in rice roots were investigated and were found to be regulated by external pH. Compared with the nitrate influx rates at pH 6.5, alkaline pH (pH 8.0) inhibited nitrate Influx, and acidic pH (pH 5.0) enhanced the nitrate influx In I h nitrate induced roots, but did not significantly affect that in 4 to 8 h nitrate induced roots.

  6. Charge transport properties of metal/metal-phthalocyanine/n-Si structures

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Afzal

    2010-12-16

    In present work the charge transport properties of metal/metal-phthalocyanine/n-Si structures with low (N{sub D} = 4 x 10{sup 14} cm{sup -3}), medium (N{sub D}=1 x 10{sup 16} cm{sup -3}) and high (N{sub D}=2 x 10{sup 19} cm{sup -3}) doped n-Si as injecting electrode and the effect of air exposure of the vacuum evaporated metal-phthalocyanine film in these structures is investigated. The results obtained through temperature dependent electrical characterizations of the structures suggest that in terms of dominant conduction mechanism in the corresponding devices Schottky-type conduction mechanism dominates the charge transport in low-bias region of these devices up to 0.8 V, 0.302 V and 0.15 V in case of low, medium and high doped n-Silicon devices. For higher voltages, in each case of devices, the space-charge-limited conduction, controlled by exponential trap distribution, is found to dominate the charge transport properties of the devices. The interface density of states at the CuPc/n-Si interface of the devices are found to be lower in case of lower work function difference at the CuPc/n-Si interface of the devices. The results also suggest that the work function difference at the CuPc/n-Si interface of these devices causes charge transfer at the interface and these phenomena results in formation of interface dipole. The width of the Schottky depletion region at the CuPc/n-Si interface of these devices is found to be higher with higher work function difference at the interface. The investigation of charge transport properties of Al/ZnPc/medium n-Si and Au/ZnPc/ medium n-Si devices suggest that the Schottky depletion region formed at the ZnPc/n-Si interface of these devices determines the charge transport in the low-bias region of both the devices. Therefore, the Schottky-type (injection limited) and the space-charge-limited (bulk limited) conduction are observed in the low and the high bias regions of these devices, respectively. The determined width of the

  7. Electronic structure and quantum transport properties of metallic and semiconducting nanowires

    Science.gov (United States)

    Simbeck, Adam J.

    The future of the semiconductor industry hinges upon new developments to combat the scaling issues that currently afflict two main chip components: transistors and interconnects. For transistors this means investigating suitable materials to replace silicon for both the insulating gate and the semiconducting channel in order to maintain device performance with decreasing size. For interconnects this equates to overcoming the challenges associated with copper when the wire dimensions approach the confinement limit, as well as continuing to develop low-k dielectric materials that can assure minimal cross-talk between lines. In addition, such challenges make it increasingly clear that device design must move from a top-down to a bottom-up approach in which the desired electronic characteristics are tailored from first-principles. It is with such fundamental hurdles in mind that ab initio calculations on the electronic and quantum transport properties of nanoscale metallic and semiconducting wires have been performed. More specifically, this study seeks to elaborate on the role played by confinement, contacts, dielectric environment, edge decoration, and defects in altering the electronic and transport characteristics of such systems. As experiments continue to achieve better control over the synthesis and design of nanowires, these results are expected to become increasingly more important for not only the interpretation of electronic and transport trends, but also in engineering the electronic structure of nanowires for the needs of the devices of the future. For the metallic atomic wires, the quantum transport properties are first investigated by considering finite, single-atom chains of aluminum, copper, gold, and silver sandwiched between gold contacts. Non-equilibrium Green's function based transport calculations reveal that even in the presence of the contact the conductivity of atomic-scale aluminum is greater than that of the other metals considered. This is

  8. Structure and Metal Binding Properties of ZnuA, a Periplasmic Zinc Transporter from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Yatsunyk,L.; Easton, J.; Kim, L.; Sugarbaker, S.; Bennett, B.; Breece, R.; Vorontsov, I.; Tierney, D.; Crowder, M.; Rosenzweig, A.

    2008-01-01

    ZnuA is the periplasmic Zn(2+)-binding protein associated with the high-affinity ATP-binding cassette ZnuABC transporter from Escherichia coli. Although several structures of ZnuA and its homologs have been determined, details regarding metal ion stoichiometry, affinity, and specificity as well as the mechanism of metal uptake and transfer remain unclear. The crystal structures of E. coli ZnuA (Eco-ZnuA) in the apo, Zn(2+)-bound, and Co(2+)-bound forms have been determined. ZnZnuA binds at least two metal ions. The first, observed previously in other structures, is coordinated tetrahedrally by Glu59, His60, His143, and His207. Replacement of Zn(2+) with Co(2+) results in almost identical coordination geometry at this site. The second metal binding site involves His224 and several yet to be identified residues from the His-rich loop that is unique to Zn(2+) periplasmic metal binding receptors. Electron paramagnetic resonance and X-ray absorption spectroscopic data on CoZnuA provide additional insight into possible residues involved in this second site. The second site is also detected by metal analysis and circular dichroism (CD) titrations. Eco-ZnuA binds Zn(2+) (estimated K (d) < 20 nM), Co(2+), Ni(2+), Cu(2+), Cu(+), and Cd(2+), but not Mn(2+). Finally, conformational changes upon metal binding observed in the crystal structures together with fluorescence and CD data indicate that only Zn(2+) substantially stabilizes ZnuA and might facilitate recognition of ZnuB and subsequent metal transfer.

  9. Structure, Magnetism, and Transport of CuCr2Se4 Thin Films

    Energy Technology Data Exchange (ETDEWEB)

    Bettinger, J.S.; Chopdekar, R.V.; Liberati, M.; Neulinger, J.R.; Chshiev, M.; Takamura, Y.; Alldredge, L.M.B.; Arenholz, E.; Idzerda,Y.U.; Stacy, A.M.; Butler, W.H.; Suzuki, Y.

    2007-04-01

    We report the successful growth of highly spin-polarized chalcogenide thin films of CuCr{sub 2}Se{sub 4}, which are promising candidates for spin-based electronic applications. We also present electronic structure calculations for CuCr{sub 2}Se{sub 4} that, together with magnetic and transport data, imply that the stoichiometric compound is a metallic ferromagnet with a relatively low density of hole-like carriers at the Fermi energy. These calculations also predict that a deficiency of Se will deplete the minority density of states at the Fermi energy perhaps leading to a half-metal. We have successfully grown thin films of CuCr{sub 2}Se{sub 4} by pulsed laser deposition on isostructural MgAl{sub 2}O{sub 4} substrates followed by an anneal in a Se-rich environment. X-ray diffraction confirms the structure of CuCr{sub 2}Se{sub 4} on MgAl{sub 2}O{sub 4} substrates as well as a secondary phase of Cr{sub 2}Se{sub 3}. X-ray absorption spectroscopy indicates that the chemical structure at the surface of the films is similar to that of bulk CuCr{sub 2}Se{sub 4} single crystals. Magnetization measurements indicate that these films saturate with a magnetic moment close to 5 {micro}{sub B} per formula unit and a T{sub c} above 400 K. X-ray magnetic circular dichroism shows that the magnetism persists to the surface of the film. Resistivity and Hall effect measurements are consistent with a p-type ferromagnetic metallic behavior and with the electronic structure calculations.

  10. Synthesis and structural, magnetic, thermal, and transport properties of several transition metal oxides and aresnides

    Energy Technology Data Exchange (ETDEWEB)

    Das, Supriyo [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    Oxide compounds containing the transition metal vanadium (V) have attracted a lot of attention in the field of condensed matter physics owing to their exhibition of interesting properties including metal-insulator transitons, structural transitions, ferromagnetic and an- tiferromagnetic orderings, and heavy fermion behavior. Binary vanadium oxides VnO2n-1 where 2 ≤ n ≤ 9 have triclinic structures and exhibit metal-insulator and antiferromagnetic transitions.[1–6] The only exception is V7O13 which remains metallic down to 4 K.[7] The ternary vanadium oxide LiV2O4 has the normal spinel structure, is metallic, does not un- dergo magnetic ordering and exhibits heavy fermion behavior below 10 K.[8] CaV2O4 has an orthorhombic structure[9, 10] with the vanadium spins forming zigzag chains and has been suggested to be a model system to study the gapless chiral phase.[11, 12] These provide great motivation for further investigation of some known vanadium compounds as well as to ex- plore new vanadium compounds in search of new physics. This thesis consists, in part, of experimental studies involving sample preparation and magnetic, transport, thermal, and x- ray measurements on some strongly correlated eletron systems containing the transition metal vanadium. The compounds studied are LiV2O4, YV4O8, and YbV4O8. The recent discovery of superconductivity in RFeAsO1-xFx (R = La, Ce, Pr, Gd, Tb, Dy, Sm, and Nd), and AFe2As2 (A = Ba, Sr, Ca, and Eu) doped with K, Na, or Cs at the A site with relatively high Tc has sparked tremendous activities in the condensed matter physics community and a renewed interest in the area of superconductivity as occurred following the discovery of the layered cuprate high Tc superconductors in 1986. To discover more supercon- ductors

  11. Communication: Unusual structure and transport in ionic liquid-hexane mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Min; Khatun, Sufia; Castner, Edward W., E-mail: ecastner@rci.rutgers.edu [Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854 (United States)

    2015-03-28

    Ionic liquids having a sufficiently amphiphilic cation can dissolve large volume fractions of alkanes, leading to mixtures with intriguing properties on molecular length scales. The trihexyl(tetradecyl)phosphonium cation paired with the bis(trifluoromethylsulfonyl)amide anion provides an ionic liquid that can dissolve large mole fractions of hexane. We present experimental results on mixtures of n-C{sub 6}D{sub 14} with this ionic liquid. High-energy X-ray scattering studies reveal a persistence of the characteristic features of ionic liquid structure even for 80% dilution with n-C{sub 6}D{sub 14}. Nuclear magnetic resonance self-diffusion results reveal decidedly non-hydrodynamic behavior where the self-diffusion of the neutral, non-polar n-C{sub 6}D{sub 14} is on average a factor of 21 times faster than for the cation. Exploitation of the unique structural and transport properties of these mixtures may lead to new opportunities for designer solvents for enhanced chemical reactivity and interface science.

  12. Ion transport and structural dynamics in homologous ammonium and phosphonium-based room temperature ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, Philip J., E-mail: pgrif@seas.upenn.edu [Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Holt, Adam P. [Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States); Tsunashima, Katsuhiko [Department of Materials Science, National Institute of Technology, Wakayama College, 77 Noshima, Nada-cho, Gobo, Wakayama 644-0023 (Japan); Sangoro, Joshua R. [Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States); Kremer, Friedrich [Institute of Experimental Physics I, University of Leipzig, Linnestr. 5, 04103 Leipzig (Germany); Sokolov, Alexei P. [Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States); Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996 (United States); Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830 (United States)

    2015-02-28

    Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphonium IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range—indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs.

  13. Charge Transport in Two-Photon Semiconducting Structures for Solar Fuels.

    Science.gov (United States)

    Liu, Guohua; Du, Kang; Haussener, Sophia; Wang, Kaiying

    2016-10-20

    Semiconducting heterostructures are emerging as promising light absorbers and offer effective electron-hole separation to drive solar chemistry. This technology relies on semiconductor composites or photoelectrodes that work in the presence of a redox mediator and that create cascade junctions to promote surface catalytic reactions. Rational tuning of their structures and compositions is crucial to fully exploit their functionality. In this review, we describe the possibilities of applying the two-photon concept to the field of solar fuels. A wide range of strategies including the indirect combination of two semiconductors by a redox couple, direct coupling of two semiconductors, multicomponent structures with a conductive mediator, related photoelectrodes, as well as two-photon cells are discussed for light energy harvesting and charge transport. Examples of charge extraction models from the literature are summarized to understand the mechanism of interfacial carrier dynamics and to rationalize experimental observations. We focus on a working principle of the constituent components and linking the photosynthetic activity with the proposed models. This work gives a new perspective on artificial photosynthesis by taking simultaneous advantages of photon absorption and charge transfer, outlining an encouraging roadmap towards solar fuels.

  14. Beta (β) tungsten thin films: Structure, electron transport, and giant spin Hall effect

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Qiang; Chen, Wenzhe; Xiao, Gang, E-mail: Gang-Xiao@Brown.edu [Department of Physics, Brown University, Providence, Rhode Island 02912 (United States)

    2015-05-04

    We use a simple magnetron sputtering process to fabricate beta (β) tungsten thin films, which are capable of generating giant spin Hall effect. As-deposited thin films are always in the metastable β-W phase from 3.0 to 26.7 nm. The β-W phase remains intact below a critical thickness of 22.1 nm even after magnetic thermal annealing at 280 °C, which is required to induce perpendicular magnetic anisotropy (PMA) in a layered structure of β-W/Co{sub 40}Fe{sub 40}B{sub 20}/MgO. Intensive annealing transforms the thicker films (>22.1 nm) into the stable α-W phase. We analyze the structure and grain size of both β- and α-W thin films. Electron transport in terms of resistivity and normal Hall effect is studied over a broad temperature range of 10 K to at least 300 K on all samples. Very low switching current densities are achieved in β-W/Co{sub 40}Fe{sub 40}B{sub 20}/MgO with PMA. These basic properties reveal useful behaviors in β-W thin films, making them technologically promising for spintronic magnetic random access memories and spin-logic devices.

  15. Beta (β) tungsten thin films: Structure, electron transport, and giant spin Hall effect

    Science.gov (United States)

    Hao, Qiang; Chen, Wenzhe; Xiao, Gang

    2015-05-01

    We use a simple magnetron sputtering process to fabricate beta (β) tungsten thin films, which are capable of generating giant spin Hall effect. As-deposited thin films are always in the metastable β-W phase from 3.0 to 26.7 nm. The β-W phase remains intact below a critical thickness of 22.1 nm even after magnetic thermal annealing at 280 °C, which is required to induce perpendicular magnetic anisotropy (PMA) in a layered structure of β-W/Co40Fe40B20/MgO. Intensive annealing transforms the thicker films (>22.1 nm) into the stable α-W phase. We analyze the structure and grain size of both β- and α-W thin films. Electron transport in terms of resistivity and normal Hall effect is studied over a broad temperature range of 10 K to at least 300 K on all samples. Very low switching current densities are achieved in β-W/Co40Fe40B20/MgO with PMA. These basic properties reveal useful behaviors in β-W thin films, making them technologically promising for spintronic magnetic random access memories and spin-logic devices.

  16. Dynamic Structure Factor and Transport Coefficients of a Homogeneously Driven Granular Fluid in Steady State

    Science.gov (United States)

    Vollmayr-Lee, Katharina; Zippelius, Annette; Aspelmeier, Timo

    2011-03-01

    We study the dynamic structure factor of a granular fluid of hard spheres, driven into a stationary nonequilibrium state by balancing the energy loss due to inelastic collisions with the energy input due to driving. The driving is chosen to conserve momentum, so that fluctuating hydrodynamics predicts the existence of sound modes. We present results of computer simulations which are based on an event driven algorithm. The dynamic structure factor F (q , ω) is determined for volume fractions 0.05, 0.1 and 0.2 and coefficients of normal restitution 0.8 and 0.9. We observe sound waves, and compare our results for F (q , ω) with the predictions of generalized fluctuating hydrodynamics which takes into account that temperature fluctuations decay either diffusively or with a finite relaxation rate, depending on wave number and inelasticity. We determine the speed of sound and the transport coefficients and compare them to the results of kinetic theory. K.V.L. thanks the Institute of Theoretical Physics, University of Goettingen, for financial support and hospitality.

  17. The structure of the COPII transport-vesicle coat assembled on membranes.

    Science.gov (United States)

    Zanetti, Giulia; Prinz, Simone; Daum, Sebastian; Meister, Annette; Schekman, Randy; Bacia, Kirsten; Briggs, John A G

    2013-09-17

    Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001.

  18. Effect of pH and soil structure on transport of sulfonamide antibiotics in agricultural soils.

    Science.gov (United States)

    Park, Jong Yol; Huwe, Bernd

    2016-06-01

    We investigated the effect of solution pH and soil structure on transport of sulfonamide antibiotics (sulfamethoxazole, sulfadimethoxine and sulfamethazine) in combination with batch sorption tests and column experiments. Sorption isotherms properly conformed to Freundlich model, and sorption potential of the antibiotics is as follows; sulfadimethoxine > sulfamethoxazole > sulfamethazine. Decreasing pH values led to increased sorption potential of the antibiotics on soil material in pH range of 4.0-8.0. This likely resulted from abundance of neutral and positive-charged sulfonamides species at low pH, which electrostatically bind to sorption sites on soil surface. Due to destruction of macropore channels, lower hydraulic conductivities of mobile zone were estimated in the disturbed soil columns than in the undisturbed soil columns, and eventually led to lower mobility of the antibiotics in disturbed column. The results suggest that knowledge of soil structure and solution condition is required to predict fate and distribution of sulfonamide antibiotics in environmental matrix.

  19. Effects of confinement and external fields on structure and transport in colloidal dispersions in reduced dimensionality.

    Science.gov (United States)

    Wilms, D; Deutschländer, S; Siems, U; Franzrahe, K; Henseler, P; Keim, P; Schwierz, N; Virnau, P; Binder, K; Maret, G; Nielaba, P

    2012-11-21

    In this work, we focus on low-dimensional colloidal model systems, via simulation studies and also some complementary experiments, in order to elucidate the interplay between phase behavior, geometric structures and transport properties. In particular, we try to investigate the (nonlinear!) response of these very soft colloidal systems to various perturbations: uniform and uniaxial pressure, laser fields, shear due to moving boundaries and randomly quenched disorder. We study ordering phenomena on surfaces or in monolayers by Monte Carlo computer simulations of binary hard-disk mixtures, the influence of a substrate being modeled by an external potential. Weak external fields allow a controlled tuning of the miscibility of the mixture. We discuss the laser induced de-mixing for the three different possible couplings to the external potential. The structural behavior of hard spheres interacting with repulsive screened Coulomb or dipolar interaction in 2D and 3D narrow constrictions is investigated using Brownian dynamics simulations. Due to misfits between multiples of the lattice parameter and the channel widths, a variety of ordered and disordered lattice structures have been observed. The resulting local lattice structures and defect probabilities are studied for various cross sections. The influence of a self-organized order within the system is reflected in the velocity of the particles and their diffusive behavior. Additionally, in an experimental system of dipolar colloidal particles confined by gravity on a solid substrate we investigate the effect of pinning on the dynamics of a two-dimensional colloidal liquid. This work contains sections reviewing previous work by the authors as well as new, unpublished results. Among the latter are detailed studies of the phase boundaries of the de-mixing regime in binary systems in external light fields, configurations for shear induced effects at structured walls, studies on the effect of confinement on the structures

  20. Structural and functional probing of the biogenic amine transporters by fluorescence spectroscopy

    DEFF Research Database (Denmark)

    Rasmussen, Søren G F; Adkins, Erika M; Carroll, F Ivy

    2003-01-01

    for the clearance of dopamine, norepinephrine, and serotonin from the synaptic cleft. In our studies, we have focused on the serotonin transporter (SERT) for which we have established a purification procedure upon expression of the transporter in Sf-9 insect cells. Importantly, the purified transporter displays...

  1. Structural and mechanistic insights into ABC-type ECF transporters for vitamin uptake

    NARCIS (Netherlands)

    Dosz-Majsnerowska, Maria

    2014-01-01

    Dit proefschrift gaat over de relatie tussen de structuur en het mechanisme van ABC-type ECF transporters voor vitamines, uit de bacterie Lactococcus lactis. Energy-Coupling Factor (ECF) transporters vormen een subgroep van de ATP-binding cassette (ABC) transporters en zijn betrokken bij de opname v

  2. Probing dopamine transporter structure and function by Zn2+-site engineering

    DEFF Research Database (Denmark)

    Loland, Claus Juul; Norgaard-Nielsen, Kristine; Gether, Ulrik

    2003-01-01

    The biogenic amine transporters belong to the class of Na+/Cl--coupled solute carriers and include the transporters for dopamine (DAT), norepinephrine (NET), and serotonin (SERT). These transporters are the primary targets for the action of many psychoactive compounds including the most commonly ...

  3. Structural and mechanistic insights into ABC-type ECF transporters for vitamin uptake

    NARCIS (Netherlands)

    Dosz-Majsnerowska, Maria

    2014-01-01

    Dit proefschrift gaat over de relatie tussen de structuur en het mechanisme van ABC-type ECF transporters voor vitamines, uit de bacterie Lactococcus lactis. Energy-Coupling Factor (ECF) transporters vormen een subgroep van de ATP-binding cassette (ABC) transporters en zijn betrokken bij de opname

  4. Influence of lithium vacancies on the polaronic transport in olivine phosphate structure

    Energy Technology Data Exchange (ETDEWEB)

    Murugavel, Sevi, E-mail: murug@physics.du.ac.in; Sharma, Monika; Shahid, Raza [Department of Physics and Astrophysics, University of Delhi, Delhi 110 007 (India)

    2016-01-28

    Intercalation and deintercalation of lithium ions in cathode materials are of principal to the operation of current rechargeable lithium ion batteries. The performance of lithium ion batteries highly relies on the active cathode material which includes cell potential, power/energy density, capacity, etc. An important issue in this class of material is to resolve the factors governing the electron and ion transport in olivine phosphate structure. In this class of material, there is still an open debate on the mechanism of charge transport including both polarons and lithium ions. On the one hand, this is due to the large disparity between the experimental results and the theoretical model predictions. On the other hand, this is also due to the lack of precise experimental measurement without any parasitic phases in a given cathode material. Here, we present the polaronic conduction in lithiated triphylite LiFePO{sub 4} (LFP) and delithiated heterosite FePO{sub 4} (FP) by means of broadband ac impedance spectroscopy over wide range temperatures and frequency. It is found that the LFP phase possess two orders of higher polaronic conductivity than FP phase despite having similar mobility of polarons in both phases. We show that the differences in the polaronic conductivity of two phases are due to the significant differences in concentration of polarons. It is found that the formation energy of polarons in individual phases is mainly determined by the corresponding defect state associated with it. The temperature dependent dc conductivity has been analyzed within the framework of Mott model of polaronic conduction and explored the origin of polaronic conduction mechanism in this class of material.

  5. Simulations of Lateral Transport and Dropout Structure of Energetic Particles from Impulsive Solar Flares

    Science.gov (United States)

    Matthaeus, W. H.; Ruffolo, D. J.; Tooprakai, P.; Seripienlert, A.; Chuychai, P.

    2016-12-01

    We simulate trajectories of energetic particles from impulsive solar flares for 2D+slab models of magnetic turbulence in spherical geometry to study dropout features, i.e., sharp, repeated changes in the particle density, and the particles' lateral transport. Among random-phase realizations of 2D turbulence, a spherical harmonic expansion can generate homogeneous turbulence over a sphere, but a 2D fast Fourier transform (FFT) locally mapped onto the lateral coordinates in the region of interest is much faster computationally, and we show that the results are qualitatively similar. We then use the 2D FFT field as input to a 2D MHD simulation, which dynamically generates realistic features of turbulence such as coherent structures. The magnetic field lines and particles spread non-diffusively (ballistically) to a patchy distribution reaching up to 25° from the injection longitude and latitude at r 1 AU. This dropout pattern in field line trajectories has sharper features in the case of the more realistic 2D MHD model, in better qualitative agreement with observations. The initial dropout pattern in particle trajectories is relatively insensitive to particle energy, though the energy affects the pattern's evolution with time. We make predictions for future observations of solar particles near the Sun (e.g., at 0.25 AU), for which we expect a sharp pulse of outgoing particles along the dropout pattern, followed by backscattering that first remains close to the dropout pattern and later exhibits cross-field transport to a distribution that is more diffusive, yet mostly contained within the dropout pattern found at greater distances. Partially supported by the Thailand Research Fund (Grants BRG5880009 and RTA5980003), the U.S. NSF (AGS-1063439), NASA (NNX14AI63G & NNX15AB88G), and the Solar Probe Plus/ISIS project.

  6. Research and design of the structure of information support of road transport

    Directory of Open Access Journals (Sweden)

    V. G. Kozlov

    2016-01-01

    Full Text Available The main issue is to study the interaction between the system of road transport and security of its information systems. The mechanism of this interaction is studied only on the basis of studies of the learning process. These two interacting systems through training react to each other. Due to the strong correlation between these two systems offer the development of the basics of management information support to carry out complex, without violating the integrity of the systems. As the methods of research used methods of system analysis and probability theory. The criteria for the study of the interaction of systems: full-scale technological and economic indicators. By the technological parameters include: completeness of use of the system (load, and performance of information security; to full-scale - the cost of labor, energy, materials; to the economic - the cost, payback, profit, profit. The stages of the development of the structure of information support: the definition of objectives; study of the problems and the choice of solution to the problem; agreed solutions (thematic plan; approval of decisions; Management and Implementation; verification of the effectiveness of decisions. Established shortcomings in the existing system of information support of decentralization processes interrelated technical planning; territorial, institutional and administrative divisions of organizations taking interdependent solutions; the lack of control most of the organizations operating information support for road transport; incomplete information of the absolute majority of publishing houses in the needs of motorists; duplication of the work of many publishers. There are two mechanisms of control information management system. Control enhances performance management system, improves the output characteristics of the system.

  7. Influence of lithium vacancies on the polaronic transport in olivine phosphate structure

    Science.gov (United States)

    Murugavel, Sevi; Sharma, Monika; Shahid, Raza

    2016-01-01

    Intercalation and deintercalation of lithium ions in cathode materials are of principal to the operation of current rechargeable lithium ion batteries. The performance of lithium ion batteries highly relies on the active cathode material which includes cell potential, power/energy density, capacity, etc. An important issue in this class of material is to resolve the factors governing the electron and ion transport in olivine phosphate structure. In this class of material, there is still an open debate on the mechanism of charge transport including both polarons and lithium ions. On the one hand, this is due to the large disparity between the experimental results and the theoretical model predictions. On the other hand, this is also due to the lack of precise experimental measurement without any parasitic phases in a given cathode material. Here, we present the polaronic conduction in lithiated triphylite LiFePO4 (LFP) and delithiated heterosite FePO4 (FP) by means of broadband ac impedance spectroscopy over wide range temperatures and frequency. It is found that the LFP phase possess two orders of higher polaronic conductivity than FP phase despite having similar mobility of polarons in both phases. We show that the differences in the polaronic conductivity of two phases are due to the significant differences in concentration of polarons. It is found that the formation energy of polarons in individual phases is mainly determined by the corresponding defect state associated with it. The temperature dependent dc conductivity has been analyzed within the framework of Mott model of polaronic conduction and explored the origin of polaronic conduction mechanism in this class of material.

  8. The Effect of Hydrophilic and Hydrophobic Structure of Amphiphilic Polymeric Micelles on Their Transportation in Rats.

    Science.gov (United States)

    Deng, Feiyang; Yu, Chao; Zhang, Hua; Dai, Wenbing; He, Bing; Zheng, Ying; Wang, Xueqing; Zhang, Qiang

    2016-01-01

    In the previous study, we have clarified how the hydrophilic and hydrophobic structures of amphiphilic polymers impact the transport of their micelles (PEEP-PCL, PEG-PCL and PEG-DSPE micelles) in epithelial MDCK cells (Biomaterials 2013, 34: 6284-6298). In this study, we attempt to clarify the behavior of the three micelles in rats. Coumarin-6 loaded micelles were injected into different sections of intestine of rats and observed by confocal laser scanning microscope (CLSM) or orally administrated and conducted pharmacokinetic study. All of the three kinds of micelles were able to cross the intestinal epithelial cells and enter blood circulation. The PEEP-PCL micelles demonstrated the fastest distribution mainly in duodenum, while the PEGDSPE micelles showed the longest distribution with the highest proportion in ileum of the three. No significant difference was observed among the pharmacokinetic parameters of the three micelles. The results were consistent in the two analysis methods mentioned above, yet there were some differences between in vivo and in vitro results reported previously. It might be the distinction between the environments in MDCK model and intestine that led to the discrepancy. The hydrophobicity of nanoparticles could both enhance uptake and hinder the transport across the mucus. However, there was no intact mucus in MDCK model, which preferred hydrophobic nanoparticles. PEEP was the most hydrophilic material constructing the micelles in the study and its uptake would be increased in rats compared to that in MDCK model, while DSPE was more hydrophobic than the others and MDCK model would be more ideal for its uptake. Considering the inconsistency of the results in the two models, whether the methods researchers were generally using at present were reasonable needs further investigation.

  9. Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t.

    Science.gov (United States)

    Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju

    2016-03-29

    Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

  10. The plasma membrane monoamine transporter (PMAT): Structure, function, and role in organic cation disposition.

    Science.gov (United States)

    Wang, J

    2016-11-01

    Plasma membrane monoamine transporter (PMAT) is a new polyspecific organic cation transporter that transports a variety of biogenic amines and xenobiotic cations. Highly expressed in the brain, PMAT represents a major uptake2 transporter for monoamine neurotransmitters. At the blood-cerebrospinal fluid (CSF) barrier, PMAT is the principal organic cation transporter for removing neurotoxins and drugs from the CSF. Here I summarize our latest understanding of PMAT and its roles in monoamine uptake and xenobiotic disposition. © 2016 American Society for Clinical Pharmacology and Therapeutics.

  11. Structures and properties of sulfonated ionomers probed by transport and mechanical measurements: The role of solute activity

    Science.gov (United States)

    Zhao, Qiao

    This work is focused on advancing the understanding of the structures and properties of sulfonated ionomer membranes in the context of Polymer Electrolyte Membrane Fuel Cell applications by transport and mechanical measurements. Transport and mechanical properties are two critical elements of ionomer membranes that govern the performance and longevity of fuel cells. Additionally, transport and mechanical property measurements can also provide valuable information about the structure of the ionomer membranes. It is essential to develop a comprehensive understanding of them under well controlled environmental conditions. The mechanism of water transport through Nafion membranes was found to be governed by water diffusivity, swelling of the hydrophilic phase and the interfacial transport across membrane/vapor interface. A transport model incorporating these parameters was developed and successfully employed to resolve water activity profiles in the membrane and make quantitative predictions under steady state and dynamic conditions. Experimental results of diffusivity, volume of mixing and tortuosity also provided hints about the hydration shell structure around in the hydrophilic domains of Nafion. The alcohol sorption and transport was found to be qualitatively similar to the behavior of water and the quantitative differences were attributed to the difference in molecular size. The transport of alcohol water mixtures through Nafion displayed significant non-ideality which was connected to the abnormal swelling and incomplete mixing within the hydrophilic domains. The mechanical properties of several perfluoro-sulfonated ionomer (PFSI) membranes were studied as functions of temperature and solute activity. The thermal transition found between 60-100°C was described as an order-disorder transition of the ionic clusters. Water and other polar solutes were found to plasticize PFSI below the transition but stiffen PFSI above the transition. The stiffening effect was

  12. Theoretical investigation of the electronic structure and quantum transport in the graphene-C(111) diamond surface system.

    Science.gov (United States)

    Selli, Daniele; Baburin, Igor; Leoni, Stefano; Zhu, Zhen; Tománek, David; Seifert, Gotthard

    2013-10-30

    We investigate the interaction of a graphene monolayer with the C(111) diamond surface using ab initio density functional theory. To accommodate the lattice mismatch between graphene and diamond, the overlayer deforms into a wavy structure that binds strongly to the diamond substrate. The detached ridges of the wavy graphene overlayer behave electronically as free-standing polyacetylene chains with delocalized π electrons, separated by regions containing only sp(3) carbon atoms covalently bonded to the (111) diamond surface. We performed quantum transport calculations for different geometries of the system to study how the buckling of the graphene layer and the associated bonding to the diamond substrate affect the transport properties. The system displays high carrier mobility along the ridges and a wide transport gap in the direction normal to the ridges. These intriguing, strongly anisotropic transport properties qualify the hybrid graphene-diamond system as a viable candidate for electronic nanodevices.

  13. Proteome scale census of major facilitator superfamily transporters in Trichoderma reesei using protein sequence and structure based classification enhanced ranking.

    Science.gov (United States)

    Chaudhary, Nitika; Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

    2016-07-01

    Trichoderma spp. have been acknowledged as potent bio-control agents against microbial pathogens and also as plant growth promoters. Various secondary metabolites are attributed for these beneficial activities. Major facilitator superfamily (MFS) includes the large proportion of efflux-pumps which are linked with membrane transport of these secondary metabolites. We have carried out a proteome-wide identification of MFS transporters using protein sequence and structure based hierarchical method in Trichoderma reesei. 448 proteins out of 9115 were detected to carry transmembrane helices. MFS specific intragenic gene duplication and its context with transport function have been presented. Finally, using homology based techniques, domains and motifs of MFS families have been identified and utilized to classify them. From query dataset of 448 transmembrane proteins, 148 proteins are identified as potential MFS transporters. Sugar porter, drug: H(+) antiporter-1, monocarboxylate porter and anion: cation symporter emerged as major MFS families with 51, 35, 17 and 11 members respectively. Representative protein tertiary structures of these families are homology modeled for structure-function analysis. This study may help to understand the molecular basis of secretion and transport of agriculturally valuable secondary metabolites produced by these bio-control fungal agents which may be exploited in future for enhancing its biotechnological applications in eco-friendly sustainable development.

  14. The transport mechanism of the human sodium/myo-inositol transporter 2 (SMIT2/SGLT6), a member of the LeuT structural family.

    Science.gov (United States)

    Sasseville, Louis J; Longpré, Jean-Philippe; Wallendorff, Bernadette; Lapointe, Jean-Yves

    2014-09-01

    The sodium/myo-inositol transporter 2 (SMIT2) is a member of the SLC5A gene family, which is believed to share the five-transmembrane segment inverted repeat of the LeuT structural family. The two-electrode voltage-clamp (TEVC) technique was used to measure the steady-state and the pre-steady-state currents mediated by human SMIT2 after expression in Xenopus laevis oocytes. Phlorizin is first shown to be a poor inhibitor of pre-steady-state currents for depolarizing voltage pulse. From an up to threefold difference between the apparent ON and OFF transferred charges during a voltage pulse, we also show that a fraction of the transient current recorded for very negative potentials is not a true pre-steady-state current coming from the cotransporter conformational changes. We suggest that this transient current comes from a time-dependent leak current that can reach large amplitudes when external Na(+) concentration is reduced. A kinetic model was generated through a simulated annealing algorithm. This algorithm was used to identify the optimal connectivity among 19 different kinetic models and obtain the numerical values of the associated parameters. The proposed 5-state model includes cooperative binding of Na(+) ions, strong apparent asymmetry of the energy barriers, a rate-limiting step that is likely associated with the translocation of the empty transporter, and a turnover rate of 21 s(-1). The proposed model is a proof of concept for a novel approach to kinetic modeling of electrogenic transporters and allows insight into the transport mechanism of members of the LeuT structural family at the millisecond timescale.

  15. The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis

    Directory of Open Access Journals (Sweden)

    King Steven C

    2004-11-01

    Full Text Available Abstract Background In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant for comparison to other transporters. Results Using the Escherichia coli GABA (4-aminobutyrate permease (GabP as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i indifference to the particular substrate concentrations used, (ii indifference to extreme changes (40-fold in transporter expression level, and within broad limits (iii indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i applicability in the analysis of membrane transport, and (ii particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations. The TSR was used to identify gab permease (GabP variants that exhibit relative changes in catalytic specificity (kcat/Km for [14C]GABA (4-aminobutyrate versus [3H]NA (nipecotic acid. Conclusions The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR, represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb that translocation catalysts rely upon to decrease activation energy (. TSR analysis is

  16. Field Measurements of Influence of Sand Transport Rate on Structure of Wind-sand Flow over Coastal Transverse Ridge

    Institute of Scientific and Technical Information of China (English)

    DONG Yuxiang; S L NAMIKAS; P A HESP; MA Jun

    2008-01-01

    The structure of wind-sand flow under different total sand transport rates was measured with field vertical anemometer and sand trap on the crest of typical coastal transverse ridge in Changli Gold Coast of Hebei Province,which is one of the most typical coastal aeolian distribution regions in China and famous for the tall and typical coastal transverse ridges.The measurement results show that,on the conditions of approximate wind velocities and same surface materials and environments,some changes happen to the structure of wind-sand flow with the increase of total sand transport rate on the crest of coastal transverse ridge.First,the sand transport rates of layers at different heights in the wind-sand flow increase,with the maximum increase at the height layer of 4-8cm.Second,the ratios of sand transport rates of layers at different heights to total sand transport rate decrease at the low height layer (0-4cm),but increase at the high height layer (4-60cm).Third,the distribution of the sand transport rate in the wind-sand flow can be expressed by an exponential function at the height layer of 0-40cm,but it changes fi'om power function model to exponential function model in the whole height layer (0-60cm) and changes into polynomial function model at the height layer of 40-60cm with the increase of total sand transport rate.Those changes have a close relationship with the limit of sand grain size of wind flow transporting and composition of sand grain size in the wind-sand flow.

  17. Organometallic B12-DNA conjugate: synthesis, structure analysis, and studies of binding to human B12-transporter proteins.

    Science.gov (United States)

    Hunger, Miriam; Mutti, Elena; Rieder, Alexander; Enders, Barbara; Nexo, Ebba; Kräutler, Bernhard

    2014-10-06

    Design, synthesis, and structural characterization of a B12-octadecanucleotide are presented herein, a new organometallic B12-DNA conjugate. In such covalent conjugates, the natural B12 moiety may be a versatile vector for controlled in vivo delivery of oligonucleotides to cellular targets in humans and animals, through the endogenous B12 transport systems. Binding of the organometallic B12 octadecanucleotide to the three important human proteins of B12 transport was studied, to examine its structural suitability for the task of eventual in vivo oligonucleotide delivery. Binding was efficient with transcobalamin (TC), but not so efficient with the homologous glycoproteins intrinsic factor and haptocorrin. Binding of the B12 octadecanucleotide to TC suggests the capacity of the B12 moiety to serve as a natural vector for specific transport of single stranded, organometallic oligonucleotide loads from the blood stream into cells.

  18. Functional characterization of the vertebrate primary ureter: Structure and ion transport mechanisms of the pronephric duct in axolotl larvae (Amphibia)

    DEFF Research Database (Denmark)

    Haugan, Birgitte M; Halberg, Kenneth Agerlin; Jespersen, Åse;

    2010-01-01

    whether the duct is involved in urine modification using larvae of the freshwater amphibian Ambystoma mexicanum (axolotl) as model. Results We investigated structural as well as physiological properties of the pronephric duct. The key elements of our methodology were: using histology, light...... duct system, which provides a model of cell structure and basic mechanisms for ion transport. Such information may be important in understanding the evolution of vertebrate kidney systems and human diseases associated with congenital malformations....

  19. Projection Structure by Single-Particle Electron Microscopy of Secondary Transport Proteins GItT, Cits, and GltS

    NARCIS (Netherlands)

    Moscicka, Katarzyna B.; Krupnik, Tomasz; Boekema, Egbert J.; Lolkema, Juke S.; Mościcka, Katarzyna B.

    2009-01-01

    The structure of three secondary transporter proteins, GltT of Bacillus stearothermophilus, CitS of Klebsiella pneumoniae, and GltS of Escherichia coli, was studied. The proteins were purified to homogeneity ill detergent solution by Ni(2+)-NTA affinity chromatography, and the complexes were determi

  20. Charge Transport Across Insulating Self-Assembled Monolayers: Non-equilibrium Approaches and Modeling To Relate Current and Molecular Structure

    NARCIS (Netherlands)

    Mirjani, F.; Thijssen, J.M.; Whitesides, G.M.; Ratner, M.A.

    2014-01-01

    This paper examines charge transport by tunneling across a series of electrically insulating molecules with the structure HS(CH2)4CONH(CH2)2R) in the form of self-assembled monolayers (SAMs), supported on silver. The molecules examined were studied experimentally by Yoon et al. (Angew. Chem. Int. Ed

  1. Soil structure, colloids, and chemical transport as affected by short-term reducing conditions: a laboratory study

    Science.gov (United States)

    Upland soils in the Midwestern US often undergo reducing conditions when soils are temporally flooded during the spring and remain water saturated for days or weeks. Short-term reducing conditions change the chemistry of the soil and may affect soil structure and solution chemical transport. The eff...

  2. Elucidation of Structural Elements for Selectivity across Monoamine Transporters: Novel 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues

    DEFF Research Database (Denmark)

    Okunola-Bakara, Oluyomi; Cao, Jianjing; Kopajtic, Theresa;

    2014-01-01

    2-[(Diphenylmethyl)sulfinyl]acetamide (modafinil, (±)-1) is a unique dopamine uptake inhibitor that binds the dopamine transporter (DAT) differently than cocaine and may have potential for the treatment of psychostimulant abuse. To further investigate structural requirements for this divergent bi...

  3. THERMOELECTRIC TRANSPORT AND STRUCTURAL-CHANGES IN CHARGE-DENSITY-WAVE SYSTEM (NBSE4)(10)I-3

    NARCIS (Netherlands)

    SMONTARA, A; VUCIC, Z; DEBOER, JL; MAZUER, J; LEVY, F; BILJAKOVIC, K

    1995-01-01

    In order to get better insight into the electrical and thermal transport of (NbSe4)(10)I-3 we performed a detailed measurements of the electrical conductivity and thermopower from 350 K down to 5 K as well as structural investigation in the vicinity of the Peierls transition on the samples selected

  4. Structural, electronic and transport properties of armorphous/crystalline silicon heterojunctions

    Energy Technology Data Exchange (ETDEWEB)

    Schulze, Tim Ferdinand

    2011-06-15

    The present dissertation is concerned with the physical aspects of the a-Si:H/c-Si heterojunction in the context of PV research. In a first step, the technological development which took place in the framework of the thesis is summarized. Its main constituent was the development and implementation of ultrathin ({<=}10 nm) undoped a-Si:H[(i)a-Si:H] layers to improve the passivation of the c-Si surface with the goal of increasing the open-circuit voltage of the solar cell. It is shown that the effect of (i)a-Si:H interlayers depends on the c-Si substrate doping type, and that challenges exist particularly on the technologically more relevant (n)c-Si substrate. A precise optimization of (i)a-Si:H thickness and the doping level of the following a-Si:H top layers is required to realize an efficiency gain in the solar cell. In this chapter, the key scientific questions to be tackled in the main part of the thesis are brought up by the technological development. In the next chapter, the charge carrier transport through a-Si:H/c-Si heterojunctions is investigated making use of current-voltage (I/V) characteristics taken at different temperatures. The dominant transport mechanisms in a-Si:H/c-Si heterojunctions are identified, and the relevance for solar cell operation is discussed. It is found that in the bias regime relevant for solar cell operation, the theoretical framework for the description of carrier transport in classical c-Si solar cells applies as well, which enables to use I/V curves for a simple characterization of a-Si:H/c-Si structures. The next chapter deals with the microscopic characterization of ultrathin a-Si:H layers. Employing infrared spectroscopy, spectroscopic ellipsometry, photoelectron spectroscopy and secondary ion mass spectroscopy, the structural, electronic and optical properties of (i)a-Si:H are analyzed. It is found that ultrathin a-Si:H essentially behaves like layers of 10..100 times the thickness. This represents the basis for the

  5. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency.

    Directory of Open Access Journals (Sweden)

    Chunlai Li

    2011-07-01

    Full Text Available Photosynthesis is the final determinator for crop yield. To gain insight into genes controlling photosynthetic capacity, we selected from our large T-DNA mutant population a rice stunted growth mutant with decreased carbon assimilate and yield production named photoassimilate defective1 (phd1. Molecular and biochemical analyses revealed that PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE, which is conserved in the plant kingdom. The chloroplast localization of PHD1 was confirmed by immunoblots, immunocytochemistry, and UGE activity in isolated chloroplasts, which was approximately 50% lower in the phd1-1 mutant than in the wild type. In addition, the amounts of UDP-glucose and UDP-galactose substrates in chloroplasts were significantly higher and lower, respectively, indicating that PHD1 was responsible for a major part of UGE activity in plastids. The relative amount of monogalactosyldiacylglycerol (MGDG, a major chloroplast membrane galactolipid, was decreased in the mutant, while the digalactosyldiacylglycerol (DGDG amount was not significantly altered, suggesting that PHD1 participates mainly in UDP-galactose supply for MGDG biosynthesis in chloroplasts. The phd1 mutant showed decreased chlorophyll content, photosynthetic activity, and altered chloroplast ultrastructure, suggesting that a correct amount of galactoglycerolipids and the ratio of glycolipids versus phospholipids are necessary for proper chloroplast function. Downregulated expression of starch biosynthesis genes and upregulated expression of sucrose cleavage genes might be a result of reduced photosynthetic activity and account for the decreased starch and sucrose levels seen in phd1 leaves. PHD1 overexpression increased photosynthetic efficiency, biomass, and grain production, suggesting that PHD1 plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity. These findings will be useful for improving crop yields and for bioenergy crop engineering.

  6. High-throughput colorimetric assays for nucleotide sugar formation and glycosyl transfer.

    Science.gov (United States)

    Gantt, Richard W; Thorson, Jon S

    2012-01-01

    Glycosyltransferases are ubiquitous in nature, catalyzing glycosidic bond formation in the context of an enormous range of substrates, which include all major classes of biological molecules. Because this wide range of substrates lacks a shared, distinguishable feature that can be altered by glycosyl transfer, general assays for detection of glycosyltransferase activity have long been largely limited to low-throughput methods. Of those high-throughput assays reported in the literature, many are confined to specific glycosyl transfer reactions with modified aglycon acceptors selected for their unique analytical properties. Herein are described a series of protocols centered on the use of 2-chloro-4-nitrophenyl glycoside donors and the reversibility of glycosyltransferase-catalyzed reactions to enable a colorimetric assay for the formation of sugar nucleotides, coupled reaction systems for the glycodiversification of small molecules, and a general colorimetric assay for glycosyltransfer, applicable to drug discovery, protein engineering, and other fundamental sugar nucleotide-dependent investigations. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Structural Biology of The sequestration & Transport of Heavy Metal Toxins: NMR Structure Determination of Proteins Containing the CYS-X-Y-Metal Binding Motif

    Energy Technology Data Exchange (ETDEWEB)

    Stanley J. Opella

    2004-03-10

    The support from the Department of Energy enabled us to initiate research on several proteins from the bacterial mercury detoxification system; in particular, we were able to determine the structures of MerP and related metal binding sequences. We have also worked on the membrane transport proteins MerF and MerT.

  8. Magnetic, structural, and transport properties at very high temperature in manganites

    Energy Technology Data Exchange (ETDEWEB)

    Nima Ramirez, Fabian Enrique; Furlan Ferreira, Fabio; Andrade Alves, Wendel; Queiruga Rey, Jose Fernando [Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo Andre, CEP 09090-400, SP (Brazil); Souza, Jose Antonio, E-mail: joseantonio.souza@ufabc.edu.br [Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo Andre, CEP 09090-400, SP (Brazil)

    2012-07-15

    Magnetic, structural, and electric transport measurements at high temperatures were carried out on La{sub 1-x}Ca{sub x}MnO{sub 3}; x=0.20, 0.25, 0.30, 0.34, 0.40, and 0.45. All samples show a first-order structural phase transition from orthorhombic Pnma to rhombohedral R3{sup Macron }c space group at T{sub R-O}. Magnetic susceptibility measurements show that the Curie-Weiss law is strictly obeyed in the rhombohedral phase as opposed to the orthorhombic phase where the effective magnetic moment has a temperature dependence. The electrical resistivity is well described by the small polaron hopping mechanism in the samples up to x=0.34. As the charge carriers are introduced into the system (x=0.40 and 0.45), this mechanism of hopping ceases to be valid. The value of Grueneisen parameter obtained through analysis of high-resolution X-ray powder diffraction as a function of temperature increases abruptly for the sample with x=0.40. This is consistent with an increase in bending and stretchinglike frequency modes observed by Raman spectroscopy. - Highlights: Black-Right-Pointing-Pointer Curie-Weiss law is strictly obeyed in the R3c phase as opposed in the Pnma one. Black-Right-Pointing-Pointer The small polaron hopping ceases to be valid as charge carriers increases. Black-Right-Pointing-Pointer The Gruneisen parameter obtained through HR X-ray diffraction increases abruptly.

  9. Cohesive band structure of carbon nanotubes for applications in quantum transport.

    Science.gov (United States)

    Arora, Vijay K; Bhattacharyya, Arkaprava

    2013-11-21

    An integrated cohesive band structure of carbon nanotubes (CNTs) applicable to all chirality directions (n, m), starting from the Dirac cone of a graphene nanolayer in k-space, is demarcated, in direct contrast to dissimilar chiral and achiral versions in the published literature. The electron wave state of a CNT is quantized into one-dimensional (1-D) nanostructure with a wrapping mode, satisfying the boundary conditions from one Dirac K-point to an equivalent neighboring one with an identical phase and returning to the same K point. The repetitive rotation for an identical configuration with added band index (n-m)mod3, yields one metallic (M) with zero bandgap corresponding to (n-m)mod3 = 0, semiconducting state SC1 with (n-m)mod3 = 1 and SC2 with (n-m)mod3 = 2. The band gap and effective mass of SC2 state are twice as large as those of SC1 state. A broad-spectrum expression signifying the linear dependence of the effective mass on the bandgap is obtained. Both the Fermi energy and the intrinsic velocity limiting the current to the saturation level is calculated as a function of the carrier concentration. Limitations of the parabolic approximation are pointed out. Several new features of the band structure are acquired in a seamlessly unified mode for all CNTs, making it suitable for all-encompassing applications. Applications of the theory to high-field transport are advocated with an example of a metallic CNT, in agreement with experimental observations. The mechanism behind the breakdown of the linear current-voltage relation of Ohm's law and the associated surge in resistance are explained on the basis of the nonequilibrium Arora's distribution function (NEADF). These results are important for the performance evaluation and characterization of a variety of applications on CNT in modern nanoscale circuits and devices.

  10. A short update on the structure of drug binding sites on neurotransmitter transporters

    Directory of Open Access Journals (Sweden)

    Gabrielsen Mari

    2011-12-01

    Full Text Available Abstract Background The dopamine (DAT, noradrenalin (NET and serotonin (SERT transporters are molecular targets for different classes of psychotropic drugs. Cocaine and the SSRI (S-citalopram block neurotransmitter reuptake competitively, but while cocaine is a non-selective reuptake inhibitor, (S-citalopram is a selective SERT inhibitor. Findings Here we present comparisons of the binding sites and the electrostatic potential surfaces (EPS of DAT, NET and SERT homology models based on two different LeuTAa templates; with a substrate (leucine in an occluded conformation (PDB id 2a65, and with an inhibitor (tryptophan in an open-to-out conformation (PDB id 3f3a. In the occluded homology models, two conserved aromatic amino acids (tyrosine and phenylalanine formed a gate between the putative binding pockets, and this contact was interrupted in the open to out conformation. The EPS of DAT and NET were generally negative in the vestibular area, whereas the EPS of the vestibular area of SERT was more neutral. Conclusions The findings presented here contribute as an update on the structure of the binding sites of DAT, NET and SERT. The updated models, which have larger ligand binding site areas than models based on other templates, may serve as improved tools for virtual ligand screening.

  11. Local structure and magneto-transport in Sr 2FeMoO 6 oxides

    Science.gov (United States)

    Liscio, F.; Bardelli, F.; Meneghini, C.; Mobilio, S.; Ray, Sugata; Sarma, D. D.

    2006-05-01

    Double perovskite oxides Sr 2FeMoO 6 have attracted a great interest for their peculiar magneto-transport properties, and, in particular, for the large values of low-field magneto-resistance (MR) which remains elevated even at room temperature, thanks to their high Curie temperature ( Tc > 400 K). These properties are strongly influenced by chemical cation disorder, that is by the relative arrangement of Fe and Mo on their sublattices: the regular alternation of Fe and Mo enhances the MR and saturation magnetization. On the contrary the disorder generally depresses the magnetization and worsen the MR response. In this work the X-ray absorption fine structure (XAFS) technique has been employed in order to probe the cation order from a local point of view. XAFS spectra were collected at the Fe and Mo K edges on Sr 2FeMoO 6 samples with different degree of long-range chemical order. The XAFS results prove that a high degree of short-range cation order is preserved, despite the different long-range order: the Fe-Mo correlations are always preferred over the Fe-Fe and Mo-Mo ones in the perfectly ordered as well as in highly disordered samples.

  12. Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.

    Science.gov (United States)

    Gawryluk, Ryan M R; Chisholm, Kenneth A; Pinto, Devanand M; Gray, Michael W

    2012-11-01

    The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of 'supernumerary' subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits.

  13. Synthesis, crystal structure and photoluminescence of phosphorescent copper (I) complexes containing hole-transporting carbazoly moiety.

    Science.gov (United States)

    Yu, Tianzhi; Chai, Haifang; Zhao, Yuling; Zhang, Chengcheng; Liu, Peng; Fan, Duowang

    2013-05-15

    Two new mononuclear Cu(I) complexes based on 2-(2'-pyridyl)benzimidazolyl derivative ligand containing hole-transporting carbazole (L), [Cu(L)(DPEphos)](BF4) and [Cu(L)(PPh3)2](BF4), where L=(4-(9H-carbazol-9-yl)phenyl)methyl-2-(2'-pyridyl)benzimidazole; DPEphos=bis[2-(diphenylphosphino)phenyl]ether and PPh3=triphenylphosphine, have been synthesized and characterized on the basis of elemental analysis, (1)H NMR and FT-IR spectra. The structures of the ligand L and the Cu(I) complexes were characterized by single crystal X-ray diffraction. The results reveal that in the Cu(I) complexes the central Cu(I) ions assume the irregular distorted tetrahedral geometry and are tetra-coordinated by the two nitrogen atoms from L ligand and two phosphorus atoms from ancillary ligands. The photophysical properties of the complexes were examined by using UV-vis, photoluminescence spectroscopic analysis. The complexes exhibit weak MLCT absorption bands ranging from 360 to 480 nm, and display strong orange phosphorescence in the solid states at room temperature, which is completely quenched in solutions.

  14. Structural phase-dependent hole localization and transport in bismuth vanadate

    Science.gov (United States)

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-05-01

    We present theoretical evidence for the phase dependence of hole localization and transport in bismuth vanadate (BiVO4). Our hybrid density-functional theory calculations predict that, in the tetragonal phase [tetragonal scheelite BiVO4 (ts-BiVO4)], an excess hole tends to localize around a BiO8 polyhedron with strong lattice distortion, whereas, in the monoclinic phase [monoclinic scheelite BiVO4 (ms-BiVO4)], it spreads over many lattice sites. The phase-dependent behavior is likely related to the higher structural stability of ms-BiVO4 than ts-BiVO4, which may suppress hole-induced lattice distortions. Our study also demonstrates that the relatively weakly localized hole in ms-BiVO4 undergoes faster diffusion compared to the case of ts-BiVO4, irrespective of the fact that the degrees of localization and mobility vary depending on the choice of exchange-correlation functional. The mobility difference may provide an explanation for the enhanced photocatalytic activity of ms-BiVO4 over ts-BiVO4 for water oxidation, considering that the increased mobility would lead to an increase in the hole current to the catalyst surface.

  15. Structure activity relationships of benzylproline-derived inhibitors of the glutamine transporter ASCT2

    Science.gov (United States)

    Singh, Kurnvir; Tanui, Rose; Gameiro, Armanda; Eisenberg, Gilad; Colas, Claire; Schlessinger, Avner; Grewer, Christof

    2017-01-01

    The glutamine transporter ASCT2 has been identified as a promising target to inhibit rapid growth of cancer cells. However, ASCT2 pharmacology is not well established. In this report, we performed a systematic structure activity analysis of a series of substituted benzylproline derivatives. Substitutions on the phenyl ring resulted in compounds with characteristics of ASCT2 inhibitors. Apparent binding affinity increased with increasing hydrophobicity of the side chain. In contrast, interaction of the ASCT2 binding site with specific positions on the phenyl ring was not observed. The most potent compound inhibits the ASCT2 anion conductance with a Ki of 3 μM, which is in the same range as that of more bulky and higher molecular weight inhibitors recently reported by others. The experimental results are consistent with computational analysis based on docking of the inhibitors against an ASCT2 homology model. The benzylproline scaffold provides a valuable tool for further improving binding potency of future ASCT2 inhibitors. PMID:28057420

  16. Measurements and theory for transport layer structure in intense bed-load

    Science.gov (United States)

    Fraccarollo, L.; Capart, H.

    2012-04-01

    We focus on sediment laden flows driven by turbulent open-channel flows where the bed surface is fully mobilized and nonetheless the thickness of the bedload layer is conveniently smaller than the flow depth. This regime presents dynamic and kinematic features which persist in the range of applied Shields stress between about 0.3 and 3. Below the lower limit the moving grains do not develop significant stresses compared to the applied ones; above the upper limit, debris-flow type frictional contacts develop in a non negligible portion of the bedload layer. We report laboratory experiments in which, using high-speed cameras and a laser light sheet, detailed profiles of granular velocity and concentration have been measured. We checked that the transversal bed profile is flat and that the sidewall measurements are representative of the interior domain. The profiles provide new information on transport layer structure and its relation to the applied Shields stress. Contrary to expectations, we find that intense bed-load layers respond to changes in flow conditions by adjusting their granular concentration at the base. Two mechanisms account for the resulting behavior: stresses generated by immersed granular collisions, and equilibration by density stratification. Without parameter adjustment, the deduced constitutive relations capture the responses of velocity, concentration, and layer thickness in the above reported ten-fold increase Shields-stress range. Away from this intermediate range, in both directions, we show how the flow features rapidly change and the theoretical inferences decay.

  17. Computational homogenization of non-stationary transport processes in masonry structures

    CERN Document Server

    Sykora, J; Kruis, J; Sejnoha, M

    2011-01-01

    A fully coupled transient heat and moisture transport in a masonry structure is examined in this paper. Supported by several successful applications in civil engineering the nonlinear diffusion model proposed by K\\"{u}nzel is adopted in the present study. A strong material heterogeneity together with a significant dependence of the model parameters on initial conditions as well as the gradients of heat and moisture fields vindicates the use of a hierarchical modeling strategy to solve the problem of this kind. Attention is limited to the classical first order homogenization in a spatial domain developed here in the framework of a two step (meso-macro) multi-scale computational scheme (FE^2 problem). Several illustrative examples are presented to investigate the influence of transient flow at the level of constituents (meso-scale) on the macroscopic response including the effect of macro-scale boundary conditions. A two-dimensional section of Charles Bridge subjected to actual climatic conditions is analyzed n...

  18. Understanding the reaction of nuclear graphite with molecular oxygen: Kinetics, transport, and structural evolution

    Science.gov (United States)

    Kane, Joshua J.; Contescu, Cristian I.; Smith, Rebecca E.; Strydom, Gerhard; Windes, William E.

    2017-09-01

    For the next generation of nuclear reactors, HTGRs specifically, an unlikely air ingress warrants inclusion in the license applications of many international regulators. Much research on oxidation rates of various graphite grades under a number of conditions has been undertaken to address such an event. However, consequences to the reactor result from the microstructural changes to the graphite rather than directly from oxidation. The microstructure is inherent to a graphite's properties and ultimately degradation to the graphite's performance must be determined to establish the safety of reactor design. To understand the oxidation induced microstructural change and its corresponding impact on performance, a thorough understanding of the reaction system is needed. This article provides a thorough review of the graphite-molecular oxygen reaction in terms of kinetics, mass and energy transport, and structural evolution: all three play a significant role in the observed rate of graphite oxidation. These provide the foundations of a microstructurally informed model for the graphite-molecular oxygen reaction system, a model kinetically independent of graphite grade, and capable of describing both the observed and local oxidation rates under a wide range of conditions applicable to air-ingress.

  19. Synthesis, crystal structure and photoluminescence of phosphorescent copper (I) complexes containing hole-transporting carbazoly moiety

    Science.gov (United States)

    Yu, Tianzhi; Chai, Haifang; Zhao, Yuling; Zhang, Chengcheng; Liu, Peng; Fan, Duowang

    2013-05-01

    Two new mononuclear Cu(I) complexes based on 2-(2'-pyridyl)benzimidazolyl derivative ligand containing hole-transporting carbazole (L), [Cu(L)(DPEphos)](BF4) and [Cu(L)(PPh3)2](BF4), where L = (4-(9H-carbazol-9-yl)phenyl)methyl-2-(2'-pyridyl)benzimidazole; DPEphos = bis[2-(diphenylphosphino)phenyl]ether and PPh3 = triphenylphosphine, have been synthesized and characterized on the basis of elemental analysis, 1H NMR and FT-IR spectra. The structures of the ligand L and the Cu(I) complexes were characterized by single crystal X-ray diffraction. The results reveal that in the Cu(I) complexes the central Cu(I) ions assume the irregular distorted tetrahedral geometry and are tetra-coordinated by the two nitrogen atoms from L ligand and two phosphorus atoms from ancillary ligands. The photophysical properties of the complexes were examined by using UV-vis, photoluminescence spectroscopic analysis. The complexes exhibit weak MLCT absorption bands ranging from 360 to 480 nm, and display strong orange phosphorescence in the solid states at room temperature, which is completely quenched in solutions.

  20. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  1. Neurotransmitter transporters

    DEFF Research Database (Denmark)

    Gether, Ulrik; Andersen, Peter H; Larsson, Orla M

    2006-01-01

    The concentration of neurotransmitters in the extracellular space is tightly controlled by distinct classes of membrane transport proteins. This review focuses on the molecular function of two major classes of neurotransmitter transporter that are present in the cell membrane of neurons and....../or glial cells: the solute carrier (SLC)1 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of glutamate, and the SLC6 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of dopamine, 5-HT, norepinephrine, glycine and GABA....... Recent research has provided substantial insight into the structure and function of these transporters. In particular, the recent crystallizations of bacterial homologs are of the utmost importance, enabling the first reliable structural models of the mammalian neurotransmitter transporters...

  2. Streambed Structure, Stream Power, and Bedload Transport: A Unified Outlook for Gravel-bed and Bedrock Streams

    Science.gov (United States)

    Chatanantavet, P.; Diplas, P.; Almedeij, J.

    2015-12-01

    Interactions among streambed structure, stream power, and sediment transport in rivers have been widely observed and documented. Perennial gravel-bed streams typically possess a surface bed layer that is coarser than the subsurface material. This coarser surface layer is, however, absent from some ephemeral gravel-bed streams and in some cases the reverse phenomenon occurs. Ephemeral streams also exhibit considerably higher efficiency in transporting sediment. In steep bedrock rivers, the hydraulic-rock interactive mechanism often self-creates step-pool or cascade bed configurations as forms of energy dissipation to control the transport efficiency of sediment. Here we aim to characterize bed structures and sediment transport in gravel-bed rivers and bedrock streams by using the concept of dimensionless stream power. We analyzed existing bed load data collected from field and experimental settings in an attempt to reach a unified outlook for both stream types and various channel bed features. We found that the mechanisms responsible for the features perceived to distinguish surface fining and surface coarsening are interrelated and triggered by different values of dimensionless stream power. The surface fining case has been attributed to fluidization of the entire bed material as demonstrated here in detail. The results also suggest that in bedrock rivers with large bedforms, such as stabled step-pool and immobile rock cascade, relatively medium-large values of stream power (i.e., floods of less than 30-year return period) do not equate with large bed load transport rates due to a portion of flow energy dissipating through local hydraulic jumps, leaving less energy to transport the bed load. Plot of transport efficiency values for each bed type and flood magnitude in bedrock rivers also helps us estimate how much fraction of flow energy is delivered to do bedrock erosive work by saltating bed load; hence, the implication for studies of landscape evolution.

  3. Neutron scattering studies of structure, hydrothermal stability and transport in porous silica catalyst supports

    Science.gov (United States)

    Pollock, Rachel A.

    Mesoporous materials are interesting as catalyst supports, because molecules can move efficiently in and out of the pore network, but they must be stable in water if they are to be used for the production of biofuels. Before investigating hydrothermal stability and transport properties, the pore structure of SBA-15 was characterized using small angle neutron scattering (SANS) and non-local density functional theory (NLDFT) analysis of nitrogen sorption isotherms. A new Contrast Matching SANS method, using a range of probe molecules to directly probe the micropore size, gave a pore size distribution onset of 6 ± 0.2 Å, consistent with cylindrical pores formed from polymer template strands that unravel into the silica matrix. Diffraction intensity analysis of SANS measurements, combined with pore size distributions calculated from NLDFT, showed that the secondary pores are distributed relatively uniformly throughout the silica framework. The hydrothermal stability of SBA-15 was evaluated using a post-calcination hydrothermal treatment in both liquid and vapor phase water. The results were consistent with a degradation mechanism in which silica dissolves from regions of small positive curvature, e.g. near the entrance to the secondary pores, and is re-deposited deeper into the framework. Under water treatment at 115 °C, the mesopore diameter increases and the intra-wall void fraction decreases significantly. The behavior is similar for steam treatment, but occurs more slowly, suggesting that transport is faster when condensation occurs in the pores. Quasielastic neutron scattering (QENS) measurements of methane in SBA-15 probed the rotational and translational motion as a function of temperature and loading. A qualitative analysis of the QENS data suggested that for the initial dose of methane at 100 K, the self diffusion constant is similar in magnitude to literature values for methane in ZSM-5 and Y-zeolite, showing that the secondary pores trap methane and limit

  4. Role of Transport Phenomena in the Evolution of Geometry, Composition and Structure

    Energy Technology Data Exchange (ETDEWEB)

    Tarasankar DebRoy

    2005-11-17

    Abstract Fusion welding is used extensively in industries that support the nation's energy supply, defense, infrastructure, and standard of living. Safety and reliability of the welded joints are affected by their geometry, composition and structure. This report provides an account of the significant advances made in quantitative understanding of the geometry, composition and various aspects of the weldment structure with financial support from DOE/BES. In particular, this report provides an account of the research conducted under the grant DE-FG02-84ER45158 in this important area and lists all the publications that document the details of the technical accomplishments that resulted from the work. Investigations of heat transfer, fluid flow and alloying element vaporization during laser welding resulted in a new technique for the determination of the peak temperature in the weld pool and provided a new method to estimate weld metal composition. Studies on the interfacial phenomena in fusion welding resulted in quantitative understanding of the interrelationship between the weld metal composition and geometry and provided new knowledge as to when the surface active elements would affect the weldment geometry and when these elements would have no effect on the geometry. Partitioning of oxygen nitrogen and hydrogen between the welding environment and the weld metal was affected by the extent of the dissociation of diatomic gaseous species which depended on the nature of the plasma formed during welding. The interfacial tension of the liquid metal was also affected by the plasma and the properties of the plasma affected the concentrations of oxygen, nitrogen and hydrogen in the weld metal. Apart from the understanding of the evolution of composition and geometry of the weldments, application of transport phenomena provided useful information about various features of the weldment structure. Quantitative understanding of microstructure of the fusion zone and heat

  5. Electronic structure and electrical transport characteristics of C60, 2C60 and 4C60 fullerene molecules

    Institute of Scientific and Technical Information of China (English)

    SHEN Haijun; MU Xiancai

    2007-01-01

    The extended Hückel method and the Green's function method were used to calculate the electronic struc-ture and electrical transport of Au electrode-C60,2C60 or 4C60 fullerene-Au electrode systems.Furthermore,their electronic structure and electrical transport characteristics were com-pared and analyzed.The results show that (I) owing to the contact with the Au electrodes,the C60,2C60 and 4C60 mole-cules change in their electronic structures ignificantly,and their energy gaps between LUMO and HOMO are narrow;(ii) the bonding between C60,2C60 or 4C60 fullerene and Au electrodes is partially covalent and partially electrovalent;and (iii) the conductance of the three fullerenes conforms to the order of C60>2C60>4C60.

  6. 3D structure of AcrB: the archetypal multidrug efflux transporter of Escherichia coli likely captures substrates from periplasm.

    Science.gov (United States)

    Elkins, Christopher A; Nikaido, Hiroshi

    2003-02-01

    Recent advances in structural biology have extended our understanding of the multiple drug efflux complex, AcrAB-TolC, of Escherichia coli. This tripartite complex and its homologs are the major mechanisms that give most Gram-negative bacteria their characteristic intrinsic resistance to a variety of lipophilic drugs, dyes, and detergents. Most recently, the structure of the transporter AcrB was elucidated at high resolution [Nature 419(2002)587]. It is a particularly significant achievement since integral membrane proteins are notoriously elusive structures for crystallography. The striking features of this trimeric pump, such as the presence of potential substrate-binding sites in the periplasmic domain and the possibility of direct interaction with the end of TolC tunnel, refine our understanding of the mode of action of this tripartite efflux transport complex.

  7. Particle transport and acceleration in a time-varying electromagnetic field with a multi-scale structure

    Energy Technology Data Exchange (ETDEWEB)

    Zelenyi, Lev [Space Research Institute, RAS, Profsoyusnaya Street 84/32, Moscow (Russian Federation); Artemyev, Anton [Space Research Institute, RAS, Profsoyusnaya Street 84/32, Moscow (Russian Federation)], E-mail: ante0226@gmail.com; Malova, Helmi [Space Research Institute, RAS, Profsoyusnaya Street 84/32, Moscow (Russian Federation); Nuclear Physics Institute, Moscow State University, Moscow (Russian Federation); Milovanov, Alexander V. [Department of Physics and Technology, University of Tromso, N-9037 Tromso (Norway); Space Research Institute, RAS, Profsoyusnaya Street 84/32, Moscow (Russian Federation); Zimbardo, Gaetano [Dipartimento di Fisica, Universita della Calabria, I-87036 Arcavacata di Rende (Italy); Istituto Nazionale di Fisica della Materia, Unita di Cosenza, I-87036 Arcavacata di Rende (Italy)

    2008-10-06

    We present the results of a numerical study of particle transport and acceleration by an ensemble of electromagnetic waves with a multi-scale spatio-temporal structure. We explore the dependence of acceleration and transport on the properties of turbulence. We found that an initially Maxwellian distribution of particle velocities evolves into a heavy-tailed distribution, which resembles the ubiquitous kappa-distribution, often used in non-thermal plasma phenomenology. The results of this study may be used to explain plasma heating and energization in turbulent current sheets such as the current sheets often observed in the Earth's magnetotail and discussed in relation to solar corona.

  8. The structural basis of modularity in ECF-type ABC transporters

    NARCIS (Netherlands)

    Erkens, Guus B.; Berntsson, Ronnie P-A; Fulyani, Faizah; Dosz-Majsnerowska, Dosz-Majsnerowska; Vujicic - Zagar, Andreja; ter Beek, Josy; Poolman, Bert; Slotboom, Dirk Jan

    2011-01-01

    Energy coupling factor (ECF) transporters are used for the uptake of vitamins in Prokarya. They consist of an integral membrane protein that confers substrate specificity (the S-component) and an energizing module that is related to ATP-binding cassette (ABC) transporters. S-components for different

  9. A method of examining the structure and topological properties of public-transport networks

    Science.gov (United States)

    Dimitrov, Stavri Dimitri; Ceder, Avishai (Avi)

    2016-06-01

    This work presents a new method of examining the structure of public-transport networks (PTNs) and analyzes their topological properties through a combination of computer programming, statistical data and large-network analyses. In order to automate the extraction, processing and exporting of data, a software program was developed allowing to extract the needed data from General Transit Feed Specification, thus overcoming difficulties occurring in accessing and collecting data. The proposed method was applied to a real-life PTN in Auckland, New Zealand, with the purpose of examining whether it showed characteristics of scale-free networks and exhibited features of "small-world" networks. As a result, new regression equations were derived analytically describing observed, strong, non-linear relationships among the probabilities of randomly chosen stops in the PTN to be serviced by a given number of routes. The established dependence is best fitted by an exponential rather than a power-law function, showing that the PTN examined is neither random nor scale-free, but a mixture of the two. This finding explains the presence of hubs that are not typical of exponential networks and simultaneously not highly connected to the other nodes as is the case with scale-free networks. On the other hand, the observed values of the topological properties of the network show that although it is highly clustered, owing to its representation as a directed graph, it differs slightly from "small-world" networks, which are characterized by strong clustering and a short average path length.

  10. Reflections of the Capitalization on Operational Leasing in Transport Subsector Companie's Structure Indicators Listed on Bovespa

    Directory of Open Access Journals (Sweden)

    Vinícius Gomes Martins

    2013-12-01

    Full Text Available Leasing is an alternative to financing the acquisition of assets for entities, and it has like modalities the operating procedures and financial leasing. This type of operation has caused several theoretical obstacles, among them the issue of off-balance sheet transactions. To reduce these accounting inconsistencies, the IASB and FASB have been working together to standardize the subject, this result was the publication of Exposure Draft 2010/09 (ED, which promises significant changes in the treatment of such transactions. Given this, this study aimed to analyze the impacts of the proposed changes contained in the ED, as the capitalization of operating leases, in the structure indicators at transportation subsector companies listed on the Bovespa. For this, we used the simulation methodology of the proposals in ED, confirming previous research. After the simulation accomplished, we proceeded with the Student's t test for paired samples, in order to check if the expected changes may cause significant differences in the indicators tested. The evidence points in the year of 2011, an amount of $ 3.8 billion, related to operating leases, not moved by the balance sheet (off-balance sheet of their respective companies. It was also observed that, on average, sample firms have operating leases to pay equivalent to 18.46% equity and 16.14% of debt. Finally, by simulating the proposals in the ED, it was found that the indicators of debt, equity and immobilization of the detention of non-current resources show significant variation from the statistical point of view, due to the capitalization of operating lease balances.

  11. Crystal Structure of the Zinc-Binding Transport Protein ZnuA from Escherichia coli Reveals an Unexpected Variation in Metal Coordination

    Energy Technology Data Exchange (ETDEWEB)

    Li,H.; Jogl, G.

    2007-01-01

    Bacterial ATP-binding cassette transport systems for high-affinity uptake of zinc and manganese use a cluster 9 solute-binding protein. Structures of four cluster 9 transport proteins have been determined previously. However, the structural determinants for discrimination between zinc and manganese remain under discussion. To further investigate the variability of metal binding sites in bacterial transporters, we have determined the structure of the zinc-bound transport protein ZnuA from Escherichia coli to 1.75 {angstrom} resolution. The overall structure of ZnuA is similar to other solute-binding transporters. A scaffolding {alpha}-helix forms the backbone for two structurally related globular domains. The metal-binding site is located at the domain interface. The bound zinc ion is coordinated by three histidine residues (His78, His161 and His225) and one glutamate residue (Glu77). The functional role of Glu77 for metal binding is unexpected, because this residue is not conserved in previously determined structures of zinc and manganese-specific transport proteins. The observed metal coordination by four protein residues differs significantly from the zinc-binding site in the ZnuA transporter from Synechocystis 6803, which binds zinc via three histidine residues. In addition, the E. coli ZnuA structure reveals the presence of a disulfide bond in the C-terminal globular domain that is not present in previously determined cluster 9 transport protein structures.

  12. Association of structural and enhanced transport properties in RE substituted cobalt nanoferrites

    Energy Technology Data Exchange (ETDEWEB)

    Abbas, S.; Fatima-tuz-Zahra; Anis-ur-Rehman, M., E-mail: marehman@comsats.edu.pk

    2016-08-25

    Spinel ferrites belong to an important class of compounds which has variety of electrical and magnetic applications. Neodymium doped cobalt ferrites with composition CoFe{sub 2-x}Nd{sub x}O{sub 4} where x = 0.00, 0.05, 0.10, 0.15, 0.20 were synthesized by wet chemical route called simplified sol-gel method. Prepared samples were characterized by X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) for structural analysis. All the samples were found spinel cubic belonging to Fd-3m space group. To analyze temperature effects on phase transition and to check thermal stability differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were done. Sample with x = 0.00 was found to be thermally more stable than remaining samples. Electrical analysis was done by using two probe method. DC electrical resistivity and drift mobility of sintered samples were measured as a function of temperature in the range from room temperature to 450 °C. It was observed that DC electrical resistivity has a direct dependence on dopant concentration but indirect dependence on temperature. Verwey hopping model was used to describe the results of DC electrical resistivity. Activation energy calculated from linear plots of DC resistivity for all samples was in the range of 0.532–0.594 eV. Rarely reported thermal transport properties that include thermal conductivity, thermal diffusivity and volumetric heat capacity were measured by Advantageous Transient Plane Source (ATPS) method. All the samples showed values near to that of thermal insulators. Thermal conductivity of all samples was increased up to 100–120 °C and then decreased. This behavior was thoroughly studied. - Highlights: • Phase pure nanoparticles of CoFe{sub 2-x}Nd{sub x}O{sub 4}(x = 0.00–0.20) by simplified sol-gel method. • XRD and FTIR spectroscopy confirmed the spinel structure of ferrites. • x = 0.00 was found to be thermally more stable than rest of the samples by TGA

  13. Metrology and characterization of impurity transport during cleaning of micro and nano structures

    Science.gov (United States)

    Yan, Jun

    A major challenge in the manufacturing of micro and nano devices is the cleaning, rinsing, and drying of very small structures. Without a technology for in situ and real-time monitoring and controlling, the rinse processes that account for a significant fraction of the total processing steps use a large amount of water and energy perhaps unnecessarily. This "blind" processing approach leads to waste that can have significant economic and environmental impacts. An electrochemical residue sensor (ECRS) has been developed and is aimed at in situ and real-time measurement of residual contamination inside the micro and nano structures. Using this technology, the mechanisms and bottlenecks of cleaning, rinsing, and drying can be investigated and the processes can be monitored and controlled. An equivalent circuit model was developed to assist the design of the sensor; its validity was proved by the first prototype. The simulation results and the experimental data predicted a good sensitivity in a wide range of operational frequency. To use the sensor in a practical rinse tank setup, the sensor-on-wafer prototype was designed and fabricated. Both the fab-scale and the lab-scale tests were performed and results illustrated many successes. The sensor is the first and the only available technology that provides the in situ and real-time cleanness information in the microstructures during the rinse processes. The sensor results distinguished four different types of rinse processes and showed high sensitivity to the ionic concentration change in the microstructures. The impacts of cleaning and rinsing parameters such as flow rate, temperature, cleaning solution concentrations, and process time on the sulfuric acid rinsing efficiency were investigated by using the sensor. The investigation discovered that sulfuric acid rinsing is a two-stage process: a flow-control stage and a desorption-control stage. A comprehensive rinse model was developed to correlate the transport process

  14. Small-scale transport structures in the Arctic winter 2009/2010

    Directory of Open Access Journals (Sweden)

    C. Kalicinsky

    2013-04-01

    Full Text Available The CRISTA-NF (Cryogenic Infrared Spectrometers and Telescope for the Atmosphere – New Frontiers instrument is an airborne infrared limb sounder operated aboard the Russian research aircraft M55-Geophysica. The instrument successfully participated in a large Arctic aircraft campaign within the RECONCILE (Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interactions project from January to March 2010 in Kiruna, Sweden. This paper concentrates on the measurements during one flight of the campaign, which took place on 2 March in the vicinity of the polar vortex. We present two-dimensional cross-sections of volume mixing ratios for the trace gases CFC-11, O3, and ClONO2 with an unprecedented vertical resolution of about 500 to 600 m for a large part of the observed altitude range and a dense horizontal sampling along flight direction of ≈ 15 km. The trace gas distributions show several structures like the polar vortex and filaments composed of air masses of different origin. The situation during the analysed flight is simulated by the chemistry and transport model CLaMS (Chemical Lagrangian Model of the Stratosphere and compared with the measurements to assess the performance of the model with respect to advection, mixing, and the chemistry in the polar vortex. These comparisons confirm the capability of CLaMS to reproduce even very small-scale structures in the atmosphere. Based on the good agreement between simulation and observation, we use a model concept utilising artificial tracers to further analyse the CRISTA-NF observations in terms of air mass origin. A characteristic of the Arctic winter 2009/10 was a sudden stratospheric warming in early December that led to a split of the polar vortex. The vortex re-established at the end of December. Our passive tracer simulations suggest that large parts of the re-established vortex consisted to about 45% of high- and

  15. Scaling of phloem structure and optimality of photoassimilate transport in conifer needles

    DEFF Research Database (Denmark)

    Ronellenfitsch, Henrik; Liesche, Johannes; Jensen, Kaare Hartvig

    2015-01-01

    The phloem vascular system facilitates transport of energy-rich sugar and signalling molecules in plants, thus permitting long-range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The flow is driven by osmotic pressure, generated...... conductive elements obeys a power law. We present a minimal model that accounts for these common traits and takes into account the transport strategy and natural constraints. This minimal model predicts a power law phloem distribution consistent with transport energy minimization, suggesting that energetics...

  16. Blocking Phonon Transport by Structural Resonances in Alloy-Based Nanophononic Metamaterials Leads to Ultralow Thermal Conductivity

    Science.gov (United States)

    Xiong, Shiyun; Sääskilahti, Kimmo; Kosevich, Yuriy A.; Han, Haoxue; Donadio, Davide; Volz, Sebastian

    2016-07-01

    Understanding the design rules to obtain materials that enable a tight control of phonon transport over a broad range of frequencies would aid major developments in thermoelectric energy harvesting, heat management in microelectronics, and information and communication technology. Using atomistic simulations we show that the metamaterials approach relying on localized resonances is very promising to engineer heat transport at the nanoscale. Combining designed resonant structures to alloying can lead to extremely low thermal conductivity in silicon nanowires. The hybridization between resonant phonons and propagating modes greatly reduces the group velocities and the phonon mean free paths in the low frequency acoustic range below 4 THz. Concurrently, alloy scattering hinders the propagation of high frequency thermal phonons. Our calculations establish a rationale between the size, shape, and period of the resonant structures, and the thermal conductivity of the nanowire, and demonstrate that this approach is even effective to block phonon transport in wavelengths much longer than the size and period of the surface resonant structures. A further consequence of using resonant structures is that they are not expected to scatter electrons, which is beneficial for thermoelectric applications.

  17. Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding.

    Science.gov (United States)

    Soysa, Radika; Venselaar, Hanka; Poston, Jacqueline; Ullman, Buddy; Hasne, Marie-Pierre

    2013-06-15

    The TcPOT1.1 gene from Trypanosoma cruzi encodes a high affinity putrescine-cadaverine transporter belonging to the APC (amino acid/polyamine/organocation) transporter superfamily. No experimental three-dimensional structure exists for any eukaryotic member of the APC family, and thus the structural determinants critical for function of these permeases are unknown. To elucidate the key residues involved in putrescine translocation and recognition by this APC family member, a homology model of TcPOT1.1 was constructed on the basis of the atomic co-ordinates of the Escherichia coli AdiC arginine/agmatine antiporter crystal structure. The TcPOT1.1 homology model consisted of 12 transmembrane helices with the first ten helices organized in two V-shaped antiparallel domains with discontinuities in the helical structures of transmembrane spans 1 and 6. The model suggests that Trp241 and a Glu247-Arg403 salt bridge participate in a gating system and that Asn245, Tyr148 and Tyr400 contribute to the putrescine-binding pocket. To test the validity of the model, 26 site-directed mutants were created and tested for their ability to transport putrescine and to localize to the parasite cell surface. These results support the robustness of the TcPOT1.1 homology model and reveal the importance of specific aromatic residues in the TcPOT1.1 putrescine-binding pocket.

  18. Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters

    Directory of Open Access Journals (Sweden)

    Norifumi Muraki

    2016-05-01

    Full Text Available Corynebacteria contain a heme uptake system encoded in hmuTUV genes, in which HmuT protein acts as a heme binding protein to transport heme to the cognate transporter HmuUV. The crystal structure of HmuT from Corynebacterium glutamicum (CgHmuT reveals that heme is accommodated in the central cleft with His141 and Tyr240 as the axial ligands and that Tyr240 forms a hydrogen bond with Arg242. In this work, the crystal structures of H141A, Y240A, and R242A mutants were determined to understand the role of these residues for the heme binding of CgHmuT. Overall and heme environmental structures of these mutants were similar to those of the wild type, suggesting that there is little conformational change in the heme-binding cleft during heme transport reaction with binding and the dissociation of heme. A loss of one axial ligand or the hydrogen bonding interaction with Tyr240 resulted in an increase in the redox potential of the heme for CgHmuT to be reduced by dithionite, though the wild type was not reduced under physiological conditions. These results suggest that the heme environmental structure stabilizes the ferric heme binding in CgHmuT, which will be responsible for efficient heme uptake under aerobic conditions where Corynebacteria grow.

  19. Blocking Phonon Transport by Structural Resonances in Alloy-Based Nanophononic Metamaterials Leads to Ultralow Thermal Conductivity.

    Science.gov (United States)

    Xiong, Shiyun; Sääskilahti, Kimmo; Kosevich, Yuriy A; Han, Haoxue; Donadio, Davide; Volz, Sebastian

    2016-07-01

    Understanding the design rules to obtain materials that enable a tight control of phonon transport over a broad range of frequencies would aid major developments in thermoelectric energy harvesting, heat management in microelectronics, and information and communication technology. Using atomistic simulations we show that the metamaterials approach relying on localized resonances is very promising to engineer heat transport at the nanoscale. Combining designed resonant structures to alloying can lead to extremely low thermal conductivity in silicon nanowires. The hybridization between resonant phonons and propagating modes greatly reduces the group velocities and the phonon mean free paths in the low frequency acoustic range below 4 THz. Concurrently, alloy scattering hinders the propagation of high frequency thermal phonons. Our calculations establish a rationale between the size, shape, and period of the resonant structures, and the thermal conductivity of the nanowire, and demonstrate that this approach is even effective to block phonon transport in wavelengths much longer than the size and period of the surface resonant structures. A further consequence of using resonant structures is that they are not expected to scatter electrons, which is beneficial for thermoelectric applications.

  20. Probing structure-function relationships and gating mechanisms in the CorA Mg2+ transport system.

    Science.gov (United States)

    Payandeh, Jian; Li, Canhui; Ramjeesingh, Mohabir; Poduch, Ewa; Bear, Christine E; Pai, Emil F

    2008-04-25

    Recent crystal structures of the CorA Mg(2+) transport protein from Thermotoga maritima (TmCorA) revealed an unusually long ion pore putatively gated by hydrophobic residues near the intracellular end and by universally conserved asparagine residues at the periplasmic entrance. A conformational change observed in an isolated funnel domain structure also led to a proposal for the structural basis of gating. Because understanding the molecular mechanisms underlying ion channel and transporter gating remains an important challenge, we have undertaken a structure-guided engineering approach to probe structure-function relationships in TmCorA. The intracellular funnel domain is shown to constitute an allosteric regulatory module that can be engineered to promote an activated or closed state. A periplasmic gate centered about a proline-induced kink of the pore-lining helix is described where "helix-straightening" mutations produce a dramatic gain-of-function. Mutation to the narrowest constriction along the pore demonstrates that a hydrophobic gate is operational within this Mg(2+)-selective transport protein and likely forms an energetic barrier to ion flux. We also provide evidence that highly conserved acidic residues found in the short periplasmic loop are not essential for TmCorA function or Mg(2+) selectivity but may be required for proper protein folding and stability. This work extends our gating model for the CorA-Alr1-Mrs2 superfamily and reveals features that are characteristic of an ion channel. Aspects of these results that have broader implications for a range of channel and transporter families are highlighted.

  1. Peering inside the granular bed: illuminating feedbacks between bed-load transport and bed-structure evolution

    Science.gov (United States)

    Houssais, M.; Jerolmack, D. J.; Martin, R. L.

    2013-12-01

    The threshold of motion is perhaps the most important quantity to determine for understanding rates of bed load transport, however it is a moving target. Decades of research show that it changes in space and in time within a river, and is highly variable among different systems; however, these differences are not mechanistically understood. Recent researchers have proposed that the critical Shields stress is strongly dependent on the local configuration of the sediment bed [Frey and Church, 2011]. Critical Shields stress has been observed to change following sediment-transporting flood events in natural rivers [e.g., Turowski et al., 2011], while small-scale laboratory experiments have produced declining bed load transport rates associated with slow bed compaction [Charru et al., 2004]. However, no direct measurements have been made of the evolving bed structure under bed load transport, so the connection between granular controls and the threshold of motion remains uncertain. A perspective we adopt is that granular effects determine the critical Shields stress, while the fluid supplies a distribution of driving stresses. In order to isolate the granular effect, we undertake laminar bed load transport experiments using plastic beads sheared by a viscous oil in a small, annular flume. The fluid and beads are refractive index matched, and the fluid impregnated with a fluorescing powder. When illuminated with a planar laser sheet, we are able to image slices of the granular bed while also tracking the overlying sediment transport. We present the first results showing how bed load transport influences granular packing, and how changes in packing influence the threshold of motion to feed back on bed load transport rates. This effect may account for much of the variability observed in the threshold of motion in natural streams, and by extension offers a plausible explanation for hysteresis in bed load transport rates observed during floods. Charru, F., H. Mouilleron, and

  2. Radio-metabolite analysis of carbon-11 biochemical partitioning to non-structural carbohydrates for integrated metabolism and transport studies.

    Science.gov (United States)

    Babst, Benjamin A; Karve, Abhijit A; Judt, Tatjana

    2013-06-01

    Metabolism and phloem transport of carbohydrates are interactive processes, yet each is often studied in isolation from the other. Carbon-11 ((11)C) has been successfully used to study transport and allocation processes dynamically over time. There is a need for techniques to determine metabolic partitioning of newly fixed carbon that are compatible with existing non-invasive (11)C-based methodologies for the study of phloem transport. In this report, we present methods using (11)C-labeled CO2 to trace carbon partitioning to the major non-structural carbohydrates in leaves-sucrose, glucose, fructose and starch. High-performance thin-layer chromatography (HPTLC) was adapted to provide multisample throughput, raising the possibility of measuring different tissues of the same individual plant, or for screening multiple plants. An additional advantage of HPTLC was that phosphor plate imaging of radioactivity had a much higher sensitivity and broader range of sensitivity than radio-HPLC detection, allowing measurement of (11)C partitioning to starch, which was previously not possible. Because of the high specific activity of (11)C and high sensitivity of detection, our method may have additional applications in the study of rapid metabolic responses to environmental changes that occur on a time scale of minutes. The use of this method in tandem with other (11)C assays for transport dynamics and whole-plant partitioning makes a powerful combination of tools to study carbohydrate metabolism and whole-plant transport as integrated processes.

  3. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies.

    Science.gov (United States)

    Kaufmann, Kristian W; Dawson, Eric S; Henry, L Keith; Field, Julie R; Blakely, Randy D; Meiler, Jens

    2009-02-15

    To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected.

  4. The Factors Influencing Satisfaction with Public City Transport: A Structural Equation Modelling Approach

    OpenAIRE

    Pawlasova Pavlina

    2015-01-01

    Satisfaction is one of the key factors which influences customer loyalty. We assume that the satisfied customer will be willing to use the ssame service provider again. The overall passengers´ satisfaction with public city transport may be affected by the overall service quality. Frequency, punctuality, cleanliness in the vehicle, proximity, speed, fare, accessibility and safety of transport, information and other factors can influence passengers´ satisfaction. The aim of this pap...

  5. Optimizing electronic structure and quantum transport at the graphene-Si(111) interface: an ab initio density-functional study.

    Science.gov (United States)

    Tayran, Ceren; Zhu, Zhen; Baldoni, Matteo; Selli, Daniele; Seifert, Gotthard; Tománek, David

    2013-04-26

    We use ab initio density-functional calculations to determine the interaction of a graphene monolayer with the Si(111) surface. We find that graphene forms strong bonds to the bare substrate and accommodates the 12% lattice mismatch by forming a wavy structure consisting of free-standing conductive ridges that are connected by ribbon-shaped regions of graphene, which bond covalently to the substrate. We perform quantum transport calculations for different geometries to study changes in the transport properties of graphene introduced by the wavy structure and bonding to the Si substrate. Our results suggest that wavy graphene combines high mobility along the ridges with efficient carrier injection into Si in the contact regions.

  6. Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution.

    Science.gov (United States)

    Eshaghi, Said; Niegowski, Damian; Kohl, Andreas; Martinez Molina, Daniel; Lesley, Scott A; Nordlund, Pär

    2006-07-21

    CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.

  7. Plant High-Affinity Potassium (HKT Transporters Involved in Salinity Tolerance: Structural Insights to Probe Differences in Ion Selectivity

    Directory of Open Access Journals (Sweden)

    Maria Hrmova

    2013-04-01

    Full Text Available High-affinity Potassium Transporters (HKTs belong to an important class of integral membrane proteins (IMPs that facilitate cation transport across the plasma membranes of plant cells. Some members of the HKT protein family have been shown to be critical for salinity tolerance in commercially important crop species, particularly in grains, through exclusion of Na+ ions from sensitive shoot tissues in plants. However, given the number of different HKT proteins expressed in plants, it is likely that different members of this protein family perform in a range of functions. Plant breeders and biotechnologists have attempted to manipulate HKT gene expression through genetic engineering and more conventional plant breeding methods to improve the salinity tolerance of commercially important crop plants. Successful manipulation of a biological trait is more likely to be effective after a thorough understanding of how the trait, genes and proteins are interconnected at the whole plant level. This article examines the current structural and functional knowledge relating to plant HKTs and how their structural features may explain their transport selectivity. We also highlight specific areas where new knowledge of plant HKT transporters is needed. Our goal is to present how knowledge of the structure of HKT proteins is helpful in understanding their function and how this understanding can be an invaluable experimental tool. As such, we assert that accurate structural information of plant IMPs will greatly inform functional studies and will lead to a deeper understanding of plant nutrition, signalling and stress tolerance, all of which represent factors that can be manipulated to improve agricultural productivity.

  8. Plant High-Affinity Potassium (HKT) Transporters involved in salinity tolerance: structural insights to probe differences in ion selectivity.

    Science.gov (United States)

    Waters, Shane; Gilliham, Matthew; Hrmova, Maria

    2013-04-09

    High-affinity Potassium Transporters (HKTs) belong to an important class of integral membrane proteins (IMPs) that facilitate cation transport across the plasma membranes of plant cells. Some members of the HKT protein family have been shown to be critical for salinity tolerance in commercially important crop species, particularly in grains, through exclusion of Na+ ions from sensitive shoot tissues in plants. However, given the number of different HKT proteins expressed in plants, it is likely that different members of this protein family perform in a range of functions. Plant breeders and biotechnologists have attempted to manipulate HKT gene expression through genetic engineering and more conventional plant breeding methods to improve the salinity tolerance of commercially important crop plants. Successful manipulation of a biological trait is more likely to be effective after a thorough understanding of how the trait, genes and proteins are interconnected at the whole plant level. This article examines the current structural and functional knowledge relating to plant HKTs and how their structural features may explain their transport selectivity. We also highlight specific areas where new knowledge of plant HKT transporters is needed. Our goal is to present how knowledge of the structure of HKT proteins is helpful in understanding their function and how this understanding can be an invaluable experimental tool. As such, we assert that accurate structural information of plant IMPs will greatly inform functional studies and will lead to a deeper understanding of plant nutrition, signalling and stress tolerance, all of which represent factors that can be manipulated to improve agricultural productivity.

  9. The Texas horned lizard as model for robust capillary structures for passive directional transport of cooling lubricants

    Science.gov (United States)

    Comanns, Philipp; Winands, Kai; Pothen, Mario; Bott, Raya A.; Wagner, Hermann; Baumgartner, Werner

    2016-04-01

    Moisture-harvesting lizards, such as the Texas horned lizard Phrynosoma cornutum, have remarkable adaptations for inhabiting arid regions. Special skin structures, in particular capillary channels in between imbricate overlapping scales, enable the lizard to collect water by capillarity and to transport it to the snout for ingestion. This fluid transport is passive and directional towards the lizard's snout. The directionality is based on geometric principles, namely on a periodic pattern of interconnected half-open capillary channels that narrow and widen. Following a biomimetic approach, these principles were transferred to technical prototype design and manufacturing. Capillary structures, 50 μm to 300 μm wide and approx. 70 μm deep, were realized by use of a pulsed picosecond laser in hot working tool steel, hardened to 52 HRC. In order to achieve highest functionality, strategies were developed to minimize potential structural inaccuracies, which can occur at the bottom of the capillary structures caused by the laser process. Such inaccuracies are in the range of 10 μm to 15 μm and form sub-capillary structures with greater capillary forces than the main channels. Hence, an Acceleration Compensation Algorithm was developed for the laser process to minimize or even avoid these inaccuracies. The capillary design was also identified to have substantial influence; by a hexagonal capillary network of non-parallel capillaries potential influences of sub-capillaries on the functionality were reduced to realize a robust passive directional capillary transport. Such smart surface structures can lead to improvements of technical systems by decreasing energy consumption and increasing the resource efficiency.

  10. Structural dynamics of the monoamine transporter homologue LeuT from accelerated conformational sampling and channel analysis

    Science.gov (United States)

    Thomas, James R.; Gedeon, Patrick C.; Madura, Jeffry D.

    2014-01-01

    The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics (aMD) simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30–D404, Y108–F253, and R5–D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport. PMID:24753369

  11. Structure-affinity relationship in the interactions of human organic anion transporter 1 with caffeine, theophylline, theobromine and their metabolites.

    Science.gov (United States)

    Sugawara, Mitsuru; Mochizuki, Takahiro; Takekuma, Yoh; Miyazaki, Katsumi

    2005-08-15

    It is well known that human organic anion transporter 1 (hOAT1) transports many kinds of drugs, endogenous compounds, and toxins. However, little is known about the structure-affinity relationship. The aim of this study was to elucidate the structure-affinity relationship using a series of structurally related compounds that interact with hOAT1. Inhibitory effects of xanthine- and uric acid-related compounds on the transport of p-aminohippuric acid were examined using CHO-K1 cells stably expressing hOAT1. The order of potency for the inhibitory effects of xanthine-related compounds on PAH uptake was 1-methyl derivative>7-methyl derivative>3-methyl derivative falling dotsxanthine>1,3,7-trimethyl derivative (caffeine). The order of potency of the inhibition was 1,3,7-trimethyluric acid>1,3-dimethyluric acid>1,7-dimethyluric acid>1-methyluric acid>uric acid. A significant correlation between inhibitory potency and lipophilicity of the tested uric acid-related compounds was observed. The main determinant of the affinity of xanthine-related compounds is the position of the methyl group. On the other hand, lipophilicity is the main determinant of the affinity of uric acid-related compounds.

  12. Structural modeling of mutant alpha-glucosidases resulting in a processing/transport defect in Pompe disease.

    Science.gov (United States)

    Sugawara, Kanako; Saito, Seiji; Sekijima, Masakazu; Ohno, Kazuki; Tajima, Youichi; Kroos, Marian A; Reuser, Arnold J J; Sakuraba, Hitoshi

    2009-06-01

    To elucidate the mechanism underlying transport and processing defects from the viewpoint of enzyme folding, we constructed three-dimensional models of human acid alpha-glucosidase encompassing 27 relevant amino acid substitutions by means of homology modeling. Then, we determined in each separate case the number of affected atoms, the root-mean-square distance value and the solvent-accessible surface area value. The analysis revealed that the amino acid substitutions causing a processing or transport defect responsible for Pompe disease were widely spread over all of the five domains comprising the acid alpha-glucosidase. They were distributed from the core to the surface of the enzyme molecule, and the predicted structural changes varied from large to very small. Among the structural changes, we paid particular attention to G377R and G483R. These two substitutions are predicted to cause electrostatic changes in neighboring small regions on the molecular surface. The quality control system of the endoplasmic reticulum apparently detects these very small structural changes and degrades the mutant enzyme precursor (G377R), but also the cellular sorting system might be misled by these minor changes whereby the precursor is secreted instead of being transported to lysosomes (G483R).

  13. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis.

    Science.gov (United States)

    Thomas, James R; Gedeon, Patrick C; Madura, Jeffry D

    2014-10-01

    The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.

  14. Sedimentary and structural controls on seismogenic slumping within mass transport deposits from the Dead Sea Basin

    Science.gov (United States)

    Alsop, G. I.; Marco, S.; Weinberger, R.; Levi, T.

    2016-10-01

    Comparatively little work has been undertaken on how sedimentary environments and facies changes can influence detailed structural development in slump sheets associated with mass transport deposits (MTDs). The nature of downslope deformation at the leading edge of MTDs is currently debated in terms of frontally emergent, frontally confined and open-toed models. An opportunity to study and address these issues occurs within the Dead Sea Basin, where six individual slump sheets (S1-S6) form MTDs in the Late Pleistocene Lisan Formation. All six slumps, which are separated from one another by undeformed beds, are traced towards the NE for up to 1 km, and each shows a change in sedimentary facies from detrital-rich in the SW, to more aragonite-rich in the NE. The detrital-rich facies is sourced predominantly from the rift margin 1.5 km further SW, while the aragonite-rich facies represents evaporitic precipitation in the hyper saline Lake Lisan. The stacked system of MTDs translates downslope towards the NE and follows a pre-determined sequence controlled by the sedimentary facies. Each individual slump roots downwards into underlying detrital-rich layers and displays a greater detrital content towards the SW, which is marked by increasing folding, while increasing aragonite content towards the NE is associated with more discrete thrusts. The MTDs thin downslope towards the NE, until they pass laterally into undeformed beds at the toe. The amount of contraction also reduces downslope from a maximum of 50% to < 10% at the toe, where upright folds form diffuse 'open-toed' systems. We suggest that MTDs are triggered by seismic events, facilitated by detrital-rich horizons, and controlled by palaeoslope orientation. The frequency of individual failures is partially controlled by local environmental influences linked to detrital input and should therefore be used with some caution in more general palaeoseismic studies. We demonstrate that MTDs display 'open toes' where

  15. STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin; Martin Keller; Joseph W. Stucki

    2011-06-15

    The objectives of this project were to: (1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), (2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and (3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee, where the subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which

  16. Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA.

    Directory of Open Access Journals (Sweden)

    Justina C Wolters

    Full Text Available BACKGROUND: The ABC transporter OpuA from Lactococcus lactis transports glycine betaine upon activation by threshold values of ionic strength. In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC was characterized. PRINCIPAL FINDINGS: The binding of glycine betaine to purified OpuA and OpuAC (K(D = 4-6 microM did not show any salt dependence or cooperative effects, in contrast to the transport activity. OpuAC is highly specific for glycine betaine and the related proline betaine. Other compatible solutes like proline and carnitine bound with affinities that were 3 to 4 orders of magnitude lower. The low affinity substrates were not noticeably transported by membrane-reconstituted OpuA. OpuAC was crystallized in an open (1.9 A and closed-liganded (2.3 A conformation. The binding pocket is formed by three tryptophans (Trp-prism coordinating the quaternary ammonium group of glycine betaine in the closed-liganded structure. Even though the binding site of OpuAC is identical to that of its B. subtilis homolog, the affinity for glycine betaine is 4-fold higher. CONCLUSIONS: Ionic strength did not affect substrate binding to OpuA, indicating that regulation of transport is not at the level of substrate binding, but rather at the level of translocation. The overlap between the crystal structures of OpuAC from L.lactis and B.subtilis, comprising the classical Trp-prism, show that the differences observed in the binding affinities originate from outside of the ligand binding site.

  17. Recent Developments in Graphene-Based Membranes: Structure, Mass-Transport Mechanism and Potential Applications.

    Science.gov (United States)

    Sun, Pengzhan; Wang, Kunlin; Zhu, Hongwei

    2016-03-23

    Significant achievements have been made on the development of next-generation filtration and separation membranes using graphene materials, as graphene-based membranes can afford numerous novel mass-transport properties that are not possible in state-of-art commercial membranes, making them promising in areas such as membrane separation, water desalination, proton conductors, energy storage and conversion, etc. The latest developments on understanding mass transport through graphene-based membranes, including perfect graphene lattice, nanoporous graphene and graphene oxide membranes are reviewed here in relation to their potential applications. A summary and outlook is further provided on the opportunities and challenges in this arising field. The aspects discussed may enable researchers to better understand the mass-transport mechanism and to optimize the synthesis of graphene-based membranes toward large-scale production for a wide range of applications.

  18. Investigation of the structure and function of a Shewanella oneidensis arsenical-resistance family transporter.

    Science.gov (United States)

    Xia, Xiaobing; Postis, Vincent L G; Rahman, Moazur; Wright, Gareth S A; Roach, Peter C J; Deacon, Sarah E; Ingram, Jean C; Henderson, Peter J F; Findlay, John B C; Phillips, Simon E V; McPherson, Michael J; Baldwin, Stephen A

    2008-12-01

    The toxic metalloid arsenic is an abundant element and most organisms possess transport systems involved in its detoxification. One such family of arsenite transporters, the ACR3 family, is widespread in fungi and bacteria. To gain a better understanding of the molecular mechanism of arsenic transport, we report here the expression and characterization of a family member, So_ACR3, from the bacterium Shewanella oneidensis MR-1. Surprisingly, expression of this transporter in the arsenic-hypersensitive Escherichia coli strain AW3110 conferred resistance to arsenate, but not to arsenite. Purification of a C-terminally His-tagged form of the protein allowed the binding of putative permeants to be directly tested: arsenate but not arsenite quenched its intrinsic fluorescence in a concentration-dependent fashion. Fourier transform infrared spectroscopy showed that the purified protein was predominantly alpha-helical. A mutant bearing a single cysteine residue at position 3 retained the ability to confer arsenate resistance, and was accessible to membrane impermeant thiol reagents in intact cells. In conjunction with successful C-terminal tagging with oligohistidine, this finding is consistent with the experimentally-determined topology of the homologous human apical sodium-dependent bile acid transporter, namely 7 transmembrane helices and a periplasmic N-terminus, although the presence of additional transmembrane segments cannot be excluded. Mutation to alanine of the conserved residue proline 190, in the fourth putative transmembrane region, abrogated the ability of the transporter to confer arsenic resistance, but did not prevent arsenate binding. An apparently increased thermal stability is consistent with the mutant being unable to undergo the conformational transitions required for permeant translocation.

  19. Integrated thermal-structural finite element analysis. [for applications to hypersonic transport design

    Science.gov (United States)

    Thornton, E. A.; Decahaumphai, P.; Wieting, A. R.

    1980-01-01

    An integrated thermal-structural finite element approach for efficient coupling of thermal and structural analysis is presented. An integrated thermal-structural rod element is developed and used in four thermal-structural applications; the accuracy of this integrated approach is illustrated by comparisons with the customary approach of finite difference thermal-finite element structural analyses. Results show that integrated thermal-structural analysis of structures modeled with rod elements is more accurate than conventional analysis, and that its further development promises significant results.

  20. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng

    2012-08-10

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Charge transport across insulating self-assembled monolayers: non-equilibrium approaches and modeling to relate current and molecular structure.

    Science.gov (United States)

    Mirjani, Fatemeh; Thijssen, Joseph M; Whitesides, George M; Ratner, Mark A

    2014-12-23

    This paper examines charge transport by tunneling across a series of electrically insulating molecules with the structure HS(CH2)4CONH(CH2)2R) in the form of self-assembled monolayers (SAMs), supported on silver. The molecules examined were studied experimentally by Yoon et al. (Angew. Chem. Int. Ed. 2012, 51, 4658-4661), using junctions of the structure AgS(CH2)4CONH(CH2)2R//Ga2O3/EGaIn. The tail group R had approximately the same length for all molecules, but a range of different structures. Changing the R entity over the range of different structures (aliphatic to aromatic) does not influence the conductance significantly. To rationalize this surprising result, we investigate transport through these SAMs theoretically, using both full quantum methods and a generic, independent-electron tight-binding toy model. We find that the highest occupied molecular orbital, which is largely responsible for the transport in these molecules, is always strongly localized on the thiol group. The relative insensitivity of the current density to the structure of the R group is due to a combination of the couplings between the carbon chains and the transmission inside the tail. Changing from saturated to conjugated tail groups increases the latter but decreases the former. This work indicates that significant control over SAMs largely composed of nominally insulating groups may be possible when tail groups are used that are significantly larger than those used in the experiments of Yoon et al.1.

  2. Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2*♦

    Science.gov (United States)

    Giménez-Mascarell, Paula; Oyenarte, Iker; Hardy, Serge; Breiderhoff, Tilman; Stuiver, Marchel; Kostantin, Elie; Diercks, Tammo; Pey, Angel L.; Ereño-Orbea, June; Martínez-Chantar, María Luz; Khalaf-Nazzal, Reham; Claverie-Martin, Felix; Müller, Dominik; Tremblay, Michel L.

    2017-01-01

    Phosphatases of regenerating liver (PRLs), the most oncogenic of all protein-tyrosine phosphatases (PTPs), play a critical role in metastatic progression of cancers. Recent findings established a new paradigm by uncovering that their association with magnesium transporters of the cyclin M (CNNM) family causes a rise in intracellular magnesium levels that promote oncogenic transformation. Recently, however, essential roles for regulation of the circadian rhythm and reproduction of the CNNM family have been highlighted. Here, we describe the crystal structure of PRL-1 in complex with the Bateman module of CNNM2 (CNNM2BAT), which consists of two cystathionine β-synthase (CBS) domains (IPR000664) and represents an intracellular regulatory module of the transporter. The structure reveals a heterotetrameric association, consisting of a disc-like homodimer of CNNM2BAT bound to two independent PRL-1 molecules, each one located at opposite tips of the disc. The structure highlights the key role played by Asp-558 at the extended loop of the CBS2 motif of CNNM2 in maintaining the association between the two proteins and proves that the interaction between CNNM2 and PRL-1 occurs via the catalytic domain of the phosphatase. Our data shed new light on the structural basis underlying the interaction between PRL phosphatases and CNNM transporters and provides a hypothesis about the molecular mechanism by which PRL-1, upon binding to CNNM2, might increase the intracellular concentration of Mg2+ thereby contributing to tumor progression and metastasis. The availability of this structure sets the basis for the rational design of compounds modulating PRL-1 and CNNM2 activities. PMID:27899452

  3. The effect of hydrophilic and hydrophobic structure of amphiphilic polymeric micelles on their transport in epithelial MDCK cells.

    Science.gov (United States)

    Yu, Chao; He, Bing; Xiong, Meng-Hua; Zhang, Hua; Yuan, Lan; Ma, Ling; Dai, Wen-Bing; Wang, Jun; Wang, Xing-Lin; Wang, Xue-Qing; Zhang, Qiang

    2013-08-01

    The interaction of nanocarriers with cells including their transcellular behavior is vital not only for a drug delivery system, but also for the safety of nanomaterials. In an attempt to clarify how the structures of polymers impact the transport mechanisms of their nanocarriers in epithelial cells, three amphiphilic polymers (PEEP-PCL, PEG-PCL and PEG-DSPE) with different hydrophilic or hydrophobic blocks were synthesized or chosen to form different micelle systems here. The endocytosis, exocytosis, intracellular colocalization, paracellular permeability and transcytosis of these micelle systems were compared using Förster resonance energy transfer analysis, real-time confocal images, colocalization assay, transepithelial electrical resistance study, and so on. All micelle systems were found intact during the studies with cells. The endocytosis and exocytosis studies with undifferentiated MDCK cells and the transcytosis study with differentiated MDCK monolayers all indicated the fact that PEG-DSPE micelles achieved the most and fastest transport, followed by PEG-PCL and PEEP-PCL in order. These might be because DSPE has higher hydrophobicity than PCL while PEG has lower hydrophilicity than PEEP. Different in hydrophilic or hydrophobic structures, all kinds of micelles demonstrated similar pathways during endocytosis and exocytosis, both caveolae- and clathrin-mediated but with difference in degree. The colocalization studies revealed different behaviors in intracellular trafficking among the three polymer micelles, suggesting the decisive role of hydrophilic shells on this process. Finally, all micelle systems did not impact the paracellular permeability of test cell monolayer. In conclusion, the hydrophilic and hydrophobic structures of test micelles could influence their transport ability, intracellular trafficking and the transport level under each pathway in MDCK cells.

  4. Logistics of water and salt transport through the plant: structure and functioning of the xylem

    NARCIS (Netherlands)

    Boer, de A.H.; Volkov, V.

    2003-01-01

    The xylem is a long-distance transport system that is unique to higher plants. It evolved into a very sophisticated plumbing system ensuring controlled loading/unloading of ions and water and their effective translocation to the required sinks. The focus of this overview will be the intrinsic

  5. Logistics of water and salt transport through the plant: structure and functioning of the xylem

    NARCIS (Netherlands)

    Boer, de A.H.; Volkov, V.

    2003-01-01

    The xylem is a long-distance transport system that is unique to higher plants. It evolved into a very sophisticated plumbing system ensuring controlled loading/unloading of ions and water and their effective translocation to the required sinks. The focus of this overview will be the intrinsic inter-

  6. Structural divergence of paralogous S components from ECF-type ABC transporters

    NARCIS (Netherlands)

    Berntsson, Ronnie P. -A.; ter Beek, Josy; Dosz-Majsnerowska, Maria; Duurkens, Ria H; Puri, Pranav; Poolman, Bert; Slotboom, Dirk-Jan

    2012-01-01

    Energy coupling factor (ECF) proteins are ATP-binding cassette transporters involved in the import of micronutrients in prokaryotes. They consist of two nucleotide-binding subunits and the integral membrane subunit EcfT, which together form the ECF module and a second integral membrane subunit that

  7. Structure, function, evolution, and application of bacterial Pnu-type vitamin transporters

    NARCIS (Netherlands)

    Jähme, Michael; Slotboom, Dirk Jan

    2015-01-01

    Many bacteria can take up vitamins from the environment via specific transport machineries. Uptake is essential for organisms that lack complete vitamin biosynthesis pathways, but even in the presence of biosynthesis routes uptake is likely preferred, because it is energetically less costly. Pnu tra

  8. How historical copper contamination affects soil structure and mobilization and transport of colloids

    DEFF Research Database (Denmark)

    Paradelo, Marcos; Møldrup, Per; Holmstrup, Martin

    of copper concentration on the movement of an inert tracer, tritium, and the mobilization and transport of colloid particles in undisturbed soil cores (10 cm diameter and 8 cm height). The cores were sampled along a copper gradient of 21 to 3837 mg Cu kg-1 soil on an abandoned arable soil polluted by copper...

  9. Origins of Anomalous Transport in Disordered Media: Structural and Dynamic Controls

    CERN Document Server

    Edery, Yaniv; Guadagnini, Alberto; Berkowitz, Brian

    2013-01-01

    We quantitatively identify the origin of anomalous transport in a representative model of a heterogeneous system---tracer migration in the complex flow patterns of a lognormally distributed hydraulic conductivity ($K$) field. The transport, determined by a particle tracking technique, is characterized by breakthrough curves; the ensemble averaged curves document anomalous transport in this system, which is entirely accounted for by a truncated power-law distribution of local transition times $\\psi(t)$ within the framework of a continuous time random walk. Unique to this study is the linking of $\\psi(t)$ directly to the system heterogeneity. We assess the statistics of the dominant preferred pathways by forming a particle-visitation weighted histogram $\\{wK\\}$. Converting the ln($K$) dependence of $\\{wK\\}$ into time yields the equivalence of $\\{wK\\}$ and $\\psi(t)$, and shows the part of $\\{wK\\}$ that forms the power-law of $\\psi(t)$, which is the origin of anomalous transport. We also derive an expression defi...

  10. Impact of urban structure on personal transportation in the context of a large Danish provincial city

    DEFF Research Database (Denmark)

    Nielsen, Thomas Alexander Sick

    2004-01-01

    This paper presents the results from a detailed study of the land use ? transport connection, with special emphasis on the location of residences, in the context of a larger Danish provincial city (the city of Aalborg with approx. 120.000 inhabitants, situated in North Jutland). The study...

  11. Effects of interfacial Fe electronic structures on magnetic and electronic transport properties in oxide/NiFe/oxide heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qianqian; Chen, Xi; Zhang, Jing-Yan [Department of Materials Physics and Chemistry, University of Science and Technology Beijing, Beijing 100083 (China); Yang, Meiyin [SKLSM, Institute of Semiconductors, CAS, P.O. Box 912, Beijing 100083 (China); Li, Xu-Jing; Jiang, Shao-Long; Liu, Yi-Wei; Cao, Yi [Department of Materials Physics and Chemistry, University of Science and Technology Beijing, Beijing 100083 (China); Wu, Zheng-Long [Analytical and Testing Center, Beijing Normal University, Beijing 100875 (China); Feng, Chun [Department of Materials Physics and Chemistry, University of Science and Technology Beijing, Beijing 100083 (China); Ding, Lei [School of Materials and Chemical Engineering, Hainan University, Haikou 570228 (China); Yu, Guang-Hua, E-mail: ghyu@mater.ustb.edu.cn [Department of Materials Physics and Chemistry, University of Science and Technology Beijing, Beijing 100083 (China)

    2015-09-15

    Highlights: • The magnetic and transport properties of oxide/NiFe/oxide films were studied. • The oxide (SiO{sub 2}, MgO and HfO{sub 2}) has different elemental electronegativity. • Redox reaction at different NiFe/oxide interface is dependent on the oxide layer. • Different interfacial electronic structures shown by XPS influence the properties. - Abstract: We report that the magnetic and electronic transport properties in oxide/NiFe(2 nm)/oxide film (oxide = SiO{sub 2}, MgO or HfO{sub 2}) are strongly influenced by the electronic structure of NiFe/oxide interface. Magnetic measurements show that there exist magnetic dead layers in the SiO{sub 2} sandwiched film and MgO sandwiched film, whereas there is no magnetic dead layer in the HfO{sub 2} sandwiched film. Furthermore, in the ultrathin SiO{sub 2} sandwiched film no magnetoresistance (MR) is detected, while in the ultrathin MgO sandwiched film and HfO{sub 2} sandwiched film the MR ratios reach 0.35% and 0.88%, respectively. The investigation by X-ray photoelectron spectroscopy reveals that the distinct interfacial redox reactions, which are dependent on the oxide layers, lead to the variation of magnetic and transport properties in different oxide/NiFe/oxide heterostructures.

  12. Fission products and structural materials release, transport and containment behaviour in Phebus FPT-0 and FPT-1

    Energy Technology Data Exchange (ETDEWEB)

    Hanniet, N.; Garnier, Y.; Jacquemain, D. [Institut de Protection et de Surete Nucleaire - IPSN, Departement de Recherches en Securite - DRS, CEA Cadarache - F 13108 Saint Paul Lez Durance (France)

    1999-07-01

    The Phebus F.P. program is a wide international effort to investigate, through a series of in-pile integral experiments, LWR severe accident phenomena, in particular bundle degradation and the subsequent release and transport of radioactive materials up to the containment. Two tests simulating a low pressure cold leg break under a steam rich environment have already been successfully performed: FPT-0 in December 1993 with trace irradiated fuel and FPT-1 in July 1996 with re-irradiated BR3 fuel. Both tests have provided experimental data of high interest, particularly in the field of fission products and structural materials release from the fuel bundle, transport in the reactor coolant system (RCS) and behaviour in the containment. The analysis of FPT-1 is currently in progress, nevertheless main observations made for FPT-10 are confirmed by first FPT-1 results, i.e.: - the main mass transport phases through the RCS correspond to bundle degradation events (fuel oxidation, material re-location, pool formation); - significant amount of gaseous iodine are injected in the model containment during bundle oxidation phases; - the aerosols are multi-component with the structural materials dominant in mass; - the retention is low in the RCS pipes but aerosol deposition on containment walls is significant; - the containment sump chemistry is marked by aerosol material dissolution and the resulting iodine trapping by silver. Those results are described in some detail in the following paper. (author)

  13. Detecting and modelling structures on the micro and the macro scales: Assessing their effects on solute transport behaviour

    Science.gov (United States)

    Haslauer, C. P.; Bárdossy, A.; Sudicky, E. A.

    2017-09-01

    This paper demonstrates quantitative reasoning to separate the dataset of spatially distributed variables into different entities and subsequently characterize their geostatistical properties, properly. The main contribution of the paper is a statistical based algorithm that matches the manual distinction results. This algorithm is based on measured data and is generally applicable. In this paper, it is successfully applied at two datasets of saturated hydraulic conductivity (K) measured at the Borden (Canada) and the Lauswiesen (Germany) aquifers. The boundary layer was successfully delineated at Borden despite its only mild heterogeneity and only small statistical differences between the divided units. The methods are verified with the more heterogeneous Lauswiesen aquifer K data-set, where a boundary layer has previously been delineated. The effects of the macro- and the microstructure on solute transport behaviour are evaluated using numerical solute tracer experiments. Within the microscale structure, both Gaussian and non-Gaussian models of spatial dependence of K are evaluated. The effects of heterogeneity both on the macro- and the microscale are analysed using numerical tracer experiments based on four scenarios: including or not including the macroscale structures and optimally fitting a Gaussian or a non-Gaussian model for the spatial dependence in the micro-structure. The paper shows that both micro- and macro-scale structures are important, as in each of the four possible geostatistical scenarios solute transport behaviour differs meaningfully.

  14. Electron transport and Goos-Haenchen shift in graphene with electric and magnetic barriers: optical analogy and band structure

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Manish [Centre for Applied Research in Electronics, Indian Institute of Technology Delhi, New Delhi-110016 (India); Ghosh, Sankalpa [Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016 (India)

    2011-02-09

    Transport of massless Dirac fermions in graphene monolayers is analysed in the presence of a combination of singular magnetic barriers and applied electrostatic potential. Extending a recently proposed (Ghosh and Sharma 2009 J. Phys.: Condens. Matter 21 292204) analogy between the transmission of light through a medium with modulated refractive index and electron transmission in graphene through singular magnetic barriers to the present case, we find the addition of a scalar potential profoundly changes the transmission. We calculate the quantum version of the Goos-Haenchen shift that the electron wave suffers upon being totally reflected by such barriers. The combined electric and magnetic barriers substantially modify the band structure near the Dirac point. This affects transport near the Dirac point significantly and has important consequences for graphene-based electronics.

  15. Electron transport and Goos-Hänchen shift in graphene with electric and magnetic barriers: optical analogy and band structure.

    Science.gov (United States)

    Sharma, Manish; Ghosh, Sankalpa

    2011-02-09

    Transport of massless Dirac fermions in graphene monolayers is analysed in the presence of a combination of singular magnetic barriers and applied electrostatic potential. Extending a recently proposed (Ghosh and Sharma 2009 J. Phys.: Condens. Matter 21 292204) analogy between the transmission of light through a medium with modulated refractive index and electron transmission in graphene through singular magnetic barriers to the present case, we find the addition of a scalar potential profoundly changes the transmission. We calculate the quantum version of the Goos-Hänchen shift that the electron wave suffers upon being totally reflected by such barriers. The combined electric and magnetic barriers substantially modify the band structure near the Dirac point. This affects transport near the Dirac point significantly and has important consequences for graphene-based electronics.

  16. Structural and functional studies of multiheme cytochromes C involved in extracellular electron transport in bacterial dissimilatory metal reduction.

    Science.gov (United States)

    Tikhonova, T V; Popov, V O

    2014-12-01

    Bacteria utilizing insoluble mineral forms of metal oxides as electron acceptors in respiratory processes are widespread in the nature. The electron transfer from a pool of reduced quinones in the cytoplasmic membrane across the periplasm to the bacterial outer membrane and then to an extracellular acceptor is a key step in bacterial dissimilatory metal reduction. Multiheme cytochromes c play a crucial role in the extracellular electron transfer. The bacterium Shewanella oneidensis MR-1 was used as a model organism to study the mechanism of extracellular electron transport. In this review, we discuss recent data on the composition, structures, and functions of multiheme cytochromes c and their functional complexes responsible for extracellular electron transport in Shewanella oneidensis.

  17. Five years of Florida Current structure and transport from the Royal Caribbean Cruise Ship Explorer of the Seas

    Science.gov (United States)

    Beal, Lisa M.; Hummon, Julia M.; Williams, Elizabeth; Brown, Otis B.; Baringer, Warner; Kearns, Edward J.

    2008-06-01

    Using ship-of-opportunity platform Explorer of the Seas, five years of full-depth velocity data have been collected across the Florida Straits at 26°N. Between May 2001 and May 2006 the mean transport of the Florida Current was 31.0 ± 4.0 Sv. This compares to a mean transport of 32.4 ± 3.2 Sv inferred from cable voltages at 27°N over the same period, implying an average 1.4 Sv transport into the Straits through the Northwest Providence Channel. The climatological core of the Florida Current is 170 cms-1 and is positioned at 79.8°W, about 10 km east of the shelf break. The largest variability in velocity occurs over the shelf and shelf break and is likely related to shelf waves. A secondary maximum occurs across much of the Straits over the top 100 m of the water column and may be associated with wind events. The annual cycle of Florida Current transports has a range of 4.7 Sv, with a maximum in May-June-July and a minimum in January. The difference between the summer and winter current structure appears as a first baroclinic mode with zero crossing at 150 m. The maximum difference is about 15 cms-1 at the surface and is centered just offshore of the mean current core. On interannual timescales, low-pass filtered Explorer and cable transports show similar downward trends between 2002 and 2005, but diverge over the last year or so of the record.

  18. Fibonacci quasiregular graphene-based superlattices: Quasiperiodicity and its effects on the transmission, transport and electronic structure properties

    Science.gov (United States)

    García-Cervantes, H.; Madrigal-Melchor, J.; Martínez-Orozco, J. C.; Rodríguez-Vargas, I.

    2015-12-01

    We study the transmission, transport and electronic structure properties of aperiodic Fibonacci monolayer graphene-based structures (AFGBSs). The transfer matrix method has been implemented to obtain the transmittance, linear-regime conductance and electronic structure. In particular, we have studied two types of aperiodic graphene-based structures: (1) electrostatic AFGBSs (EAFGBSs), structures formed with electrostatic potentials, and (2) substrate AFGBSs (SAFGBSs), obtained alternating substrates that can open and non-open, such as SiC and SiO2, an energy bandgap on graphene. We have found that the transmission properties can be modulated readily by changing the main parameters of the systems: well and barrier widths, energy and angle of incident electrons and the degree of aperiodicity. In the case of the linear-regime conductance turns out that it diminishes various orders of magnitude increasing the barrier width for SAFGBSs. On the contrary, Klein tunneling sustains the conductance in EAFGBSs. Calculating the electronic structure or miniband-structure formation and its fragmentation we establish a direct connection between the conductance peaks and the opening, closure and degeneration of energy minibands for both EAFGSLs and SAFGSLs.

  19. Fibonacci quasiregular graphene-based superlattices: Quasiperiodicity and its effects on the transmission, transport and electronic structure properties

    Energy Technology Data Exchange (ETDEWEB)

    García-Cervantes, H.; Madrigal-Melchor, J.; Martínez-Orozco, J.C.; Rodríguez-Vargas, I., E-mail: isaac@fisica.uaz.edu.mx

    2015-12-01

    We study the transmission, transport and electronic structure properties of aperiodic Fibonacci monolayer graphene-based structures (AFGBSs). The transfer matrix method has been implemented to obtain the transmittance, linear-regime conductance and electronic structure. In particular, we have studied two types of aperiodic graphene-based structures: (1) electrostatic AFGBSs (EAFGBSs), structures formed with electrostatic potentials, and (2) substrate AFGBSs (SAFGBSs), obtained alternating substrates that can open and non-open, such as SiC and SiO{sub 2}, an energy bandgap on graphene. We have found that the transmission properties can be modulated readily by changing the main parameters of the systems: well and barrier widths, energy and angle of incident electrons and the degree of aperiodicity. In the case of the linear-regime conductance turns out that it diminishes various orders of magnitude increasing the barrier width for SAFGBSs. On the contrary, Klein tunneling sustains the conductance in EAFGBSs. Calculating the electronic structure or miniband-structure formation and its fragmentation we establish a direct connection between the conductance peaks and the opening, closure and degeneration of energy minibands for both EAFGSLs and SAFGSLs.

  20. Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material.

    Science.gov (United States)

    Huang, Jin-Dou; Li, Wen-Liang; Wen, Shu-Hao; Dong, Bin

    2015-04-15

    Recently, diketopyrrolopyrrole (DPP)-based materials have attracted much interest due to their promising performance as a subunit in organic field effect transistors. Using density functional theory and charge-transport models, we investigated the electronic structure and microscopic charge transport properties of the cyanated bithiophene-functionalized DPP molecule (compound 1). First, we analyzed in detail the partition of the total relaxation (polaron) energy into the contributions from each vibrational mode and the influence of bond-parameter variations on the local electron-vibration coupling of compound 1, which well explains the effects of different functional groups on internal reorganization energy (λ). Then, we investigated the structural and electronic properties of compound 1 in its isolated molecular state and in the solid state form, and further simulated the angular resolution anisotropic mobility for both electron- and hole-transport using two different simulation methods: (i) the mobility orientation function proposed in our previous studies (method 1); and (ii) the master equation approach (method 2). The calculated electron-transfer mobility (0.00003-0.784 cm(2) V(-1) s(-1) from method 1 and 0.02-2.26 cm(2) V(-1) s(-1) from method 2) matched reasonably with the experimentally reported value (0.07-0.55 cm(2) V(-1) s(-1) ). To the best of our knowledge, this is the first time that the transport parameters of compound 1 were calculated in the context of band model and hopping models, and both calculation results suggest that the intrinsic hole mobility is higher than the corresponding intrinsic electron mobility. Our calculation results here will be instructive to further explore the potential of other higher DPP-containing quinoidal small molecules.

  1. Grain boundary effects on the structural, microstructural and transport behavior of sol - gel grown PrMnO3 nanoparticles

    Science.gov (United States)

    Keshvani, M. J.; Katba, Savan; Jethva, Sadaf; Udeshi, Malay; Pandya, D. D.; Shah, N. A.; Ravalia, Ashish; Kataria, Bharat; Kuberkar, D. G.

    2017-05-01

    In this communication, we report the results of the studies on the grain boundary (GB) effect on the structural, microstructural and transport properties of nanostructured PrMnO3 (PMO) manganites synthesized by acetate precursor based sol - gel method. As synthesized PMO samples were sintered at various temperatures to understand the role of sintering temperature in modifying the structure - property correlations in the context of GB effects. Structural analysis using X-ray diffraction studies reveal the single phasic nature of all the PMO samples while TEM analysis reveals uniform particle size distribution with agglomeration effect observed in samples sintered at higher temperatures. SEM micrographs depict the increase in grain size with sharp grain boundaries in the samples sintered at a higher temperature. Size-dependent resistivity behavior of the PMO samples have been understood in the light of grain size modification and GB effect.

  2. An ab initio study of the structure and atomic transport in bulk liquid Ag and its liquid-vapor interface

    Science.gov (United States)

    del Rio, Beatriz G.; González, David J.; González, Luis E.

    2016-10-01

    Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.

  3. Determination of assurance сoefficient by supporting structures fatigue of car bodies during transportation by the railway ferries

    Directory of Open Access Journals (Sweden)

    A. A. Lovskaya

    2014-12-01

    Full Text Available Purpose. To determine assurance coefficient by supporting structures fatigue of car bodies during transportation by the railway ferries. Methodology. The operating conditions of cars in international railway-water communication have been investigated in previous works for the solution of this problem. To solve the problem there were conducted researches of dynamic features of car bodies transporting by the railway ferries in conditions of the sea storm. A mathematical model of car bodies movement was made up and accelerations acting on them in placements on the decks were determined. During determination of accelerations the actual meteorological characteristics of the Black Sea during a storm were taken into account. The assurance coefficient fatigue by supporting structures of car bodies by the railway ferries was determined and it was found that under regular loading of the car body n ≈ 2,0 . It is higher than the admissible value. Findings. Comparison of obtained acceleration values with the accelerations acting on car bodies when operating on main-line routes showed that they have exceeded the acceleration specified in the regulations approximately on 40%. It proves the need of accounting the loads acting on car bodies during transportations by the railway ferries when designing new generation cars. Originality. There was proposed a mathematical model of car bodies movement by the railway ferries in the conditions of sea storm. It gives the possibility of determining the accelerations of car bodies placed on the decker rail ferries taking into account the hydrometeorology characteristics. Practical value. The results of researches can be used when designing new generation cars to provide their strength during the combination of railway and water transportation. It gives an opportunity to develop measures as to the adaptation of cars bodies to the interaction with the fastenings of railway ferries by means of equipping their bearing

  4. Research Advances: Less Expensive and More Convenient Gaucher's Disease Treatment; Structural Loop Regions: Key to Multidrug-Resistance Transporters?; New Method Identifies Proteins in Old Artwork

    Science.gov (United States)

    King, Angela G.

    2006-01-01

    The X-ray structure of EmrD, a multidrug transporter protein from Escherichia coli, common bacteria known to cause several food-borne illnesses was determined by scientists at The Scripps Research Institute. The hydrophobic residues in the EmrD internal cavity are likely to contribute to the general mechanism transporting various compounds through…

  5. Mobilization and transport of soil colloids as influenced by texture, organic matter, and structure

    DEFF Research Database (Denmark)

    Vendelboe, Anders Lindblad

    , but via colloid-facilitated transport they may bypass the purification stage and be leached to the groundwater reservoir and via tile drains to surface waters. The main focus of the work presented in this thesis as part of the SOIL-IT-IS project was to increase knowledge about the processes controlling...... mobilization and transport of colloids. This was done using a series of state-of-the-art methods, including end-over-end dispersion measurements of soil aggregates and undisturbed soil cores, and irrigation experiments using undisturbed soil cores. In addition, a novel laser diffraction method was used...... in combination with a wet-dispersion unit proved to be an accurate and highly efficient method for measuring colloid dispersion from aggregates. The method gave highly detailed temporal data, enabling more detailed studies of dispersion kinetics. The contents of water-dispersible colloids measured...

  6. The Integration of a Structural Water Gas Shift Catalyst with a Vanadium Alloy Hydrogen Transport Device

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Thomas; Argyle, Morris; Popa, Tiberiu

    2009-06-30

    This project is in response to a requirement for a system that combines water gas shift technology with separation technology for coal derived synthesis gas. The justification of such a system would be improved efficiency for the overall hydrogen production. By removing hydrogen from the synthesis gas stream, the water gas shift equilibrium would force more carbon monoxide to carbon dioxide and maximize the total hydrogen produced. Additional benefit would derive from the reduction in capital cost of plant by the removal of one step in the process by integrating water gas shift with the membrane separation device. The answer turns out to be that the integration of hydrogen separation and water gas shift catalysis is possible and desirable. There are no significant roadblocks to that combination of technologies. The problem becomes one of design and selection of materials to optimize, or at least maximize performance of the two integrated steps. A goal of the project was to investigate the effects of alloying elements on the performance of vanadium membranes with respect to hydrogen flux and fabricability. Vanadium was chosen as a compromise between performance and cost. It is clear that the vanadium alloys for this application can be produced, but the approach is not simple and the results inconsistent. For any future contracts, large single batches of alloy would be obtained and rolled with larger facilities to produce the most consistent thin foils possible. Brazing was identified as a very likely choice for sealing the membranes to structural components. As alloying was beneficial to hydrogen transport, it became important to identify where those alloying elements might be detrimental to brazing. Cataloging positive and negative alloying effects was a significant portion of the initial project work on vanadium alloying. A water gas shift catalyst with ceramic like structural characteristics was the second large goal of the project. Alumina was added as a

  7. The Integration of a Structural Water Gas Shift Catalyst with a Vanadium Alloy Hydrogen Transport Device

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Thomas; Argyle, Morris; Popa, Tiberiu

    2009-06-30

    This project is in response to a requirement for a system that combines water gas shift technology with separation technology for coal derived synthesis gas. The justification of such a system would be improved efficiency for the overall hydrogen production. By removing hydrogen from the synthesis gas stream, the water gas shift equilibrium would force more carbon monoxide to carbon dioxide and maximize the total hydrogen produced. Additional benefit would derive from the reduction in capital cost of plant by the removal of one step in the process by integrating water gas shift with the membrane separation device. The answer turns out to be that the integration of hydrogen separation and water gas shift catalysis is possible and desirable. There are no significant roadblocks to that combination of technologies. The problem becomes one of design and selection of materials to optimize, or at least maximize performance of the two integrated steps. A goal of the project was to investigate the effects of alloying elements on the performance of vanadium membranes with respect to hydrogen flux and fabricability. Vanadium was chosen as a compromise between performance and cost. It is clear that the vanadium alloys for this application can be produced, but the approach is not simple and the results inconsistent. For any future contracts, large single batches of alloy would be obtained and rolled with larger facilities to produce the most consistent thin foils possible. Brazing was identified as a very likely choice for sealing the membranes to structural components. As alloying was beneficial to hydrogen transport, it became important to identify where those alloying elements might be detrimental to brazing. Cataloging positive and negative alloying effects was a significant portion of the initial project work on vanadium alloying. A water gas shift catalyst with ceramic like structural characteristics was the second large goal of the project. Alumina was added as a

  8. Electron Transport in Graphene-Based Double-Barrier Structure under a Time Periodic Field

    Institute of Scientific and Technical Information of China (English)

    LU Wei-Tao; WANG Shun-Jin

    2011-01-01

    The transport property of electron through graphene-based double-barrier under a time periodic field is investigated. We study the influence of the system parameters and external field strength on the transmission probability.The results show that transmission exhibits various kinds of behavior with the change of parameters due to its angular anisotropy. One could control the values of transmission and conductivity as well as their distribution in each band by tuning the parameters.

  9. Spin-dependent quantum transport through an Aharonov-Bohm structure spin splitter

    Institute of Scientific and Technical Information of China (English)

    Li Yu-Xian

    2008-01-01

    Using the tight-binding model approximation, this paper investigates theoretically spin-dependent quantum trans-port through an Aharonov-Bohm (AB) interferometer. An external magnetic field is applied to produce the spin-polarization and spin current. The AB interferometer, acting as a spin splitter, separates the opposite spin polarization current. By adjusting the energy and the direction of the magnetic field, large spin-polarized current can be obtained.

  10. Observations of pockmark flow structure in Belfast Bay, Maine, Part 3: implications for sediment transport

    Science.gov (United States)

    Fandel, Christina L.; Lippmann, Thomas C.; Foster, Diane L.; Brothers, Laura L.

    2017-01-01

    Current observations and sediment characteristics acquired within and along the rim of two pockmarks in Belfast Bay, Maine, were used to characterize periods of sediment transport and to investigate conditions favorable to the settling of suspended sediment. Hourly averaged Shields parameters determined from horizontal current velocity profiles within the center of each pockmark never exceed the critical value (approximated with the theoretical model of Dade et al. 1992). However, Shields parameters estimated at the pockmark rims periodically exceed the critical value, consistent with conditions that support the onset of sediment transport and suspension. Below the rim in the near-center of each pockmark, depth-averaged vertical velocities were less than zero (downward) 60% and 55% of the time in the northern and southern pockmarks, and were often comparable to depth-averaged horizontal velocities. Along the rim, depth-averaged vertical velocities over the lower 8 m of the water column were primarily downward but much less than depth-averaged horizontal velocities indicating that suspended sediment may be moved to distant locations. Maximum grain sizes capable of remaining in suspension under terminal settling flow conditions (ranging 10–170 μm) were typically much greater than the observed median grain diameter (about 7 μm) at the bed. During upwelling flow within the pockmarks, and in the absence of flocculation, suspended sediment would not settle. The greater frequency of predicted periods of sediment transport along the rim of the southern pockmark is consistent with pockmark morphology in Belfast Bay, which transitions from more spherical to more elongated toward the south, suggesting near-bed sediment transport may contribute to post-formation pockmark evolution during typical conditions in Belfast Bay.

  11. Observations of pockmark flow structure in Belfast Bay, Maine, Part 3: implications for sediment transport

    Science.gov (United States)

    Fandel, Christina L.; Lippmann, Thomas C.; Foster, Diane L.; Brothers, Laura L.

    2017-02-01

    Current observations and sediment characteristics acquired within and along the rim of two pockmarks in Belfast Bay, Maine, were used to characterize periods of sediment transport and to investigate conditions favorable to the settling of suspended sediment. Hourly averaged Shields parameters determined from horizontal current velocity profiles within the center of each pockmark never exceed the critical value (approximated with the theoretical model of Dade et al. 1992). However, Shields parameters estimated at the pockmark rims periodically exceed the critical value, consistent with conditions that support the onset of sediment transport and suspension. Below the rim in the near-center of each pockmark, depth-averaged vertical velocities were less than zero (downward) 60% and 55% of the time in the northern and southern pockmarks, and were often comparable to depth-averaged horizontal velocities. Along the rim, depth-averaged vertical velocities over the lower 8 m of the water column were primarily downward but much less than depth-averaged horizontal velocities indicating that suspended sediment may be moved to distant locations. Maximum grain sizes capable of remaining in suspension under terminal settling flow conditions (ranging 10-170 μm) were typically much greater than the observed median grain diameter (about 7 μm) at the bed. During upwelling flow within the pockmarks, and in the absence of flocculation, suspended sediment would not settle. The greater frequency of predicted periods of sediment transport along the rim of the southern pockmark is consistent with pockmark morphology in Belfast Bay, which transitions from more spherical to more elongated toward the south, suggesting near-bed sediment transport may contribute to post-formation pockmark evolution during typical conditions in Belfast Bay.

  12. Transporting particulate material

    Science.gov (United States)

    Aldred, Derek Leslie [North Hollywood, CA; Rader, Jeffrey A [North Hollywood, CA; Saunders, Timothy W [North Hollywood, CA

    2011-08-30

    A material transporting system comprises a material transporting apparatus (100) including a material transporting apparatus hopper structure (200, 202), which comprises at least one rotary transporting apparatus; a stationary hub structure (900) constraining and assisting the at least one rotary transporting apparatus; an outlet duct configuration (700) configured to permit material to exit therefrom and comprising at least one diverging portion (702, 702'); an outlet abutment configuration (800) configured to direct material to the outlet duct configuration; an outlet valve assembly from the material transporting system venting the material transporting system; and a moving wall configuration in the material transporting apparatus capable of assisting the material transporting apparatus in transporting material in the material transporting system. Material can be moved from the material transporting apparatus hopper structure to the outlet duct configuration through the at least one rotary transporting apparatus, the outlet abutment configuration, and the outlet valve assembly.

  13. Raising Climate Finance from International Transport Sectors. Identification and Analysis of Governance Structures

    Energy Technology Data Exchange (ETDEWEB)

    Faber, J. [CE Delft, Delft (Netherlands); Pahuja, N.; Garg, A. [The Energy and Resources Institute TERI, New Delhi (India)

    2012-03-15

    Market based instruments (MBIs) for maritime transport have the potential to reduce emissions while at the same time raising funds for climate policies in developing countries. GHG emissions from international aviation and maritime transport accounted for approximately 5% of global anthropogenic emissions in 2005 and are rising rapidly. There is a clear need to address these emissions in order not to undermine policies for mitigating land based emissions. Developing countries need financial support to carry out climate policies, both adaptation and mitigation. The UN Framework Convention on Climate Change (UNFCCC) makes policies by developing countries conditional on climate finance. In the current economic and financial circumstances, there is a need for new sources of finance. The governance of such MBIs should ensure that they are neither an international tax nor require hypothecation of fiscal revenues, while they should provide new and additional finance. MBIs which are in fact an international tax would not be politically feasible, and likewise hypothecation would be opposed by many states. This report finds that an emissions trading scheme (ETS) can satisfy these criteria, provided that: (1) it transfers a share of allowances directly to developing countries in order to ensure there is no net incidence on them; developing countries could auction these allowances in order to raise revenue; (2) it transfers allowances to the Green Climate Fund to support climate policies; auctioning these allowances would provide revenues for the Fund; (3) it transfers allowances to IMO or another organisation in order to finance fuel-efficiency improvements in international transport.

  14. A fully resolved fluid-structure-muscle-activation model for esophageal transport

    Science.gov (United States)

    Kou, Wenjun; Bhalla, Amneet P. S.; Griffith, Boyce E.; Johnson, Mark; Patankar, Neelesh A.

    2013-11-01

    Esophageal transport is a mechanical and physiological process that transfers the ingested food bolus from the pharynx to the stomach through a multi-layered esophageal tube. The process involves interactions between the bolus, esophageal wall composed of mucosal, circular muscle (CM) and longitudinal muscle (LM) layers, and neurally coordinated muscle activation including CM contraction and LM shortening. In this work, we present a 3D fully-resolved model of esophageal transport based on the immersed boundary method. The model describes the bolus as a Newtonian fluid, the esophageal wall as a multi-layered elastic tube represented by springs and beams, and the muscle activation as a traveling wave of sequential actuation/relaxation of muscle fibers, represented by springs with dynamic rest lengths. Results on intraluminal pressure profile and bolus shape will be shown, which are qualitatively consistent with experimental observations. Effects of activating CM contraction only, LM shortening only or both, for the bolus transport, are studied. A comparison among them can help to identify the role of each type of muscle activation. The support of grant R01 DK56033 and R01 DK079902 from NIH is gratefully acknowledged.

  15. Improving transportation networks: Effects of population structure and decision making policies.

    Science.gov (United States)

    Pablo-Martí, Federico; Sánchez, Angel

    2017-07-03

    Transportation networks are one of the fundamental tools for human society to work, more so in our globalized world. The importance of a correct, efficient design of a transportation network for a given region or country cannot be overstated. We here study how network design is affected by the geography of the towns or nuclei to be connected, and also by the decision process necessary to choose which connections should be improved (in a generic sense) first. We begin by establishing that Delaunay networks provide an efficient starting point for the network design and at the same time allow us to introduce a computationally amenable model. Subsequent improvements lead to decentralized designs in geographies where towns are more or less homogeneously distributed, whereas radial designs arise when there is a core-periphery distribution of nodes. We also show that optimization of Delaunay networks outperforms that of complete networks at a lower cost, by allowing for a proper selection of the links to improve. In closing, we draw conclusions relevant to policy making applied to designing transportation networks and point our how our study can be useful to identify mechanisms relevant to the historical development of a region.

  16. Quantitative Analysis of Major Factors Affecting Black Carbon Transport and Concentrations in the Unique Atmospheric Structures of Urban Environment

    Science.gov (United States)

    Liang, Marissa Shuang

    Black carbon (BC) from vehicular emission in transportation is a principal component of particulate matters ≤ 2.5 mum (PM2.5). PM2.5 and other diesel emission pollutants (e.g., NOx) are regulated by the Clean Air Act (CAA) according to the National Ambient Air Quality standards (NAAQS). This doctoral dissertation details a study on transport behaviors of black carbon and PM2.5 from transportation routes, their relations with the atmospheric structure of an urban formation, and their relations with the use of biodiesel fuels. The results have implications to near-road risk assessment and to the development of sustainable transportation solutions in urban centers. The first part of study quantified near-roadside black carbon transport as a function of particulate matter (PM) size and composition, as well as microclimatic variables (temperature and wind fields) at the interstate highway I-75 in northern Cincinnati, Ohio. Among variables examined, wind speed and direction significantly affect the roadside transport of black carbon and hence its effective emission factor. Observed non-Gaussian dispersion occurred during low wind and for wind directions at acute angles or upwind to the receptors, mostly occurring in the morning hours. Meandering of air pollutant mass under thermal inversion is likely the driving force. In contrary, Gaussian distribution predominated in daytime of strong downwinds. The roles of urban atmospheric structure, wind fields, and the urban heat island (UHI) effects were further examined on pollutant dispersion and transport. Spatiotemporal variations of traffic flow, atmospheric structure, ambient temperature and PM2.5 concentration data from 14 EPA-certified NAAQS monitoring stations, were analyzed in relation to land-use in the Cincinnati metropolitan area. The results show a decade-long UHI effects with higher interior temperature than that in exurban, and a prominent nocturnal thermal inversion frequent in urban boundary layer. The

  17. Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity.

    Science.gov (United States)

    Esser, Lothar; Zhou, Fei; Pluchino, Kristen M; Shiloach, Joseph; Ma, Jichun; Tang, Wai-Kwan; Gutierrez, Camilo; Zhang, Alex; Shukla, Suneet; Madigan, James P; Zhou, Tongqing; Kwong, Peter D; Ambudkar, Suresh V; Gottesman, Michael M; Xia, Di

    2017-01-13

    P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancer; it plays important roles in determining the pharmacokinetics of many drugs. Understanding the structural basis of P-gp, substrate polyspecificity has been hampered by its intrinsic flexibility, which is facilitated by a 75-residue linker that connects the two halves of P-gp. Here we constructed a mutant murine P-gp with a shortened linker to facilitate structural determination. Despite dramatic reduction in rhodamine 123 and calcein-AM transport, the linker-shortened mutant P-gp possesses basal ATPase activity and binds ATP only in its N-terminal nucleotide-binding domain. Nine independently determined structures of wild type, the linker mutant, and a methylated P-gp at up to 3.3 Å resolution display significant movements of individual transmembrane domain helices, which correlated with the opening and closing motion of the two halves of P-gp. The open-and-close motion alters the surface topology of P-gp within the drug-binding pocket, providing a mechanistic explanation for the polyspecificity of P-gp in substrate interactions.

  18. Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity*♦

    Science.gov (United States)

    Esser, Lothar; Zhou, Fei; Pluchino, Kristen M.; Shiloach, Joseph; Ma, Jichun; Tang, Wai-kwan; Gutierrez, Camilo; Zhang, Alex; Shukla, Suneet; Madigan, James P.; Zhou, Tongqing; Kwong, Peter D.; Ambudkar, Suresh V.; Gottesman, Michael M.; Xia, Di

    2017-01-01

    P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancer; it plays important roles in determining the pharmacokinetics of many drugs. Understanding the structural basis of P-gp, substrate polyspecificity has been hampered by its intrinsic flexibility, which is facilitated by a 75-residue linker that connects the two halves of P-gp. Here we constructed a mutant murine P-gp with a shortened linker to facilitate structural determination. Despite dramatic reduction in rhodamine 123 and calcein-AM transport, the linker-shortened mutant P-gp possesses basal ATPase activity and binds ATP only in its N-terminal nucleotide-binding domain. Nine independently determined structures of wild type, the linker mutant, and a methylated P-gp at up to 3.3 Å resolution display significant movements of individual transmembrane domain helices, which correlated with the opening and closing motion of the two halves of P-gp. The open-and-close motion alters the surface topology of P-gp within the drug-binding pocket, providing a mechanistic explanation for the polyspecificity of P-gp in substrate interactions. PMID:27864369

  19. Observation of charge transport through CdSe/ZnS quantum dots in a single-electron transistor structure

    Science.gov (United States)

    Kobo, Masanori; Yamamoto, Makoto; Ishii, Hisao; Noguchi, Yutaka

    2016-10-01

    We fabricated single-electron transistors (SETs) having CdSe/ZnS core-shell-type quantum dots (CdSe/ZnS-QDs) as a Coulomb island using a wet chemistry technique. The CdSe/ZnS-QDs were deposited onto Au electrodes with or without the assistance of a self-assembled monolayer of octane(di)thiols. The CdSe/ZnS-QDs were adsorbed onto the Au electrodes even without the interlayer of thiol molecules depending on the concentration of the CdSe/ZnS-QD solution. The electron-transport characteristics through the CdSe/ZnS-QDs were examined in an SET structure at 13 K. Coulomb blockade behavior with typical gate voltage dependence was clearly observed. The estimated charge addition energies of a CdSe/ZnS-QD ranged from 70 to 280 meV. Moreover, additional structures, including negative differential conductance, appeared in the stability diagram in the source-drain bias region beyond 100 mV; these structures are specific to single-charge transport through the discrete energy levels in the Coulomb island.

  20. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

    Science.gov (United States)

    Laponogov, Ivan; Veselkov, Dennis A; Crevel, Isabelle M-T; Pan, Xiao-Su; Fisher, L Mark; Sanderson, Mark R

    2013-11-01

    Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.

  1. MODERN APPROACHES FOR PROTECTION OF TRANSPORT STRUCTURES FROM INFLUENCES CAUSED BY MOVING DISPLACEMENTS AND FOR PROVIDING OF THEIR SAFE LONG TERM EXPLOITATION

    Directory of Open Access Journals (Sweden)

    M. M. Bresler

    2010-04-01

    Full Text Available The conception and new developments of Company «Maurer Soehne» intended for protection of transport structures from influences caused by displacements and for providing of their safe long-term exploitation are presented.

  2. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis

    National Research Council Canada - National Science Library

    Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M Joanne; Möhlmann, Torsten

    2014-01-01

    .... We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens...

  3. Self-similar Hierarchical Wrinkles as a Potential Multifunctional Smart Window with Simultaneously Tunable Transparency, Structural Color, and Droplet Transport.

    Science.gov (United States)

    Lin, Gaojian; Chandrasekaran, Prashant; Lv, Cunjing; Zhang, Qiuting; Tang, Yichao; Han, Lin; Yin, Jie

    2017-08-09

    Smart window has immense potential for energy savings in architectural and vehicular applications, while most studies focus on the tunability of a single property of optical transmittance. Here we explore harnessing dynamically tunable hierarchical wrinkles for design of a potential multifunctional smart window with combined structural color and water droplet transport control. The self-similar hierarchical wrinkles with both nanoscale and microscale features are generated on a prestrained poly(dimethylsiloxane) elastomer through sequential strain release and multistep oxygen plasma treatment. We show that the hierarchically wrinkled elastomer displays both opaqueness and iridescent structural color. We find that restretching/releasing the elastomer leads to the reversible and repeatable switch from opaqueness to transparency, arising from the flattening of large wrinkles (micrometer scale), while a nonvanishing structural color occurs due to the nondisappearing small wrinkles (nanoscale). The unique features of combined reversible large wrinkles and irreversible small wrinkles during hierarchical wrinkling are well reproduced by corresponding finite element simulation. The criteria for generating self-similar hierarchical wrinkles is revealed through a simplified theoretical model and validated by experiments. In addition to its tunable optical property, we further show its ability in control of water droplet transport on demand through mechanical stretching and release. We find that an initially pinned water droplet on the tilted hierarchically wrinkled surface starts to slide when the surface is stretched, and becomes pinned again upon strain release. Such a process is reversible and repeatable. The hierarchically wrinkled surface could find broad potential applications not only in multifunctional smart windows with additional features of aesthetics and water collection, but in microfluidics, design of slippery surfaces, and directional water transportation.

  4. Molecular physiology of the insect K-activated amino acid transporter 1 (KAAT1) and cation-anion activated amino acid transporter/channel 1 (CAATCH1) in the light of the structure of the homologous protein LeuT.

    Science.gov (United States)

    Castagna, M; Bossi, E; Sacchi, V F

    2009-06-01

    K-activated amino acid transporter 1 (KAAT1) and cation-anion-activated amino acid transporter/channel 1 (CAATCH1) are amino acid cotransporters, belonging to the Na/Cl-dependent neurotransmitter transporter family (also called SLC6/NSS), that have been cloned from Manduca sexta midgut. They have been thoroughly studied by expression in Xenopus laevis oocytes, and structure/function analyses have made it possible to identify the structural determinants of their cation and amino acid selectivity. About 40 mutants of these proteins have been studied by measuring amino acid uptake and current/voltage relationships. The results obtained since the cloning of KAAT1 and CAATCH1 are here discussed in the light of the 3D model of the first crystallized member of the family, the leucine transporter LeuT.

  5. Structural, optical, and electrical-transport properties of Al-P-O inorganic layer coated on flexible stainless steel substrate

    Science.gov (United States)

    Kim, Moojin; Min, Jinhyuk; Kwak, Yongsu; Kim, Doori; Kim, Kyoung-Bo; Song, Jonghyun

    2017-03-01

    We coated inorganic layer containing oxygen, aluminium, phosphorus, and negligible sodium (APO) on stainless steel (STS) by using slot-die coating method and studied its application prospects as a substrate for flexible devices. The APO layer was compositionally uniform in overall area with an amorphous crystal structure. Surface morphology characterization of STS exhibited an improved flatness after the APO layer coating process. The optical property characterization of the APO film carried out by measuring optical reflectance spectrum and refractive index. We also investigated the electrical-transport mechanism in the APO layer. These experimental observations imply the possibility of potential application of APO-STS as a substrate for flexible devices.

  6. Multidrug efflux pumps: the structures of prokaryotic ATP-binding cassette transporter efflux pumps and implications for our understanding of eukaryotic P-glycoproteins and homologues.

    Science.gov (United States)

    Kerr, Ian D; Jones, Peter M; George, Anthony M

    2010-02-01

    One of the Holy Grails of ATP-binding cassette transporter research is a structural understanding of drug binding and transport in a eukaryotic multidrug resistance pump. These transporters are front-line mediators of drug resistance in cancers and represent an important therapeutic target in future chemotherapy. Although there has been intensive biochemical research into the human multidrug pumps, their 3D structure at atomic resolution remains unknown. The recent determination of the structure of a mouse P-glycoprotein at subatomic resolution is complemented by structures for a number of prokaryotic homologues. These structures have provided advances into our knowledge of the ATP-binding cassette exporter structure and mechanism, and have provided the template data for a number of homology modelling studies designed to reconcile biochemical data on these clinically important proteins.

  7. A nano-grid structure made of perovskite SrTiO3 nanowires for efficient electron transport layers in inverted polymer solar cells.

    Science.gov (United States)

    Kim, Jeong Won; Suh, Yo-han; Lee, Chang-Lyoul; Kim, Yong Seok; Kim, Won Bae

    2015-03-14

    A nano-grid structure of perovskite SrTiO3 NWs is developed for a novel electron transport layer in inverted polymer solar cells. Due to the excellent charge transporting properties of the SrTiO3 nano-grid structure, the device employing this nanostructure showed ∼32% enhanced photovoltaic performance, compared to the solar cell using a TiO2 thin film.

  8. Theoretical studies on electronic structures and photophysical properties of anthracene derivatives as hole-transporting materials for OLEDs.

    Science.gov (United States)

    Chitpakdee, Chirawat; Namuangruk, Supawadee; Khongpracha, Pipat; Jungsuttiwong, Siriporn; Tarsang, Ruangchai; Sudyoadsuk, Taweesak; Promarak, Vinich

    2014-05-05

    The electronic structures and photophysical properties of anthracene derivatives as hole-transporting materials (HTM) in OLEDs have been studied by DFT and TD-DFT methods. Thiophene and triphenylamine (TPA) moieties are used as substituents in anthracene based HTMs providing FATn and FAPn compounds (n=1-2), respectively. The calculated electronic levels by B3LYP show proper energy matching of FAPn and hole-injecting layer (HIL), indicating that the hole-transports of the FAPn compounds are better than the FATn compounds. The photophysical properties calculated by TD-B3LYP elucidate that TPA in FAPn compounds acts as electron donating group and induces charge transfer character in the absorptions. Furthermore, the calculated ionization potential (IP), electron affinity (EA) and reorganization energies also revealed that the extended FAP2 compound has the highest charge-transporting ability among the studied compounds. The calculated results are consistent to our experimental observations showing that FAP2 exhibits bright fluorescence with highest quantum yield in electroluminescent devices. Understanding of these properties is useful for further design of new HTMs of desired properties, such as high efficiency and stability.

  9. Trimmed simulation of a transport aircraft using fluid-structure coupling

    NARCIS (Netherlands)

    Michler, A.K.; Dwight, R.P.; Heinrich, R.

    2009-01-01

    The accurate prediction of the aerodynamic coefficients under cruise conditions is of major importance for assessing the aircraft’s fuel consumption. To this end, fluid dynamics, structural mechanics and flight mechanics have to be considered: on the one hand, the structure elastically deforms under

  10. Intermittent convective transport carried by propagating electromagnetic filamentary structures in nonuniformly magnetized plasma

    DEFF Research Database (Denmark)

    Xu, G.S.; Naulin, Volker; Fundamenski, W.

    2010-01-01

    Drift-Alfvén vortex filaments associated with electromagnetic turbulence were recently identified in reversed field pinch devices. Similar propagating filamentary structures were observed in the Earth magnetosheath, magnetospheric cusp and Saturn’s magnetosheath by spacecrafts. The characteristic......, heat, and momentum in the fusion plasmas can be interpreted in terms of the ballistic motion of these solitary electromagnetic filamentary structures....

  11. Stability and structure of the membrane protein transporter Ffh is modulated by substrates and lipids

    DEFF Research Database (Denmark)

    Reinau, Marika Ejby; Otzen, Daniel

    2009-01-01

    The cytosolic protein Ffh transports membrane proteins from the ribosome to the inner membrane in complex with 4.5S RNA. Here we show that native Ffh binds to the hydrophobic probe ANS in a 1 Ffh:3 ANS stoichiometry, revealing a hydrophobic binding site. Thermal precipitation of Ffh is shifted...... upwards by ∼10 °C by ANS or substrate protein, suggesting that the hydrophobic binding site makes the protein aggregation prone. Chemical denaturation confirm that Ffh is a rather unstable protein. 4.5S RNA destabilizes Ffh further, suggesting it keeps the protein in a more open conformation than...

  12. Water retention, gas transport, and pore network complexity during short-term regeneration of soil structure

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Møldrup, Per; Schjønning, Per

    2013-01-01

    was done using water retention (pore size distribution), soil gas diffusivity, air permeability, and derived pore network complexity parameters. Significant decreases in bulk density (increased total porosity) and increases in pores > 100 1m was observed for incubated samples compared with SR samples....... The proportion of pores > 100 1m increased in order: smectite gas diffusivity, air permeability, and derived pore network indices was greater for incubated samples than SR. For illitic soils...... for convective air transport when analyzing pore network complexity. Overall, our results showed that short-term regeneration...

  13. Charge and spin transport in nanoscopic structures with spin-orbit coupling

    Energy Technology Data Exchange (ETDEWEB)

    Reynoso, A. [Instituto Balseiro and Centro Atomico Bariloche, Comision Nacional de Energia Atomica, 8400 San Carlos de Bariloche (Argentina); Gonzalo Usaj [Instituto Balseiro and Centro Atomico Bariloche, Comision Nacional de Energia Atomica, 8400 San Carlos de Bariloche (Argentina); Balseiro, C.A. [Instituto Balseiro and Centro Atomico Bariloche, Comision Nacional de Energia Atomica, 8400 San Carlos de Bariloche (Argentina)]. E-mail: balseiro@cab.cnea.gov.ar

    2006-10-01

    During the last years there has been much interest, and theoretical discussion, about the possibility to use spin-orbit coupling to control the carriers spins in two-dimensional semiconducting heterostructures. Spin polarization at the sample edges may occur as the response of systems with strong SO-coupling to an external transport current, an effect known as spin Hall effect. Here, we show that in a 2DEG with Rashba SO-coupling, spin polarization near the sample edge can develop kinematically for low electron densities. We also discuss the effect in quantum wires where lateral confinement plays an important role.

  14. Simulation Studies of Charge Transport on Resistive Structures in Gaseous Ionization Detectors

    CERN Document Server

    Budanur, Nazmi Burak

    2012-01-01

    We developed a tool for the simulation of charge transport on a conducting plate of finite dimensions. This tool is named Chani. Main motivation of developing Chani was to provide a tool for the optimization of the dimensions and resistivity of the anode electrodes in spark-protected Micropattern Gaseous Detectors (MPGD). In this thesis, we start with the general description of the LHC and the ATLAS Experiment. Then, we review the gaseous ionization detector technologies and in particular, the micromegas technology. We then present the working principles of Chani along with the example calculations. These examples include comparisons with the analytically solvable problems which shows that the simulation results are reasonable.

  15. Electronic Transport Through Carbon Nanotubes: Effects of Structural Deformation and the Tube Chirality

    Science.gov (United States)

    Maiti, Amitesh; Svizhenko, Alexei; Anantram, M. P.; Biegel, Bryan (Technical Monitor)

    2001-01-01

    Atomistic simulations using a combination of classical force field and Density-Functional-Theory (DFT) show that carbon atoms remain essentially sp2 coordinated in either bent tubes or tubes pushed by an atomically sharp AFM tip. Subsequent Green's-function-based transport calculations reveal that for armchair tubes there is no significant drop in conductance, while for zigzag tubes the conductance can drop by several orders of magnitude in AFM-pushed tubes. The effect can be attributed to simple stretching of the tube under tip deformation, which opens up an energy gap at the Fermi surface.

  16. Cosmic ray transport in heliospheric magnetic structures. I. Modeling background solar wind using the CRONOS magnetohydrodynamic code

    Energy Technology Data Exchange (ETDEWEB)

    Wiengarten, T.; Kleimann, J.; Fichtner, H. [Institut für Theoretische Physik IV, Ruhr-Universität Bochum (Germany); Kühl, P.; Kopp, A.; Heber, B. [Institut für Experimentelle und Angewandte Physik, Christian-Albrecht-Universität zu Kiel (Germany); Kissmann, R. [Institut für Astro- und Teilchenphysik, Universität Innsbruck (Austria)

    2014-06-10

    The transport of energetic particles such as cosmic rays is governed by the properties of the plasma being traversed. While these properties are rather poorly known for galactic and interstellar plasmas due to the lack of in situ measurements, the heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric transport of energetic particles are structures such as corotating interaction regions, which, due to strongly enhanced magnetic field strengths, turbulence, and associated shocks, can act as diffusion barriers on the one hand, but also as accelerators of low energy CRs on the other hand as well. In a two-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with a numerical magnetohydrodynamic (MHD) setup (this paper), which will serve as an input to a transport code employing a stochastic differential equation approach (second paper). In this first paper, we present results from 3D MHD simulations with our code CRONOS: for validation purposes we use analytic boundary conditions and compare with similar work by Pizzo. For a more realistic modeling of solar wind conditions, boundary conditions derived from synoptic magnetograms via the Wang-Sheeley-Arge (WSA) model are utilized, where the potential field modeling is performed with a finite-difference approach in contrast to the traditional spherical harmonics expansion often utilized in the WSA model. Our results are validated by comparing with multi-spacecraft data for ecliptical (STEREO-A/B) and out-of-ecliptic (Ulysses) regions.

  17. The Role of Shape on Electronic Structure and Charge Transport in Faceted PbSe Nanocrystals

    KAUST Repository

    Kaushik, Ananth P.

    2014-03-25

    We have determined the effect of shape on the charge transport characteristics of nanocrystals. Our study looked at the explicit determination of the electronic properties of faceted nanocrystals that essentially probe the limit of current computational reach, i.e., nanocrystals from 1.53 to 2.1 nm in diameter. These nanocrystals, which resemble PbSe systems, are either bare or covered in short ligands. They also differ in shape, octahedral vs cube-octahedral, and in superlattice symmetry (fcc vs bcc). We have provided insights on electron and hole coupling along different facets and overall charge mobility in bcc and fcc superlattices. We have determined that the relative areas of (100) to (111) facets, and facet atom types are important factors governing the optimization of charge transport. The calculated electronic density of states shows no role of -SCH3 - ligands on states near the band gap. Electron coupling between nanocrystals is significantly higher than that of hole coupling; thiol ligands lower the ratio between electron and hole couplings. Stronger coupling exists between smaller nanocrystals. © 2014 American Chemical Society.

  18. Ballistic phonon thermal transport across topologically structured nanojunctions on Gold wires

    Science.gov (United States)

    Belhadi, M.; Khater, A.

    2017-04-01

    We investigate the coherent phonon thermal transport at low temperatures in Gold nanowires, in order to study the effects of scattering on the lattice thermal conductivity. Three types of shaped joint nanostructures are employed in our calculation. We present a detailed study of the thermal conductance as a function of the temperature for different shaped joint. This is done by solving the phonon Boltzmann transport equation in the ballistic regime and calculating the transmission rates of the vibration modes through the consideration of the phonon group velocity modification in the system. The transmission properties are calculated by use of the matching method in the harmonic approximation with nearest and next nearest neighbor force constants. The results show that the transmission probabilities depend on the type of joint nanostructure. The pronounced fluctuations of the transmission spectra as a function of the frequency can be understood as Fano resonances. It is also found that the behavior of the thermal conductance versus temperature is qualitatively different for different nanostructures and depends sensitively on the width of the shaped joint.

  19. Research on Some Bus Transport Networks with Random Overlapping Clique Structure

    Institute of Scientific and Technical Information of China (English)

    YANG Xu-Hua; WANG Bo; WANG Wan-Liang; SUN You-Xian

    2008-01-01

    On the basis of investigating the statistical data of bus transport networks of three big cities in China, we propose that each bus route is a clique (maximal complete subgraph) and a bus transport network (BTN) consists of a lot of cliques, which intensively connect and overlap with each other. We study the network properties, which include the degree distribution, multiple edges' overlapping time distribution, distribution of the overlap size between any two overlapping cliques, distribution of the number of cliques that a node belongs to. Naturally, the cliques also constitute a network, with the overlapping nodes being their multiple links. We' also research its network properties such as degree distribution, clustering, average path length, and so on. We propose that a BTN has the properties of random clique increment and random overlapping clique, at the same time, a BTN is a small-world network with highly clique-clustered and highly clique-overlapped. Finally, we introduce a BTN evolution model, whose simulation results agree well with the statistical laws that emerge in real BTNs.