WorldWideScience

Sample records for surface structure revealed

  1. The interior structure of Ceres as revealed by surface topography

    Science.gov (United States)

    Fu, Roger R.; Ermakov, Anton I.; Marchi, Simone; Castillo-Rogez, Julie C.; Raymond, Carol A.; Hager, Bradford H.; Zuber, Maria T.; King, Scott D.; Bland, Michael T.; Cristina De Sanctis, Maria; Preusker, Frank; Park, Ryan S.; Russell, Christopher T.

    2017-10-01

    Ceres, the largest body in the asteroid belt (940 km diameter), provides a unique opportunity to study the interior structure of a volatile-rich dwarf planet. Variations in a planetary body's subsurface rheology and density affect the rate of topographic relaxation. Preferential attenuation of long wavelength topography (≥150 km) on Ceres suggests that the viscosity of its crust decreases with increasing depth. We present finite element (FE) geodynamical simulations of Ceres to identify the internal structures and compositions that best reproduce its topography as observed by the NASA Dawn mission. We infer that Ceres has a mechanically strong crust with maximum effective viscosity ∼1025 Pa s. Combined with density constraints, this rheology suggests a crustal composition of carbonates or phyllosilicates, water ice, and at least 30 volume percent (vol.%) low-density, high-strength phases most consistent with salt and/or clathrate hydrates. The inference of these crustal materials supports the past existence of a global ocean, consistent with the observed surface composition. Meanwhile, we infer that the uppermost ≥60 km of the silicate-rich mantle is mechanically weak with viscosity history that avoided igneous differentiation due to late accretion or efficient heat loss through hydrothermal processes.

  2. Structure of Est3 reveals a bimodal surface with differential roles in telomere replication.

    Science.gov (United States)

    Rao, Timsi; Lubin, Johnathan W; Armstrong, Geoffrey S; Tucey, Timothy M; Lundblad, Victoria; Wuttke, Deborah S

    2014-01-01

    Telomerase is essential for continuous cellular proliferation. Substantial insights have come from studies of budding yeast telomerase, which consists of a catalytic core in association with two regulatory proteins, ever shorter telomeres 1 and 3 (Est1 and Est3). We report here a high-resolution structure of the Est3 telomerase subunit determined using a recently developed strategy that combines minimal NMR experimental data with Rosetta de novo structure prediction algorithms. Est3 adopts an overall protein fold which is structurally similar to that adopted by the shelterin component TPP1. However, the characteristics of the surface of the experimentally determined Est3 structure are substantially different from those predicted by prior homology-based models of Est3. Structure-guided mutagenesis of the complete surface of the Est3 protein reveals two adjacent patches on a noncanonical face of the protein that differentially mediate telomere function. Mapping these two patches on the Est3 structure defines a set of shared features between Est3 and HsTPP1, suggesting an analogous multifunctional surface on TPP1.

  3. Crystal Structure of West Nile Virus Envelope Glycoprotein Reveals Viral Surface Epitopes

    Energy Technology Data Exchange (ETDEWEB)

    Kanai,R.; Kar, K.; Anthony, K.; Gould, L.; Ledizet, M.; Fikrig, E.; Marasco, W.; Koski, R.; Modis, Y.

    2006-01-01

    West Nile virus, a member of the Flavivirus genus, causes fever that can progress to life-threatening encephalitis. The major envelope glycoprotein, E, of these viruses mediates viral attachment and entry by membrane fusion. We have determined the crystal structure of a soluble fragment of West Nile virus E. The structure adopts the same overall fold as that of the E proteins from dengue and tick-borne encephalitis viruses. The conformation of domain II is different from that in other prefusion E structures, however, and resembles the conformation of domain II in postfusion E structures. The epitopes of neutralizing West Nile virus-specific antibodies map to a region of domain III that is exposed on the viral surface and has been implicated in receptor binding. In contrast, we show that certain recombinant therapeutic antibodies, which cross-neutralize West Nile and dengue viruses, bind a peptide from domain I that is exposed only during the membrane fusion transition. By revealing the details of the molecular landscape of the West Nile virus surface, our structure will assist the design of antiviral vaccines and therapeutics.

  4. Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface.

    Science.gov (United States)

    Ayres, Chapelle A; Schormann, Norbert; Senkovich, Olga; Fry, Alexandra; Banerjee, Surajit; Ulett, Glen C; Chattopadhyay, Debasish

    2014-10-01

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294-307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.

  5. Anatase (101)-like Structural Model Revealed for Metastable Rutile TiO2(011) Surface.

    Science.gov (United States)

    Xu, Meiling; Shao, Sen; Gao, Bo; Lv, Jian; Li, Quan; Wang, Yanchao; Wang, Hui; Zhang, Lijun; Ma, Yanming

    2017-03-08

    Titanium dioxide has been widely used as an efficient transition metal oxide photocatalyst. However, its photocatalytic activity is limited to the ultraviolet spectrum range due to the large bandgap beyond 3 eV. Efforts to reduce the bandgap to achieve a broader spectrum range of light absorption have been successfully attempted via the experimental synthesis of dopant-free metastable surface structures of rutile-type TiO2 (011) 2 × 1. This new surface phase possesses a reduced bandgap of ∼2.1 eV, showing great potential for an excellent photocatalyst covering a wide range of visible light. There is a need to establish the atomistic structure of this metastable surface to understand the physical cause for the bandgap reduction and to improve the future design of photocatalysts. Here, we report computational investigations in an effort to unravel this surface structure via swarm structure-searching simulations. The established structure adopts the anatase (101)-like structure model, where the topmost 2-fold O atoms form a quasi-hexagonal surface pattern and bond with the unsaturated 5-fold and 4-fold Ti atoms in the next layer. The predicted anatase (101)-like surface model can naturally explain the experimental observation of the STM images, the electronic bandgap, and the oxidation state of Ti(4+). Dangling bonds on the anatase (101)-like surface are abundant making it a superior photocatalyst. First-principles molecular dynamics simulations have supported the high photocatalytic activity by showing that water and formic acid molecules dissociate spontaneously on the anatase (101)-like surface.

  6. Structure of DNA-Cationic Surfactant Complexes at Hydrophobically Modified and Hydrophilic Silica Surfaces as Revealed by Neutron Reflectometry

    DEFF Research Database (Denmark)

    Cardenas Gomez, Marite; Wacklin, Hanna; Campbell, Richard A.

    2011-01-01

    In this article, we discuss the structure and composition of mixed DNA-cationic surfactant adsorption layers on both hydrophobic and hydrophilic solid surfaces. We have focused on the effects of the bulk concentrations, the surfactant chain length, and the type solid surface on the interfacial...... layer structure (the location, coverage, and conformation the e DNA and surfactant molecules). Neutron reflectometry is the technique of choice for revealing the surface layer structure by means of selective deuteration. We start by studying the interfacial complexation of DNA...... with dodecyltrimethylammonium bromide (DTAB) and hexadecyltrimethylammonium bromide (CTAB) on hydrophobic surfaces, where we show that DNA molecules are located on top of a self-assembled surfactant monolayer, with the thickness of the DNA layer and the surfactant DNA ratio determined by the surface coverage of the underlying...

  7. Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul

    2006-01-27

    We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.

  8. Elements of the Chicxulub Impact Structure as Revealed in SRTM and Surface GPS Topographic Data

    Science.gov (United States)

    Kinsland, Gary L.; Sanchez, Gary; Kobrick, Michael; Cardador, Manuel Hurtado

    2003-01-01

    Pope et al. [1] utilized the elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxulub Impact Structure is a roughly semi-circular, lowrelief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact, which possibly led to the development of these features. These are summarized in Table 1. Kinsland et al. [2] presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Very recently we have acquired digital topography data from NASA s Shuttle Radar Topography Mission (SRTM). Our subset covers 6 square degrees from 20deg N 91degW to 22deg N 88degW (corner to corner) with a pixel size of about 90m. This area includes all of the identified portion of the crater on land.

  9. Amyloid plaque structure and cell surface interactions of β-amyloid fibrils revealed by electron tomography

    Science.gov (United States)

    Han, Shen; Kollmer, Marius; Markx, Daniel; Claus, Stephanie; Walther, Paul; Fändrich, Marcus

    2017-01-01

    The deposition of amyloid fibrils as plaques is a key feature of several neurodegenerative diseases including in particular Alzheimer’s. This disease is characterized, if not provoked, by amyloid aggregates formed from Aβ peptide that deposit inside the brain or are toxic to neuronal cells. We here used scanning transmission electron microscopy (STEM) to determine the fibril network structure and interactions of Aβ fibrils within a cell culture model of Alzheimer’s disease. STEM images taken from the formed Aβ amyloid deposits revealed three main types of fibril network structures, termed amorphous meshwork, fibril bundle and amyloid star. All three were infiltrated by different types of lipid inclusions from small-sized exosome-like structures (50–100 nm diameter) to large-sized extracellular vesicles (up to 300 nm). The fibrils also presented strong interactions with the surrounding cells such that fibril bundles extended into tubular invaginations of the plasma membrane. Amyloid formation in the cell model was previously found to have an intracellular origin and we show here that it functionally destroys the integrity of the intracellular membranes as it leads to lysosomal leakage. These data provide a mechanistic link to explain why intracellular fibril formation is toxic to the cell. PMID:28240273

  10. Elements of the Chicxulub Impact Structure as revealed in SRTM and surface GPS topographic data

    Science.gov (United States)

    Kobrick, M.; Kinsland, G. L.; Sanchez, G.; Cardador, M. H.

    2003-04-01

    Pope et al have utilized elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxu-lub Impact Structure is a roughly semi-circular, low-relief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact which possibly led to the development of these features. Kinsland et al presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Shaded relief images from recently acquired SRTM elevation data clearly show the circular depression of the crater and the moat/cenote ring. In addition we can readily identify Inner trough 1, Inner trough 2 and Outer trough as defined by Pope et al. The agreement between the topographic maps of Pope et al, Kinsland et al and SRTM data are remarkable considering that the distribution and types of data in the sets are so different. We also have ground topographic data collected with a special "autonomous differ-ential GPS" system during summer 2002. Profiles from these data generally agree with both the gravity data based topographic maps and profiles extracted from the SRTM data. Preliminary analyses of our new data, SRTM and GPS, have uncovered features not previously recognized: 1) as shown by the GPS data the moat/cenote ring consists of two distinct depressions separated by about 10 km...perhaps separate ring faults, 2) in the SRTM data over the southern part of the crater and on southward for perhaps 20 km beyond the moat/ cenote ring there exists a pattern, as yet unexplained, of roughly concentric topographic features whose center lies at about 21deg 40min N and 89deg 25min W, about 50km NNE of the moat/cenote ring center. The corroboration and better definition of the previously recognized topographic features yielded by the two new forms of data strengthens the cases for these fea-tures and for their relevance to the underlying

  11. Internal structure and physicochemical properties of corn starches as revealed by chemical surface gelatinization.

    Science.gov (United States)

    Kuakpetoon, Daris; Wang, Ya-Jane

    2007-11-05

    The organization of amylose and amylopectin within starch granules is still not well elucidated. This study investigates the radial distribution of amylose and amylopectin in different corn starches varying in amylose content (waxy corn starch (WC), common corn starch (CC), and 50% and 70% amylose corn starches (AMC)). Corn starches were surface gelatinized by 13 M LiCl at room temperature to different extents (approximately 10%, 20%, 30%, and 40%). The gelatinized surface starch and remaining granules were characterized for amylose content, amylopectin chain-length distribution, thermal properties, swelling power (SP), and water solubility index (WSI). Except for the outmost 10% layer, the amylose content in CC increased slightly with increasing surface removal. In contrast, amylose was more concentrated at the periphery than at the core for 50% and 70% AMC. The proportion of amylopectin A chains generally decreased while that of B1 chains generally increased with increasing surface removal for all corn starches. The gelatinization enthalpy usually decreased, except for 70% AMC, whereas the retrogradation enthalpy relatively remained unchanged for CC but increased for WC, 50% and 70% AMC with increasing surface removal. The SP and WSI increased with increasing surface removal for all corn starches, with WC showing a significant increase in SP after the removal of the outmost 10% layer. The results of this study indicated that there were similarities and differences in the distribution of amylose and amylopectin chains along the radial location of corn starch granules with varying amylose contents. More amylose-lipid complex and amylopectin long chains were present at the periphery than at the core for amylose-containing corn starches.

  12. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

    Directory of Open Access Journals (Sweden)

    Moffatt Barbara A

    2010-08-01

    Full Text Available Abstract Background Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB for coplanar aromatic motifs similar to those found in known glycan-binding proteins. Results The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192 in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Conclusions Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

  13. Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch.

    Science.gov (United States)

    Hwang, Hyo-Jeong; Min, Hye Jung; Yun, Hyosuk; Pelton, Jeffery G; Wemmer, David E; Cho, Kyoung-Oh; Kim, Jeong-Sun; Lee, Chul Won

    2015-04-17

    Viral protein genome-linked (VPg) proteins play a critical role in the life cycle of vertebrate and plant positive-sense RNA viruses by acting as a protein primer for genome replication and as a protein cap for translation initiation. Here we report the solution structure of the porcine sapovirus VPg core (VPg(C)) determined by multi-dimensional NMR spectroscopy. The structure of VPg(C) is composed of three α-helices stabilized by several conserved hydrophobic residues that form a helical bundle core similar to that of feline calicivirus VPg. The putative nucleotide acceptor Tyr956 within the first helix of the core is completely exposed to solvent accessible surface to facilitate nucleotidylation by viral RNA polymerase. Comparison of VPg structures suggests that the surface for nucleotidylation site is highly conserved among the Caliciviridae family, whereas the backbone core structures are different. These structural features suggest that caliciviruses share common mechanisms of VPg-dependent viral replication and translation. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Metal-like Band Structures of Ultrathin Si {111} and {112} Surface Layers Revealed through Density Functional Theory Calculations.

    Science.gov (United States)

    Tan, Chih-Shan; Huang, Michael H

    2017-07-11

    Density functional theory calculations have been performed on Si (100), (110), (111), and (112) planes with tunable number of planes for evaluation of their band structures and density of states profiles. The purpose is to see whether silicon can exhibit facet-dependent properties derived from the presence of a thin surface layer having different band structures. No changes have been observed for single to multiple layers of Si (100) and (110) planes with a consistent band gap between the valence band and the conduction band. However, for 1, 2, 4, and 5 Si (111) and (112) planes, metal-like band structures were obtained with continuous density of states going from the valence band to the conduction band. For 3, 6, and more Si (111) planes, as well as 3 and 6 Si (112) planes, the same band structure as that seen for Si (100) and (110) planes has been obtained. Thus, beyond a layer thickness of five Si (111) planes at ≈1.6 nm, normal semiconductor behavior can be expected. The emergence of metal-like band structures for the Si (111) and (112) planes are related to variation in Si-Si bond length and bond distortion plus 3s and 3p orbital electron contributions in the band structure. This work predicts possession of facet-dependent electrical properties of silicon with consequences in FinFET transistor design. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics

    Science.gov (United States)

    Fahrenfeld, N.L.; Reyes, Hannah Delos; Eramo, Alessia; Akob, Denise M.; Mumford, Adam; Cozzarelli, Isabelle M.

    2017-01-01

    Unconventional oil and gas (UOG) production produces large quantities of wastewater with complex geochemistry and largely uncharacterized impacts on surface waters. In this study, we assessed shifts in microbial community structure and function in sediments and waters upstream and downstream from a UOG wastewater disposal facility. To do this, quantitative PCR for 16S rRNA and antibiotic resistance genes along with metagenomic sequencing were performed. Elevated conductivity and markers of UOG wastewater characterized sites sampled downstream from the disposal facility compared to background sites. Shifts in overall high level functions and microbial community structure were observed between background sites and downstream sediments. Increases in Deltaproteobacteria and Methanomicrobia and decreases in Thaumarchaeota were observed at downstream sites. Genes related to dormancy and sporulation and methanogenic respiration were 18–86 times higher at downstream, impacted sites. The potential for these sediments to serve as reservoirs of antimicrobial resistance was investigated given frequent reports of the use of biocides to control the growth of nuisance bacteria in UOG operations. A shift in resistance profiles downstream of the UOG facility was observed including increases in acrB and mexB genes encoding for multidrug efflux pumps, but not overall abundance of resistance genes. The observed shifts in microbial community structure and potential function indicate changes in respiration, nutrient cycling, and markers of stress in a stream impacted by UOG waste disposal operations.

  16. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation

    Directory of Open Access Journals (Sweden)

    Morroll Shaun

    2009-08-01

    Full Text Available Abstract Background The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Proliferating cell nuclear antigen (PCNA is a fundamental protein involved in maintaining genome integrity, with roles in both DNA replication and repair. To investigate the halophilic adaptation of such a key protein we have crystallised and solved the structure of Haloferax volcanii PCNA (HvPCNA to a resolution of 2.0 Å. Results The overall architecture of HvPCNA is very similar to other known PCNAs, which are highly structurally conserved. Three commonly observed adaptations in halophilic proteins are higher surface acidity, bound ions and increased numbers of intermolecular ion pairs (in oligomeric proteins. HvPCNA possesses the former two adaptations but not the latter, despite functioning as a homotrimer. Strikingly, the positive surface charge considered key to PCNA's role as a sliding clamp is dramatically reduced in the halophilic protein. Instead, bound cations within the solvation shell of HvPCNA may permit sliding along negatively charged DNA by reducing electrostatic repulsion effects. Conclusion The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as

  17. Crystal Structures of Mite Allergens Der f 1 and Der p 1 Reveal Differences in Surface-Exposed Residues that May Influence Antibody Binding

    Energy Technology Data Exchange (ETDEWEB)

    Chruszcz, Maksymilian; Chapman, Martin D.; Vailes, Lisa D.; Stura, Enrico A.; Saint-Remy, Jean-Marie; Minor, Wladek; Pomés, Anna; (INDOOR Bio.); (CEAS); (Leuven); (UV)

    2009-12-01

    The Group 1 mite allergens, Der f 1 and Der p 1, are potent allergens excreted by Dermatophagoides farinae and Dermatophagoides pteronyssinus, respectively. The human IgE antibody responses to the Group 1 allergens show more cross-reactivity than the murine IgG antibody responses which are largely species-specific. Here, we report the crystal structure of the mature form of Der f 1, which was isolated from its natural source, and a new, high-resolution structure of mature recombinant Der p 1. Unlike Der p 1, Der f 1 is monomeric both in the crystalline state and in solution. Moreover, no metal binding is observed in the structure of Der f 1, despite the fact that all amino acids involved in Ca{sup 2+} binding in Der p 1 are completely conserved in Der f 1. Although Der p 1 and Der f 1 share extensive sequence identity, comparison of the crystal structures of both allergens revealed structural features which could explain the differences in murine and human IgE antibody responses to these allergens. There are structural differences between Der f 1 and Der p 1 which are unevenly distributed on the allergens' surfaces. This uneven spatial arrangement of conserved versus altered residues could explain both the specificity and cross-reactivity of antibodies against Der f 1 and Der p 1.

  18. X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface.

    Science.gov (United States)

    Graebsch, Almut; Roche, Stéphane; Niessing, Dierk

    2009-11-03

    The PUR protein family is a distinct and highly conserved class that is characterized by its sequence-specific RNA- and DNA-binding. Its best-studied family member, Pur-alpha, acts as a transcriptional regulator, as host factor for viral replication, and as cofactor for mRNP localization in dendrites. Pur-alpha-deficient mice show severe neurologic defects and die after birth. Nucleic-acid binding by Pur-alpha is mediated by its central core region, for which no structural information is available. We determined the x-ray structure of residues 40 to 185 from Drosophila melanogaster Pur-alpha, which constitutes a major part of the core region. We found that this region contains two almost identical structural motifs, termed "PUR repeats," which interact with each other to form a PUR domain. DNA- and RNA-binding studies confirmed that PUR domains are indeed functional nucleic-acid binding domains. Database analysis show that PUR domains share a fold with the Whirly class of nucleic-acid binding proteins. Structural analysis combined with mutational studies suggest that a PUR domain binds nucleic acids through two independent surface regions involving concave beta-sheets. Structure-based sequence alignment revealed that the core region harbors a third PUR repeat at its C terminus. Subsequent characterization by small-angle x-ray scattering (SAXS) and size-exclusion chromatography indicated that PUR repeat III mediates dimerization of Pur-alpha. Surface envelopes calculated from SAXS data show that the Pur-alpha dimer consisting of repeats I to III is arranged in a Z-like shape. This unexpected domain organization of the entire core domain of Pur-alpha has direct implications for ssDNA/ssRNA and dsDNA binding.

  19. Structural characterization of S100A15 reveals a novel zinc coordination site among S100 proteins and altered surface chemistry with functional implications for receptor binding

    Directory of Open Access Journals (Sweden)

    Murray Jill I

    2012-07-01

    Full Text Available Abstract Background S100 proteins are a family of small, EF-hand containing calcium-binding signaling proteins that are implicated in many cancers. While the majority of human S100 proteins share 25-65% sequence similarity, S100A7 and its recently identified paralog, S100A15, display 93% sequence identity. Intriguingly, however, S100A7 and S100A15 serve distinct roles in inflammatory skin disease; S100A7 signals through the receptor for advanced glycation products (RAGE in a zinc-dependent manner, while S100A15 signals through a yet unidentified G-protein coupled receptor in a zinc-independent manner. Of the seven divergent residues that differentiate S100A7 and S100A15, four cluster in a zinc-binding region and the remaining three localize to a predicted receptor-binding surface. Results To investigate the structural and functional consequences of these divergent clusters, we report the X-ray crystal structures of S100A15 and S100A7D24G, a hybrid variant where the zinc ligand Asp24 of S100A7 has been substituted with the glycine of S100A15, to 1.7 Å and 1.6 Å resolution, respectively. Remarkably, despite replacement of the Asp ligand, zinc binding is retained at the S100A15 dimer interface with distorted tetrahedral geometry and a chloride ion serving as an exogenous fourth ligand. Zinc binding was confirmed using anomalous difference maps and solution binding studies that revealed similar affinities of zinc for S100A15 and S100A7. Additionally, the predicted receptor-binding surface on S100A7 is substantially more basic in S100A15 without incurring structural rearrangement. Conclusions Here we demonstrate that S100A15 retains the ability to coordinate zinc through incorporation of an exogenous ligand resulting in a unique zinc-binding site among S100 proteins. The altered surface chemistry between S100A7 and S100A15 that localizes to the predicted receptor binding site is likely responsible for the differential recognition of distinct

  20. Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.

    Science.gov (United States)

    Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-Suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B; Nauck, Markus; Kaminski, Wolfgang E

    2017-01-01

    The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its "a" determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the "a" determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of "a" determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated.

  1. Surface structure of AU3Cu(001)

    DEFF Research Database (Denmark)

    Eckstein, G.A.; Maupai, S.; Dakkouri, A.S.

    1999-01-01

    The surface morphology, composition, and structure of Au3Cu(001) as determined by scanning tunneling microscopy and surface x-ray diffraction are presented. Atomic resolution STM images reveal distinctive geometric features. The analysis of the surface x-ray diffraction data provides clear evidence...... for the surface structure. [S0163-1829(99)04535-X]....

  2. Helical surface structures

    CERN Document Server

    Brandenburg, A; Brandenburg, Axel; Blackman, Eric G.

    2002-01-01

    Over the past few years there has been growing interest in helical magnetic field structures seen at the solar surface, in coronal mass ejections, as well as in the solar wind. Although there is a great deal of randomness in the data, on average the extended structures are mostly left-handed on the northern hemisphere and right-handed on the southern. Surface field structures are also classified as dextral (= right bearing) and sinistral (= left bearing) occurring preferentially in the northern and southern hemispheres respectively. Of particular interest here is a quantitative measurement of the associated emergence rates of helical structures, which translate to magnetic helicity fluxes. In this review, we give a brief survey of what has been found so far and what is expected based on models. Particular emphasis is put on the scale dependence of the associated fields and an attempt is made to estimate the helicity flux of the mean field vs. fluctuating field.

  3. Cortical and Subcortical Structural Plasticity Associated with the Glioma Volumes in Patients with Cerebral Gliomas Revealed by Surface-Based Morphometry

    Directory of Open Access Journals (Sweden)

    Jinping Xu

    2017-06-01

    Full Text Available Postlesional plasticity has been identified in patients with cerebral gliomas by inducing a large functional reshaping of brain networks. Although numerous non-invasive functional neuroimaging methods have extensively investigated the mechanisms of this functional redistribution in patients with cerebral gliomas, little effort has been made to investigate the structural plasticity of cortical and subcortical structures associated with the glioma volume. In this study, we aimed to investigate whether the contralateral cortical and subcortical structures are able to actively reorganize by themselves in these patients. The compensation mechanism following contralateral cortical and subcortical structural plasticity is considered. We adopted the surface-based morphometry to investigate the difference of cortical and subcortical gray matter (GM volumes in a cohort of 14 healthy controls and 13 patients with left-hemisphere cerebral gliomas [including 1 patients with World Health Organization (WHO I, 8 WHO II, and 4 WHO III]. The glioma volume ranges from 5.1633 to 208.165 cm2. Compared to healthy controls, we found significantly increased GM volume of the right cuneus and the left thalamus, as well as a trend toward enlargement in the right globus pallidus in patients with cerebral gliomas. Moreover, the GM volumes of these regions were positively correlated with the glioma volumes of the patients. These results provide evidence of cortical and subcortical enlargement, suggesting the usefulness of surface-based morphometry to investigate the structural plasticity. Moreover, the structural plasticity might be acted as the compensation mechanism to better fulfill its functions in patients with cerebral gliomas as the gliomas get larger.

  4. Brain surface parameterization using Riemann surface structure.

    Science.gov (United States)

    Wang, Yalin; Gu, Xianfeng; Hayashi, Kiralee M; Chan, Tony F; Thompson, Paul M; Yau, Shing-Tung

    2005-01-01

    We develop a general approach that uses holomorphic 1-forms to parameterize anatomical surfaces with complex (possibly branching) topology. Rather than evolve the surface geometry to a plane or sphere, we instead use the fact that all orientable surfaces are Riemann surfaces and admit conformal structures, which induce special curvilinear coordinate systems on the surfaces. Based on Riemann surface structure, we can then canonically partition the surface into patches. Each of these patches can be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable. To illustrate the technique, we computed conformal structures for several types of anatomical surfaces in MRI scans of the brain, including the cortex, hippocampus, and lateral ventricles. We found that the resulting parameterizations were consistent across subjects, even for branching structures such as the ventricles, which are otherwise difficult to parameterize. Compared with other variational approaches based on surface inflation, our technique works on surfaces with arbitrary complexity while guaranteeing minimal distortion in the parameterization. It also offers a way to explicitly match landmark curves in anatomical surfaces such as the cortex, providing a surface-based framework to compare anatomy statistically and to generate grids on surfaces for PDE-based signal processing.

  5. The Surface Structure of Relative Clauses

    Science.gov (United States)

    Lucas, Michael A.

    1974-01-01

    This article attempts to show that a more rigorous approach to surface structure analysis can reveal distinctions just as subtle as those discovered through analyzing deep structures or transformations. Relative clauses are examined in relation to nominal constructions, and alternatives to restrictive and non-restrictive classifications are…

  6. Revealing digital documents. Concealed structures in data

    CERN Document Server

    Voß, Jakob

    2011-01-01

    This short paper gives an introduction to a research project to analyze how digital documents are structured and described. Using a phenomenological approach, this research will reveal common patterns that are used in data, independent from the particular technology in which the data is available. The ability to identify these patterns, on different levels of description, is important for several applications in digital libraries. A better understanding of data structuring will not only help to better capture singular characteristics of data by metadata, but will also recover intended structures of digital objects, beyond long term preservation.

  7. Revealing Surface Modifications of Potassium-Fluoride-Treated Cu(In,Ga)Se 2 : A Study of Material Structure, Chemistry, and Photovoltaic Performance

    Energy Technology Data Exchange (ETDEWEB)

    Aguiar, Jeffery A. [National Renewable Energy Laboratory, Golden CO 80401 USA; Stokes, Adam [National Renewable Energy Laboratory, Golden CO 80401 USA; Colorado School of Mines, Golden CO 80401 USA; Jiang, Chun-Sheng [National Renewable Energy Laboratory, Golden CO 80401 USA; Aoki, Toshihiro [Arizona State University, Tempe AZ 85281 USA; Kotula, Paul G. [Sandia National Laboratories, Albuquerque NM 87185-0886 USA; Patel, Maulik K. [University of Tennessee-Knoxville, Knoxville TN 37996 USA; Gorman, Brian [Colorado School of Mines, Golden CO 80401 USA; Al-Jassim, Mowafak [National Renewable Energy Laboratory, Golden CO 80401 USA

    2016-07-06

    The effects of alkali post-deposition treatments and device properties for polycrystalline thin film Cu(In,Ga)Se2 have been investigated. It is reported that these surface treatments lead to differences in interface chemistry and device properties. The behavior of defects in the space charge region as a function of different growth parameters is investigated by correlative analytical microscopy. The latter combines electron microscopy based imaging, Kelvin probe force microscopy, and atom probe tomography. Alkali treatments lead to copper depletion and consequent sharpening of the compositional profiles, and the measured electric potential differences of exposed Cu(In1-x,Gax)Se2 surfaces. Measurable differences in resistivity and potential have also been observed, which are expected to relate to the improved open-circuit voltage, fill-factor, and device efficiency. This study frames one perspective as to why post-deposition alkaline treatments lead to copper depletion, a mildly n-type semiconductor interface, and higher efficiency for a Cu(In,Ga)Se2 thin-film photovoltaic device.

  8. Flat surfaces and stability structures

    OpenAIRE

    2014-01-01

    We identify spaces of half-translation surfaces, equivalently complex curves with quadratic differential, with spaces of stability structures on Fukaya-type categories of punctured surfaces. This is achieved by new methods involving the complete classification of objects in these categories, which are defined in an elementary way. We also introduce a number of tools to deal with surfaces of infinite area, where structures similar to those in cluster algebra appear.

  9. Bioinspired structured surfaces.

    Science.gov (United States)

    Bhushan, Bharat

    2012-01-24

    Nature has evolved objects with desired functionality using commonly found materials. Nature capitalizes on hierarchical structures to achieve functionality. The understanding of the functions provided by objects and processes found in nature can guide us to produce nanomaterials, nanodevices, and processes with desirable functionality. Various natural objects which provide functionality of commercial interest have been characterized to understand how a natural object provides functionality. We have modeled and fabricated structures in the lab using nature's route and developed optimum structures. Once it is understood how nature does it, optimum structures have been fabricated using smart materials and fabrication techniques. This feature article provides an overview of four topics: Lotus effect, rose petal effect, gecko feet, and shark skin.

  10. Melamine structures on the Au(111) surface

    NARCIS (Netherlands)

    Silly, Fabien; Shaw, Adam Q.; Castell, Martin R.; Briggs, G. A. D.; Mura, Manuela; Martsinovich, Natalia; Kantorovich, Lev

    2008-01-01

    We report on a joint experimental and theoretical study of the ordered structures of melamine molecules formed on the Au(111)-(22 x root 3) surface. Scanning tunneling microscopy (STM) images taken under UHV conditions reveal two distinct monolayers one of which has never been reported before on gol

  11. Structural models of human eEF1A1 and eEF1A2 reveal two distinct surface clusters of sequence variation and potential differences in phosphorylation.

    Directory of Open Access Journals (Sweden)

    Dinesh C Soares

    Full Text Available BACKGROUND: Despite sharing 92% sequence identity, paralogous human translation elongation factor 1 alpha-1 (eEF1A1 and elongation factor 1 alpha-2 (eEF1A2 have different but overlapping functional profiles. This may reflect the differential requirements of the cell-types in which they are expressed and is consistent with complex roles for these proteins that extend beyond delivery of tRNA to the ribosome. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the structural basis of these functional differences, we created and validated comparative three-dimensional (3-D models of eEF1A1 and eEF1A2 on the basis of the crystal structure of homologous eEF1A from yeast. The spatial location of amino acid residues that vary between the two proteins was thereby pinpointed, and their surface electrostatic and lipophilic properties were compared. None of the variations amongst buried amino acid residues are judged likely to have a major structural effect on the protein fold, or to affect domain-domain interactions. Nearly all the variant surface-exposed amino acid residues lie on one face of the protein, in two proximal but distinct sub-clusters. The result of previously performed mutagenesis in yeast may be interpreted as confirming the importance of one of these clusters in actin-bundling and filament disorganization. Interestingly, some variant residues lie in close proximity to, and in a few cases show differences in interactions with, residues previously inferred to be directly involved in binding GTP/GDP, eEF1Balpha and aminoacyl-tRNA. Additional sequence-based predictions, in conjunction with the 3-D models, reveal likely differences in phosphorylation sites that could reconcile some of the functional differences between the two proteins. CONCLUSIONS: The revelation and putative functional assignment of two distinct sub-clusters on the surface of the protein models should enable rational site-directed mutagenesis, including homologous reverse

  12. Structural and functional studies of titin's fn3 modules reveal conserved surface patterns and binding to myosin S1--a possible role in the Frank-Starling mechanism of the heart.

    Science.gov (United States)

    Muhle-Goll, C; Habeck, M; Cazorla, O; Nilges, M; Labeit, S; Granzier, H

    2001-10-19

    The A-band part of titin, a striated-muscle specific protein spanning from the Z-line to the M-line, mainly consists of a well-ordered super-repeat array of immunoglobulin-like and fibronectin-type III (fn3)-like domains. Since it has been suspected that the fn3 domains might represent titin's binding sites to myosin, we have developed structural models for all of titin's 132 fn3-like domains. A subset of eight experimentally determined fn3 structures from a range of proteins, including titin itself, was used as homology templates. After grouping the models according to their position within the super-repeat segment of the central A-band titin region, we analyzed the models with respect to side-chain conservation. This showed that conserved residues form an extensive surface pattern predominantly at one side of the domains, whereas domains outside the central C-zone super-repeat region show generally less conserved surfaces. Since the conserved surface residues may function as protein-binding sites, we experimentally studied the binding properties of expressed multi-domain fn3 fragments. This revealed that fn3 fragments specifically bind to the sub-fragment 1 of myosin. We also measured the effect of fn3 fragments on the contractile properties of single cardiac myocytes. At sub-maximal Ca(2+) concentrations, fn3 fragments significantly enhance active tension. This effect is most pronounced at short sarcomere length, and as a result the length-dependence of Ca(2+) activation is reduced. A model of how titin's fn3-like domains may influence actomyosin interaction is proposed.

  13. Structure of the moon's surface

    CERN Document Server

    Fielder, Gilbert

    1961-01-01

    Structure of the Moon's Surface aims to assemble and marshal relevant matter, and to produce a largely unprejudiced text which brings lunar studies up to date and stresses the importance of certain features of the Moon which have frequently been disregarded in the past, largely because of lack of knowledge about them. The book contains 14 chapters organized into two parts. Part I reviews and summarizes important physical problems. These include the liberations of the moon; height determinations of points of the moon's surface; the figure of the moon; and the moon's temperature and atmosphere.

  14. Structural unsafety revealed by failure databases

    NARCIS (Netherlands)

    Terwel, K.C.; Boot, W.; Nelisse, M.

    2014-01-01

    After several major structural incidents in the Netherlands, such as the collapse of five balconies in Maastricht in 2001 resulting in two fatalities, various initiatives have been started to improve structural safety. Research studies were initiated on the characteristics, causes and consequences

  15. Structural unsafety revealed by failure databases

    NARCIS (Netherlands)

    Terwel, K.; Boot, W.; Nelisse, M.

    2014-01-01

    After several major structural incidents in the Netherlands, such as the collapse of five balconies in Maastricht in 2001 resulting in two fatalities, various initiatives have been started to improve structural safety. Research studies were initiated on the characteristics, causes and consequences o

  16. Structural and spectroscopic studies of surfaces

    CERN Document Server

    Laitenberger, P

    1996-01-01

    and on a 10ML thick Ar spacer layer, a remarkable substrate dependence is revealed. A new STM-based technique for fabricating simple metal-structures with dimensions in the 10-100nm regime which are partially electrically isolated from their environment was developed in collaboration with Dr. L. A. Silva. This technique employs the STM tip as a mechanical nanofabrication tool to machine gaps into a thin metallic film deposited on an insulating substrate, which laterally confine and electrically isolate the desired metal regions. Several metal structures, such as nanoscale wires and pads, were successfully created. Finally, the conceptual basis and present stage of construction of a new surface analytical tool, the Scanning Probe Energy Loss Spectrometer (SPELS), is discussed. The SPELS offers the exciting prospect of collecting structural as well as spectroscopic information with a spatial resolution of a few nanometres. Once successfully developed, it will be ideally suited for spectroscopic studies of nanos...

  17. The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease.

    Science.gov (United States)

    Bunick, Christopher G; Milstone, Leonard M

    2017-01-01

    Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401(K10) disulfide link, although the bond angle is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20-25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.

  18. On real structures on rigid surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kulikov, Vik S [Steklov Mathematical Institute, Russian Academy of Sciences (Russian Federation); Kharlamov, V M [Institut de Recherche Matematique Avanee Universite Louis Pasteur et CNRS 7 rue Rene Descartes (France)

    2002-02-28

    We construct examples of rigid surfaces (that is, surfaces whose deformation class consists of a unique surface) with a particular behaviour with respect to real structures. In one example the surface has no real structure. In another it has a unique real structure, which is not maximal with respect to the Smith-Thom inequality. These examples give negative answers to the following problems: the existence of real surfaces in each deformation class of complex surfaces, and the existence of maximal real surfaces in every complex deformation class that contains real surfaces. Moreover, we prove that there are no real surfaces among surfaces of general type with p{sub g}=q=0 and K{sup 2}=9. These surfaces also provide new counterexamples to the 'Dif = Def' problem.

  19. The Meaning of Surface Structure and Deep Structure to Translation

    Institute of Scientific and Technical Information of China (English)

    罗源

    2014-01-01

    Surface structure and deep structure first come up with by Chomsky is an innovative action in linguistics. Despite the arguments involved around surface structure and deep structure, it is instructional to English-Chinese translation to some degree and its scientific connotation is meaningful to deepen language study and construct related disciplinary both in theory and practice.

  20. Locally homogeneous structures on Hopf surfaces

    CERN Document Server

    McKay, Benjamin

    2009-01-01

    We study holomorphic locally homogeneous geometric structures modelled on line bundles over the projective line. We classify these structures on primary Hopf surfaces. We write out the developing map and holonomy morphism of each of these structures explicitly on each primary Hopf surface.

  1. Tuning Wettability and Adhesion of Structured Surfaces

    Science.gov (United States)

    Badge, Ila

    Structured surfaces with feature size ranging from a few micrometers down to nanometers are of great interest in the applications such as design of anti-wetting surfaces, tissue engineering, microfluidics, filtration, microelectronic devices, anti-reflective coatings and reversible adhesives. A specific surface property demands particular roughness geometry along with suitable surface chemistry. Plasma Enhanced Chemical Vapor Deposition (PECVD) is a technique that offers control over surface chemistry without significantly affecting the roughness and thus, provides a flexibility to alter surface chemistry selectively for a given structured surface. In this study, we have used PECVD to fine tune wetting and adhesion properties. The research presented focuses on material design aspects as well as the fundamental understanding of wetting and adhesion phenomena of structured surfaces. In order to study the effect of surface roughness and surface chemistry on the surface wettability independently, we developed a model surface by combination of colloidal lithography and PECVD. A systematically controlled hierarchical roughness using spherical colloidal particles and surface chemistry allowed for quantitative prediction of contact angles corresponding to metastable and stable wetting states. A well-defined roughness and chemical composition of the surface enabled establishing a correlation between theory predictions and experimental measurements. We developed an extremely robust superhydrophobic surface based on Carbon-Nanotubes (CNT) mats. The surface of CNTs forming a nano-porous mesh was modified using PECVD to deposit a layer of hydrophobic coating (PCNT). The PCNT surface thus formed is superhydrophobic with almost zero contact angle hysteresis. We demonstrated that the PCNT surface is not wetted under steam condensation even after prolonged exposure and also continues to retain its superhydrophobicity after multiple frosting-defrosting cycles. The anti

  2. Rheological characteristics of soft rock structural surface

    Institute of Scientific and Technical Information of China (English)

    陈沅江; 吴超; 傅衣铭

    2008-01-01

    There are two mechanisms of the coarse surface asperity resistance effect and rubbing resistance effect in the course of the soft rock structural surface creep,of which the former plays a dominant role in hindering the deformation in the starting creep phase,so that the structural surface creep usually displays the strong surface roughness effect,and so does the latter when the asperities in the coarse surface were fractured by shearing.Under the low stress condition,there are only two phases of the decelerating creep and the constant creep for the soft rock structural surface,and as the stress increases and overcomes the rubbing resistance,the accelerating creep failure of the structural surface will happen suddenly.Therefore,a multiple rheological model,which combines the nonlinear NEWTON body(NN) of a certain mass and the empirical plastic body(EM) with the classical SAINT VENANT body,NEWTON body,KELVIN body and HOOKE body,could be used to comprehensively describe the creep characteristics of the soft rock structural surface.Its mechanical parameter values will vary owing to the different surface roughness of the structural surface.The parameters of GH,GK and ηL are positively linearly correlative to the surface roughness.The surface roughness and m are negative exponential function correlation.The long-term strength τS is positively correlative to the surface roughness.

  3. Exotic geometric structures on Kodaira surfaces

    CERN Document Server

    McKay, Benjamin

    2012-01-01

    On all compact complex surfaces (modulo finite unramified coverings), we classify all of the locally homogeneous geometric structures which are locally isomorphic to the exotic homogeneous surfaces of Lie.

  4. Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions.

    Science.gov (United States)

    Natarajan, Padmaja; Punta, Marco; Kumar, Abhinav; Yeh, Andrew P; Godzik, Adam; Aravind, L

    2015-01-16

    N-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified. Crystal structures of both BVU_4064 and BF1687 proteins, solved at the JCSG center, show strikingly similar three-dimensional structures. The main difference between the two is that the two domains in the BVU_4064 protein are connected by a short linker, as opposed to a longer insertion made of 4 helices placed linearly along with a strand that is added to the C-terminal domain in the BF1687 protein. The N-terminal domain in both proteins, corresponding to the PF12985 (DUF3869) domain is a β-sandwich with pre-albumin-like fold, found in many proteins belonging to the Transthyretin clan of Pfam. The structures of C-terminal domains of both proteins, corresponding to the PF12986 (DUF3870) domain in BVU_4064 protein and an unclassified domain in the BF1687 protein, show significant structural similarity to bacterial pore-forming toxins. A helix in this domain is in an analogous position to a loop connecting the second and third strands in the toxin structures, where this loop is implicated to play a role in the toxin insertion into the host cell membrane. The same helix also points to the groove between the N- and C-terminal domains that are loosely held together by hydrophobic and hydrogen bond interactions. The presence of several conserved residues in this region together with these structural determinants could make it a functionally important region in these proteins. Structural

  5. Silicon surface structure-controlled oleophobicity.

    Science.gov (United States)

    Liu, Yan; Xiu, Yonghao; Hess, Dennis W; Wong, C P

    2010-06-01

    Superoleophobic surfaces display contact angles >150 degrees with liquids that have lower surface energies than does water. The design of superoleophobic surfaces requires an understanding of the effect of the geometrical shape of etched silicon surfaces on the contact angle and hysteresis observed when different liquids are brought into contact with these surfaces. This study used liquid-based metal-assisted etching and various silane treatments to create superoleophobic surfaces on a Si(111) surface. Etch conditions such as the etch time and etch solution concentration played critical roles in establishing the oleophobicity of Si(111). When compared to Young's contact angle, the apparent contact angle showed a transition from a Cassie to a Wenzel state for low-surface-energy liquids as different silane treatments were applied to the silicon surface. These results demonstrated the relationship between the re-entrant angle of etched surface structures and the contact angle transition between Cassie and Wenzel behavior on etched Si(111) surfaces.

  6. Moulding of Sub-micrometer Surface Structures

    DEFF Research Database (Denmark)

    Pranov, Henrik; Rasmussen, Henrik K.; Larsen, Niels Bent

    2006-01-01

    The experiments strongly suggest that the possibility to injection mould sub-micrometer surface structures in polymers mainly relates to the forces originating from the adhesive energy between polymer and shim.......The experiments strongly suggest that the possibility to injection mould sub-micrometer surface structures in polymers mainly relates to the forces originating from the adhesive energy between polymer and shim....

  7. Evidence for water structuring forces between surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, Christopher B [ORNL; Rau, Dr. Donald [National Institutes of Health

    2011-01-01

    Structured water on apposing surfaces can generate significant energies due to reorganization and displacement as the surfaces encounter each other. Force measurements on a multitude of biological structures using the osmotic stress technique have elucidated commonalities that point toward an underlying hydration force. In this review, the forces of two contrasting systems are considered in detail: highly charged DNA and nonpolar, uncharged hydroxypropyl cellulose. Conditions for both net repulsion and attraction, along with the measured exclusion of chemically different solutes from these macromolecular surfaces, are explored and demonstrate features consistent with a hydration force origin. Specifically, the observed interaction forces can be reduced to the effects of perturbing structured surface water.

  8. Modeling of laser induced periodic surface structures

    NARCIS (Netherlands)

    Skolski, J.Z.P.; Römer, G.R.B.E.; Huis in 't Veld, A.J.; Mitko, V.S.; Obona, J.V.; Ocelik, V.; Hosson, J.T.M. de

    2010-01-01

    In surfaces irradiated by short laser pulses, Laser Induced Periodic Surface Structures (LIPSS) have been observed on all kind of materials for over forty years. These LIPSS, also referred to as ripples, consist of wavy surfaces with periodicity equal or smaller than the wavelength of the laser radi

  9. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    Science.gov (United States)

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.

  10. Electron backscatter diffraction characterization of laser-induced periodic surface structures on nickel surface

    Energy Technology Data Exchange (ETDEWEB)

    Sedao, Xxx, E-mail: sedao.xxx@gmail.com [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France); Maurice, Claire [Laboratoire Georges Friedel, Ecole Nationale Supérieure des Mines, 42023 St-Etienne (France); Garrelie, Florence; Colombier, Jean-Philippe; Reynaud, Stéphanie [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France); Quey, Romain; Blanc, Gilles [Laboratoire Georges Friedel, Ecole Nationale Supérieure des Mines, 42023 St-Etienne (France); Pigeon, Florent [Laboratoire Hubert Curien, Université Jean Monnet, 42000 St-Etienne (France)

    2014-05-01

    Graphical abstract: -- Highlight: •Lattice rotation and its distribution in laser-induced periodic surface structures (LIPSS) and the subsurface region on a nickel substrate are revealed using electron backscatter diffraction (EBSD). -- Abstract: We report on the structural investigation of laser-induced periodic surface structures (LIPSS) generated in polycrystalline nickel target after multi-shot irradiation by femtosecond laser pulses. Electron backscatter diffraction (EBSD) is used to reveal lattice rotation caused by dislocation storage during LIPSS formation. Localized crystallographic damages in the LIPSS are detected from both surface and cross-sectional EBSD studies. A surface region (up to 200 nm) with 1–3° grain disorientation is observed in localized areas from the cross-section of the LIPSS. The distribution of the local disorientation is inhomogeneous across the LIPSS and the subsurface region.

  11. Numerical simulation of condensation on structured surfaces.

    Science.gov (United States)

    Fu, Xiaowu; Yao, Zhaohui; Hao, Pengfei

    2014-11-25

    Condensation of liquid droplets on solid surfaces happens widely in nature and industrial processes. This phase-change phenomenon has great effect on the performance of some microfluidic devices. On the basis of micro- and nanotechnology, superhydrophobic structured surfaces can be well-fabricated. In this work, the nucleating and growth of droplets on different structured surfaces are investigated numerically. The dynamic behavior of droplets during the condensation is simulated by the multiphase lattice Boltzmann method (LBM), which has the ability to incorporate the microscopic interactions, including fluid-fluid interaction and fluid-surface interaction. The results by the LBM show that, besides the chemical properties of surfaces, the topography of structures on solid surfaces influences the condensation process. For superhydrophobic surfaces, the spacing and height of microridges have significant influence on the nucleation sites. This mechanism provides an effective way for prevention of wetting on surfaces in engineering applications. Moreover, it suggests a way to prevent ice formation on surfaces caused by the condensation of subcooled water. For hydrophilic surfaces, however, microstructures may be submerged by the liquid films adhering to the surfaces. In this case, microstructures will fail to control the condensation process. Our research provides an optimized way for designing surfaces for condensation in engineering systems.

  12. Super water repellent surface 'strictly' mimicking the surface structure of lotus leaf

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Tae Gon; Kim, Ho Young [Seoul National University, Seoul (Korea, Republic of); Yi, Jin Woo; Lee, Kwang Ryeol; Moon, Myoung Woon [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2009-07-01

    To achieve the hierarchy of roughness as observed in lotus leaves, most artificial water-repellent surfaces have nano-asperities on top of micropillars. However, observation of real lotus leaves through SEM reveals that nonoscale roughness covers the entire surface including the base as well as bumps. Thus we fabricate surfaces having the same hierarchical roughness structure as the lotus leaf by forming nanopillars on both micropillars and base. We compare the measures of water-repellency (static contact angle, contact angle hysteresis, and transition pressure between the Cassie and Wenzel states) of the lotus-like surface with those of surfaces having single micro- and nano- roughness. The results show that nanoscale roughness covering entire surface area leads to superior water-repellency to other surface roughness structures. We also give a theoretical consideration of this observation.

  13. [Oligoglycine surface structures: molecular dynamics simulation].

    Science.gov (United States)

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  14. Structure and functions of fungal cell surfaces

    Science.gov (United States)

    Nozawa, Y.

    1984-01-01

    A review with 24 references on the biochemistry, molecular structure, and function of cell surfaces of fungi, especially dermatophytes: the chemistry and structure of the cell wall, the effect of polyene antibiotics on the morphology and function of cytoplasmic membranes, and the chemical structure and function of pigments produced by various fungi are discussed.

  15. Revealing how network structure affects accuracy of link prediction

    Science.gov (United States)

    Yang, Jin-Xuan; Zhang, Xiao-Dong

    2017-08-01

    Link prediction plays an important role in network reconstruction and network evolution. The network structure affects the accuracy of link prediction, which is an interesting problem. In this paper we use common neighbors and the Gini coefficient to reveal the relation between them, which can provide a good reference for the choice of a suitable link prediction algorithm according to the network structure. Moreover, the statistical analysis reveals correlation between the common neighbors index, Gini coefficient index and other indices to describe the network structure, such as Laplacian eigenvalues, clustering coefficient, degree heterogeneity, and assortativity of network. Furthermore, a new method to predict missing links is proposed. The experimental results show that the proposed algorithm yields better prediction accuracy and robustness to the network structure than existing currently used methods for a variety of real-world networks.

  16. Beyond the surface atlas: A roadmap and gazetteer for surface symmetry and structure

    Science.gov (United States)

    Jenkins, Stephen J.; Pratt, Stephanie J.

    2007-10-01

    , highlights elementary one-dimensional (1D) features lying parallel to the surface plane. Crucial to the utility of these concepts is that both structure and symmetry can conveniently be represented independently within a single stereographic projection; this then serves as a "roadmap" that fully embodies the essential relationships between different surfaces and facilitates navigation amongst them. Key locations on the map identify surfaces of particular structural simplicity, which are collated in a "gazetteer" with an accompanying description of their essential symmetry and structural character. Our symmetry-structure surface stereography (4S) analysis of fcc, bcc and hcp crystals reveals various new insights about the types of surface that they present. For instance, although the asymmetry of chiral fcc planes has hitherto been associated with the presence of kink sites, we show that the same is not always true of either bcc or hcp chiral surfaces. Kink-free chiral bcc planes offer particular advantages as model systems for asymmetric applications. We further reveal that the hcp crystal structure gives rise to intriguing types of surface that are not observed for either fcc or bcc materials. These include surfaces with intrinsic glide symmetry, surfaces with intrinsic racemic character and others displaying intrinsic double-chirality, analogous to the existence of diastereoisomers in molecular chemistry. We also identify several elementary surface structural categories that are specific to the hcp case. Having thus established a secure framework via ideal bulk-terminated crystalline surfaces, we subsequently demonstrate its extension to real surfaces. In considering how these differ from ideal surfaces we discuss relaxation and reconstruction within the same symmetry-resolved and structure-resolved perspective, drawing on numerous examples from the literature. Finally we illustrate the application of our scheme in one selected branch of surface science by exploring the

  17. Flood damage claims reveal insights about surface runoff in Switzerland

    Science.gov (United States)

    Bernet, D. B.; Prasuhn, V.; Weingartner, R.

    2015-12-01

    A few case studies in Switzerland exemplify that not only overtopping water bodies frequently cause damages to buildings. Reportedly, a large share of the total loss due to flooding in Switzerland goes back to surface runoff that is formed and is propagating outside of regular watercourses. Nevertheless, little is known about when, where and why such surface runoff occurs. The described process encompasses surface runoff formation, followed by unchannelised overland flow until a water body is reached. It is understood as a type of flash flood, has short response times and occurs diffusely in the landscape. Thus, the process is difficult to observe and study directly. A promising source indicating surface runoff indirectly are houseowners' damage claims recorded by Swiss Public Insurance Companies for Buildings (PICB). In most of Switzerland, PICB hold a monopoly position and insure (almost) every building. Consequently, PICB generally register all damages to buildings caused by an insured natural hazard (including surface runoff) within the respective zones. We have gathered gapless flood related claim records of most of all Swiss PICB covering more than the last two decades on average. Based on a subset, we have developed a methodology to differentiate claims related to surface runoff from other causes. This allows us to assess the number of claims as well as total loss related to surface runoff and compare these to the numbers of overtopping watercourses. Furthermore, with the good data coverage, we are able to analyze surface runoff related claims in space and time, from which we can infer spatial and temporal characteristics of surface runoff. Although the delivered data of PICB are heterogeneous and, consequently, time-consuming to harmonize, our first results show that exploiting these damage claim records is feasible and worthwhile to learn more about surface runoff in Switzerland.

  18. Electron backscatter diffraction characterization of laser-induced periodic surface structures on nickel surface

    Science.gov (United States)

    Sedao, Xxx; Maurice, Claire; Garrelie, Florence; Colombier, Jean-Philippe; Reynaud, Stéphanie; Quey, Romain; Blanc, Gilles; Pigeon, Florent

    2014-05-01

    We report on the structural investigation of laser-induced periodic surface structures (LIPSS) generated in polycrystalline nickel target after multi-shot irradiation by femtosecond laser pulses. Electron backscatter diffraction (EBSD) is used to reveal lattice rotation caused by dislocation storage during LIPSS formation. Localized crystallographic damages in the LIPSS are detected from both surface and cross-sectional EBSD studies. A surface region (up to 200 nm) with 1-3° grain disorientation is observed in localized areas from the cross-section of the LIPSS. The distribution of the local disorientation is inhomogeneous across the LIPSS and the subsurface region.

  19. Coherent flow structures at earth's surface

    National Research Council Canada - National Science Library

    Venditti, J.G; Best, J.L; Church, M; Hardy, R.J

    2013-01-01

    This book reviews the recent progress in the study of the turbulent flows that sculpt the Earth's surface, focusing in particular on the organized structures that have been identified in recent years...

  20. Protein Adsorption to Surface Chemistry and Crystal Structure Modification of Titanium Surfaces

    Directory of Open Access Journals (Sweden)

    Ryo Jimbo

    2010-07-01

    Full Text Available Objectives: To observe the early adsorption of extracellular matrix and blood plasma proteins to magnesium-incorporated titanium oxide surfaces, which has shown superior bone response in animal models.Material and Methods: Commercially pure titanium discs were blasted with titanium dioxide (TiO2 particles (control, and for the test group, TiO2 blasted discs were further processed with a micro-arc oxidation method (test. Surface morphology was investigated by scanning electron microscopy, surface topography by optic interferometry, characterization by X-ray photoelectron spectroscopy (XPS, and by X-ray diffraction (XRD analysis. The adsorption of 3 different proteins (fibronectin, albumin, and collagen type I was investigated by an immunoblotting technique.Results: The test surface showed a porous structure, whereas the control surface showed a typical TiO2 blasted structure. XPS data revealed magnesium-incorporation to the anodic oxide film of the surface. There was no difference in surface roughness between the control and test surfaces. For the protein adsorption test, the amount of albumin was significantly higher on the control surface whereas the amount of fibronectin was significantly higher on the test surface. Although there was no significant difference, the test surface had a tendency to adsorb more collagen type I.Conclusions: The magnesium-incorporated anodized surface showed significantly higher fibronectin adsorption and lower albumin adsorption than the blasted surface. These results may be one of the reasons for the excellent bone response previously observed in animal studies.

  1. Correlating simulated surface marks with near-surface tornado structure

    Science.gov (United States)

    Zimmerman, Michael I.

    Tornadoes often leave behind patterns of debris deposition, or "surface marks", which provide a direct signature of their near surface winds. The intent of this thesis is to investigate what can be learned about near-surface tornado structure and intensity through the properties of surface marks generated by simulated, debris-laden tornadoes. Earlier work showed through numerical simulations that the tornado's structure and intensity is highly sensitive to properties of the near-surface flow and can change rapidly in time for some conditions. The strongest winds often occur within tens of meters of the surface where the threat to human life and property is highest, and factors such as massive debris loadings and asymmetry of the main vortex have proven to be critical complications in some regimes. However, studying this portion of the flow in the field is problematic; while Doppler radar provides the best tornado wind field measurements, it cannot probe below about 20 m, and interpretation of Doppler data requires assumptions about tornado symmetry, steadiness in time, and correlation between scatterer and air velocities that are more uncertain near the surface. As early as 1967, Fujita proposed estimating tornado wind speeds from analysis of aerial photography and ground documentation of surface marks. A handful of studies followed but were limited by difficulties in interpreting physical origins of the marks, and little scientific attention has been paid to them since. Here, Fujita's original idea is revisited in the context of three-dimensional, large-eddy simulations of tornadoes with fully-coupled debris. In this thesis, the origins of the most prominent simulated marks are determined and compared with historical interpretations of real marks. The earlier hypothesis that cycloidal surface marks were directly correlated with the paths of individual vortices (either the main vortex or its secondary vortices, when present) is unsupported by the simulation results

  2. Long Range Surface Plasmons in Multilayer Structures

    CERN Document Server

    Delfan, Aida

    2013-01-01

    We present a new strategy, based on a Fresnel coefficient pole analysis, for designing an asymmetric multilayer structure that supports long range surface plasmons (LRSP). We find that the electric field intensity in the metal layer of a multilayer LRSP structure can be even slightly smaller than in the metal layer of the corresponding symmetric LRSP structure, minimizing absorption losses and resulting in LRSP propagation lengths up to 2mm. With a view towards biosensing applications, we also present semi-analytic expressions for a standard surface sensing parameter in arbitrary planar resonant structures, and in particular show that for an asymmetric structure consisting of a gold film deposited on a multilayer of SiO2 and TiO2 a surface sensing parameter G = 1.28(1/nm) can be achieved.

  3. Structure of mega-hemocyanin reveals protein origami in snails.

    Science.gov (United States)

    Gatsogiannis, Christos; Hofnagel, Oliver; Markl, Jürgen; Raunser, Stefan

    2015-01-06

    Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters.

  4. A genetic algorithm approach in interface and surface structure optimization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    The thesis is divided into two parts. In the first part a global optimization method is developed for the interface and surface structures optimization. Two prototype systems are chosen to be studied. One is Si[001] symmetric tilted grain boundaries and the other is Ag/Au induced Si(111) surface. It is found that Genetic Algorithm is very efficient in finding lowest energy structures in both cases. Not only existing structures in the experiments can be reproduced, but also many new structures can be predicted using Genetic Algorithm. Thus it is shown that Genetic Algorithm is a extremely powerful tool for the material structures predictions. The second part of the thesis is devoted to the explanation of an experimental observation of thermal radiation from three-dimensional tungsten photonic crystal structures. The experimental results seems astounding and confusing, yet the theoretical models in the paper revealed the physics insight behind the phenomena and can well reproduced the experimental results.

  5. Sub-µm structured lotus surfaces manufacturing

    DEFF Research Database (Denmark)

    Worgull, Matthias; Heckele, Mathias; Mappes, Timo

    2009-01-01

    . Unlike to stochastic methods, patterning with a LIGA-mold insert it is possible to structure surfaces very uniformly or even with controlled variations (e.g., with gradients). In this paper we present the process chain to realize polymer sub-lm structures with minimum lateral feature size of 400 nm...

  6. Sub-µ structured Lotus Surfaces Manufacturing

    DEFF Research Database (Denmark)

    Worgull, Matthias; Heckele, Mathias; Mappes, Timo

    2008-01-01

    . Unlike to stochastic methods, patternin¬g with a LIGA-mold insert it is possible to structure surfaces very uniformly or even with controlled variations (e.g. with gradients). In this paper we present the process chain to realize polymer sub-micro structures with minimum lateral feature size of 400 nm...

  7. Pressurizable structures comprising different surface sections

    NARCIS (Netherlands)

    Koussios, S.; Bergsma, O.K.; Beukers, A.

    2004-01-01

    The invention relates to composite pressurizable structures which are overwound with fibres or are braided. The pressurizable structures comprise axial sections which in turn comprise both concave and convex surfaces. The shape characteristics are related to geodesic as well as non-geodesic trajecto

  8. Longitudinal surface structures (flowstripes on Antarctic glaciers

    Directory of Open Access Journals (Sweden)

    N. F. Glasser

    2011-11-01

    Full Text Available Longitudinal surface structures (''flowstripes'' are common on many glaciers but their origin and significance are poorly understood. In this paper we present observations of the development of these longitudinal structures from four different Antarctic glacier systems (the Lambert Glacier/Amery Ice Shelf area, outlet glaciers in the Ross Sea sector, ice-shelf tributary glaciers on the Antarctic Peninsula, and the onset zone of a tributary to the Recovery Glacier Ice Stream in the Filchner Ice Shelf area. Mapping from optical satellite images demonstrates that longitudinal surface structures develop in two main situations: (1 as relatively wide flow stripes within glacier flow units and (2 as relatively narrow flow stripes where there is convergent flow around nunataks or at glacier confluence zones. Our observations indicate that the confluence features are narrower, sharper, and more clearly defined features. They are characterised by linear troughs or depressions on the ice surface and are much more common than the former type. Longitudinal surface structures within glacier flow units have previously been explained as the surface expression of localised bed perturbations but a universal explanation for those forming at glacier confluences is lacking. Here we propose that these features are formed at zones of ice acceleration and extensional flow at glacier confluences. We provide a schematic model for the development of longitudinal surface structures based on extensional flow that can explain their ridge and trough morphology as well as their down-ice persistence.

  9. Colloids with high-definition surface structures

    Science.gov (United States)

    Chen, Hsien-Yeh; Rouillard, Jean-Marie; Gulari, Erdogan; Lahann, Joerg

    2007-01-01

    Compared with the well equipped arsenal of surface modification methods for flat surfaces, techniques that are applicable to curved, colloidal surfaces are still in their infancy. This technological gap exists because spin-coating techniques used in traditional photolithographic processes are not applicable to the curved surfaces of spherical objects. By replacing spin-coated photoresist with a vapor-deposited, photodefinable polymer coating, we have now fabricated microstructured colloids with a wide range of surface patterns, including asymmetric and chiral surface structures, that so far were typically reserved for flat substrates. This high-throughput method can yield surface-structured colloidal particles at a rate of ≈107 to 108 particles per operator per day. Equipped with spatially defined binding pockets, microstructured colloids can engage in programmable interactions, which can lead to directed self-assembly. The ability to create a wide range of colloids with both simple and complex surface patterns may contribute to the genesis of previously unknown colloidal structures and may have important technological implications in a range of different applications, including photonic and phononic materials or chemical sensors. PMID:17592149

  10. Colloids with high-definition surface structures.

    Science.gov (United States)

    Chen, Hsien-Yeh; Rouillard, Jean-Marie; Gulari, Erdogan; Lahann, Joerg

    2007-07-03

    Compared with the well equipped arsenal of surface modification methods for flat surfaces, techniques that are applicable to curved, colloidal surfaces are still in their infancy. This technological gap exists because spin-coating techniques used in traditional photolithographic processes are not applicable to the curved surfaces of spherical objects. By replacing spin-coated photoresist with a vapor-deposited, photodefinable polymer coating, we have now fabricated microstructured colloids with a wide range of surface patterns, including asymmetric and chiral surface structures, that so far were typically reserved for flat substrates. This high-throughput method can yield surface-structured colloidal particles at a rate of approximately 10(7) to 10(8) particles per operator per day. Equipped with spatially defined binding pockets, microstructured colloids can engage in programmable interactions, which can lead to directed self-assembly. The ability to create a wide range of colloids with both simple and complex surface patterns may contribute to the genesis of previously unknown colloidal structures and may have important technological implications in a range of different applications, including photonic and phononic materials or chemical sensors.

  11. Predator-guided sampling reveals biotic structure in the bathypelagic.

    Science.gov (United States)

    Benoit-Bird, Kelly J; Southall, Brandon L; Moline, Mark A

    2016-02-24

    We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1,200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column.

  12. Nature inspired structured surfaces for biomedical applications.

    Science.gov (United States)

    Webb, H K; Hasan, J; Truong, V K; Crawford, R J; Ivanova, E P

    2011-01-01

    Nature has created an array of superhydrophobic surfaces that possess water-repellent, self-cleaning and anti-icing properties. These surfaces have a number of potential applications in the biomedical industry, as they have the potential to control protein adsorption and cell adhesion. Natural superhydrophobic surfaces are typically composed of materials with a low intrinsic surface free-energy (e.g the cuticular waxes of lotus leaves and insect wings) with a hierarchical structural configuration. This hierarchical surface topography acts to decrease the contact area of water droplets in contact with the surface, thereby increasing the extent of the air/water interface, resulting in water contact angles greater than 150º. In order to employ these surfaces in biotechnological applications, fabrication techniques must be developed so that these multi-scale surface roughness characteristics can be reproduced. Additionally, these fabrication techniques must also be able to be applied to the material required for the intended application. An overview of some of the superhydrophobic surfaces that exist in nature is presented, together with an explanation of the theories of their wettability. Also included is a description of some of the biomedical applications of superhydrophobic surfaces and fabrication techniques that can be used to mimic superhydrophobic surfaces found in nature.

  13. An alternative RNA polymerase I structure reveals a dimer hinge.

    Science.gov (United States)

    Kostrewa, Dirk; Kuhn, Claus-D; Engel, Christoph; Cramer, Patrick

    2015-09-01

    RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engel et al. (2013), Nature (London), 502, 650-655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.

  14. Maps of random walks on complex networks reveal community structure.

    Science.gov (United States)

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  15. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: fengyg@qibebt.ac.cn [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  16. Col-OSSOS: z-Band Photometry Reveals Three Distinct TNO Surface Types

    Science.gov (United States)

    Pike, Rosemary E.; Fraser, Wesley C.; Schwamb, Megan E.; Kavelaars, J. J.; Marsset, Michael; Bannister, Michele T.; Lehner, Matthew J.; Wang, Shiang-Yu; Alexandersen, Mike; Chen, Ying-Tung; Gladman, Brett J.; Gwyn, Stephen; Petit, Jean-Marc; Volk, Kathryn

    2017-09-01

    Several different classes of trans-Neptunian objects (TNOs) have been identified based on their optical and near-infrared colors. As part of the Colours of the Outer Solar System Origins Survey (Col-OSSOS), we have obtained g-, r-, and z-band photometry of 26 TNOs using Subaru and Gemini Observatories. Previous color surveys have not utilized z-band reflectance, and the inclusion of this band reveals significant surface reflectance variations between sub-populations. The colors of TNOs in g - r and r - z show obvious structure, and appear consistent with the previously measured bi-modality in g - r. The distribution of colors of the two dynamically excited surface types can be modeled using the two-component mixing models from Fraser & Brown. With the combination of g - r and r - z, the dynamically excited classes can be separated cleanly into red and neutral surface classes. In g - r and r - z, the two dynamically excited surface groups are also clearly distinct from the cold classical TNO surfaces, which are red, with g-r≳ 0.85 and r - z ≲ 0.6, while all dynamically excited objects with similar g - r colors exhibit redder r - z colors. The z-band photometry makes it possible for the first time to differentiate the red excited TNO surfaces from the red cold classical TNO surfaces. The discovery of different r - z colors for these cold classical TNOs makes it possible to search for cold classical surfaces in other regions of the Kuiper Belt and to completely separate cold classical TNOs from the dynamically excited population, which overlaps in orbital parameter space.

  17. Electric arc surfacing on low carbon steel: Structure and properties

    Science.gov (United States)

    Ivanov, Yurii; Gromov, Victor; Kormyshev, Vasilii; Konovalov, Sergey; Kapralov, Evgenii; Semin, Alexander

    2016-11-01

    By the methods of modern materials science, the structure-phase state and microhardness distribution along the cross-section of single and double coatings surfaced on martensite low carbon steel by alloy powder-cored wire were studied. It was established that the increased mechanical properties of surfaced layer are determined by the sub-micro and nanodispersed martensite structure formation, containing iron borides forming the eutectic of lamellar form. The plates of Fe2B are formed mainly in the eutectic of a single-surfaced layer, while FeB is formed in a double-surfaced layer. The existence of bend extinction contours indicating the internal stress fields formation at the boundaries of Fe borides-α-Fe phases were revealed.

  18. Surface Plasmon Coupling and Control Using Spherical Cap Structures

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Yu; Joly, Alan G.; Zhang, Xin; El-Khoury, Patrick Z.; Hess, Wayne P.

    2017-06-05

    Propagating surface plasmons (PSPs) launched from a protruded silver spherical cap structure are investigated using photoemission electron microscopy (PEEM) and finite difference time domain (FDTD) calculations. Our combined experimental and theoretical findings reveal that PSP coupling efficiency is comparable to conventional etched-in plasmonic coupling structures. Additionally, plasmon propagation direction can be varied by a linear rotation of the driving laser polarization. A simple geometric model is proposed in which the plasmon direction selectivity is proportional to the projection of the linear laser polarization on the surface normal. An application for the spherical cap coupler as a gate device is proposed. Overall, our results indicate that protruded cap structures hold great promise as elements in emerging surface plasmon applications.

  19. Persistent Near-Surface Flow Structures from Local Helioseismology

    CERN Document Server

    Howe, R; Baker, D; Harra, L; van Driel-Gesztelyi, L; Bogart, R S

    2015-01-01

    Near-surface flows measured by the ring-diagram technique of local helioseismology show structures that persist over multiple rotations. We examine these phenomena using data from the {\\em Global Oscillation Network Group} (GONG) and the {\\em Helioseismic and Magnetic Imager} (HMI) and show that a correlation analysis of the structures can be used to estimate the rotation rate as a function of latitude, giving a result consistent with the near-surface rate from global helioseismology and slightly slower than that obtained from a similar analysis of the surface magnetic field strength. At latitudes of 60$^{\\circ}$ and above the HMI flow data reveal a strong signature of a two-sided zonal flow structure. This signature may be related to recent reports of "giant cells" in solar convection.

  20. Surface structure and electronic properties of materials

    Science.gov (United States)

    Siekhaus, W. J.; Somorjai, G. A.

    1975-01-01

    A surface potential model is developed to explain dopant effects on chemical vapor deposition. Auger analysis of the interaction between allotropic forms of carbon and silicon films has shown Si-C formation for all forms by glassy carbon. LEED intensity measurements have been used to determine the mean square displacement of surface atoms of silicon single crystals, and electron loss spectroscopy has shown the effect of structure and impurities on surface states located within the band gap. A thin film of Al has been used to enhance film crystallinity at low temperature.

  1. Revealing the hidden structural phases of FeRh

    Science.gov (United States)

    Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

    2016-11-01

    Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.

  2. Structure and reactivity of water at biomaterial surfaces.

    Science.gov (United States)

    Vogler, E A

    1998-02-01

    Molecular self association in liquids is a physical process that can dominate cohesion (interfacial tension) and miscibility. In water, self association is a powerful organizational force leading to a three-dimensional hydrogen-bonded network (water structure). Localized perturbations in the chemical potential of water as by, for example, contact with a solid surface, induces compensating changes in water structure that can be sensed tens of nanometers from the point of origin using the surface force apparatus (SFA) and ancillary techniques. These instruments reveal attractive or repulsive forces between opposing surfaces immersed in water, over and above that anticipated by continuum theory (DLVO), that are attributed to a variable density (partial molar volume) of a more-or-less ordered water structure, depending on the water wettability (surface energy) of the water-contacting surfaces. Water structure at surfaces is thus found to be a manifestation of hydrophobicity and, while mechanistic/theoretical interpretation of experimental results remain the subject of some debate in the literature, convergence of experimental observations permit, for the first time, quantitative definition of the relative terms 'hydrophobic' and 'hydrophilic'. In particular, long-range attractive forces are detected only between surfaces exhibiting a water contact angle theta > 65 degrees (herein defined as hydrophobic surfaces with pure water adhesion tension tau O = gamma O cos theta 30 dyn/cm). These findings suggest at least two distinct kinds of water structure and reactivity: a relatively less-dense water region against hydrophobic surfaces with an open hydrogen-bonded network and a relatively more-dense water region against hydrophilic surfaces with a collapsed hydrogen-bonded network. Importantly, membrane and SFA studies reveal a discrimination between biologically-important ions that preferentially solubilizes divalent ions in more-dense water regions relative to less

  3. Designing visual appearance using a structured surface

    DEFF Research Database (Denmark)

    Johansen, Villads Egede; Thamdrup, Lasse Højlund; Smitrup, Christian;

    2015-01-01

    We present an approach for designing nanostructured surfaces with prescribed visual appearances, starting at design analysis and ending with a fabricated sample. The method is applied to a silicon wafer structured using deep ultraviolet lithography and dry etching and includes preliminary design ...

  4. The regulatory SCR-1/5 and cell surface-binding SCR-16/20 fragments of factor H reveal partially folded-back solution structures and different self-associative properties.

    Science.gov (United States)

    Okemefuna, Azubuike I; Gilbert, Hannah E; Griggs, Kim M; Ormsby, Rebecca J; Gordon, David L; Perkins, Stephen J

    2008-01-04

    Factor H (FH) is a plasma glycoprotein that plays a central role in regulation of the alternative pathway of complement. It is composed of 20 short complement regulator (SCR) domains. The SCR-1/5 fragment is required for decay acceleration and cofactor activity, while the SCR-16/20 fragment possesses binding sites for complement C3d and heparin. X-ray scattering and analytical ultracentrifugation showed that SCR-1/5 was monomeric, while SCR-16/20 formed dimers. The Guinier radius of gyration R(G) of 4.3 nm for SCR-1/5 and those of 4.7 nm and about 7.8 nm for monomeric and dimeric SCR-16/20, respectively, showed that their structures are partially folded back and bent. The distance distribution function P(r) showed that SCR-1/5 has a maximum dimension of 15 nm while monomeric and dimeric SCR-16/20 are 17 nm and about 27 nm long, respectively. The sedimentation coefficient of 2.4 S for SCR-1/5 showed no concentration-dependence, while that for SCR-16/20 was 2.8 S for the monomer and 3.9 S for the dimer. Sedimentation equilibrium data showed that SCR-1/5 is monomeric while SCR-16/20 exhibited a weak monomer-dimer equilibrium with a dissociation constant of 16 microM. The constrained scattering and sedimentation modelling of SCR-1/5 and SCR-16/20 showed that partially folded-back and bent flexible SCR arrangements fitted both data sets better than extended linear arrangements, and that the dimer was best modelled in the SCR-16/20 model by an end-to-end association of two SCR-20 domains. The SCR-1/5 and SCR-16/20 models were conformationally similar to the previously determined partially folded-back structure for intact wild-type FH, hence suggesting a partial explanation of the intact FH structure. Comparison of the SCR-16/20 model with the crystal structure of C3b clarified reasons for the distribution of mutations leading to atypical haemolytic uraemic syndrome.

  5. Surface and Core Electronic Structure of Oxidized Silicon Nanocrystals

    Directory of Open Access Journals (Sweden)

    Noor A. Nama

    2010-01-01

    Full Text Available Ab initio restricted Hartree-Fock method within the framework of large unit cell formalism is used to simulate silicon nanocrystals between 216 and 1000 atoms (1.6–2.65 nm in diameter that include Bravais and primitive cell multiples. The investigated properties include core and oxidized surface properties. Results revealed that electronic properties converge to some limit as the size of the nanocrystal increases. Increasing the size of the core of a nanocrystal resulted in an increase of the energy gap, valence band width, and cohesive energy. The lattice constant of the core and oxidized surface parts shows a decreasing trend as the nanocrystal increases in a size that converges to 5.28 Ǻ in a good agreement with the experiment. Surface and core convergence to the same lattice constant reflects good adherence of oxide layer at the surface. The core density of states shows highly degenerate states that split at the oxygenated (001-(1×1 surface due to symmetry breaking. The nanocrystal surface shows smaller gap and higher valence and conduction bands when compared to the core part, due to oxygen surface atoms and reduced structural symmetry. The smaller surface energy gap shows that energy gap of the nanocrystal is controlled by the surface part. Unlike the core part, the surface part shows a descending energy gap that proves its obedience to quantum confinement effects. Nanocrystal geometry proved to have some influence on all electronic properties including the energy gap.

  6. Local structure of nanosized tungstates revealed by evolutionary algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Timoshenko, Janis; Anspoks, Andris; Kuzmin, Alexei [Institute of Solid State Physics, University of Latvia, Riga (Latvia); Kalinko, Alexandr [Institute of Solid State Physics, University of Latvia, Riga (Latvia); Synchrotron SOLEIL, l' Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette (France)

    2015-02-01

    Nanostructured tungstates, such as CoWO{sub 4} and CuWO{sub 4}, are very promising catalytic materials, particularly for photocatalytic oxidation of water. The high catalytic activity of tungstate nanoparticles partially is a result of their extremely small sizes, and, consequently, high surface-to-volume ratio. Therefore their properties depend strongly on the atomic structure, which differ significantly from that of the bulk material. X-ray absorption spectroscopy is a powerful technique to address the challenging problem of the local structure determination in nanomaterials. In order to fully exploit the structural information contained in X-ray absorption spectra, in this study we employ a novel evolutionary algorithm (EA) for the interpretation of the Co and Cu K-edges as well as the W L{sub 3}-edge extended X-ray absorption fine structure (EXAFS) of nanosized CoWO{sub 4} and CuWO{sub 4}. The combined EA-EXAFS approach and simultaneous analysis of the W L{sub 3} and Co(Cu) K-edge EXAFS spectra allowed us for the first time to obtain a 3D structure model of the tungstate nanoparticles and to explore in details the effect of size, temperature and transition metal type. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Nanoscale electrochemical patterning reveals the active sites for catechol oxidation at graphite surfaces.

    Science.gov (United States)

    Patel, Anisha N; McKelvey, Kim; Unwin, Patrick R

    2012-12-19

    Graphite-based electrodes (graphite, graphene, and nanotubes) are used widely in electrochemistry, and there is a long-standing view that graphite step edges are needed to catalyze many reactions, with the basal surface considered to be inert. In the present work, this model was tested directly for the first time using scanning electrochemical cell microscopy reactive patterning and shown to be incorrect. For the electro-oxidation of dopamine as a model process, the reaction rate was measured at high spatial resolution across a surface of highly oriented pyrolytic graphite. Oxidation products left behind in a pattern defined by the scanned electrochemical cell served as surface-site markers, allowing the electrochemical activity to be correlated directly with the graphite structure on the nanoscale. This process produced tens of thousands of electrochemical measurements at different locations across the basal surface, unambiguously revealing it to be highly electrochemically active, with step edges providing no enhanced activity. This new model of graphite electrodes has significant implications for the design of carbon-based biosensors, and the results are additionally important for understanding electrochemical processes on related sp(2)-hybridized materials such as pristine graphene and nanotubes.

  8. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    Science.gov (United States)

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; Basu, Shibom; Grotjohann, Ingo; Kupitz, Christopher; Rendek, Kimberley; Weierstall, Uwe; Zatsepin, Nadia A.; Cherezov, Vadim; Liu, Wei; Bandaru, Sateesh; English, Niall J.; Gati, Cornelius; Barty, Anton; Yefanov, Oleksandr; Chapman, Henry N.; Diederichs, Kay; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Marvin Seibert, M.; Caffrey, Martin

    2015-12-01

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

  9. Dramatic changes in electronic structure revealed by fractionally charged nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Aron J. [Department of Chemistry, Lensfield Rd., University of Cambridge, Cambridge CB2 1EW (United Kingdom); Mori-Sánchez, Paula, E-mail: paula.mori@uam.es [Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid (Spain)

    2014-01-28

    Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. These are revealed in one and two electron molecular systems by full configuration interaction (FCI) calculations when the realm of the nuclear charge is extended to be fractional. FCI electron densities in these systems show dramatic changes in real space and illustrate the transfer, hopping, and removal of electrons. This is due to the particle nature of electrons seen in stretched systems and is a manifestation of an energy derivative discontinuity at constant number of electrons. Dramatic errors of density functional theory densities are seen in real space as this physics is missing from currently used approximations. The movements of electrons in these simple systems encapsulate those in real physical processes, from chemical reactions to electron transport and pose a great challenge for the development of new electronic structure methods.

  10. Dramatic changes in electronic structure revealed by fractionally charged nuclei

    Science.gov (United States)

    Cohen, Aron J.; Mori-Sánchez, Paula

    2014-01-01

    Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. These are revealed in one and two electron molecular systems by full configuration interaction (FCI) calculations when the realm of the nuclear charge is extended to be fractional. FCI electron densities in these systems show dramatic changes in real space and illustrate the transfer, hopping, and removal of electrons. This is due to the particle nature of electrons seen in stretched systems and is a manifestation of an energy derivative discontinuity at constant number of electrons. Dramatic errors of density functional theory densities are seen in real space as this physics is missing from currently used approximations. The movements of electrons in these simple systems encapsulate those in real physical processes, from chemical reactions to electron transport and pose a great challenge for the development of new electronic structure methods.

  11. Pool Boiling Heat Transfer on structured Surfaces

    Science.gov (United States)

    Addy, J.; Olbricht, M.; Müller, B.; Luke, A.

    2016-09-01

    The development in the process and energy sector shows the importance of efficient utilization of available resources to improve thermal devices. To achieve this goal, all thermal components have to be optimized continuously. Various applications of multi-phase heat and mass transfer have to be improved. Therefore, the heat transfer and the influence of surface roughness in nucleate boiling with the working fluid propane is experimentally investigated on structured mild steel tubes, because only few data are available in the literature. The mild steel tube is sandblasted to obtain different surface roughness. The measurements are carried out over wide ranges of heat flux and pressure. The experimental results are compared with correlations from literature and the effect of surface roughness on the heat transfer is discussed. It is shown that the heat transfer coefficient increases with increasing surface roughness, heat flux and reduced pressure at nucleate pool boiling.

  12. How quantum bound states bounce and the structure it reveals

    CERN Document Server

    Lee, Dean

    2010-01-01

    We investigate how quantum bound states bounce from a hard surface. Our analysis has applications to ab initio calculations of nuclear structure and elastic deformation, energy levels of excitons in semiconductor quantum dots and wells, and cold atomic few-body systems on optical lattices with sharp boundaries. We develop the general theory of elastic reflection for a composite body from a hard wall. On the numerical side we present universal results for two-body states and discuss ab initio calculations for general few-body systems. On the analytical side we derive a universal effective potential that gives the reflection scattering length for shallow two-body states.

  13. Towards revealing the structure of bacterial inclusion bodies.

    Science.gov (United States)

    Wang, Lei

    2009-01-01

    Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

  14. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

    Science.gov (United States)

    Tempel, Wolfram; Rabeh, Wael M; Bogan, Katrina L; Belenky, Peter; Wojcik, Marzena; Seidle, Heather F; Nedyalkova, Lyudmila; Yang, Tianle; Sauve, Anthony A; Park, Hee-Won; Brenner, Charles

    2007-10-02

    The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.

  15. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

    Directory of Open Access Journals (Sweden)

    Wolfram Tempel

    2007-10-01

    Full Text Available The eukaryotic nicotinamide riboside kinase (Nrk pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+ by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.

  16. Comparison of the Genome Sequence of the Poultry Pathogen Bordetella avium with Those of B. bronchiseptica, B. pertussis, and B. parapertussis Reveals Extensive Diversity in Surface Structures Associated with Host Interaction

    Science.gov (United States)

    Sebaihia, Mohammed; Preston, Andrew; Maskell, Duncan J.; Kuzmiak, Holly; Connell, Terry D.; King, Natalie D.; Orndorff, Paul E.; Miyamoto, David M.; Thomson, Nicholas R.; Harris, David; Goble, Arlette; Lord, Angela; Murphy, Lee; Quail, Michael A.; Rutter, Simon; Squares, Robert; Squares, Steven; Woodward, John; Parkhill, Julian; Temple, Louise M.

    2006-01-01

    Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness of Bordetella species and further the understanding of pathogenesis, we obtained the complete genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the smallest genome and gene complement of the sequenced bordetellae. In this study, the presence or absence of previously reported virulence factors from B. avium was confirmed, and the genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium but not in B. bronchiseptica were identified, and most were predicted to encode surface or secreted proteins that are likely to define an organism adapted to the avian rather than the mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three apparently complete prophages are also present. The BvgAS virulence regulatory system appears to have polymorphisms at a poly(C) tract that is involved in phase variation in other bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from the sequence, and this regulation was confirmed experimentally for five of these. PMID:16885469

  17. Surface structure of oriented PET films

    CERN Document Server

    Kirov, K

    2001-01-01

    crystallinity and the level of molecular orientation of the polymer are highest at the film surface and gradually decrease away from it. The same trend for an increase in structural order nearer the film surface was observed in a series of PET films drawn uniaxially in laboratory conditions. The observed strong dependence of stratification in the oriented films on drawing ratio, lead to the conclusion, that the structural gradients arise as a result of viscous flow. The molecular mechanism of stratification is discussed and leads to the idea of enhanced chain mobility at the PET film surface. The idea is in line with recent studies showing a depression of the glass transition temperature of free polymer surfaces. In addition, the results on structure formation in PET films during drawing, give support to the existing view that polymer crystallisation is assisted by a spinodal-decomposition nucleation process. Polymer films are widely used as substrates in nano-composite materials and therefore have to possess...

  18. Structurally tuned iridescent surfaces inspired by nature

    Energy Technology Data Exchange (ETDEWEB)

    Deparis, Olivier; Rassart, Marie; Vandenbem, Cedric; Welch, Victoria; Vigneron, Jean Pol [Laboratoire de Physique du Solide, University of Namur, 61 rue de Bruxelles, 5000 Namur (Belgium); Lucas, Stephane [Laboratoire d' Analyses par Reactions Nucleaires, University of Namur, 61 rue de Bruxelles, 5000 Namur (Belgium)], E-mail: olivier.deparis@fundp.ac.be

    2008-01-15

    Iridescent surfaces exhibit vivid colours which change with the angle of incidence or viewing due to optical wave interference in the multilayer structure present at the wavelength scale underneath the surface. In nature, one can find examples of iridescent Coleoptera for which the hue changes either greatly or slightly with the angle. Because these species typically make these structures from a single biological material (usually chitin) and air or water as the low refractive index component, they have evolved by adjusting the layer thicknesses in order to display quite different iridescent aspects. Taking inspiration from this proven strategy, we have designed and fabricated periodic TiO{sub 2}/SiO{sub 2} multilayer films in order to demonstrate the concept of structurally tuned iridescent surfaces. Titanium or silicon oxide layers were deposited on a glass substrate using dc reactive or RF magnetron sputtering techniques, respectively. Two structures were designed for which the period and the TiO{sub 2}/SiO{sub 2} layer thickness ratio were varied in such a way that the films displayed radically different iridescent aspects: a reddish-to-greenish changing hue and a stable bluish hue. The fabricated samples were characterized through specular reflectance/transmittance measurements. Modelling of transmittance spectra using standard multilayer film theory confirmed the high quality of the twelve-period Bragg reflectors. The chromaticity coordinates, which were calculated from measured reflectance spectra taken at different angles, were in accordance with theoretical predictions.

  19. Superhydrophobic Behavior on Nano-structured Surfaces

    Science.gov (United States)

    Schaeffer, Daniel

    2008-05-01

    Superhydrophobic behavior is observed in natural occurrences and has been thoroughly studied over the past few years. Water repellant properties on uniform arrays of vertically aligned nano-cones were investigated to determine the highest achievable contact angle (a measure of water drop repellency), which is measured from the reference plane on which the water drop sits to the tangent line of the point at which the drop makes contact with the reference plane. At low aspect ratios (height vs. width of the nano-cones), surface tension pulls the water into the nano-cone array, resulting in a wetted surface. Higher aspect ratios reverse the effect of the surface tension, resulting in a larger contact angle that causes water drops to roll off the surface. Fiber drawing, bundling, and redrawing are used to produce the structured array glass composite surface. Triple-drawn fibers are fused together, annealed, and sliced into thin wafers. The surface of the composite glass is etched to form nano-cones through a differential etching process and then coated with a fluorinated self-assembled monolayer (SAM). Cone aspect ratios can be varied through changes in the chemistry and concentration of the etching acid solution. Superhydrophobic behavior occurs at contact angles >150 and it is predicted and measured that optimal behavior is achieved when the aspect ratio is 4:1, which displays contact angles >=175 .

  20. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein.

    Science.gov (United States)

    Horejs, Christine; Ristl, Robin; Tscheliessnig, Rupert; Sleytr, Uwe B; Pum, Dietmar

    2011-08-05

    Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

  1. Gross Morphological Features of the Organ Surface Primo-Vascular System Revealed by Hemacolor Staining

    Directory of Open Access Journals (Sweden)

    Chae Jeong Lim

    2013-01-01

    Full Text Available The primo-vascular system (PVS, which consists of primo-vessels (PVs and primo-nodes (PNs, is a novel thread-like structure identified in many animal species. Various observational methods have been used to clarify its anatomical properties. Here, we used Hemacolor staining to examine the gross morphology of organ-surface PVS in rats. We observed a sinus structure (20–50 μm with a remarkably low cellularity within PNs and PVs and several lines of ductules (3–5 μm filled with single cells or granules (~1 μm in PV. Both sinuses and ductules were linearly aligned along the longitudinal axis of the PVS. Such morphology of the PVS was further confirmed by acridine orange staining. In PN slices, there was a honeycomb-like structure containing the granules with pentagonal lumens (~10 μm. Both PVs and PNs were densely filled with WBCs, RBCs, and putative mast cells (MCs, which were 90.3%, 5.9%, and 3.8% of the cell population, respectively. Granules in putative MCs showed spontaneous vibrating movements. In conclusion, the results show that Hemacolor, a simple and rapid staining system, can reveal the gross morphological features reported previously. Our findings may help to elucidate the structure and function of the PVS in normal and disease states in future studies.

  2. Advances on surface structural determination by LEED

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Edmar A; De Carvalho, Vagner E [Departamento de Fisica, ICEX, Universidade Federal de Minas Gerais, 31270-090, Belo Horizonte, MG (Brazil); De Castilho, Caio M C, E-mail: edmar@fisica.ufmg.br [Grupo de Fisica de SuperfIcies e Materiais, Instituto de Fisica and Instituto Nacional de Ciencia e Tecnologia em Energia e Ambiente (CIENAM)INCT-E and A, Universidade Federal da Bahia, Campus Universitario da Federacao, 40170-115, Salvador, BA (Brazil)

    2011-08-03

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail. (topical review)

  3. Advances on surface structural determination by LEED.

    Science.gov (United States)

    Soares, Edmar A; de Castilho, Caio M C; de Carvalho, Vagner E

    2011-08-03

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail.

  4. Structured light for focusing surface plasmon polaritons.

    Science.gov (United States)

    Hu, Z J; Tan, P S; Zhu, S W; Yuan, X-C

    2010-05-10

    We propose a structureless method for focusing surface plasmon polaritons (SPPs) on a flat metal film under illumination of radially polarized cogwheel-like structured light beams. Without metal structures, the locally induced SPPs can further be propagated following the predefined patterns to form symmetric focal spots with dimensions beyond diffraction limit. Benefiting from the radial polarization, this method can be employed to pattern various center-symmetric evanescent distributions for generating SPPs reconfigurably. The SPPs will be propagating and focusing in radial directions.

  5. Bacterial cell surface structures in Yersinia enterocolitica.

    Science.gov (United States)

    Białas, Nataniel; Kasperkiewicz, Katarzyna; Radziejewska-Lebrecht, Joanna; Skurnik, Mikael

    2012-06-01

    Yersinia enterocolitica is a widespread member of the family of Enterobacteriaceae that contains both non-virulent and virulent isolates. Pathogenic Y. enterocolitica strains, especially belonging to serotypes O:3, O:5,27, O:8 and O:9 are etiologic agents of yersiniosis in animals and humans. Y. enterocolitica cell surface structures that play a significant role in virulence have been subject to many investigations. These include outer membrane (OM) glycolipids such as lipopolysaccharide (LPS) and enterobacterial common antigen (ECA) and several cell surface adhesion proteins present only in virulent Y. enterocolitica, i.e., Inv, YadA and Ail. While the yadA gene is located on the Yersinia virulence plasmid the Ail, Inv, LPS and ECA are chromosomally encoded. These structures ensure the correct architecture of the OM, provide adhesive properties as well as resistance to antimicrobial peptides and to host innate immune response mechanisms.

  6. Single crystal surface structure by bragg scattering

    DEFF Research Database (Denmark)

    Nielsen, Mogens

    1985-01-01

    X-ray diffraction is becoming an important tool in the measurements of surface structures. Single crystalline samples are used as in Low Energy Electron Diffraction (LEED)-studies. The X-ray technique is somewhat more involved due to the need of bright, collimated photon sources, in general...... synchrotron X-rays, and of very accurate angular settings in the ultrahigh-vacuum environment of the sample. We present the technique and discuss examples of experimental results....

  7. Structural information revealed by the dispersion of ADC with frequency.

    Science.gov (United States)

    Li, Hua; Jiang, Xiaoyu; Wang, Feng; Xu, Junzhong; Gore, John C

    2015-11-01

    Diffusion MRI provides a non-invasive means to characterize tissue microstructure at varying length scales. Temporal diffusion spectra reveal how the apparent diffusion coefficient (ADC) varies with frequency. When measured using oscillating gradient spin echo sequences, the manner in which ADC disperses with gradient frequency (which is related to the reciprocal of diffusion time) provides information on the characteristic dimensions of restricting structures within the medium. For example, the dispersion of ADC with oscillating gradient frequency (ΔfADC) has been shown to correlate with axon sizes in white matter and provide novel tissue contrast in images of mouse hippocampus and cerebellum. However, despite increasing interest in applying frequency-dependent ADC to derive novel information on tissue, the interpretations of ADC spectra are not always clear. In this study, the relation between ADC spectra and restricting dimensions are further elucidated and used to derive novel image contrast related to the sizes of intrinsic microstructures.

  8. Revealing alteration of membrane structures during ischema using impedance spectroscopy

    Directory of Open Access Journals (Sweden)

    Mihaela Gheorghiu

    2002-11-01

    Full Text Available Alterations of membrane structure and function are essential characteristics of cells undergoing ischemia. Noninvasive monitoring of tissue alterations during ischemia and the estimation of the reversibility domain (corresponding to organ capability to fully recover its functions after shifting back to normal blood perfusion are important for biomedical applications allowing better time management during surgical interventions, especially in organ transplantation. Due to it’s capability to reveal inhomogeneities, as well as it’s noninvasive character, impedance spectroscopy was used for continuous monitoring of the progression of excised tissue samples during ischemia. We have developed a fast, noninvasive, automated method for quantitative analysis of impedance spectra of tissue samples, capable of revealing, through characteristic parameters (dispersion amplitudes, time constants and distribution parameters membrane based microscopic processes like the closure ofgap-junctions (a characteristic of the early alterations of ischemic tissues in the reversibility phase. Microscopic and equivalent circuit modeling was used to probe the effect of closure of cell connections and of changes in electrical properties of cell constituents on impedance spectra. We have developed a normalizing procedure emphasizing the pattern of ischemic alterations and enabling the comparison of different data sets.

  9. Random field model reveals structure of the protein recombinational landscape.

    Directory of Open Access Journals (Sweden)

    Philip A Romero

    Full Text Available We are interested in how intragenic recombination contributes to the evolution of proteins and how this mechanism complements and enhances the diversity generated by random mutation. Experiments have revealed that proteins are highly tolerant to recombination with homologous sequences (mutation by recombination is conservative; more surprisingly, they have also shown that homologous sequence fragments make largely additive contributions to biophysical properties such as stability. Here, we develop a random field model to describe the statistical features of the subset of protein space accessible by recombination, which we refer to as the recombinational landscape. This model shows quantitative agreement with experimental results compiled from eight libraries of proteins that were generated by recombining gene fragments from homologous proteins. The model reveals a recombinational landscape that is highly enriched in functional sequences, with properties dominated by a large-scale additive structure. It also quantifies the relative contributions of parent sequence identity, crossover locations, and protein fold to the tolerance of proteins to recombination. Intragenic recombination explores a unique subset of sequence space that promotes rapid molecular diversification and functional adaptation.

  10. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  11. Architectural Surfaces and Structures from Circular Arcs

    KAUST Repository

    Shi, Ling

    2013-12-01

    In recent decades, the popularity of freeform shapes in contemporary architecture poses new challenges to digital design. One of them is the process of rationalization, i.e. to make freeform skins or structures affordable to manufacture, which draws the most attention from geometry researchers. In this thesis, we aim to realize this process with simple geometric primitives, circular arcs. We investigate architectural surfaces and structures consisting of circular arcs. Our focus is lying on how to employ them nicely and repetitively in architectural design, in order to decrease the cost in manufacturing. Firstly, we study Darboux cyclides, which are algebraic surfaces of order ≤ 4. We provide a computational tool to identify all families of circles on a given cyclide based on the spherical model of M ̈obius geometry. Practical ways to design cyclide patches that pass through certain inputs are presented. In particular, certain triples of circle families on Darboux cyclides may be suitably arranged as 3-webs. We provide a complete classification of all possible 3-webs of circles on Darboux cyclides. We then investigate the circular arc snakes, which are smooth sequences of circu- lar arcs. We evolve the snakes such that their curvature, as a function of arc length, remains unchanged. The evolution of snakes is utilized to approximate given surfaces by circular arcs or to generated freeform shapes, and it is realized by a 2-step pro- cess. More interestingly, certain 6-arc snake with boundary constraints can produce a smooth self motion, which can be employed to build flexible structures. Another challenging topic is approximating smooth freeform skins with simple panels. We contribute to this problem area by approximating a negatively-curved 5 surface with a smooth union of rational bilinear patches. We provide a proof for vertex consistency of hyperbolic nets using the CAGD approach of the rational B ́ezier form. Moreover, we use Darboux transformations for the

  12. Neisserial surface lipoproteins: structure, function and biogenesis.

    Science.gov (United States)

    Hooda, Yogesh; Shin, Hyejin E; Bateman, Thomas J; Moraes, Trevor F

    2017-03-01

    The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of the bacterial stress response. The focus of this review is on the SLPs present in Neisseria, a genus of bacteria that colonise the mucosal surfaces of animals. Neisseria contains two pathogens of medical interest, namely Neisseria meningitidis and N. gonorrhoeae. Several SLPs have been identified in Neisseria and their study has elucidated key strategies used by these pathogens to survive inside the human body. Herein, we focus on the identification, structure and function of SLPs that have been identified in Neisseria. We also survey the translocation pathways used by these SLPs to reach the cell surface. Specifically, we elaborate on the strategies used by neisserial SLPs to translocate across the outer membrane with an emphasis on Slam, a novel outer membrane protein that has been implicated in SLP biogenesis. Taken together, the study of SLPs in Neisseria illustrates the widespread roles played by this family of proteins in Gram-negative bacteria. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Electronic Structure and Catalysis on Metal Surfaces

    Science.gov (United States)

    Greeley, Jeff; Norskov, Jens K.; Mavrikakis, Manos

    2002-10-01

    The powerful computational resources available to scientists today, together with recent improvements in electronic structure calculation algorithms, are providing important new tools for researchers in the fields of surface science and catalysis. In this review, we discuss first principles calculations that are now capable of providing qualitative and, in many cases, quantitative insights into surface chemistry. The calculations can aid in the establishment of chemisorption trends across the transition metals, in the characterization of reaction pathways on individual metals, and in the design of novel catalysts. First principles studies provide an excellent fundamental complement to experimental investigations of the above phenomena and can often allow the elucidation of important mechanistic details that would be difficult, if not impossible, to determine from experiments alone.

  14. Structure and thermodynamics of surface recognition

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Interactions of the surface glycoprotein, gp120, with the receptors of host cells define the pathogenesis of HIV-1, the virus that causes AIDS. gp120 is made of several disulfide-bridged loops--the amino acid sequences of some of these loops are fairly conserved whereas the rest are variable. The third variable (V3) loop has been the target of vaccine design for quite some time since this loop is involved in various steps of viral pathogenesis. However, this loop also happens to be the most variable one. The authors have carried out structural and immunological studies to determine the sequence-structure-antigenicity correlations of the HIV-1 V3 loops. This resulted in the identification of a secondary structure at the tip of the V3 loop that remains invariant in spite of the sequence variation. The authors designed a multi-valent V3-based antigen that presents multiple copies of the same tip element several times in the same structure. During the course of this project, they realized that the protective epitopes of gp120 should be judged in the context of the native structure. Therefore, the authors developed a method to obtain a model of gp120 that is consistent with all the immunology and virology data. This model is useful in choosing or designing gp120 subdomains for vaccine development.

  15. The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens

    Energy Technology Data Exchange (ETDEWEB)

    Geisbrecht, B V; Hamaoka, B Y; Perman, B; Zemla, A; Leahy, D J

    2005-10-14

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  16. APPLICATIONS OF SURFACE SPLINEFUNCTIONS TO STRUCTURAL ANALYSIS IN COAL GEOLOGY

    Institute of Scientific and Technical Information of China (English)

    HanJinyan; YuZhiwei

    1996-01-01

    A surface spline function is used to fit a coal seam surface in structural analysis in coal geology. From the surface spline function, the first and second partial derivatives can also be derived and used to structural analysis, especially for recognition of the concealed structures. The detection of structures related to faulting is emphasized.

  17. Nanoscale surface topographies for structural colors

    DEFF Research Database (Denmark)

    Clausen, Jeppe Sandvik

    The thesis describes and demonstrates the possibilities for utilization of structural colors in mass fabricated plastic products as replacement for or in combination with pigments and inks. The motivation is the possible advantages related to re-cycling and re-use of plastic by limiting the number...... of materials in a given plastic part. Also, the reduction of process steps and materials leads to a reduction of the fabrication costs. In the thesis only surfaces, which may be fabricated using replication based methods, such as injection molding, are considered. Nanostructures with sizes comparable......-polymer interface is suppressed. This improves the ability to see through a clear plastic in the presence of specular reflection. The tapered nanostructures are also utilized to enhance the chroma of pigmented polymers. Larger tapered structures fabricated in a similar manor are shown to work as color filters...

  18. Fine-scaled human genetic structure revealed by SNP microarrays.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

    2009-05-01

    We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

  19. Statistical universals reveal the structures and functions of human music.

    Science.gov (United States)

    Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

    2015-07-21

    Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.

  20. Revealing structural effects: electrochemical reactions of butanols on platinum.

    Science.gov (United States)

    Rodríguez, José L; Souto, Ricardo M; Fernández-Mérida, Luis; Pastor, Elena

    2002-05-01

    Spectroelectrochemical studies on the reactivity of butanol isomers on Pt electrodes in perchloric acid medium led to the observation of structural effects that result from the different arrangements of atoms in the organic molecules. The use of differential electrochemical mass spectrometry (DEMS) to detect volatile products showed that all four isomers react on the electrode, though different product yields were observed for each compound. In spite of the differences in the electrochemical behaviour of the butanol isomers, a series of general processes accounts for the results obtained. The formation of strongly adsorbed residues by a dehydration process leading to the formation of a C=C bond was proposed for all isomers. Electroreduction of the adsorbates produces C(4) and C(3) alkanes, and the latter reveal the existence of a fragmentation process. The C(4) hydrocarbons can be formed by hydrogenation of these residues and by hydrogenolysis of alcohol molecules in the bulk solution which react at the electrode with adsorbed hydrogen. On the other hand, CO(2) is formed during electrooxidation of the adsorbed species. Partial-oxidation products containing a carbonyl group were detected from 0.2 M solutions of 1-butanol, isobutyl alcohol and sec-butyl alcohol. The tertiary alcohol tert-butyl alcohol only reacts in its adsorbed state.

  1. Learning surface molecular structures via machine vision

    Science.gov (United States)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  2. Structure and Evolution of the Lunar Procellarum Region as Revealed by GRAIL Gravity Data

    Science.gov (United States)

    Andrews-Hanna, Jeffrey C.; Besserer, Jonathan; Head, James W., III; Howett, Carly J. A.; Kiefer, Walter S.; Lucey, Paul J.; McGovern, Patrick J.; Melosh, H. Jay; Neumann, Gregory A.; Phillips, Roger J.; Schenk, Paul M.; Smith, David E.; Solomon, Sean C.; Zuber, Maria T.

    2014-01-01

    The Procellarum region is a broad area on the nearside of the Moon that is characterized by low elevations, thin crust, and high surface concentrations of the heat-producing elements uranium, thorium, and potassium. The Procellarum region has been interpreted as an ancient impact basin approximately 3200 km in diameter, though supporting evidence at the surface would have been largely obscured as a result of the great antiquity and poor preservation of any diagnostic features. Here we use data from the Gravity Recovery and Interior Laboratory (GRAIL) mission to examine the subsurface structure of Procellarum. The Bouguer gravity anomalies and gravity gradients reveal a pattern of narrow linear anomalies that border the Procellarum region and are interpreted to be the frozen remnants of lava-filled rifts and the underlying feeder dikes that served as the magma plumbing system for much of the nearside mare volcanism. The discontinuous surface structures that were earlier interpreted as remnants of an impact basin rim are shown in GRAIL data to be a part of this continuous set of quasi-rectangular border structures with angular intersections, contrary to the expected circular or elliptical shape of an impact basin. The spatial pattern of magmatic-tectonic structures bounding Procellarum is consistent with their formation in response to thermal stresses produced by the differential cooling of the province relative to its surroundings, coupled with magmatic activity driven by the elevated heat flux in the region.

  3. Design of a lunar surface structure

    Science.gov (United States)

    Mottaghi, Sohrob

    The next step for manned exploration and settlement is a return to the Moon. In such a return, the most challenging task is the construction of structures for habitation, considering the Moon's hostile environment. Therefore the question is: What is the best way to erect habitable structures on the lunar surface? Given the cost associated with bringing material to the Moon, In-Situ Resource Utilization (ISRU) is viewed by most as the basis for a successful manned exploration and settlement of the Solar system. Along these lines, we propose an advanced concept where the use of freeform fabrication technologies by autonomous mini-robots can form the basis for habitable lunar structures. Also, locally-available magnesium is proposed as the structural material. While it is one of the most pervasive metals in the regolith, magnesium has been only suggested only briefly as a viable option in the past. Therefore, a study has been conducted on magnesium and its alloys, taking into account the availability of the alloying elements on the Moon. An igloo-shaped magnesium structure, covered by sandbags of regolith shielding and supported on a sintered regolith foundation, is considered as a potential design of a lunar base, as well as the test bed for the proposed vision. Three studies are carried out: First a static analysis is conducted which proves the feasibility of the proposed material and method. Second, a thermal analysis is carried out to study the effect of the regolith shielding as well as the sensitivity of such designs to measurement uncertainties of regolith and sintered thermal properties. The lunar thermal environment is modeled for a potential site at 88º latitude in the lunar South Pole Region. Our analysis shows that the uncertainties are in an acceptable range where a three-meter thick shield is considered. Also, the required capacity of a thermal rejection system is estimated, choosing the thermal loads to be those of the Space Station modules. In the

  4. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Science.gov (United States)

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  5. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Directory of Open Access Journals (Sweden)

    Bénédicte Coupat-Goutaland

    Full Text Available Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM. Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis. They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  6. Femtosecond laser surface structuring technique for making human enamel and dentin surfaces superwetting

    Science.gov (United States)

    Vorobyev, A. Y.; Guo, Chunlei

    2013-12-01

    It is known that good wettability of enamel and dentin surfaces is a key factor in enhancing adhesion of restorative materials in dentistry. Here, we report on a femtosecond laser surface texturing approach that makes both the enamel and dentine surfaces superwetting. In contrast to the traditional chemical etching that yields random surface structures, this new approach produces engineered surface structures. The surface structure engineered and tested here is an array of femtosecond laser-produced parallel microgrooves that generates a strong capillary force. Due to the powerful capillary action, water is rapidly sucked into this engineered surface structure and spreads even on a vertical surface.

  7. Structure of the airflow above surface waves

    Science.gov (United States)

    Buckley, Marc; Veron, Fabrice

    2016-04-01

    Weather, climate and upper ocean patterns are controlled by the exchanges of momentum, heat, mass, and energy across the ocean surface. These fluxes are, in turn, influenced by the small-scale physics at the wavy air-sea interface. We present laboratory measurements of the fine-scale airflow structure above waves, achieved in over 15 different wind-wave conditions, with wave ages Cp/u* ranging from 1.4 to 66.7 (where Cp is the peak phase speed of the waves, and u* the air friction velocity). The experiments were performed in the large (42-m long) wind-wave-current tank at University of Delaware's Air-Sea Interaction laboratory (USA). A combined Particle Image Velocimetry and Laser Induced Fluorescence system was specifically developed for this study, and provided two-dimensional airflow velocity measurement as low as 100 um above the air-water interface. Starting at very low wind speeds (U10~2m/s), we directly observe coherent turbulent structures within the buffer and logarithmic layers of the airflow above the air-water interface, whereby low horizontal velocity air is ejected away from the surface, and higher velocity fluid is swept downward. Wave phase coherent quadrant analysis shows that such turbulent momentum flux events are wave-phase dependent. Airflow separation events are directly observed over young wind waves (Cp/u*wind waves (Cp/u*=3.7). Over slightly older wind waves (Cp/u* = 6.5), the measured wave-induced airflow perturbations are qualitatively consistent with linear critical layer theory.

  8. Thermal Tomography of Asteroid Surface Structure

    CERN Document Server

    Harris, Alan

    2016-01-01

    Knowledge of the surface thermal inertia of an asteroid can provide insight into surface structure: porous material has a lower thermal inertia than rock. We develop a means to estimate thermal inertia values of asteroids and use it to show that thermal inertia appears to increase with spin period in the case of main-belt asteroids (MBAs). Similar behavior is found on the basis of thermophysical modeling for near-Earth objects (NEOs). We interpret our results in terms of rapidly increasing material density and thermal conductivity with depth, and provide evidence that thermal inertia increases by factors of 10 (MBAs) to 20 (NEOs) within a depth of just 10 cm. Our results are consistent with a very general picture of rapidly changing material properties in the topmost regolith layers of asteroids and have important implications for calculations of the Yarkovsky effect, including its perturbation of the orbits of potentially hazardous objects and those of asteroid family members after the break-up event. Eviden...

  9. Protein-mediated surface structuring in biomembranes

    Directory of Open Access Journals (Sweden)

    Maggio B.

    2005-01-01

    Full Text Available The lipids and proteins of biomembranes exhibit highly dissimilar conformations, geometrical shapes, amphipathicity, and thermodynamic properties which constrain their two-dimensional molecular packing, electrostatics, and interaction preferences. This causes inevitable development of large local tensions that frequently relax into phase or compositional immiscibility along lateral and transverse planes of the membrane. On the other hand, these effects constitute the very codes that mediate molecular and structural changes determining and controlling the possibilities for enzymatic activity, apposition and recombination in biomembranes. The presence of proteins constitutes a major perturbing factor for the membrane sculpturing both in terms of its surface topography and dynamics. We will focus on some results from our group within this context and summarize some recent evidence for the active involvement of extrinsic (myelin basic protein, integral (Folch-Lees proteolipid protein and amphitropic (c-Fos and c-Jun proteins, as well as a membrane-active amphitropic phosphohydrolytic enzyme (neutral sphingomyelinase, in the process of lateral segregation and dynamics of phase domains, sculpturing of the surface topography, and the bi-directional modulation of the membrane biochemical reactivity.

  10. Thermal Tomography of Asteroid Surface Structure

    Science.gov (United States)

    Harris, Alan W.; Drube, Line

    2016-12-01

    Knowledge of the surface thermal inertia of an asteroid can provide insight into its surface structure: porous material has a lower thermal inertia than rock. We develop a means to estimate thermal inertia values of asteroids and use it to show that thermal inertia appears to increase with spin period in the case of main-belt asteroids (MBAs). Similar behavior is found on the basis of thermophysical modeling for near-Earth objects (NEOs). We interpret our results in terms of rapidly increasing material density and thermal conductivity with depth, and provide evidence that thermal inertia increases by factors of 10 (MBAs) to 20 (NEOs) within a depth of just 10 cm. Our results are consistent with a very general picture of rapidly changing material properties in the topmost regolith layers of asteroids and have important implications for calculations of the Yarkovsky effect, including its perturbation of the orbits of potentially hazardous objects and those of asteroid family members after the break-up event. Evidence of a rapid increase of thermal inertia with depth is also an important result for studies of the ejecta-enhanced momentum transfer of impacting vehicles (“kinetic impactors”) in planetary defense.

  11. Photoelectron spectroscopy bulk and surface electronic structures

    CERN Document Server

    Suga, Shigemasa

    2014-01-01

    Photoelectron spectroscopy is now becoming more and more required to investigate electronic structures of various solid materials in the bulk, on surfaces as well as at buried interfaces. The energy resolution was much improved in the last decade down to 1 meV in the low photon energy region. Now this technique is available from a few eV up to 10 keV by use of lasers, electron cyclotron resonance lamps in addition to synchrotron radiation and X-ray tubes. High resolution angle resolved photoelectron spectroscopy (ARPES) is now widely applied to band mapping of materials. It attracts a wide attention from both fundamental science and material engineering. Studies of the dynamics of excited states are feasible by time of flight spectroscopy with fully utilizing the pulse structures of synchrotron radiation as well as lasers including the free electron lasers (FEL). Spin resolved studies also made dramatic progress by using higher efficiency spin detectors and two dimensional spin detectors. Polarization depend...

  12. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities

    Energy Technology Data Exchange (ETDEWEB)

    Chitnumsub, Penchit, E-mail: penchit@biotec.or.th; Ittarat, Wanwipa; Jaruwat, Aritsara; Noytanom, Krittikar [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Amornwatcharapong, Watcharee [Mahidol University, Bangkok (Thailand); Pornthanakasem, Wichai [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Chaiyen, Pimchai [Mahidol University, Bangkok (Thailand); Yuthavong, Yongyuth; Leartsakulpanich, Ubolsree, E-mail: penchit@biotec.or.th [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand)

    2014-06-01

    The crystal structure of P. falciparum SHMT revealed snapshots of an intriguing disulfide/sulfhydryl switch controlling the functional activity. Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.

  13. Upper crustal structure of Madeira Island revealed from ambient noise tomography

    Science.gov (United States)

    Matos, Catarina; Silveira, Graça; Matias, Luís; Caldeira, Rita; Ribeiro, M. Luísa; Dias, Nuno A.; Krüger, Frank; Bento dos Santos, Telmo

    2015-06-01

    We present the first image of the Madeira upper crustal structure, using ambient seismic noise tomography. 16 months of ambient noise, recorded in a dense network of 26 seismometers deployed across Madeira, allowed reconstructing Rayleigh wave Green's functions between receivers. Dispersion analysis was performed in the short period band from 1.0 to 4.0 s. Group velocity measurements were regionalized to obtain 2D tomographic images, with a lateral resolution of 2.0 km in central Madeira. Afterwards, the dispersion curves, extracted from each cell of the 2D group velocity maps, were inverted as a function of depth to obtain a 3D shear wave velocity model of the upper crust, from the surface to a depth of 2.0 km. The obtained 3D velocity model reveals features throughout the island that correlates well with surface geology and island evolution.

  14. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

    Science.gov (United States)

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.

  15. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs

    DEFF Research Database (Denmark)

    Edmondson, Jill L; Stott, Iain; Davies, Zoe G

    2016-01-01

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface...... in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce...... the adverse impacts of urbanization on microclimate, soil processes and human health....

  16. [Function of surface membrane structures in Thiobacillus thiooxidans].

    Science.gov (United States)

    Pivovarova, T A; Karavaĭko, G I

    1975-01-01

    The function of the surface membrane structures was studied with cytochemical techniques on ultrathin sections of Thiobacillus thiooxidans. The transport of elementary sulphur inside the cell involves the surface membrane structures, while oxidation of the sulphur to sulphuric acid takes place on the outer surface of the cytoplasmic membrane. The surface membrane structures are supposed also to participate in the primary dissolution of elementary sulphur at the site of contact of the cells with the mineral.

  17. Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features.

    Directory of Open Access Journals (Sweden)

    Manidip Shasmal

    Full Text Available Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria.

  18. Microwetting of Supported Graphene on Hydrophobic Surfaces Revealed by Polymerized Interfacial Femtodroplets

    NARCIS (Netherlands)

    Peng, Shuhua; Lohse, Detlef; Zhang, Xuehua

    2014-01-01

    Understanding the wettability of graphene is the crucial step toward the design and control of graphene-based surface in contact with liquids. In this work, the static microwettability of a supported single layer graphene (SLG) immersed in water or alcoholic aqueous solutions is revealed by the

  19. Microwetting of Supported Graphene on Hydrophobic Surfaces Revealed by Polymerized Interfacial Femtodroplets

    NARCIS (Netherlands)

    Peng, Shuhua; Lohse, Detlef; Zhang, Xuehua

    2014-01-01

    Understanding the wettability of graphene is the crucial step toward the design and control of graphene-based surface in contact with liquids. In this work, the static microwettability of a supported single layer graphene (SLG) immersed in water or alcoholic aqueous solutions is revealed by the morp

  20. Mechanically robust superhydrophobicity on hierarchically structured Si surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Xiu Yonghao; Hess, Dennis W [School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0100 (United States); Liu Yan; Wong, C P, E-mail: dennis.hess@chbe.gatech.edu, E-mail: cp.wong@mse.gatech.edu [School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Drive, Atlanta, GA 30332-0245 (United States)

    2010-04-16

    Improvement of the robustness of superhydrophobic surfaces is critical in order to achieve commercial applications of these surfaces in such diverse areas as self-cleaning, water repellency and corrosion resistance. In this study, the mechanical robustness of superhydrophobic surfaces was evaluated on hierarchically structured silicon surfaces. The effect of two-scale hierarchical structures on robustness was investigated using an abrasion test and the results compared to those of superhydrophobic surfaces fabricated from polymeric materials and from silicon that contains only nanostructures. Unlike the polymeric and nanostructure-only surfaces, the hierarchical structures retained superhydrophobic behavior after mechanical abrasion.

  1. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting.

    Directory of Open Access Journals (Sweden)

    Md Imtaiyaz Hassan

    Full Text Available Human β-glucuronidase (GUS cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII. Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene.

  2. On the structure of Si(100) surface

    DEFF Research Database (Denmark)

    Back, Seoin; Schmidt, Johan Albrecht; Ji, Hyunjun;

    2013-01-01

    We revisit a dangling theoretical question of whether the surface reconstruction of the Si(100) surface would energetically favor the symmetric or buckled dimers on the intrinsic potential energy surfaces at 0 K. This seemingly simple question is still unanswered definitively since all existing...

  3. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  4. Phylogenetic clusters of rhizobia revealed by genome structures

    Institute of Scientific and Technical Information of China (English)

    ZHENG Junfang; LIU Guirong; ZHU Wanfu; ZHOU Yuguang; LIU Shulin

    2004-01-01

    Rhizobia, bacteria that fix atmospheric nitrogen, are important agricultural resources. In order to establish the evolutionary relationships among rhizobia isolated from different geographic regions and different plant hosts for systematic studies, we evaluated the use of physical structure of the rhizobial genomes as a phylogenetic marker to categorize these bacteria. In this work, we analyzed the features of genome structures of 64 rhizobial strains. These rhizobial strains were divided into 21 phylogenetic clusters according to the features of genome structures evaluated by the endonuclease I-CeuI. These clusters were supported by 16S rRNA comparisons and genomic sequences of four rhizobial strains, but they are largely different from those based on the current taxonomic scheme (except 16S rRNA).

  5. Real-Time Visualization of Platelet Interaction With Micro Structured Surfaces.

    Science.gov (United States)

    Gester, Kathrin; Birtel, Stephan; Clauser, Johanna; Steinseifer, Ulrich; Sonntag, Simon Johannes

    2016-02-01

    Improving the hemocompatibility of artificial implants by micro structuring their surfaces has shown promising results, but the mechanisms which lead to this improvement are not yet understood. Therefore, we built a test setup for real-time visualization of platelet interaction with a plain and two micro structured surfaces. The micro structures, defined by the distance of the plain surface area between the structures, were chosen to be 3 and 30 μm, representing a positive and a negative effect on the hemocompatibility. The main part of the test setup was a flow chamber containing films of low density polyethylene (LDPE) with the differently structured surfaces. For different wall shear stresses, no considerable differences were observed in the platelet-surface interaction for all surface types. Whereas, major differences in flow behavior were observed when comparing the surfaces to each other. The platelets "rolled" along the smooth surface, being in constant contact with the surface material. Although the platelets "rolled" over the surface with small structures as well, they were only in contact with the tips of the structure and therefore had less surface contact with the foreign material. The increased distance and height of the structures of the last surface led to a trapping of platelets between the structures. This resulted in a longer contact time with the foreign material as well as a larger contact area, which both increase the risk of platelet activation, adhesion, and finally clotting. Our results showed the mechanisms which lead to these effects and thus revealed why micro structuring of surfaces impacts the hemocompatibility. Furthermore, we established a test setup which can be used for future investigations on the platelet-structure interactions.

  6. Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT*

    Science.gov (United States)

    Kemble, David J.; Whitby, Frank G.; Robinson, Howard; McCullough, Laura L.; Formosa, Tim; Hill, Christopher P.

    2013-01-01

    The histone chaperone FACT is an essential and abundant heterodimer found in all eukaryotes. Here we report a crystal structure of the middle domain of the large subunit of FACT (Spt16-M) to reveal a double pleckstrin homology architecture. This structure was found previously in the Pob3-M domain of the small subunit of FACT and in the related histone chaperone Rtt106, although Spt16-M is distinguished from these structures by the presence of an extended α-helix and a C-terminal addition. Consistent with our finding that the double pleckstrin homology structure is common to these three histone chaperones and reports that Pob3 and Rtt106 double pleckstrin homology domains bind histones H3-H4, we also find that Spt16-M binds H3-H4 with low micromolar affinity. Our structure provides a framework for interpreting a large body of genetic data regarding the physiological functions of FACT, including the identification of potential interaction surfaces for binding histones or other proteins. PMID:23417676

  7. Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges

    Science.gov (United States)

    Min, Hye Jung; Yun, Hyosuk; Ji, Sehyeon; Rajasekaran, Ganesan; Kim, Jae Il; Kim, Jeong-Sun; Shin, Song Yub; Lee, Chul Won

    2017-01-01

    Defensin peptides are essential for innate immunity in humans and other living systems, as they provide protection against infectious pathogens and regulate the immune response. Here, we report the solution structure of rattusin (RTSN), an α-defensin-related peptide, which revealed a novel C2-symmetric disulfide-linked dimeric structure. RTSN was synthesized by solid-phase peptide synthesis (SPPS) and refolded by air oxidation in vitro. Dimerization of the refolded RTSN (r-RTSN) resulted from five intermolecular disulfide (SS) bond exchanges formed by ten cysteines within two protomer chains. The SS bond pairings of r-RTSN were determined by mass analysis of peptide fragments cleaved by trypsin digestion. In addition to mass analysis, nuclear magnetic resonance (NMR) experiments for a C15S mutant and r-RTSN confirmed that the intermolecular SS bond structure of r-RTSN showed an I-V’, II-IV’, III-III’, IV-II’, V-I’ arrangement. The overall structure of r-RTSN exhibited a cylindrical array, similar to that of β-sandwich folds, with a highly basic surface. Furthermore, fluorescence spectroscopy results suggest that r-RTSN exerts bactericidal activity by damaging membrane integrity. Collectively, these results provide a novel structural scaffold for designing highly potent peptide-based antibiotics suitable for use under various physiological conditions. PMID:28345637

  8. Surface molecular aggregation structure and surface physicochemical properties of poly(fluoroalkyl acrylate) thin films

    Science.gov (United States)

    Honda, K.; Yamaguchi, H.; Kobayashi, M.; Morita, M.; Takahara, A.

    2008-03-01

    Effect of side chain length on the molecular aggregation states and surface properties of poly(fluoroalkyl acrylate)s [PFA-Cy, where y is fluoromethylene number in Rf group] thin films were systematically investigated. Spin-coated PFA-Cy thin films were characterized by static and dynamic contact angle measurements, X-ray photoelectron spectroscopy (XPS), and grazing- incidence X-ray diffraction (GIXD). The receding contact angles showed small values for PFA-Cy with short side chain (y=8. GIXD revealed that fluoroalkyl side chain of PFA-Cy with y>=8 was crystallized and formed ordered structures at the surface region as well as bulk one. These results suggest that water repellent mechanism of PFA-Cy can be attributed to the presence of highly ordered fluoroalkyl side chains at the outermost surfaces. The results of XPS in the dry and hydrated states and contact angle measurement in water support the mechanism of lowering contact angle for water by exposure of carbonyl group to the water interface through reorientation of short fluoroalkyl chains. The surface nanotextured PFA-C8 through imprinting of anodic aluminum oxide mold showed extremely high hydrophobicity as well as high oleophobicity.

  9. Surface molecular aggregation structure and surface physicochemical properties of poly(fluoroalkyl acrylate) thin films

    Energy Technology Data Exchange (ETDEWEB)

    Honda, K; Yamaguchi, H; Takahara, A [Graduate School of Engineering, Kyushu University, Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan); Kobayashi, M [Institute for Materials Chemistry and Engineering, Kyushu University, Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan); Morita, M [Fundamental Research Department, Chemical Division, Daikin Industries, Ltd., 1-1 Nishi Hitotsuya, Settsu-shi, Osaka 566-8585 (Japan)], E-mail: takahara@cstf.kyushu-u.ac.jp

    2008-03-15

    Effect of side chain length on the molecular aggregation states and surface properties of poly(fluoroalkyl acrylate)s [PFA-C{sub y}, where y is fluoromethylene number in R{sub f} group] thin films were systematically investigated. Spin-coated PFA-C{sub y} thin films were characterized by static and dynamic contact angle measurements, X-ray photoelectron spectroscopy (XPS), and grazing- incidence X-ray diffraction (GIXD). The receding contact angles showed small values for PFA-C{sub y} with short side chain (y{<=}6) and increased above y{>=}8. GIXD revealed that fluoroalkyl side chain of PFA-C{sub y} with y{>=}8 was crystallized and formed ordered structures at the surface region as well as bulk one. These results suggest that water repellent mechanism of PFA-C{sub y} can be attributed to the presence of highly ordered fluoroalkyl side chains at the outermost surfaces. The results of XPS in the dry and hydrated states and contact angle measurement in water support the mechanism of lowering contact angle for water by exposure of carbonyl group to the water interface through reorientation of short fluoroalkyl chains. The surface nanotextured PFA-C{sub 8} through imprinting of anodic aluminum oxide mold showed extremely high hydrophobicity as well as high oleophobicity.

  10. Polymer surface functionalities that control human embryoid body cell adhesion revealed by high throughput surface characterization of combinatorial material microarrays.

    Science.gov (United States)

    Yang, Jing; Mei, Ying; Hook, Andrew L; Taylor, Michael; Urquhart, Andrew J; Bogatyrev, Said R; Langer, Robert; Anderson, Daniel G; Davies, Martyn C; Alexander, Morgan R

    2010-12-01

    High throughput materials discovery using combinatorial polymer microarrays to screen for new biomaterials with new and improved function is established as a powerful strategy. Here we combine this screening approach with high throughput surface characterization (HT-SC) to identify surface structure-function relationships. We explore how this combination can help to identify surface chemical moieties that control protein adsorption and subsequent cellular response. The adhesion of human embryoid body (hEB) cells to a large number (496) of different acrylate polymers synthesized in a microarray format is screened using a high throughput procedure. To determine the role of the polymer surface properties on hEB cell adhesion, detailed HT-SC of these acrylate polymers is carried out using time of flight secondary ion mass spectrometry (ToF SIMS), X-ray photoelectron spectroscopy (XPS), pico litre drop sessile water contact angle (WCA) measurement and atomic force microscopy (AFM). A structure-function relationship is identified between the ToF SIMS analysis of the surface chemistry after a fibronectin (Fn) pre-conditioning step and the cell adhesion to each spot using the multivariate analysis technique partial least squares (PLS) regression. Secondary ions indicative of the adsorbed Fn correlate with increased cell adhesion whereas glycol and other functionalities from the polymers are identified that reduce cell adhesion. Furthermore, a strong relationship between the ToF SIMS spectra of bare polymers and the cell adhesion to each spot is identified using PLS regression. This identifies a role for both the surface chemistry of the bare polymer and the pre-adsorbed Fn, as-represented in the ToF SIMS spectra, in controlling cellular adhesion. In contrast, no relationship is found between cell adhesion and wettability, surface roughness, elemental or functional surface composition. The correlation between ToF SIMS data of the surfaces and the cell adhesion demonstrates

  11. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.

    Science.gov (United States)

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-03-11

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

  12. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga*

    Science.gov (United States)

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-01-01

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ′, a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ′ subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ′ were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII. PMID:26757821

  13. The structural basis of non-photochemical quenching is revealed?

    Science.gov (United States)

    Cogdell, Richard J

    2006-02-01

    Light-harvesting complex II (LHCII, the major plant light-harvesting pigment-protein complex, efficiently harvests light-energy. However, if the incident light intensity is too high and photosynthesis becomes saturated, LHCII can switch into a quenching state that prevents photodamage. This important process is called non-photochemical quenching, or NPQ, and represents feedback control. Andrew Pascal et al. have recently proposed a detailed model of NPQ based upon the crystal structure of LHCII from spinach.

  14. Cellular structural biology as revealed by cryo-electron tomography.

    Science.gov (United States)

    Irobalieva, Rossitza N; Martins, Bruno; Medalia, Ohad

    2016-02-01

    Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology. © 2016. Published by The Company of Biologists Ltd.

  15. Multiscale structure of time series revealed by the monotony spectrum.

    Science.gov (United States)

    Vamoş, Călin

    2017-03-01

    Observation of complex systems produces time series with specific dynamics at different time scales. The majority of the existing numerical methods for multiscale analysis first decompose the time series into several simpler components and the multiscale structure is given by the properties of their components. We present a numerical method which describes the multiscale structure of arbitrary time series without decomposing them. It is based on the monotony spectrum defined as the variation of the mean amplitude of the monotonic segments with respect to the mean local time scale during successive averagings of the time series, the local time scales being the durations of the monotonic segments. The maxima of the monotony spectrum indicate the time scales which dominate the variations of the time series. We show that the monotony spectrum can correctly analyze a diversity of artificial time series and can discriminate the existence of deterministic variations at large time scales from the random fluctuations. As an application we analyze the multifractal structure of some hydrological time series.

  16. Clique topology reveals intrinsic geometric structure in neural correlations.

    Science.gov (United States)

    Giusti, Chad; Pastalkova, Eva; Curto, Carina; Itskov, Vladimir

    2015-11-03

    Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using only the intrinsic pattern of neural correlations. Remarkably, we found similar results during nonspatial behaviors such as wheel running and rapid eye movement (REM) sleep. This suggests that the geometric structure of correlations is shaped by the underlying hippocampal circuits and is not merely a consequence of position coding. We propose that clique topology is a powerful new tool for matrix analysis in biological settings, where the relationship of observed quantities to more meaningful variables is often nonlinear and unknown.

  17. Clique topology reveals intrinsic geometric structure in neural correlations

    Science.gov (United States)

    Giusti, Chad; Pastalkova, Eva; Curto, Carina; Itskov, Vladimir

    2015-01-01

    Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using only the intrinsic pattern of neural correlations. Remarkably, we found similar results during nonspatial behaviors such as wheel running and rapid eye movement (REM) sleep. This suggests that the geometric structure of correlations is shaped by the underlying hippocampal circuits and is not merely a consequence of position coding. We propose that clique topology is a powerful new tool for matrix analysis in biological settings, where the relationship of observed quantities to more meaningful variables is often nonlinear and unknown. PMID:26487684

  18. Revealing the structure of the world airline network

    CERN Document Server

    Verma, Trivik; Herrmann, Hans J

    2014-01-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their ...

  19. Surface morphologic and structural analysis of IR irradiated silver

    Energy Technology Data Exchange (ETDEWEB)

    Latif, Anwar, E-mail: anwarlatif@uet.edu.p [Department of Physics, University of Engineering and Technology, Lahore 54890 (Pakistan); Khaleeq-ur-Rahman, M.; Rafique, M.S.; Bhatti, K.A. [Department of Physics, University of Engineering and Technology, Lahore 54890 (Pakistan)

    2011-04-15

    The microstructural morphological changes in laser irradiated targets are investigated. Nd:YAG laser (1064 nm, {approx}12 ns nominal, 1.1 MW) is used to irradiate 4 N pure (99.99%) fine polished and annealed silver samples in ambient air and under vacuum {approx}10{sup -6} Torr. The laser spot size and power density at tight focus are 12 {mu}m and 3x10{sup 11} W/cm{sup 2}, respectively. SEM micrographs and X-ray diffractograms of the exposed and unexposed targets reveal the surface texture and structural changes, respectively. Amongst the ablation mechanisms involved, exfoliation and hydrodynamic sputtering are found to be dominant. Surface modifications appear in the form of craters and ripples formation. Heat is conducted non-uniformly through narrow channels at the surface. Thermal stresses induced by the laser do not disturb inter planar distance of the target. On the other hand irradiation causes significant variations in grain size and diffracted X-rays intensities.

  20. Surface, structural and tensile properties of proton beam irradiated zirconium

    Science.gov (United States)

    Rafique, Mohsin; Chae, San; Kim, Yong-Soo

    2016-02-01

    This paper reports the surface, structural and tensile properties of proton beam irradiated pure zirconium (99.8%). The Zr samples were irradiated by 3.5 MeV protons using MC-50 cyclotron accelerator at different doses ranging from 1 × 1013 to 1 × 1016 protons/cm2. Both un-irradiated and irradiated samples were characterized using Field Emission Scanning Electron Microscope (FESEM), X-ray Diffraction (XRD) and Universal Testing Machine (UTM). The average surface roughness of the specimens was determined by using Nanotech WSxM 5.0 develop 7.0 software. The FESEM results revealed the formation of bubbles, cracks and black spots on the samples' surface at different doses whereas the XRD results indicated the presence of residual stresses in the irradiated specimens. Williamson-Hall analysis of the diffraction peaks was carried out to investigate changes in crystallite size and lattice strain in the irradiated specimens. The tensile properties such as the yield stress, ultimate tensile stress and percentage elongation exhibited a decreasing trend after irradiation in general, however, an inconsistent behavior was observed in their dependence on proton dose. The changes in tensile properties of Zr were associated with the production of radiation-induced defects including bubbles, cracks, precipitates and simultaneous recovery by the thermal energy generated with the increase of irradiation dose.

  1. Characteristics of ripple structures revealed in OH airglow images

    Science.gov (United States)

    Li, Jing; Li, Tao; Dou, Xiankang; Fang, Xin; Cao, Bing; She, Chiao-Yao; Nakamura, Takuji; Manson, Alan; Meek, Chris; Thorsen, Denise

    2017-03-01

    Small-scale ripple structures observed in OH airglow images are most likely induced by either dynamic instability due to large wind shear or convective instability due to superadiabatic lapse rate. Using the data set taken in the mesopause region with an OH all-sky imager at Yucca Ridge Field Station, Colorado (40.7°N, 104.9°W), from September 2003 to December 2005, we study the characteristics and seasonal variations of ripple structures. By analyzing the simultaneous background wind and temperature observed by the nearby sodium temperature/wind lidar at Fort Collins, Colorado (40.6°N, 105°W), and a nearby medium-frequency radar at Platteville, Colorado (40.2°N, 105.8°W), we are able to statistically study the possible relation between ripples and the background atmosphere conditions. Characteristics and seasonal variations of ripples are presented in detail in this study. The occurrence frequency of ripples exhibits clear seasonal variability, with peak in autumn. The occurrence of ripples shows a local time dependence, which is most likely associated with the solar tides. The lifetime and spatial scale of these ripples are typically 5-20 min and 5-10 km, respectively, and most of the ripples move preferentially either southward or northward. However, more than half of the observed ripples do not advect with background flow; they have higher Richardson numbers than those ripples that advect with background flow. It is possible that they are not instability features but wave structures that are hard to be distinguished from the real instability features.

  2. Band Structure Asymmetry of Bilayer Graphene Revealed by Infrared Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Li, Z.Q.; Henriksen, E.A.; Jiang, Z.; Hao, Zhao; Martin, Michael C.; Kim, P.; Stormer, H.L.; Basov, Dimitri N.

    2008-12-10

    We report on infrared spectroscopy of bilayer graphene integrated in gated structures. We observe a significant asymmetry in the optical conductivity upon electrostatic doping of electrons and holes. We show that this finding arises from a marked asymmetry between the valence and conduction bands, which is mainly due to the inequivalence of the two sublattices within the graphene layer and the next-nearest-neighbor interlayer coupling. From the conductivity data, the energy difference of the two sublattices and the interlayer coupling energy are directly determined.

  3. Biofilm formation assessment in Sinorhizobium meliloti reveals interlinked control with surface motility

    OpenAIRE

    Amaya-Gomez, CV; Hirsch, AM; Soto, MJ

    2015-01-01

    Background Swarming motility and biofilm formation are opposite, but related surface-associated behaviors that allow various pathogenic bacteria to colonize and invade their hosts. In Sinorhizobium meliloti, the alfalfa endosymbiont, these bacterial processes and their relevance for host plant colonization are largely unexplored. Our previous work demonstrated distinct swarming abilities in two S. meliloti strains (Rm1021 and GR4) and revealed that both environmental cues (iron concentration)...

  4. Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion

    Directory of Open Access Journals (Sweden)

    Gerald eLosensky

    2015-01-01

    Full Text Available It was recently shown that haloarchaeal strains of different genera are able to adhere to surfaces and form surface-attached biofilms. However the surface structures mediating the adhesion were still unknown. We have identified a novel surface structure with Halobacterium salinarum strain R1, crucial for surface adhesion. Electron microscopic studies of surface-attached cells frequently showed pili-like surface structures of two different diameters that were irregularly distributed on the surface. The thinner filaments, 7 - 8 nm in diameter, represented a so far unobserved novel pili-like structure. Examination of the Hbt. salinarum R1 genome identified two putative gene loci (pil-1 and pil-2 encoding type IV pilus biogenesis complexes besides the archaellum encoding fla gene locus. Both pil-1 and pil-2 were expressed as transcriptional units, and the transcriptional start of pil-1 was identified. In silico analyses revealed that the pil-1 locus is present with other euryarchaeal genomes whereas the pil-2 is restricted to haloarchaea. Comparative real time qRT-PCR studies indicated that the general transcriptional activity was reduced in adherent versus planktonic cells. In contrast, the transcription of pilB1 and pilB2, encoding putative type IV pilus assembly ATPases, was induced in comparison to the archaella assembly/motor ATPase (flaI and the ferredoxin gene. Mutant strains were constructed that incurred a flaI deletion or flaI/pilB1 gene deletions. The absence of flaI caused the loss of the archaella while the additional absence of pilB1 led to loss of the novel pili-like surface structures. The ΔflaI/ΔpilB1 double mutants showed a 10-fold reduction in surface adhesion compared to the parental strain. Since surface adhesion was not reduced with the non-archaellated ΔflaI mutants, the pil-1 filaments have a distinct function in the adhesion process.

  5. Microbial community structure of Arctic seawater as revealed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    LI Yang; WANG Zhen; LIN Xuezheng

    2016-01-01

    This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95%and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.

  6. Revealing the structure of the world airline network.

    Science.gov (United States)

    Verma, T; Araújo, N A M; Herrmann, H J

    2014-07-09

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their relevance, more than 90% of the world airports are still interconnected upon removal of this core. With standard and unconventional removal measures we compare both empirical and topological perceptions for the fragmentation of the world. We identify how the WAN is organized into different classes of clusters based on the physical proximity of airports and analyze the consequence of this fragmentation.

  7. Revealing the structure of the world airline network

    Science.gov (United States)

    Verma, T.; Araújo, N. A. M.; Herrmann, H. J.

    2014-07-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their relevance, more than 90% of the world airports are still interconnected upon removal of this core. With standard and unconventional removal measures we compare both empirical and topological perceptions for the fragmentation of the world. We identify how the WAN is organized into different classes of clusters based on the physical proximity of airports and analyze the consequence of this fragmentation.

  8. Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Kober, Daniel L.; Alexander-Brett, Jennifer M.; Karch, Celeste M.; Cruchaga, Carlos; Colonna, Marco; Holtzman, Michael J.; Brett, Thomas J. (WU-MED)

    2016-12-20

    Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.

  9. Iron Isotope Fractionation Reveals Structural Change upon Microbial and Chemical Reduction of Nontronite NAu-1

    Science.gov (United States)

    Liu, K.; Wu, L.; Shi, B.; Smeaton, C. M.; Li, W.; Beard, B. L.; Johnson, C.; Roden, E. E.; Van Cappellen, P.

    2015-12-01

    Iron (Fe) isotope fractionations were determined during reduction of structural Fe(III) in nontronite NAu-1 biologically by Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA and chemically by dithionite. ~10% reduction was achieved in biological reactors, with similar reduction extents obtained by dithionite. We hypothesize that two stages occurred in our reactors. Firstly, reduction started from edge sites of clays and the produced Fe(II) partially remained in situ and partially was released into solution. Next aqueous Fe(II) adsorbed onto basal planes. The basal sorbed Fe(II) then undergoes electron transfer and atom exchange (ETAE) with octahedral Fe(III) in clays, with the most negative fractionation factor Δ56Febasal Fe(II)-structural Fe(III)of -1.7‰ when basal sorption reached a threshold value. Secondly, when the most reactive Fe(III) was exhausted, bioreduction significantly slowed down and chemical reduction was able to achieve 24% due to diffusion of small size dithionite. Importantly, no ETAE occurred between basal Fe(II) and structural Fe(III) due to blockage of pathways by collapsed clay layers. This two-stage process in our reduction experiments is distinctive from abiotic exchange experiments by mixing aqueous Fe(II) and NAu-1, where no structural change of clay would block ETAE between basal Fe(II) and structural Fe(III). The separation of reduction sites (clay edges) and sorption sites (basal planes) is unique to clay minerals with layered structure. In contrast, reduction and sorption occur on the same sites on the surfaces of Fe oxyhydroxides, where reduction does not induce structure change. Thus, the Fe isotope fractionations are the same for reduction and abiotic exchange experiments for Fe oxides. Our study reveals important changes in electron transfer and atom exchange pathways upon reduction of clay minerals by dissimilatory Fe reducing bacteria, which is prevalent in anoxic soils and sediments.

  10. Phonons on the clean metal surfaces and in adsorption structures

    Science.gov (United States)

    Rusina, Galina G.; Chulkov, Evgenii V.

    2013-06-01

    The state-of-the-art studies of the vibrational dynamics of clean metal surfaces and metal surface structures formed upon the sub-monolayer adsorption of the atoms of various elements are considered. A brief historical survey of the milestones of investigations of surface phonons is presented. The results of studies of the atomic structure and vibration characteristics of surfaces with low and high Miller indices and adsorption structures are analyzed. It is demonstrated that vicinal surfaces of FCC metals tend to exhibit specific vibrational modes located on the step and polarized along the step. Irrespective of the type and position of adsorption or the substrate structure, the phonon spectra of sub-monolayer adsorption structures always tend to display two modes for combined translational displacements of adatoms and for coupled vibrations of substrate atoms and adatoms polarized in the direction normal to the surface. The bibliography includes 202 references.

  11. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs.

    Science.gov (United States)

    Edmondson, J L; Stott, I; Davies, Z G; Gaston, K J; Leake, J R

    2016-09-19

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface temperature extremes, but their effects have not been investigated at a city-wide scale. Across a mid-sized UK city we buried temperature loggers at the surface of greenspace soils at 100 sites, stratified by proximity to city centre, vegetation cover and land-use. Mean daily soil surface temperature over 11 months increased by 0.6 °C over the 5 km from the city outskirts to the centre. Trees and shrubs in non-domestic greenspace reduced mean maximum daily soil surface temperatures in the summer by 5.7 °C compared to herbaceous vegetation, but tended to maintain slightly higher temperatures in winter. Trees in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce the adverse impacts of urbanization on microclimate, soil processes and human health.

  12. Soil surface temperatures reveal moderation of the urban heat island effect by trees and shrubs

    Science.gov (United States)

    Edmondson, J. L.; Stott, I.; Davies, Z. G.; Gaston, K. J.; Leake, J. R.

    2016-09-01

    Urban areas are major contributors to air pollution and climate change, causing impacts on human health that are amplified by the microclimatological effects of buildings and grey infrastructure through the urban heat island (UHI) effect. Urban greenspaces may be important in reducing surface temperature extremes, but their effects have not been investigated at a city-wide scale. Across a mid-sized UK city we buried temperature loggers at the surface of greenspace soils at 100 sites, stratified by proximity to city centre, vegetation cover and land-use. Mean daily soil surface temperature over 11 months increased by 0.6 °C over the 5 km from the city outskirts to the centre. Trees and shrubs in non-domestic greenspace reduced mean maximum daily soil surface temperatures in the summer by 5.7 °C compared to herbaceous vegetation, but tended to maintain slightly higher temperatures in winter. Trees in domestic gardens, which tend to be smaller, were less effective at reducing summer soil surface temperatures. Our findings reveal that the UHI effects soil temperatures at a city-wide scale, and that in their moderating urban soil surface temperature extremes, trees and shrubs may help to reduce the adverse impacts of urbanization on microclimate, soil processes and human health.

  13. Dissipative surface solitons in periodic structures

    CERN Document Server

    Kartashov, Yaroslav V; Vysloukh, Victor A

    2010-01-01

    We report dissipative surface solitons forming at the interface between a semi-infinite lattice and a homogeneous Kerr medium. The solitons exist due to balance between amplification in the near-surface lattice channel and two-photon absorption. The stable dissipative surface solitons exist in both focusing and defocusing media, when propagation constants of corresponding states fall into a total semi-infinite and or into one of total finite gaps of the spectrum (i.e. in a domain where propagation of linear waves is inhibited for the both media). In a general situation, the surface solitons form when amplification coefficient exceeds threshold value. When a soliton is formed in a total finite gap there exists also the upper limit for the linear gain.

  14. Coal surface structure and thermodynamics. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, J.W.; Wernett, P.C.; Glass, A.S.; Quay, D.; Roberts, J.

    1994-05-01

    Coals surfaces were studied using static surface adsorption measurements, low angle x-ray scattering (LAXS), inverse gas chromatography (IGC) and a new {sup 13}C NMR relaxation technique. A comparison of surface areas determined by hydrocarbon gas adsorption and LAXS led to the twin conclusions that the hydrocarbons had to diffuse through the solid to reach isolated pores and that the coal pores do not form interconnected networks, but are largely isolated. This conclusion was confirmed when IGC data for small hydrocarbons showed no discontinuities in their size dependence as usually observed with porous solids. IGC is capable of providing adsorption thermodynamics of gases on coal surfaces. The interactions of non-polar molecules and coal surfaces are directly proportioned to the gas molecular polarizability. For bases, the adsorption enthalpy is equal to the polarizability interaction plus the heat of hydrogen bond formation with phenol. Amphoteric molecules have more complex interactions. Mineral matter can have highly specific effects on surface interactions, but with most of the molecules studied is not an important factor.

  15. Importance of bulk states for the electronic structure of semiconductor surfaces: implications for finite slabs.

    Science.gov (United States)

    Sagisaka, Keisuke; Nara, Jun; Bowler, David

    2017-04-12

    We investigate the influence of slab thickness on the electronic structure of the Si(1 0 0)- p([Formula: see text]) surface in density functional theory (DFT) calculations, considering both density of states and band structure. Our calculations, with slab thicknesses of up to 78 atomic layers, reveal that the slab thickness profoundly affects the surface band structure, particularly the dangling bond states of the silicon dimers near the Fermi level. We find that, to precisely reproduce the surface bands, the slab thickness needs to be large enough to completely converge the bulk bands in the slab. In the case of the Si(1 0 0) surface, the dispersion features of the surface bands, such as the band shape and width, converge when the slab thickness is larger than 30 layers. Complete convergence of both the surface and bulk bands in the slab is only achieved when the slab thickness is greater than 60 layers.

  16. Structure-activity relationships in carbohydrates revealed by their hydration.

    Science.gov (United States)

    Maugeri, Laura; Busch, Sebastian; McLain, Sylvia E; Pardo, Luis Carlos; Bruni, Fabio; Ricci, Maria Antonietta

    2016-12-21

    One of the more intriguing aspects of carbohydrate chemistry is that despite having very similar molecular structures, sugars have very different properties. For instance, there is a sensible difference in sweet taste between glucose and trehalose, even though trehalose is a disaccharide that comprised two glucose units, suggesting a different ability of these two carbohydrates to bind to sweet receptors. Here we have looked at the hydration of specific sites and at the three-dimensional configuration of water molecules around three carbohydrates (glucose, cellobiose, and trehalose), combining neutron diffraction data with computer modelling. Results indicate that identical chemical groups can have radically different hydration patterns depending on their location on a given molecule. These differences can be linked with the specific activity of glucose, cellobiose, and trehalose as a sweet substance, as building block of cellulose fiber, and as a bioprotective agent, respectively. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editors: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.

  17. Probabilistic diffusion tractography reveals improvement of structural network in musicians.

    Directory of Open Access Journals (Sweden)

    Jianfu Li

    Full Text Available PURPOSE: Musicians experience a large amount of information transfer and integration of complex sensory, motor, and auditory processes when training and playing musical instruments. Therefore, musicians are a useful model in which to investigate neural adaptations in the brain. METHODS: Here, based on diffusion-weighted imaging, probabilistic tractography was used to determine the architecture of white matter anatomical networks in musicians and non-musicians. Furthermore, the features of the white matter networks were analyzed using graph theory. RESULTS: Small-world properties of the white matter network were observed in both groups. Compared with non-musicians, the musicians exhibited significantly increased connectivity strength in the left and right supplementary motor areas, the left calcarine fissure and surrounding cortex and the right caudate nucleus, as well as a significantly larger weighted clustering coefficient in the right olfactory cortex, the left medial superior frontal gyrus, the right gyrus rectus, the left lingual gyrus, the left supramarginal gyrus, and the right pallidum. Furthermore, there were differences in the node betweenness centrality in several regions. However, no significant differences in topological properties were observed at a global level. CONCLUSIONS: We illustrated preliminary findings to extend the network level understanding of white matter plasticity in musicians who have had long-term musical training. These structural, network-based findings may indicate that musicians have enhanced information transmission efficiencies in local white matter networks that are related to musical training.

  18. The NH$_2$D hyperfine structure revealed by astrophysical observations

    CERN Document Server

    Daniel, F; Punanova, A; Harju, J; Faure, A; Roueff, E; Sipilä, O; Caselli, P; Güsten, R; Pon, A; Pineda, J E

    2016-01-01

    The 1$_{11}$-1$_{01}$ lines of ortho and para--NH$_2$D (o/p-NH$_2$D), respectively at 86 and 110 GHz, are commonly observed to provide constraints on the deuterium fractionation in the interstellar medium. In cold regions, the hyperfine structure due to the nitrogen ($^{14}$N) nucleus is resolved. To date, this splitting is the only one which is taken into account in the NH$_2$D column density estimates. We investigate how the inclusion of the hyperfine splitting caused by the deuterium (D) nucleus affects the analysis of the rotational lines of NH$_2$D. We present 30m IRAM observations of the above mentioned lines, as well as APEX o/p-NH$_2$D observations of the 1$_{01}$-0$_{00}$ lines at 333 GHz. The hyperfine spectra are first analyzed with a line list that only includes the hyperfine splitting due to the $^{14}$N nucleus. We find inconsistencies between the line widths of the 1$_{01}$-0$_{00}$ and 1$_{11}$-1$_{01}$ lines, the latter being larger by a factor of $\\sim$1.6$\\pm0.3$. Such a large difference is...

  19. Hydroxyl migration disorders the surface structure of hydroxyapatite nanoparticles

    Science.gov (United States)

    Cheng, Xiajie; Wu, Hong; Zhang, Li; Ma, Xingtao; Zhang, Xingdong; Yang, Mingli

    2017-09-01

    The surface structure of nano-hydroxyapatite (HAP) was investigated using a combined simulated annealing and molecular dynamics method. The stationary structures of nano-HAP with 4-7 nm in diameter and annealed under different temperatures were analyzed in terms of pair distribution function, structural factor, mean square displacement and atomic coordination number. The particles possess different structures from bulk crystal. A clear radial change in their atomic arrangements was noted. From core to surface the structures change from ordered to disordered. A three-shell model was proposed to describe the structure evolution of nano-HAP. Atoms in the core zone keep their arrangements as in crystal, while atoms in the surface shell are in short-range order and long-range disorder, adopting a typically amorphous structure. Atoms in the middle shell have small displacements and/or deflections but basically retain their original locations as in crystal. The disordered shell is about 1 nm in thickness, in agreement with experimental observations. The disordering mainly stems from hydroxyl migration during which hydroxyls move to the surface and bond with the exposed Ca ions, and their left vacancies bring about a rearrangement of nearby atoms. The disordering is to some extent different for particles unannealed under different temperatures, resulting from fewer number of migrated hydroxyls at lower temperatures. Particles with different sizes have similar surface structures, and their surface energy decreases with increasing size. Moreover, the surface energy is reduced by hydroxyl migration because the exposed Ca ions on the surface are ionically bonded with the migrated hydroxyls. Our calculations proposed a new structure model for nano-HAP, which indicates a surface structure with activities different from those without surface reorganization. This is particularly interesting because most bioactivities of biomaterials are dominated by their surface activity.

  20. Controlled anisotropic wetting behaviour of multi-scale slippery surface structure of non fluoro polymer composite

    Directory of Open Access Journals (Sweden)

    B. Sabarish

    2013-11-01

    Full Text Available A facile process for in-situ modification of surface properties of Waste Expanded Polystyrene (WEP/graphite film produced by spin coating technique has been described. The additives undergo spontaneous surface agglomeration with formation of islands of forest of flake structure during the spinning process. This results in polymer films with enhanced roughness and highly hydrophobic surfaces. Wettability was analyzed using static water contact angle, surface morphology was observed using atomic force microscopy (AFM and field emission scanning electron microscopy (FE-SEM. The polymer composite exhibited maximum water contact angle (WCA of 129°. Surface texture reveals the variation of surface roughness which enables anisotropic surface wettability property. The present work exhibits promising approach for fabricating nano flake forest in polymer structures for various industrial applications.

  1. UV spectral filtering by surface structured multilayer mirrors

    NARCIS (Netherlands)

    Huang, Q.; Paardekooper, Daniel Mathijs; Zoethout, E.; Medvedev, V. V.; van de Kruijs, Robbert; Bosgra, Jeroen; Louis, Eric; F. Bijkerk,

    2014-01-01

    A surface structured extreme ultraviolet multilayer mirror was developed showing full band suppression of UV (lambda = 100-400 nm) and simultaneously a high reflectance of EUV light (lambda = 13.5 nm). The surface structure consists of Si pyramids, which are substantially transparent for EUV but

  2. UV spectral filtering by surface structured multilayer mirrors

    NARCIS (Netherlands)

    Huang, Q.; Paardekooper, Daniel Mathijs; Zoethout, E.; Medvedev, V. V.; van de Kruijs, Robbert; Bosgra, Jeroen; Louis, Eric; F. Bijkerk,

    2014-01-01

    A surface structured extreme ultraviolet multilayer mirror was developed showing full band suppression of UV (lambda = 100-400 nm) and simultaneously a high reflectance of EUV light (lambda = 13.5 nm). The surface structure consists of Si pyramids, which are substantially transparent for EUV but ref

  3. Structures of surface and interface of amorphous ice

    Science.gov (United States)

    Kumagai, Yu; Ikeda-Fukazawa, Tomoko

    2017-06-01

    To investigate the surface structure, we performed molecular dynamics calculations of amorphous ice. The result shows that a low density layer, which forms a few hydrogen bonds with weaker strength, exists in the surface. Furthermore, the sintering processes were simulated to investigate the structure of grain boundary formed from the adsorption of two surfaces. The result indicates that a low density region exists in a boundary between amorphous ice grains. The structures of surface and interface of amorphous ice have important implications for adsorption, diffusion, and chemical reaction in ice grains of interstellar molecular clouds.

  4. Hierarchically structured superoleophobic surfaces with ultralow contact angle hysteresis.

    Science.gov (United States)

    Kota, Arun K; Li, Yongxin; Mabry, Joseph M; Tuteja, Anish

    2012-11-14

    Hierarchically structured, superoleophobic surfaces are demonstrated that display one of the lowest contact angle hysteresis values ever reported - even with extremely low-surface-tension liquids such as n-heptane. Consequently, these surfaces allow, for the first time, even ≈2 μL n-heptane droplets to bounce and roll-off at tilt angles. ≤ 2°.

  5. Metrology of sub-micron structured polymer surfaces

    DEFF Research Database (Denmark)

    Quagliotti, Danilo; Tosello, Guido; Salaga, J.

    surface replication of the tool insert component when moulding the polymer melt [1]. This aspect is particularly critical when dealing with increasingly small dimensional scales in micro- and nano-structured surfaces [2, 3].In this context, a metrological investigation of polymer replicated surfaces using...

  6. Structure dependence of Pt surface activated ammonia oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Santen, R A van; Offermans, W K [Schuit Institute of Catalysis, Laboratory of Inorganic Chemistry and Catalysis, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands); Ricart, J M; Novell-Leruth, G [Department of Chemical Physics and Inorganic Chemistry, University Rovira I Virgili, C/ Marcel.lI Domingo s/n, 43007 Tarragona (Spain); Perez-RamIrez, J [Institute of Chemical Research of Catalonia (ICIQ) and Catalan, Institution for Research and Advanced Studies (ICREA), Avinguda Paisos Catalans 16, 43007, Tarragona (Spain)], E-mail: r.a.v.santen@tue.nl

    2008-06-01

    Computational advances that enable the prediction of the structures and the energies of surface reaction intermediates are providing essential information to the formulation of theories of surface chemical reactivity. In this contribution this is illustrated for the activation of ammonia by coadsorbed oxygen and hydroxyl on the Pt(111), Pt(100), and Pt(211) surfaces.

  7. Surface Nano-Structuring by Adsorption and Chemical Reactions

    OpenAIRE

    Ken-ichi Tanaka

    2010-01-01

    Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species are reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembl...

  8. Structural characterization of surface glycans from Clostridium difficile.

    Science.gov (United States)

    Reid, Christopher W; Vinogradov, Evgeny; Li, Jianjun; Jarrell, Harold C; Logan, Susan M; Brisson, Jean-Robert

    2012-06-01

    Whole-cell high-resolution magic angle spinning (HR-MAS) NMR was employed to survey the surface polysaccharides of a group of clinical and environmental isolates of Clostridium difficile. Results indicated that a highly conserved surface polysaccharide profile among all strains studied. Multiple additional peaks in the anomeric region were also observed which prompted further investigation. Structural characterization of the isolated surface polysaccharides from two strains confirmed the presence of the conserved water soluble polysaccharide originally described by Ganeshapillai et al. which was composed of a hexaglycosyl phosphate repeat consisting of [→6)-β-D-Glcp-(1-3)-β-D-GalpNAc-(1-4)-α-D-Glcp-(1-4)-[β-D-Glcp(1-3]-β-D-GalpNAc-(1-3)-α-D-Manp-(1-P→]. In addition, analysis of phenol soluble polysaccharides revealed a similarly conserved lipoteichoic acid (LTA) which could be detected on whole cells by HR-MAS NMR. Conventional NMR and mass spectrometry analysis indicated that the structure of this LTA consisted of the repeat unit [→6)-α-D-GlcpNAc-(1-3)-[→P-6]-α-D-GlcpNAc-(1-2)-D-GroA] where GroA is glyceric acid. The repeating units were linked by a phosphodiester bridge between C-6 of the two GlcNAc residues (6-P-6). A minor component consisted of GlcpN-(1-3) instead of GlcpNAc-(1-3) in the repeat unit. Through a 6-6 phosphodiester bridge this polymer was linked to →6)-β-D-Glcp-(1-6)-β-D-Glcp-(1-6)-β-D-Glcp-(1-1)-Gro, with glycerol (Gro) substituted by fatty acids. This is the first report of the utility of HR-MAS NMR in the examination of surface carbohydrates of Gram positive bacteria and identification of a novel LTA structure from Clostridium difficile.

  9. Fragmentation pathways of nanofractal structures on surfaces

    DEFF Research Database (Denmark)

    Dick, Veronika V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2011-01-01

    We present a theoretical analysis of the post-growth processes occurring in nanofractals grown on a surface. For this study we have developed a method that accounts for the internal dynamics of particles in a fractal. We demonstrate that the detachment of particles from the fractal and their diff......We present a theoretical analysis of the post-growth processes occurring in nanofractals grown on a surface. For this study we have developed a method that accounts for the internal dynamics of particles in a fractal. We demonstrate that the detachment of particles from the fractal...... and their diffusion within the fractal and over the surface determines the shape of the islands remaining on a surface after the fractal fragmentation. We consider different scenarios of fractal post-growth relaxation and analyze the time evolution of the island's morphology. The results of our calculations...... are compared with available experimental observations, and experiments in which the post-growth relaxation of deposited nanostructures can be tested are suggested....

  10. Structural optimization of super-repellent surfaces

    DEFF Research Database (Denmark)

    Cavalli, Andrea; Bøggild, Peter; Okkels, Fridolin

    2013-01-01

    Micro-patterning is an effective way to achieve surfaces with extreme liquid repellency. This technique does not rely on chemical coatings and is therefore a promising concept for application in food processing and bio-compatibile coatings. This super-repellent behaviour is obtained by suspending...

  11. Fragmentation pathways of nanofractal structures on surfaces

    DEFF Research Database (Denmark)

    Dick, Veronika V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2011-01-01

    We present a theoretical analysis of the post-growth processes occurring in nanofractals grown on a surface. For this study we have developed a method that accounts for the internal dynamics of particles in a fractal. We demonstrate that the detachment of particles from the fractal and their diff...

  12. The high resolution structure of tyrocidine A reveals an amphipathic dimer.

    Science.gov (United States)

    Loll, Patrick J; Upton, Elizabeth C; Nahoum, Virginie; Economou, Nicoleta J; Cocklin, Simon

    2014-05-01

    Tyrocidine A, one of the first antibiotics ever to be discovered, is a cyclic decapeptide that binds to membranes of target bacteria, disrupting their integrity. It is active against a broad spectrum of Gram-positive organisms, and has recently engendered interest as a potential scaffold for the development of new drugs to combat antibiotic-resistant pathogens. We present here the X-ray crystal structure of tyrocidine A at a resolution of 0.95Å. The structure reveals that tyrocidine forms an intimate and highly amphipathic homodimer made up of four beta strands that associate into a single, highly curved antiparallel beta sheet. We used surface plasmon resonance and potassium efflux assays to demonstrate that tyrocidine binds tightly to mimetics of bacterial membranes with an apparent dissociation constant (K(D)) of 10 μM, and efficiently permeabilizes bacterial cells at concentrations equal to and below the K(D). Using variant forms of tyrocidine in which the fluorescent probe p-cyano-phenylalanine had been inserted on either the polar or apolar face of the molecule, we performed fluorescence quenching experiments, using both water-soluble and membrane-embedded quenchers. The quenching results, together with the structure, strongly support a membrane association model in which the convex, apolar face of tyrocidine's beta sheet is oriented toward the membrane interior, while the concave, polar face is presented to the aqueous phase.

  13. X-ray CT Scanning Reveals Long-Term Copper Pollution Effects on Functional Soil Structure

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Homstrup, Martin

    Soil structure plays the main role in the ability of the soil to fulfill essential soil functions such as the root growth, rate of water infiltration and retention, transport of gaseous and chemicals/pollutants through the soil. Soil structure is a dynamic soil property and affected by various...... factors such as soil type, land use, and soil contamination. In this study, we quantified the soil structure using X-ray CT scanning and revealed the effect of a long history of Copper (Cu) pollution on it. A fallow field at Hygum Denmark provides this opportunity as it had a long history of Copper...... sulphate contamination in a gradient with Cu content varies from 21 mg kg-1 to 3837 mg kg-1. Total 20 intact soil columns (diameter of 10 cm and height of 8 cm) were sampled at five locations along the Cu-gradient from a depth of 5 to 15 cm below surface level. The soil columns were scanned at a voxel...

  14. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    Science.gov (United States)

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-03

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  15. Laser Surface Preparation and Bonding of Aerospace Structural Composites

    Science.gov (United States)

    Belcher, M. A.; Wohl, C. J.; Hopkins, J. W.; Connell, J. W.

    2010-01-01

    Adhesive bonds are critical to the integrity of built-up structures. Disbonds can often be detected but the strength of adhesion between surfaces in contact is not obtainable without destructive testing. Typically the number one problem in a bonded structure is surface contamination, and by extension, surface preparation. Standard surface preparation techniques, including grit blasting, manual abrasion, and peel ply, are not ideal because of variations in their application. Etching of carbon fiber reinforced plastic (CFRP) panels using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser appears to be a highly precise and promising way to both clean a composite surface prior to bonding and provide a bond-promoting patterned surface akin to peel ply without the inherent drawbacks from the same (i.e., debris and curvature). CFRP surfaces prepared using laser patterns conducive to adhesive bonding were compared to typical prebonding surface treatments through optical microscopy, contact angle goniometry, and post-bonding mechanical testing.

  16. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius).

    Science.gov (United States)

    Milano, Ilaria; Babbucci, Massimiliano; Cariani, Alessia; Atanassova, Miroslava; Bekkevold, Dorte; Carvalho, Gary R; Espiñeira, Montserrat; Fiorentino, Fabio; Garofalo, Germana; Geffen, Audrey J; Hansen, Jakob H; Helyar, Sarah J; Nielsen, Einar E; Ogden, Rob; Patarnello, Tomaso; Stagioni, Marco; Tinti, Fausto; Bargelloni, Luca

    2014-01-01

    Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

  17. Local Environment and Interactions of Liquid and Solid Interfaces Revealed by Spectral Line Shape of Surface Selective Nonlinear Vibrational Probe

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shun-Li; Fu, Li; Chase, Zizwe A.; Gan, Wei; Wang, Hong-Fei

    2016-11-10

    Vibrational spectral lineshape contains important detailed information of molecular vibration and reports its specific interactions and couplings to its local environment. In this work, recently developed sub-1 cm-1 high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) was used to measure the -C≡N stretch vibration in the 4-n-octyl-4’-cyanobiphenyl (8CB) Langmuir or Langmuir-Blodgett (LB) monolayer as a unique vibrational probe, and the spectral lineshape analysis revealed the local environment and interactions at the air/water, air/glass, air/calcium fluoride and air/-quartz interfaces for the first time. The 8CB Langmuir or LB film is uniform and the vibrational spectral lineshape of its -C≡N group has been well characterized, making it a good choice as the surface vibrational probe. Lineshape analysis of the 8CB -C≡N stretch SFG vibrational spectra suggests the coherent vibrational dynamics and the structural and dynamic inhomogeneity of the -C≡N group at each interface are uniquely different. In addition, it is also found that there are significantly different roles for water molecules in the LB films on different substrate surfaces. These results demonstrated the novel capabilities of the surface nonlinear spectroscopy in characterization and in understanding the specific structures and chemical interactions at the liquid and solid interfaces in general.

  18. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob;

    2002-01-01

    , the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations...

  19. Biomembrane interactions reveal the mechanism of action of surface-immobilized host defense IDR-1010 peptide.

    Science.gov (United States)

    Gao, Guangzheng; Cheng, John T J; Kindrachuk, Jason; Hancock, Robert E W; Straus, Suzana K; Kizhakkedathu, Jayachandran N

    2012-02-24

    Dissecting the mechanism of action of surface-tethered antimicrobial and immunomodulatory peptides is critical to the design of optimized anti-infection coatings on biomedical devices. To address this, we compared the biomembrane interactions of host defense peptide IDR-1010cys (1) in free form, (2) as a soluble polymer conjugate, and (3) with one end tethered to a solid support with model bacterial and mammalian lipid membranes. Our results show that IDR-1010cys in all three distinct forms interacted with bacterial and mammalian lipid vesicles, but the extent of the interactions as monitored by the induction of secondary structure varied. The enhanced interaction of surface-tethered peptides is well correlated with their very good antimicrobial activities. Our results demonstrate that there may be a difference in the mechanism of action of surface-tethered versus free IDR-1010cys.

  20. Structural and electronic properties of hydrosilylated silicon surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Baumer, A.

    2005-11-15

    The structural and electronic properties of alkyl-terminated Si surfaces prepared by thermallyinduced hydrosilylation have been studied in detail in the preceding chapters. Various surfaces have been used for the functionalization ranging from crystalline Si over amorphous hydrogenated Si to nanoscaled materials such as Si nanowires and nanoparticles. In each case, the alkyl-terminated surfaces have been compared to the native oxidized and H-terminated surfaces. (orig.)

  1. Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-06-01

    In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  2. Carbon Nanomaterials: Surface Structure and Morphology

    Science.gov (United States)

    Mansurov, Z. A.; Shabanova, T. A.; Mofa, N. N.; Glagolev, V. A.

    2014-09-01

    We propose a classification of individual nanoparticles on the basis of the form of the surface and the internal architectural packing for investigations carried out with the help of transmission electron microscopy. The investigated samples contain individual nanoparticles of seven kinds in different ratios: rounded, tubular, fibrous, fi lm, "veil," "active" particles and "particles with regular geometric contours." The classification was made on the basis of an analysis of the results of investigations of the surfaces and internal architectural packing of carbon particles obtained in different physiochemical processes (carbonization, carburizing, arc discharge, mechanochemical treatment, plasma chemistry, and in carbon-containing fl ames). For the source materials, we used waste of farming products and widely distributed mineral raw materials.

  3. Dyeing of Snow Surfaces to Observe Structure

    Science.gov (United States)

    1993-06-01

    of freezeup problems important to obtain a clear visual perspective and with water. We found that both coloring agents to obtain good photographic...a dye of methanol coloring in with floodlights, whereas Figure 7b is a view of the water. Freezeup at the sprayer nozzle was one same area lighted...from behind, problem and the snow surface had a blemished appearance because of the addition of the water, which then froze. Freezeup may not be a

  4. Surface Structure Enhanced Microchannel Flow Boiling

    OpenAIRE

    Zhu, Yangying; Antao, Dion Savio; Chu, Kuang-Han; Chen, Siyu; Hendricks, Terry J.; Zhang, Tiejun; Wang, Evelyn N.

    2016-01-01

    We investigated the role of surface microstructures in two-phase microchannels on suppressing flow instabilities and enhancing heat transfer. We designed and fabricated microchannels with well-defined silicon micropillar arrays on the bottom heated microchannel wall to promote capillary flow for thin film evaporation while facilitating nucleation only from the sidewalls. Our experimental results show significantly reduced temperature and pressure drop fluctuation especially at high heat fluxe...

  5. Compositional variability across Mercury's surface revealed by MESSENGER measurements of variations in thermal neutron count rates

    Science.gov (United States)

    Peplowski, P. N.; Lawrence, D. J.; Goldsten, J. O.; Nittler, L. R.; Solomon, S. C.

    2013-12-01

    Measurements by MESSENGER's Gamma-Ray and Neutron Spectrometer (GRNS) have revealed variations in the flux of thermal neutrons across Mercury's northern hemisphere. These variations are interpreted to originate from spatial variations in surface elemental composition. In particular, the measurements are sensitive to the near-surface abundances of elements that absorb thermal neutrons, including major rock-forming elements such as Fe and Ti, minor elements such as Mn and Cl, and rare-earth elements such as Gd and Sm. We have constructed a map of thermal neutron variability across the surface and compared it with known variations in elemental composition and with the distribution of geologic units. Development of the map included the derivation of the macroscopic thermal neutron absorption cross section across the surface, a quantity whose value and variability provides useful constraints on the formation and geochemical evolution of Mercury's crust. Finally, by combining the thermal neutron measurements with previously reported elemental measurements from the GRNS and MESSENGER's X-Ray Spectrometer, we have derived constraints on the abundances of neutron-absorbing elements, including previously unreported limits for some minor and rare-earth elements.

  6. Cell-material interactions revealed via material techniques of surface patterning.

    Science.gov (United States)

    Yao, Xiang; Peng, Rong; Ding, Jiandong

    2013-10-04

    Cell-material interactions constitute a key fundamental topic in biomaterials study. Various cell cues and matrix cues as well as soluble factors regulate cell behaviors on materials. These factors are coupled with each other as usual, and thus it is very difficult to unambiguously elucidate the role of each regulator. The recently developed material techniques of surface patterning afford unique ways to reveal the underlying science. This paper reviews the pertinent material techniques to fabricate patterns of microscale and nanoscale resolutions, and corresponding cell studies. Some issues are emphasized, such as cell localization on patterned surfaces of chemical contrast, and effects of cell shape, cell size, cell-cell contact, and seeding density on differentiation of stem cells. Material cues to regulate cell adhesion, cell differentiation and other cell events are further summed up. Effects of some physical properties, such as surface topography and matrix stiffness, on cell behaviors are also discussed; nanoscaled features of substrate surfaces to regulate cell fate are summarized as well. The pertinent work sheds new insight into the cell-material interactions, and is stimulating for biomaterial design in regenerative medicine, tissue engineering, and high-throughput detection, diagnosis, and drug screening. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Scanning tunneling microscopy characterization of the geometric and electronic structure of hydrogen-terminated silicon surfaces

    Science.gov (United States)

    Kaiser, W. J.; Bell, L. D.; Hecht, M. H.; Grunthaner, F. J.

    1988-01-01

    Scanning tunneling microscopy (STM) methods are used to characterize hydrogen-terminated Si surfaces prepared by a novel method. The surface preparation method is used to expose the Si-SiO2 interface. STM images directly reveal the topographic structure of the Si-SiO2 interface. The dependence of interface topography on oxide preparation conditions observed by STM is compared to the results of conventional surface characterization methods. Also, the electronic structure of the hydrogen-terminated surface is studied by STM spectroscopy. The near-ideal electronic structure of this surface enables direct tunnel spectroscopy measurements of Schottky barrier phenomena. In addition, this method enables probing of semiconductor subsurface properties by STM.

  8. Imprinted and injection-molded nano-structured optical surfaces

    DEFF Research Database (Denmark)

    Christiansen, Alexander Bruun; Højlund-Nielsen, Emil; Clausen, Jeppe Sandvik

    2013-01-01

    Inspired by nature, nano-textured surfaces have attracted much attention as a method to realize optical surface functionality. The moth-eye antireflective structure and the structural colors of Morpho butterflies are wellknown examples used for inspiration for such biomimetic research...... of light from polymer surfaces and their implication for creating structural colors is discussed. In the case of injection-moulding compatible designs, the maximum reflection of nano-scale textured surfaces cannot exceed the Fresnel reflection of a corresponding flat polymer surface, which is approx. 4...... % for normal incidence. Diffraction gratings provide strong color reflection defined by the diffraction orders. However, the apperance varies strongly with viewing angles. Three different methods to address the strong angular-dependence of diffraction grating based structural color are discussed....

  9. Highly charged ions interacting with carbon surfaces : An influence of surface structure?

    NARCIS (Netherlands)

    Morgenstern, R; Winters, D; Schlatholter, T; Hoekstra, R

    Auger electron spectroscopy has been used to investigate the reaction of various carbon surfaces - including fullerene covered metal surfaces - on the impact of highly charged ions. An influence of the electronic surface structure on the interaction is clearly observed. However, the goal of

  10. The Dynamics and Structures of Adsorbed Surfaces

    DEFF Research Database (Denmark)

    Nielsen, M; Ellenson, W. D.; McTague, J. P.

    1978-01-01

    Reviews neutron scattering work performed on films of simple gas atoms and molecules adsorbed primarily on graphite surfaces. Exfoliated graphite substrates such as Grafoil were first used in this kind of measurements about five years ago and new results have been reported at an increasing pace...... of molecules such as NH3 or the internal modes of adsorbed molecules such as C4H10. Neutron scattering measurements where substrates other than graphite products are used as the adsorbents will not be reviewed here. However, the power of the technique will be demonstrated in an example of H2 physisorbed...

  11. Structure and surface properties of supported oxides

    Energy Technology Data Exchange (ETDEWEB)

    Leyrer, J.; Vielhaber, B.; Zaki, M.I.; Zhuang Shuxian; Weitkamp, J.; Knoezinger, H.

    1985-09-15

    Supported molybdate catalysts have been prepared on Al/sub 2/O/sub 3/,TiO/sub 2/, CeO/sub 2/, ZrO/sub 2/ and SiO/sub 2/ by impregnation from aqueous solution. The isoelectric point (IEPS) of the support surfaces determines the primary adsorption interaction of the molybdate species with the surface at a given pH. Raman spectroscopy shows monolayer formation on Al/sub 2/O/sub 3/, TiO/sub 2/ and CeO/sub 2/, while high proportions of MoO/sub 3/ are detected on SiO/sub 2/ and ZrO/sub 2/. Strong support effects influence the reducibility of the supported molybdate, which decreases in the sequence Mo/TiO/sub 2/ > Mo/ > CeO/sub 2/ > Mo/Al/sub 2/O/sub 3/ > Mo/ZrO/sub 2/. The dispersion of the monolayer on TiO/sub 2/, CeO/sub 2/ and Al/sub 2/O/sub 3/ seems to be fairly stable under reduction conditions, indicating strong chemical interaction with the supports.

  12. Evolution of kinetically controlled In-induced surface structure on Si(5 5 7) surface

    Science.gov (United States)

    Chauhan, Amit Kumar Singh; Eldose, Nirosh M.; Mishra, Monu; Niazi, Asad; Nair, Lekha; Gupta, Govind

    2014-09-01

    This paper introduces issue of kinetically controlled and temperature driven superstructural phase transition of Indium (In) on atomically clean high index Si(5 5 7)-7 × 1 surface. Auger electron spectroscopy analysis reveals that at room-temperature (RT) with a controlled incident flux of 0.002 ML/s; In overlayers evolve through the Frank-van der Merwe growth mode and yield a (1 × 1) diffraction pattern for coverage ≥1 ML. For substrate temperature 500 °C island growth is observed. On annealing the In/Si(5 5 7) interface in the temperature range 250-340 °C, clusters to two dimensional (2D) layer transformation on top of a stable monolayer is predominated. In-situ RT and HT adsorption and thermal desorption phenomena revealed the formation of coverage and temperature dependent thermally stable In induced superstructural phases such as (4 × 1) at 0.5 ML (520 °C), (√3 × √3-R30°) at 0.3 ML (560 °C) and (7 × 7) at 0.1 ML (580 °C). These indium induced superstructures could be utilized as potential substrate for the growth of various exotic 1D/2D structures.

  13. Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Hasler Madlen

    2010-03-01

    Full Text Available Abstract Background Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE, a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F or produced with an old-young smearing process (M. Results TTGE revealed nine bacterial species common to both F and M consortia, but consortium F exhibited a higher diversity than consortium M, with thirteen and ten species, respectively. Population dynamics were studied after application of the consortia on fresh-produced Raclette cheeses. TTGE analyses revealed a similar sequential development of the nine species common to both consortia. Beside common cheese surface bacteria (Staphylococcus equorum, Corynebacterium spp., Brevibacterium linens, Microbacterium gubbeenense, Agrococcus casei, the two consortia contained marine lactic acid bacteria (Alkalibacterium kapii, Marinilactibacillus psychrotolerans that developed early in ripening (day 14 to 20, shortly after the growth of staphylococci (day 7. A decrease of Listeria counts was observed on cheese surface inoculated at day 7 with 0.1-1 × 102 CFU cm-2, when cheeses were smeared with consortium F or M. Listeria counts went below the detection limit of the method between day 14 and 28 and no subsequent regrowth was detected over 60 to 80 ripening days. In contrast, Listeria grew to high counts (105 CFU cm-2 on cheeses smeared with a defined surface culture

  14. Architecture and High-Resolution Structure of Bacillus thuringiensis and Bacillus cereus Spore Coat Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Plomp, M; Leighton, T; Wheeler, K; Malkin, A

    2005-02-18

    We have utilized atomic force microscopy (AFM) to visualize the native surface topology and ultrastructure of Bacillus thuringiensis and Bacillus cereus spores in water and in air. AFM was able to resolve the nanostructure of the exosporium and three distinctive classes of appendages. Removal of the exosporium exposed either a hexagonal honeycomb layer (B. thuringiensis) or a rodlet outer spore coat layer (B. cereus). Removal of the rodlet structure from B. cereus spores revealed an underlying honeycomb layer similar to that observed with B. thuringiensis spores. The periodicity of the rodlet structure on the outer spore coat of B. cereus was {approx}8 nm, and the length of the rodlets was limited to the cross-patched domain structure of this layer to {approx}200 nm. The lattice constant of the honeycomb structures was {approx}9 nm for both B. cereus and B. thuringiensis spores. Both honeycomb structures were composed of multiple, disoriented domains with distinct boundaries. Our results demonstrate that variations in storage and preparation procedures result in architectural changes in individual spore surfaces, which establish AFM as a useful tool for evaluation of preparation and processing ''fingerprints'' of bacterial spores. These results establish that high-resolution AFM has the capacity to reveal species-specific assembly and nanometer scale structure of spore surfaces. These species-specific spore surface structural variations are correlated with sequence divergences in a spore core structural protein SspE.

  15. Nematic films at chemically structured surfaces

    Science.gov (United States)

    Silvestre, N. M.; Telo da Gama, M. M.; Tasinkevych, M.

    2017-02-01

    We investigate theoretically the morphology of a thin nematic film adsorbed at flat substrate patterned by stripes with alternating aligning properties, normal and tangential respectively. We construct a simple ‘exactly-solvable’ effective interfacial model where the liquid crystal distortions are accounted for via an effective interface potential. We find that chemically patterned substrates can strongly deform the nematic-air interface. The amplitude of this substrate-induced undulations increases with decreasing average film thickness and with increasing surface pattern pitch. We find a regime where the interfacial deformation may be described in terms of a material-independent universal scaling function. Surprisingly, the predictions of the effective interfacial model agree semi-quantitatively with the results of the numerical solution of a full model based on the Landau-de Gennes theory coupled to a square-gradient phase field free energy functional for a two phase system.

  16. Imprinted and injection-molded nano-structured optical surfaces

    Science.gov (United States)

    Christiansen, Alexander B.; Højlund-Nielsen, Emil; Clausen, Jeppe; Caringal, Gideon P.; Mortensen, N. Asger; Kristensen, Anders

    2013-09-01

    Inspired by nature, nano-textured surfaces have attracted much attention as a method to realize optical surface functionality. The moth-eye antireflective structure and the structural colors of Morpho butterflies are well- known examples used for inspiration for such biomimetic research. In this paper, nanostructured polymer surfaces suitable for up-scalable polymer replication methods, such as imprinting/embossing and injection-molding, are discussed. The limiting case of injection-moulding compatible designs is investigated. Anti-reflective polymer surfaces are realized by replication of Black Silicon (BSi) random nanostructure surfaces. The optical transmission at normal incidence is measured for wavelengths from 400 nm to 900 nm. For samples with optimized nanostructures, the reflectance is reduced by 50 % compared to samples with planar surfaces. The specular and diffusive reflection of light from polymer surfaces and their implication for creating structural colors is discussed. In the case of injection-moulding compatible designs, the maximum reflection of nano-scale textured surfaces cannot exceed the Fresnel reflection of a corresponding flat polymer surface, which is approx. 4 % for normal incidence. Diffraction gratings provide strong color reflection defined by the diffraction orders. However, the apperance varies strongly with viewing angles. Three different methods to address the strong angular-dependence of diffraction grating based structural color are discussed.

  17. Evolution of kinetically controlled In-induced surface structure on Si(5 5 7) surface

    Energy Technology Data Exchange (ETDEWEB)

    Chauhan, Amit Kumar Singh [Physics of Energy Harvesting, (CSIR-NPL), Dr. K.S. Krishnan Road, New Delhi 110012 (India); Department of Physics, JMI, New Delhi 110025 (India); Eldose, Nirosh M.; Mishra, Monu [Physics of Energy Harvesting, (CSIR-NPL), Dr. K.S. Krishnan Road, New Delhi 110012 (India); Niazi, Asad; Nair, Lekha [Department of Physics, JMI, New Delhi 110025 (India); Gupta, Govind, E-mail: govind@nplindia.org [Physics of Energy Harvesting, (CSIR-NPL), Dr. K.S. Krishnan Road, New Delhi 110012 (India)

    2014-09-30

    Highlights: • Evolution of In induced superstructures on Si(5 5 7) surface during RT and HT adsorption/desorption process. • Kinetics is governed by substrate temperature which exhibits various growth modes (FM, SK, VB) under different conditions. • Strain relaxation play significant role in the commencement of desorption/rearrangement of atoms. • A consolidated phase diagram of In/Si(5 5 7) interface has been reported with new √3 × √3-R30° and 4 × 1 phases. - Abstract: This paper introduces issue of kinetically controlled and temperature driven superstructural phase transition of Indium (In) on atomically clean high index Si(5 5 7)-7 × 1 surface. Auger electron spectroscopy analysis reveals that at room-temperature (RT) with a controlled incident flux of 0.002 ML/s; In overlayers evolve through the Frank-van der Merwe growth mode and yield a (1 × 1) diffraction pattern for coverage ≥1 ML. For substrate temperature <500°C, growth of In follows Stranski–Krastanov growth mode while for temperature >500°C island growth is observed. On annealing the In/Si(5 5 7) interface in the temperature range 250–340°C, clusters to two dimensional (2D) layer transformation on top of a stable monolayer is predominated. In-situ RT and HT adsorption and thermal desorption phenomena revealed the formation of coverage and temperature dependent thermally stable In induced superstructural phases such as (4 × 1) at 0.5 ML (520°C), (√3 × √3-R30°) at 0.3 ML (560°C) and (7 × 7) at 0.1 ML (580°C). These indium induced superstructures could be utilized as potential substrate for the growth of various exotic 1D/2D structures.

  18. Structured teleconnections reveal the South American monsoon onset: A network approach

    Science.gov (United States)

    Ciemer, Catrin; Ekhtiari, Nikoo; Barbosa, Henrique; Boers, Niklas; Donner, Reik; Kurths, Jürgen; Rammig, Anja; Winkelmann, Ricarda

    2017-04-01

    The regional onset dates of the global monsoon systems are, to first order, determined by the seasonal shift of the intertropical convergence zone. However, precise onset dates vary substantially from year to year due to the complexity of the involved mechanisms. In this study, we investigate processes determining the onset of the South American monsoon system (SAMS). In recent years, a trend towards later onset dates of the SAMS has been observed. A later onset of the monsoon can have severe impacts on agriculture and infrastructure such as farming, water transport routes, and the stability of the Amazon rainforest in the long term. Possible reasons for this shift involve a multitude of climatic phenomena and variables relevant for the SAMS. To account for the highly interactive nature of the SAMS, we here investigate it with the help of complex networks. By studying the temporal changes of the correlation structure in spatial rainfall networks, we are able to determine coherent areas of similar precipitation patterns, spot teleconnections in terms of strongly correlated areas, detect key regions for precipitation correlations, and finally reveal the monsoon onset by an abrupt shift from an unordered to an ordered correlation structure of the network. To further evaluate the shift in the monsoon onset, we couple our rainfall network to a network of climate networks using sea surface temperature as a second variable. We are thereby able to emphasize oceanic regions that are particularly important for the SAMS and anticipate the influence of future changes of sea-surface temperature on the SAMS.

  19. Structure sensitivity of CO dissociation on Rh surfaces

    DEFF Research Database (Denmark)

    Mavrikakis, Manos; Baumer, M.; Freund, H.J.;

    2002-01-01

    Using periodic self-consistent density functional calculations it is shown that the barrier for CO dissociation is similar to120 kJ/mol lower on the stepped Rh(211) surface than on the close-packed Rh(111) surface. The stepped surface binds molecular CO and the dissociation products more strongly...... than the flat surface, but the effect is considerably weaker than the effect of surface structure on the dissociation barrier. Our findings are compared with available experimental data, and the consequences for CO activation in methanation and Fischer-Tropsch reactions are discussed....

  20. The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology.

    Science.gov (United States)

    Tecon, Robin; Leveau, Johan H J

    2012-05-01

    Bacteria that colonize the leaves of terrestrial plants often occur in clusters whose size varies from a few to thousands of cells. For the formation of such bacterial clusters, two non-mutually exclusive but very different mechanisms may be proposed: aggregation of multiple cells or clonal reproduction of a single cell. Here we assessed the contribution of both mechanisms on the leaves of bean plants that were colonized by the bacterium Pantoea agglomerans. In one approach, we used a mixture of green and red fluorescent P. agglomerans cells to populate bean leaves. We observed that this resulted in clusters made up of only one colour as well as two-colour clusters, thus providing evidence for both mechanisms. Another P. agglomerans bioreporter, designed to quantify the reproductive success of bacterial colonizers by proxy to the rate at which green fluorescent protein is diluted from dividing cells, revealed that during the first hours on the leaf surface, many bacteria were dividing, but not staying together and forming clusters, which is suggestive of bacterial relocation. Together, these findings support a dynamic model of leaf surface colonization, where both aggregative and reproductive mechanisms take place. The bioreporter-based approach we employed here should be broadly applicable towards a more quantitative and mechanistic understanding of bacterial colonization of surfaces in general. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  1. Electronic structure of disordered alloys, surfaces and interfaces

    CERN Document Server

    Turek, Ilja; Kudrnovský, Josef; Šob, Mojmír; Weinberger, Peter

    1997-01-01

    At present, there is an increasing interest in the prediction of properties of classical and new materials such as substitutional alloys, their surfaces, and metallic or semiconductor multilayers. A detailed understanding based on a thus of the utmost importance for fu­ microscopic, parameter-free approach is ture developments in solid state physics and materials science. The interrela­ tion between electronic and structural properties at surfaces plays a key role for a microscopic understanding of phenomena as diverse as catalysis, corrosion, chemisorption and crystal growth. Remarkable progress has been made in the past 10-15 years in the understand­ ing of behavior of ideal crystals and their surfaces by relating their properties to the underlying electronic structure as determined from the first principles. Similar studies of complex systems like imperfect surfaces, interfaces, and mul­ tilayered structures seem to be accessible by now. Conventional band-structure methods, however, are of limited use ...

  2. Functional oxide structures on a surface of metals and alloys

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ The investigations of the plasma electrolytic processes in our laboratory are aimed to the development of conditions of formation of oxide layers with determined composition, structure and functional properties on the surface of valve metals (Al, Ti) and their alloys.

  3. Surface structure of polymer Gels and emerging functions

    CERN Document Server

    Kobiki, Y

    1999-01-01

    We report the surface structure of polymer gels on a submicrometer scale during the volume phase transition. Sponge-like domains with a mesoscopic scale were directly observed in water by using at atomic force microscope (AFM). The surface structure characterized by the domains is discussed in terms of the root-mean-square roughness and the auto-correlation function, which were calculated from the AFM images. In order to demonstrate the role of surface structure in determining the macroscopic properties of film-like poly (N-isopropylacrylamide: NIPA) gels. It was found that the temperature dependence, as well as the absolute values of the static contact angle, were strongly dependent on the bulk network inhomogeneities. The relation between the mesoscopic structure and the macroscopic properties is qualitatively discussed in terms of not only the changes in the chemical, but also in the physical, surface properties of the NIPA gels in response to a temperature change.

  4. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    Directory of Open Access Journals (Sweden)

    Vasily F. Shabanov

    2013-08-01

    Full Text Available Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface.

  5. Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

    Science.gov (United States)

    Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

    2014-04-28

    Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

  6. The effect of surfaces on the domain structure

    Science.gov (United States)

    Korneta, W.; Pytel, Z.

    1987-12-01

    The second-order phase transition from the paramagnetic phase to the ferromagnetic phase with domain structure in a ferromagnetic film with strong uniaxial anisotropy is studied. The easy axis is perpendicular to the surface of the film. It is assumed that the short range interactions depend on the distance to the surface. The phase diagram of the film and the form of the domain structure which occurs at the phase transition temperature are obtained.

  7. Underwater 3D Surface Scanning using Structured Light

    OpenAIRE

    Törnblom, Nils

    2010-01-01

    In this thesis project, an underwater 3D scanner based on structured light has been constructed and developed. Two other scanners, based on stereoscopy and a line-swept laser, were also tested. The target application is to examine objects inside the water filled reactor vessel of nuclear power plants. Structured light systems (SLS) use a projector to illuminate the surface of the scanned object, and a camera to capture the surfaces' reflection. By projecting a series of specific line-patterns...

  8. Dimers on Surface Graphs and Spin Structures. I

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai

    2007-01-01

    Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures.......Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures....

  9. Analysis of surface protein expression reveals the growth pattern of the gram-negative outer membrane.

    Directory of Open Access Journals (Sweden)

    Tristan S Ursell

    Full Text Available The outer membrane (OM of Gram-negative bacteria is a complex bilayer composed of proteins, phospholipids, lipoproteins, and lipopolysaccharides. Despite recent advances revealing the molecular pathways underlying protein and lipopolysaccharide incorporation into the OM, the spatial distribution and dynamic regulation of these processes remain poorly understood. Here, we used sequence-specific fluorescent labeling to map the incorporation patterns of an OM-porin protein, LamB, by labeling proteins only after epitope exposure on the cell surface. Newly synthesized LamB appeared in discrete puncta, rather than evenly distributed over the cell surface. Further growth of bacteria after labeling resulted in divergence of labeled LamB puncta, consistent with a spatial pattern of OM growth in which new, unlabeled material was also inserted in patches. At the poles, puncta remained relatively stationary through several rounds of division, a salient characteristic of the OM protein population as a whole. We propose a biophysical model of growth in which patches of new OM material are added in discrete bursts that evolve in time according to Stokes flow and are randomly distributed over the cell surface. Simulations based on this model demonstrate that our experimental observations are consistent with a bursty insertion pattern without spatial bias across the cylindrical cell surface, with approximately one burst of ≈ 10(-2 µm(2 of OM material per two minutes per µm(2. Growth by insertion of discrete patches suggests that stochasticity plays a major role in patterning and material organization in the OM.

  10. The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese.

    Directory of Open Access Journals (Sweden)

    Christophe Monnet

    Full Text Available Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

  11. Synthesis, Structure and Reactivity of Molecules Attached to Electrode Surfaces.

    Science.gov (United States)

    2014-09-26

    Structure and Reactivity of Molecules Attached to Electrode Surfaces", AFOSR #81-0149 III. REPORTING PERIOD: April 15, 1981 through April 14, 1985 IV...Adsorption .... ............... 17 9. Effect of Surface Roughness on Adsorbate Orientation and Reactivity . 20 10. Ordered/ Disordered Packing in Chemisorbed... reactivity only when present in the edge-pendant orientation. Clearly, molecular orientation (i.e., mode of +. .4 o,, -12- attachment to the surface) is a

  12. Electron-Hole Counting Approach to Surface Atomic Structure

    Science.gov (United States)

    Chadi, D. J.

    The observed reconstructions of III-V semiconductor surfaces are shown to be consistent with constraints imposed by a simple "electron-hole" counting rule proposed by Pashley. The rule ensures that the predicted surfaces are nonmetallic, nonpolar, and at least, metastable since the compensation of the "donor" electrons leaves no occupied states in the upper part of the band gap which can easily induce other reconstructions. Applications of the method to the problem of surface structure and passivation are examined.

  13. Effective Quantification of the Paper Surface 3D Structure

    OpenAIRE

    Fidjestøl, Svein

    2005-01-01

    This thesis covers the topic of image processing in relation to the segmentation and analysis of pores protruding the surface in the three dimensional surface structure of paper. The successful analysis of pores is related to a greater goal of relating such an analysis to the perceived quality of the surface of a paper sample. The first part of the thesis gives an introduction to the context of image processing in relation to paper research. Also, an overview of the image processing framewor...

  14. Orogen-scale anticline revealed in the Southern Alps of New Zealand by structural thermochronology

    Science.gov (United States)

    Zhou, Renjie; Brandon, Mark

    2017-04-01

    A dense set of cooling ages from the Southern Alps reveals an orogen-scale anticline of cooling-age isosurfaces (isochrones) and provides an interesting example of structural thermochronology, where isochrones are used as structural markers. The isochrone concept is an integral aspect of the age-elevation method, but the latter implicitly assumes that all isochrones are horizontal. Our experience in New Zeland and elsewhere is that isochrones are commonly tilted after formation. We use a more general approach that solves for orientation of the isochrone surfaces, and also the slope of the age-elevation trend, where "elevation" is measured normal to the isochrone surfaces. In New Zealand, collision and convergence between the Pacific and Australian plates have resulted in the formation and continuing growth of the Southern Alps, a prototypical orogenic wedge. In the western side, the Southern Alps is bounded by the Alpine fault, along with deeply exhumed rocks from depths up to 25 km. There are 150 apatite and 200 zircon fission-track (AFT, ZFT) ages that cover the vast region of the South Island of New Zealand from Lake Summer to Lake Wanaka. The AFT ages range from Letters, 2010, doi: 10.1016/j.epsl.2010.05.022). We use a least-squares method to solve for a best-fit sequence of dipping isochrone surfaces. The solution specifies the strike, dip and spacing of the parallel isochrones, the last of which indicates the velocity of the isochrones passing through the closure depth. We find that the calculation of the entire dataset failed to yield reasonable results, implying nonplanar structures at the regional scale. Using subsets of data, we observed three distinct zones of isochrones from E to W across the South Island. 1) The large area east of the Southern Alps in the central South Island contains ZFT isochrones that dip shallowly (young age and spacing, but dip 10-30 degrees to the west. Collectively, these observations indicate an anticlinal structure across the

  15. Surface structure of coherently strained ceria ultrathin films

    Science.gov (United States)

    Shi, Yezhou; Stone, Kevin H.; Guan, Zixuan; Monti, Matteo; Cao, Chuntian; El Gabaly, Farid; Chueh, William C.; Toney, Michael F.

    2016-11-01

    Cerium oxide, or ceria, is an important material for solid oxide fuel cells and water splitting devices. Although the ceria surface is active in catalytic and electrochemical reactions, how its catalytic properties are affected by the surface structure under operating conditions is far from understood. We investigate the structure of the coherently strained Ce O2 ultrathin films on yttria-stabilized zirconia (001) single crystals by specular synchrotron x-ray diffraction (XRD) under oxidizing conditions as a first step to study the surface structure in situ. An excellent agreement between the experiment data and the model is achieved by using a "stacks and islands" model that has a two-component roughness. One component is due to the tiny clusters of nanometer scale in lateral dimensions on each terrace, while the other component is due to slightly different Ce O2 thickness that span over hundreds of nanometers on neighboring terraces. We attribute the nonuniform thickness to step depairing during the thin film deposition that is supported by the surface morphology results on the microscopic level. Importantly, our model also shows that the polarity of the ceria surface is removed by a half monolayer surface coverage of oxygen. The successful resolution of the ceria surface structure using in situ specular synchrotron XRD paves the way to study the structural evolution of ceria as a fuel cell electrode under catalytically relevant temperatures and gas pressures.

  16. UGC 4599: Revealing the Extended Structure of a Hoag’s Object Analog with HERON

    Science.gov (United States)

    Fusco, Michael; Thilker, David A.; Wen, Fufang; Xia, Junjie; Storment, Stephen; Brosch, Noah; Longstaff, Francis; Kennefick, Julia D.; Rich, Robert Michael; Halos and Environments of Nearby galaxies (HERON) Team

    2017-01-01

    The Halos and Environments of Nearby Galaxies (HERON) survey utilizes a specialized telescope for imaging low surface brightness halos and galaxy environments. One such galaxy is UGC 4599, whose HERON images show improvements in observing the extended low luminosity structure as compared to previous studies. UGC 4599 is a nearby Hoag-Type Ring Galaxy with an extremely extended HI disk. Hoag's Object is characterized by a blue star-forming ring surrounding an older yellow nucleus. In the case of UGC 4599, the nuclear region was previously revealed to closely follow a De Vaucouleurs luminosity profile, suggesting the object to be at least elliptical-like. While previous photometric studies of UGC 4599 were focused mainly on the bright core and star forming ring of the galaxy, the HERON survey is able to probe the fainter, extended halo. With an eight hour integration time, we find spiral structure surrounding the core and ring of UGC 4599. The main ring of the galaxy is broken with an m=2 (180 degree) symmetry, suggesting a two armed spiral structure. However, once the core and ring of UGC 4599 are modeled with the software GALFIT, a well defined m=1 (single arm) spiral emerges, extending from the central region to several times the radius of the ring. Though the ring appears to break in two places, the spiral structure may be comprised of mainly one dominant arm. In late type galaxies, the pitch angle of spiral arms has been shown to correlate well with the mass of the central Supermassive Black Hole (SMBH) in an M-P relation. The pitch angle of the one arm spiral of UGC 4599 is measured to be roughly P=9 degrees, corresponding to a SMBH mass for UGC 4599 of between 107 and 108 solar masses (further constrained pitch angle measurements forthcoming). The outermost edge of UGC 4599 as detected in our imaging may be modeled as an extension of this one armed spiral, or as yet another ring feature. Due to many bright foreground stars, there is difficulty in ascertaining

  17. Laser Induced Periodic Surface Structures induced by surface plasmons coupled via roughness

    Science.gov (United States)

    Gurevich, E. L.; Gurevich, S. V.

    2014-05-01

    In this paper the formation mechanisms of the femtosecond laser-induced periodic surface structures (LIPSS) are discussed. One of the most frequently used theories explains the structures by interference between the incident laser beam and surface plasmon-polariton waves. The latter is most commonly attributed to the coupling of the incident laser light to the surface roughness. We demonstrate that this excitation of surface plasmons contradicts the results of laser-ablation experiments. As an alternative approach to the excitation of LIPSS we analyse development of hydrodynamic instabilities in the melt layer.

  18. Laser Induced Periodic Surface Structures induced by surface plasmons coupled via roughness

    Energy Technology Data Exchange (ETDEWEB)

    Gurevich, E.L., E-mail: gurevich@lat.rub.de [Chair of Applied Laser Technology, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum (Germany); Gurevich, S.V., E-mail: gurevics@uni-muenster.de [Institute for Theoretical Physics, University of Münster, Wilhelm-Klemm-Straße 9, 48149 Münster (Germany)

    2014-05-01

    In this paper the formation mechanisms of the femtosecond laser-induced periodic surface structures (LIPSS) are discussed. One of the most frequently used theories explains the structures by interference between the incident laser beam and surface plasmon-polariton waves. The latter is most commonly attributed to the coupling of the incident laser light to the surface roughness. We demonstrate that this excitation of surface plasmons contradicts the results of laser-ablation experiments. As an alternative approach to the excitation of LIPSS we analyse development of hydrodynamic instabilities in the melt layer.

  19. Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias toward the Bacterial Surface

    Science.gov (United States)

    Dowdell, Alexander S.; Murphy, Maxwell D.; Azodi, Christina; Swanson, Selene K.; Florens, Laurence

    2017-01-01

    ABSTRACT The Lyme disease spirochete Borrelia burgdorferi is unique among bacteria in its large number of lipoproteins that are encoded by a small, exceptionally fragmented, and predominantly linear genome. Peripherally anchored in either the inner or outer membrane and facing either the periplasm or the external environment, these lipoproteins assume varied roles. A prominent subset of lipoproteins functioning as the apparent linchpins of the enzootic tick-vertebrate infection cycle have been explored as vaccine targets. Yet, most of the B. burgdorferi lipoproteome has remained uncharacterized. Here, we comprehensively and conclusively localize the B. burgdorferi lipoproteome by applying established protein localization assays to a newly generated epitope-tagged lipoprotein expression library and by validating the obtained individual protein localization results using a sensitive global mass spectrometry approach. The derived consensus localization data indicate that 86 of the 125 analyzed lipoproteins encoded by B. burgdorferi are secreted to the bacterial surface. Thirty-one of the remaining 39 periplasmic lipoproteins are retained in the inner membrane, with only 8 lipoproteins being anchored in the periplasmic leaflet of the outer membrane. The localization of 10 lipoproteins was further defined or revised, and 52 surface and 23 periplasmic lipoproteins were newly localized. Cross-referencing prior studies revealed that the borrelial surface lipoproteome contributing to the host-pathogen interface is encoded predominantly by plasmids. Conversely, periplasmic lipoproteins are encoded mainly by chromosomal loci. These studies close a gap in our understanding of the functional lipoproteome of an important human pathogen and set the stage for more in-depth studies of thus-far-neglected spirochetal lipoproteins. IMPORTANCE The small and exceptionally fragmented genome of the Lyme disease spirochete Borrelia burgdorferi encodes over 120 lipoproteins. Studies in the

  20. Osteoblast Behavior on Hierarchical Micro-/Nano-Structured Titanium Surface

    Institute of Scientific and Technical Information of China (English)

    Weiyan Meng; Yanmin Zhou; Yanjing Zhang; Qing Cai; Liming Yang; Jinghui Zhao; Chnnyan Li

    2011-01-01

    In the present work, osteoblast behavior on a hierarchical micro-/nano-structured titanium surface was investigated. A hierarchical hybrid micro-/nano-structured titanium surface topography was produced via Electrolytic Etching (EE). MG-63 cells were cultured on disks for 2 h to 7 days. The osteoblast response to the hierarchical hybrid micro-/nano-structured titanium surface was evaluated through the osteoblast cell morphology, attachment and proliferation. For comparison, MG-63 cells were also cultured on Sandblasted and Acid-etched (SLA) as well as Machined (M) surfaces respectively. The results show significant differences in the adhesion rates and proliferation levels of MG-63 cells on EE, SLA, and M surfaces. Both adhesion rate and proliferation level on EE surface are higher than those on SLA and M surfaces. Therefore, we may expect that, comparing with SLA and M surfaces, bone growth on EE surface could be accelerated and bone formation could be promoted at an early stage, which could be applied in the clinical practices for immediate and early-stage loadings.

  1. Structures of multidomain proteins adsorbed on hydrophobic interaction chromatography surfaces.

    Science.gov (United States)

    Gospodarek, Adrian M; Sun, Weitong; O'Connell, John P; Fernandez, Erik J

    2014-12-05

    In hydrophobic interaction chromatography (HIC), interactions between buried hydrophobic residues and HIC surfaces can cause conformational changes that interfere with separations and cause yield losses. This paper extends our previous investigations of protein unfolding in HIC chromatography by identifying protein structures on HIC surfaces under denaturing conditions and relating them to solution behavior. The thermal unfolding of three model multidomain proteins on three HIC surfaces of differing hydrophobicities was investigated with hydrogen exchange mass spectrometry (HXMS). The data were analyzed to obtain unfolding rates and Gibbs free energies for unfolding of adsorbed proteins. The melting temperatures of the proteins were lowered, but by different amounts, on the different surfaces. In addition, the structures of the proteins on the chromatographic surfaces were similar to the partially unfolded structures produced in the absence of a surface by temperature as well as by chemical denaturants. Finally, it was found that patterns of residue exposure to solvent on different surfaces at different temperatures can be largely superimposed. These findings suggest that protein unfolding on various HIC surfaces might be quantitatively related to protein unfolding in solution and that details of surface unfolding behavior might be generalized.

  2. Upper mantle structure of the Pacific and Philippine Sea plates revealed by seafloor seismic array observations

    Science.gov (United States)

    Isse, Takehi; Shiobara, Hajime; Suetsugu, Daisuke; Sugioka, Hiroko; Ito, Aki

    2016-04-01

    Seismic tomography studies have revealed the structure and dynamics of Earth's interior since the 1980s. However, the spatial resolution of the oceanic region is not good enough caused by sparse distribution of the seismic stations. The observations with broadband ocean-bottom seismographs (BBOBSs) since the 2000s enabled us to obtain seismic tomography models with higher spatial resolution. Our Japanese BBOBS group deployed more than 100 BBOBSs in the Pacific Ocean and obtained a high-resolution (300-500 km) three-dimensional shear wave velocity structure in the upper mantle beneath northwestern and south Pacific Ocean by using surface wave tomography technique. In the northwestern Pacific Ocean, where the Pacific plate subducts beneath the Philippine Sea plate, we found that the shear wave structure in the Philippine sea plate is well correlated with the seafloor age in the upper 120 km, three separate slow anomalies in the mantle wedge at depth shallower than 100 km beneath the Izu-Bonin-Mariana arc, which have a close relationship with the three groups of frontal and rear arc volcanoes having distinct Sr, Nd, and Pb isotope ratios, and that the Philippine Sea plate, which is a single plate, shows very large lateral variations in azimuthal and radial anisotropies compared with the Pacific plate. In the South Pacific Ocean, where midplate hotspots are concentrated, we found that the localized slow anomalies are found near hotspots in the upper mantle, estimated thickness of the lithosphere is about 90 km in average and is thinned by ~20 km in the vicinity of hotspots, which may represent thermal erosion due to mantle plumes.

  3. Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating.

    Science.gov (United States)

    Seitsonen, Jani J T; Shakeel, Shabih; Susi, Petri; Pandurangan, Arun P; Sinkovits, Robert S; Hyvönen, Heini; Laurinmäki, Pasi; Ylä-Pelto, Jani; Topf, Maya; Hyypiä, Timo; Butcher, Sarah J

    2012-07-01

    Coxsackievirus A7 (CAV7) is a rarely detected and poorly characterized serotype of the Enterovirus species Human enterovirus A (HEV-A) within the Picornaviridae family. The CAV7-USSR strain has caused polio-like epidemics and was originally thought to represent the fourth poliovirus type, but later evidence linked this strain to the CAV7-Parker prototype. Another isolate, CAV7-275/58, was also serologically similar to Parker but was noninfectious in a mouse model. Sequencing of the genomic region encoding the capsid proteins of the USSR and 275/58 strains and subsequent comparison with the corresponding amino acid sequences of the Parker strain revealed that the Parker and USSR strains are nearly identical, while the 275/58 strain is more distant. Using electron cryomicroscopy and three-dimensional image reconstruction, the structures of the CAV7-USSR virion and empty capsid were resolved to 8.2-Å and 6.1-Å resolutions, respectively. This is one of the first detailed structural analyses of the HEV-A species. Using homology modeling, reconstruction segmentation, and flexible fitting, we constructed a pseudoatomic T = 1 (pseudo T = 3) model incorporating the three major capsid proteins (VP1 to VP3), addressed the conformational changes of the capsid and its constituent viral proteins occurring during RNA release, and mapped the capsid proteins' variable regions to the structure. During uncoating, VP4 and RNA are released analogously to poliovirus 1, the interfaces of VP2 and VP3 are rearranged, and VP1 rotates. Variable regions in the capsid proteins were predicted to map mainly to the surface of VP1 and are thus likely to affect the tropism and pathogenicity of CAV7.

  4. Structural changes of radial forging die surface during service under thermo-mechanical fatigue

    Energy Technology Data Exchange (ETDEWEB)

    Nematzadeh, Fardin [Materials and Energy Research Center, Tehran (Iran, Islamic Republic of); Akbarpour, Mohammad Reza, E-mail: mreza.akbarpour@gmail.com [Materials and Energy Research Center, Tehran (Iran, Islamic Republic of); Kokabi, Amir Hosein; Sadrnezhaad, Seyed Khatiboleslam [Department of Materials Science and Engineering, Sharif University of Technology, Tehran (Iran, Islamic Republic of)

    2009-12-15

    Radial forging is one of the modern open die forging techniques and has a wide application in producing machine parts. During operation at high temperatures, severe temperature change associated with mechanical loads and the resultant wearing of the die surface lead to intense variation in strain on the die surface. Therefore, under this operating condition, thermo-mechanical fatigue (TMF) occurs on the surface of the radial forging die. TMF decreases the life of the die severely. In the present research, different layers were deposited on a 1.2714 steel die by SMAW and GTAW, with a weld wire of UDIMET 520. The microstructure of the radial forging die surface was investigated during welding and service using an optical microscope and scanning electron microscope. The results revealed that, after welding, the structure of the radial forging die surface includes the {gamma} matrix with a homogeneous distribution of fine semi-spherical carbides. The weld structure consisted mostly of columnar dendrites with low grain boundaries. Also, microstructural investigation of the die surface during operation showed that the weld structure of the die surface has remained without any considerable change. Only dendrites were deformed and broken. Moreover, grain boundaries of the dendrites were revealed during service.

  5. Color effects from scattering on random surface structures in dielectrics

    DEFF Research Database (Denmark)

    Clausen, Jeppe; Christiansen, Alexander B; Garnæs, Jørgen;

    2012-01-01

    We show that cheap large area color filters, based on surface scattering, can be fabricated in dielectric materials by replication of random structures in silicon. The specular transmittance of three different types of structures, corresponding to three different colors, have been characterized....... The angle resolved scattering has been measured and compared to predictions based on the measured surface topography and by the use of non-paraxial scalar diffraction theory. From this it is shown that the color of the transmitted light can be predicted from the topography of the randomly textured surfaces....

  6. Bionic Duplication of Fresh Navodon septentrionalis Fish Surface Structures

    Directory of Open Access Journals (Sweden)

    Bing Qu

    2011-01-01

    Full Text Available Biomimetic superhydrophobic surface was fabricated by replicating topography of the fresh fish skin surface of Navodon septentrionalis with polydimethylsiloxane (PDMS elastomer. A two-step replicating method was developed to make the surface structure of the fresh fish skin be replicated with high fidelity. After duplication, it was found that the static contact angle of the replica was as large as 173°. Theoretic analysis based on Young's and Cassie-Baxter (C-B model was performed to explain the relationship between structure and hydrophobicity.

  7. Femtosecond laser-induced periodic surface structures on silica

    Energy Technology Data Exchange (ETDEWEB)

    Hoehm, S.; Rosenfeld, A. [Max-Born-Institut fuer Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Strasse 2A, D-12489 Berlin (Germany); Krueger, J.; Bonse, J. [BAM Bundesanstalt fuer Materialforschung und-pruefung, Unter den Eichen 87, D-12205 Berlin (Germany)

    2012-07-01

    The formation of laser-induced periodic surface structures (LIPSS) on two different silica polymorphs (single-crystalline synthetic quartz and commercial fused silica glass) upon irradiation in air with multiple linearly polarized single- and double-fs-laser pulse sequences ({tau} = 150 fs pulse duration, {lambda} = 800 nm center wavelength, temporal pulse separation {Delta}t < 40 ps) is studied experimentally and theoretically. Two distinct types of fs-LIPSS [so-called low-spatial-frequency LIPSS (LSFL) and high-spatial-frequency LIPSS (HSFL)] with different spatial periods and orientations were identified. Their appearance was characterized with respect to the experimental parameters peak laser fluence and number of laser pulses per spot. Additionally, the 'dynamics' of the LIPSS formation was addressed in complementary double-fs-pulse experiments with varying delays, revealing a characteristic change of the LSFL periods. The experimental results are interpreted on the basis of a Sipe-Drude model considering the carrier dependence of the optical properties of fs-laser excited silica. This new approach provides an explanation of the LSFL orientation parallel to the laser beam polarisation in silica - as opposed to the behaviour of most other materials.

  8. Micro-structuring of polycarbonate-urethane surfaces in order to reduce platelet activation and adhesion.

    Science.gov (United States)

    Clauser, Johanna; Gester, Kathrin; Roggenkamp, Jan; Mager, Ilona; Maas, Judith; Jansen, Sebastian V; Steinseifer, Ulrich

    2014-01-01

    In the development of new hemocompatible biomaterials, surface modification appears to be a suitable method in order to reduce the thrombogenetic potential of such materials. In this study, polycarbonate-urethane (PCU) tubes with different surface microstructures to be used for aortic heart valve models were investigated with regard to the thrombogenicity. The surface structures were produced by using a centrifugal casting process for manufacturing PCU tubes with defined casting mold surfaces which are conferred to the PCU surface during the process. Tubes with different structures defined by altering groove widths were cut into films and investigated under dynamic flow conditions in contact with porcine blood. The analysis was carried out by laser scanning microscopy which allowed for counting various morphological types of platelets with regard to the grade of activation. The comparison between plain and shaped PCU samples showed that the surface topography led to a decline of the activation of the coagulation cascade and thus to the reduction of the fibrin synthesis. Comparing different types of structures revealed that smooth structures with a small groove width (d ~ 3 μm) showed less platelet activation as well as less adhesion in contrast to a distinct wave structure (d ~ 90 μm). These results prove surface modification of polymer biomaterials to be a suitable method for reducing thrombogenicity and hence give reason for further alterations and improvements.

  9. Surface N-glycoproteome patterns reveal key proteins of neuronal differentiation.

    Science.gov (United States)

    Tyleckova, Jirina; Valekova, Ivona; Zizkova, Martina; Rakocyova, Michaela; Marsala, Silvia; Marsala, Martin; Gadher, Suresh Jivan; Kovarova, Hana

    2016-01-30

    Pluripotent stem cell-derived committed neural precursors are an important source of cells to treat neurodegenerative diseases including spinal cord injury. There remains an urgency to identify markers for monitoring of neural progenitor specificity, estimation of neural fate and follow-up correlation with therapeutic effect in preclinical studies using animal disease models. Cell surface capture technology was used to uncover the cell surface exposed N-glycoproteome of neural precursor cells upon neuronal differentiation as well as post-mitotic mature hNT neurons. The data presented depict an extensive study of surfaceome during neuronal differentiation, confirming glycosylation at a particular predicted site of many of the identified proteins. Quantitative changes detected in cell surface protein levels reveal a set of proteins that highlight the complexity of the neuronal differentiation process. Several of these proteins including the cell adhesion molecules ICAM1, CHL1, and astrotactin1 as well as LAMP1 were validated by SRM. Combination of immunofluorescence staining of ICAM1 and flow cytometry indicated a possible direction for future scrutiny of such proteins as targets for enrichment of the neuronal subpopulation from mixed cultures after differentiation of neural precursor cells. These surface proteins hold an important key for development of safe strategies in cell-replacement therapies of neuronal disorders. Neural stem and/or precursor cells have a great potential for cell-replacement therapies of neuronal diseases. Availability of well characterised and expandable neural cell lineage specific populations is critical for addressing such a challenge. In our study we identified and relatively quantified several hundred surface N-glycoproteins in the course of neuronal differentiation. We further confirmed the abundant changes for several cell adhesion proteins by SRM and outlined a strategy for utilisation of such N-glycoproteins in antibody based cell

  10. Structure and electronic properties of graphene on ferroelectric LiNbO{sub 3} surface

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Jun, E-mail: dingjun@haue.edu.cn [College of Science, Henan University of Engineering, Zhengzhou 451191 (China); Wen, LiWei; Li, HaiDong [College of Science, Henan University of Engineering, Zhengzhou 451191 (China); Zhang, Ying, E-mail: yingzhang@bnu.edu.cn [Department of Physics, Beijing Normal University, Beijing 100875 (China)

    2017-05-25

    Highlights: • Interface structure of graphene on O terminated LiNbO{sub 3} surface. • Asymmetry gap around Dirac point. • Berry phase calculations confirm a valley Hall effect. - Abstract: We investigate the structural and electronic properties of graphene on the O terminated LiNbO{sub 3}(001) surface by density functional theory simulations. We observe that the first graphene layer is covalent bonded with the surface O atoms and buckles a lot. While considering second layer graphene upon the first layer, it almost recovers the planar structure and the interface interaction breaks the AB sublattice symmetry which leads to a valley Hall effect. Our results reveal the interface structure of graphene-ferroelectric heterostructure and provide the way for valleytronic applications with graphene.

  11. Riblet Sensor -- Light Scattering on Micro Structured Surface Coatings

    CERN Document Server

    Imlau, Mirco; Voit, Kay-Michael; Tschentscher, Juliane; Dieckmann, Volker

    2016-01-01

    With the application of appropriate surface structuring on aircrafts, up to 8\\% fuel may be saved in regular air traffic. Before these techniques can be introduced into productive environments, a controlling method for the quality of surface structuring is needed to be used during fabrication and service, ensuring persistent quality of the structured coatings and a justified decision for surface renewal. In this project, these important requirements for achieving the improvements defined above are fulfilled. We have shown that fast sampling is possible using noncontacting laser probing, and we have presented a working preliminary configuration for the sensor. In the theoretical part, a model for the interaction between a probing laser beam and the surface is developed and the resulting wavefront is derived. This is done using a combination of Huygens-Fresnel diffraction theory and geometrical optics. The model is then used to counsel the design of the experimental setup, to interpret the emerging data and to ...

  12. Structure of adsorbed monolayers. The surface chemical bond

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.; Bent, B.E.

    1984-06-01

    This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table.

  13. Surface Structures Formed by a Copper(II Complex of Alkyl-Derivatized Indigo

    Directory of Open Access Journals (Sweden)

    Akinori Honda

    2016-10-01

    Full Text Available Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM analysis revealed that the copper(II complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed.

  14. Surface Polysaccharide Mutants Reveal that Absence of O Antigen Reduces Biofilm Formation of Actinobacillus pleuropneumoniae.

    Science.gov (United States)

    Hathroubi, S; Hancock, M A; Bossé, J T; Langford, P R; Tremblay, Y D N; Labrie, J; Jacques, M

    2015-10-19

    Actinobacillus pleuropneumoniae is a Gram-negative bacterium belonging to the Pasteurellaceae family and the causative agent of porcine pleuropneumonia, a highly contagious lung disease causing important economic losses. Surface polysaccharides, including lipopolysaccharides (LPS) and capsular polysaccharides (CPS), are implicated in the adhesion and virulence of A. pleuropneumoniae, but their role in biofilm formation is still unclear. In this study, we investigated the requirement for these surface polysaccharides in biofilm formation by A. pleuropneumoniae serotype 1. Well-characterized mutants were used: an O-antigen LPS mutant, a truncated core LPS mutant with an intact O antigen, a capsule mutant, and a poly-N-acetylglucosamine (PGA) mutant. We compared the amount of biofilm produced by the parental strain and the isogenic mutants using static and dynamic systems. Compared to the findings for the biofilm of the parental or other strains, the biofilm of the O antigen and the PGA mutants was dramatically reduced, and it had less cell-associated PGA. Real-time PCR analyses revealed a significant reduction in the level of pgaA, cpxR, and cpxA mRNA in the biofilm cells of the O-antigen mutant compared to that in the biofilm cells of the parental strain. Specific binding between PGA and LPS was consistently detected by surface plasmon resonance, but the lack of O antigen did not abolish these interactions. In conclusion, the absence of the O antigen reduces the ability of A. pleuropneumoniae to form a biofilm, and this is associated with the reduced expression and production of PGA. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Novel Secondary Structure of Calcitonin in Solid State as Revealed by Circular Dichroism Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    DU,Hai-Ning(杜海宁); DING,Jin-Guo(丁金国); CUI,Da-Fu(崔大敷); HU,Hong-Yu(胡红雨)

    2002-01-01

    The solid-state circular dichroic study reveals that salmon calcitonin presents a typical α-helical structure while human calcitonin appears to form a β-sheet in solid state, although both of them adopt random coil structures in aqueous solution.

  16. Formation of Surface Corrosion-Resistant Nanocrystalline Structures on Steel.

    Science.gov (United States)

    Nykyforchyn, Hryhoriy; Kyryliv, Volodymyr; Maksymiv, Olha; Slobodyan, Zvenomyra; Tsyrulnyk, Oleksandr

    2016-12-01

    Engineering materials with nanocrystalline structure could be exploited under simultaneous action of mechanical loading and corrosion environments; therefore, their corrosion resistance is important. Surface nanocrystalline structure was generated on middle carbon steels by severe plastic deformation using the method of mechanical pulse friction treatment. This treatment additionally includes high temperature phase transformation and alloying. Using a complex of the corrosive, electrochemical and physical investigations, it was established that nanocrystalline structures can be characterized by lower or increased corrosion resistance in comparison with the reference material. It is caused by the action of two confronting factors: arising energy level and anticorrosive alloying of the surface layer.

  17. Surface Appendages of Archaea: Structure, Function, Genetics and Assembly

    Directory of Open Access Journals (Sweden)

    Sarah Siu

    2013-01-01

    Full Text Available Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain.

  18. Sliding surface searching method for slopes containing a potential weak structural surface

    Directory of Open Access Journals (Sweden)

    Aijun Yao

    2014-06-01

    Full Text Available Weak structural surface is one of the key factors controlling the stability of slopes. The stability of rock slopes is in general concerned with set of discontinuities. However, in soft rocks, failure can occur along surfaces approaching to a circular failure surface. To better understand the position of potential sliding surface, a new method called simplex-finite stochastic tracking method is proposed. This method basically divides sliding surface into two parts: one is described by smooth curve obtained by random searching, the other one is polyline formed by the weak structural surface. Single or multiple sliding surfaces can be considered, and consequently several types of combined sliding surfaces can be simulated. The paper will adopt the arc-polyline to simulate potential sliding surface and analyze the searching process of sliding surface. Accordingly, software for slope stability analysis using this method was developed and applied in real cases. The results show that, using simplex-finite stochastic tracking method, it is possible to locate the position of a potential sliding surface in the slope.

  19. Sliding surface searching method for slopes containing a potential weak structural surface

    Institute of Scientific and Technical Information of China (English)

    Aijun Yao; Zhizhou Tian; Yongjun Jin

    2014-01-01

    Weak structural surface is one of the key factors controlling the stability of slopes. The stability of rock slopes is in general concerned with set of discontinuities. However, in soft rocks, failure can occur along surfaces approaching to a circular failure surface. To better understand the position of potential sliding surface, a new method called simplex-finite stochastic tracking method is proposed. This method basically divides sliding surface into two parts: one is described by smooth curve obtained by random searching, the other one is polyline formed by the weak structural surface. Single or multiple sliding surfaces can be considered, and consequently several types of combined sliding surfaces can be simu-lated. The paper will adopt the arc-polyline to simulate potential sliding surface and analyze the searching process of sliding surface. Accordingly, software for slope stability analysis using this method was developed and applied in real cases. The results show that, using simplex-finite stochastic tracking method, it is possible to locate the position of a potential sliding surface in the slope.

  20. The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

    OpenAIRE

    Yurtsever, Zeynep; Scheaffer, Suzanne M.; Romero, Arthur G.; Holtzman, Michael J.; Brett, Tom J.

    2015-01-01

    The p38 MAP kinases are an important family of drug targets for a myriad of inflammatory, as well as other, diseases. Presented here is the crystal structure of the active form of MAPK13 (p38d) as well as a comprehensive analysis of all known apo inactive and active p38 MAPK structures, revealing a common mode of activation as well as some unique structural features.

  1. Nanoscale Structuring of Surfaces by Using Atomic Layer Deposition.

    Science.gov (United States)

    Sobel, Nicolas; Hess, Christian

    2015-12-01

    Controlled structuring of surfaces is interesting for a wide variety of areas, including microelectronic device fabrication, optical devices, bio(sensing), (electro-, photo)catalysis, batteries, solar cells, fuel cells, and sorption. A unique feature of atomic layer deposition (ALD) is the possibility to form conformal uniform coatings on arbitrarily shaped materials with controlled atomic-scale thickness. In this Minireview, we discuss the potential of ALD for the nanoscale structuring of surfaces, highlighting its versatile application to structuring both planar substrates and powder materials. Recent progress in the application of ALD to porous substrates has even made the nanoscale structuring of high-surface-area materials now feasible, thereby enabling novel applications, such as those in the fields of catalysis and alternative energy.

  2. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting

    National Research Council Canada - National Science Library

    Hassan, Md Imtaiyaz; Waheed, Abdul; Grubb, Jeffery H; Klei, Herbert E; Korolev, Sergey; Sly, William S

    2013-01-01

    ...). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases...

  3. High Resolution Crystal Structure of Human [beta]-Glucuronidase Reveals Structural Basis of Lysosome Targeting

    National Research Council Canada - National Science Library

    Hassan, Md; Waheed, Abdul; Grubb, Jeffery; Klei, Herbert; Korolev, Sergey; Sly, William

    2013-01-01

    ...). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases...

  4. Sorting of droplets by migration on structured surfaces

    Directory of Open Access Journals (Sweden)

    Wilfried Konrad

    2011-04-01

    Full Text Available Background: Controlled transport of microdroplets is a topic of interest for various applications. It is well known that liquid droplets move towards areas of minimum contact angle if placed on a flat solid surface exhibiting a gradient of contact angle. This effect can be utilised for droplet manipulation. In this contribution we describe how controlled droplet movement can be achieved by a surface pattern consisting of cones and funnels whose length scales are comparable to the droplet diameter.Results: The surface energy of a droplet attached to a cone in a symmetry-preserving way can be smaller than the surface energy of a freely floating droplet. If the value of the contact angle is fixed and lies within a certain interval, then droplets sitting initially on a cone can gain energy by moving to adjacent cones.Conclusion: Surfaces covered with cone-shaped protrusions or cavities may be devised for constructing “band-conveyors” for droplets. In our approach, it is essentially the surface structure which is varied, not the contact angle. It may be speculated that suitably patterned surfaces are also utilised in biological surfaces where a large variety of ornamentations and surface structuring are often observed.

  5. The Moisture Structure of ISO in Western North Pacific Revealed by AIRS

    Institute of Scientific and Technical Information of China (English)

    TAO Li; FU Xiouhua; WANG Bin

    2009-01-01

    Using the humidity profiles from the Atmospheric Infrared Sounder (AIRS) dataset, rainfall from the Tropical Rainfall Measuring Mission (TRMM) Global Precipitation Index (GPI), and surface winds from QuickSCAT (QSCAT) as well as SST from the Advanced Microwave Scanning Radiometer for NASA's Earth Observing System (AMSR_E), we analyzed the structure of summer intraseasonal oscillation (ISO) over the western North Pacific region in 2003-2004. We find that the signal of 20-90-day oscillations in the western North Pacific originates from the equatorial Indian Ocean, and propagates eastward to Philippine Sea and then moves northwestward to South China. The AIRS humidity data reveal that the boundary-layer moisture leads the mid-troposphere moisture during the ISO propagation. The positive SST anomaly may play an important role to moistening the boundary-layer, which preconditions the ISO propagation. Therefore, the intraseasonal SST anomaly could positively feed back to the atmosphere through moistening the boundary-layer, destabilizing the troposphere, and contributing to the northwestward propagation of the ISO in western North Pacific. On the other hand, the salient feature that the boundary-layer moisture anomaly leads mid-troposphere moisture does not exist in ECMWF/TOGA analysis.

  6. Femtosecond diffraction dynamics of laser-induced periodic surface structures on fused silica

    Energy Technology Data Exchange (ETDEWEB)

    Hoehm, S.; Rosenfeld, A. [Max-Born-Institut fuer Nichtlineare Optik und Kurzzeitspektroskopie (MBI), Max-Born-Strasse 2A, D-12489 Berlin (Germany); Krueger, J.; Bonse, J. [BAM Bundesanstalt fuer Materialforschung und - pruefung, Unter den Eichen 87, D-12205 Berlin (Germany)

    2013-02-04

    The formation of laser-induced periodic surface structures (LIPSS) on fused silica upon irradiation with linearly polarized fs-laser pulses (50 fs pulse duration, 800 nm center wavelength) is studied experimentally using a transillumination femtosecond time-resolved (0.1 ps-1 ns) pump-probe diffraction approach. This allows to reveal the generation dynamics of near-wavelength-sized LIPSS showing a transient diffraction at specific spatial frequencies even before a corresponding permanent surface relief was observed. The results confirm that the ultrafast energy deposition to the materials surface plays a key role and triggers subsequent physical mechanisms such as carrier scattering into self-trapped excitons.

  7. 10Be surface exposure dating reveals strong active deformation in the central Andean backarc interior

    Science.gov (United States)

    García Morabito, Ezequiel; Terrizzano, Carla; Zech, Roland; Willett, Sean; Yamin, Marcela; Haghipour, Negar; Wuethrich, Lorenz; Christl, Marcus; María Cortes, José; Ramos, Victor

    2016-04-01

    Understanding the deformation associated with active thrust wedges is essential to evaluate seismic hazard. How is active faulting distributed throughout the wedge, and how much deformation is taken up by individual structures? We address these questions for our study region, the central Andean backarc of Argentina. We combined a structural and geomorphological approach with surface exposure dating (10Be) of alluvial fans and strath terraces in two key localities at ~32° S: the Cerro Salinas, located in the active orogenic front of the Precordillera, and the Barreal block in the interior of the Andean mountain range. We analysed 22 surface samples and 6 depth profiles. At the thrust front, the oldest terrace (T1) yields an age of 100-130 ka, the intermediate terrace (T2) between 40-95 ka, and the youngest terrace (T3) an age of ~20 ka. In the Andean interior, T1´ dates to 117-146 ka, T2´ to ~70 ka, and T3´ to ~20 ka, all calculations assuming negligible erosion and using the scaling scheme for spallation based on Lal 1991, Stone 2000. Vertical slip rates of fault offsets are 0.3-0.5 mm/yr and of 0.6-1.2 mm/yr at the thrust front and in the Andean interior, respectively. Our results highlight: i) fault activity related to the growth of the Andean orogenic wedge is not only limited to a narrow thrust front zone. Internal structures have been active during the last 150 ka, ii) deformation rates in the Andean interior are comparable or even higher that those estimated and reported along the emerging thrust front, iii) distribution of active faulting seems to account for unsteady state conditions, and iv) seismic hazards may be more relevant in the internal parts of the Andean orogen than assumed so far. References Lal, D., 1991: Cosmic ray labeling of erosion surfaces: In situ nuclide production rates and erosion models. Earth and Planetary Science Letters 104: 424-439. Stone, J.O., 2000: Air pressure and cosmogenic isotope production. Journal of Geophysical

  8. Understanding surface structure and chemistry of single crystal lanthanum aluminate

    KAUST Repository

    Pramana, Stevin S.

    2017-03-02

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10−10 Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10−6 Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures.

  9. Fabrication of micro/nano hierarchical structures with analysis on the surface mechanics

    Science.gov (United States)

    Jheng, Yu-Sheng; Lee, Yeeu-Chang

    2016-10-01

    Biomimicry refers to the imitation of mechanisms and features found in living creatures using artificial methods. This study used optical lithography, colloidal lithography, and dry etching to mimic the micro/nano hierarchical structures covering the soles of gecko feet. We measured the static contact angle and contact angle hysteresis to reveal the behavior of liquid drops on the hierarchical structures. Pulling tests were also performed to measure the resistance of movement between the hierarchical structures and a testing plate. Our results reveal that hierarchical structures at the micro-/nano-scale are considerably hydrophobic, they provide good flow characteristics, and they generate more contact force than do surfaces with micro-scale cylindrical structures.

  10. Crystallography and surface structure an introduction for surface scientists and nanoscientists

    CERN Document Server

    Hermann, Klaus

    2017-01-01

    A valuable learning tool as well as a reference, this book provides students and researchers in surface science and nanoscience with the theoretical crystallographic foundations, which are necessary to understand local structure and symmetry of bulk crystals, including ideal and real single crystal surfaces. The author deals with the subject at an introductory level, providing numerous graphic examples to illustrate the mathematical formalism. The book brings together and logically connects many seemingly disparate structural issues and notations used frequently by surface scientists and nanoscientists. Numerous exercises of varying difficulty, ranging from simple questions to small research projects, are included to stimulate discussions about the different subjects.

  11. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    Science.gov (United States)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-01

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  12. Condensation and Wetting Dynamics on Micro/Nano-Structured Surfaces

    Science.gov (United States)

    Olceroglu, Emre

    Because of their adjustable wetting characteristics, micro/nanostructured surfaces are attractive for the enhancement of phase-change heat transfer where liquid-solid-vapor interactions are important. Condensation, evaporation, and boiling processes are traditionally used in a variety of applications including water harvesting, desalination, industrial power generation, HVAC, and thermal management systems. Although they have been studied by numerous researchers, there is currently a lack of understanding of the underlying mechanisms by which structured surfaces improve heat transfer during phase-change. This PhD dissertation focuses on condensation onto engineered surfaces including fabrication aspect, the physics of phase-change, and the operational limitations of engineered surfaces. While superhydrophobic condensation has been shown to produce high heat transfer rates, several critical issues remain in the field. These include surface manufacturability, heat transfer coefficient measurement limitations at low heat fluxes, failure due to surface flooding at high supersaturations, insufficient modeling of droplet growth rates, and the inherent issues associated with maintenance of non-wetted surface structures. Each of these issues is investigated in this thesis, leading to several contributions to the field of condensation on engineered surfaces. A variety of engineered surfaces have been fabricated and characterized, including nanostructured and hierarchically-structured superhydrophobic surfaces. The Tobacco mosaic virus (TMV) is used here as a biological template for the fabrication of nickel nanostructures, which are subsequently functionalized to achieve superhydrophobicity. This technique is simple and sustainable, and requires no applied heat or external power, thus making it easily extendable to a variety of common heat transfer materials and complex geometries. To measure heat transfer rates during superhydrophobic condensation in the presence of non

  13. Structural and chemical control in assembly of multicomponent metal-organic coordination networks on a surface.

    Science.gov (United States)

    Shi, Ziliang; Lin, Nian

    2010-08-11

    Surface-supported supramolecular self-assembly has been used to generate multicomponent two-dimensional metal-organic coordination networks on a Au(111) surface. The networks consist of linker ligands of 4',4''''-(1,4-phenylene)bis(2,2':6',2''-terpyridine) and nodal ligands of 5,10,15,20-tetra(4-pyridyl)porphyrin that are connected by pyridine-Fe-terpyridine motifs. Scanning tunneling microscopy revealed the coexistence of two polymorphic types of network structures (rhombus and Kagome). Through control of the dosage of the constituent ligands, homogeneous structural phases were obtained selectively. In particular, the rhombus structure could be converted into the more complex and more open Kagome structure by inclusion of guest molecules. Finally, coordination networks providing structural and chemical homogeneity were realized by judiciously choosing the dosages of the constituent ligands and the chemical substitution of the porphyrin ligands.

  14. Basic reactions of osteoblasts on structured material surfaces

    Directory of Open Access Journals (Sweden)

    B�chter A.

    2005-04-01

    Full Text Available In order to assess how bone substitute materials determine bone formation in vivo it is useful to understand the mechanisms of the material surface/tissue interaction on a cellular level. Artificial materials are used in two applications, as biomaterials alone or as a scaffold for osteoblasts in a tissue engineering approach. Recently, many efforts have been undertaken to improve bone regeneration by the use of structured material surfaces. In vitro studies of bone cell responses to artificial materials are the basic tool to determine these interactions. Surface properties of materials surfaces as well as biophysical constraints at the biomaterial surface are of major importance since these features will direct the cell responses. Studies on osteoblastlike cell reactivity towards materials will have to focus on the different steps of protein and cell reactions towards defined surface properties. The introduction of new techniques allows nowadays the fabrication of materials with ordered surface structures. This paper gives a review of present knowledge on the various stages of osteoblast reactions on material surfaces, focused on basic cell events under in vitro conditions. Special emphasis is given to cellular reactions towards ordered nano-sized topographies.

  15. Laser Surface Preparation for Adhesive Bonding of Aerospace Structural Composites

    Science.gov (United States)

    Belcher, M. A.; Wohl, C. J.; Hopkins, J. W.; Connell, J. W.

    2010-01-01

    Adhesive bonds are critical to the integrity of built-up structures. Disbonds can often be detected but the strength of adhesion between surfaces in contact is not obtainable without destructive testing. Typically the number one problem in a bonded structure is surface contamination, and by extension, surface preparation. Standard surface preparation techniques, including grit blasting, manual abrasion, and peel ply, are not ideal because of variations in their application. Etching of carbon fiber reinforced plastic (CFRP) panels using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser appears to be a highly precise and promising way to both clean a composite surface prior to bonding and provide a bond-promoting patterned surface akin to peel ply without the inherent drawbacks from the same (i.e., debris and curvature). CFRP surfaces prepared using laser patterns conducive to adhesive bonding were compared to typical pre-bonding surface treatments through optical microscopy, contact angle goniometry, and post-bonding mechanical testing.

  16. Determination of surface structure and the depth profile of silica glass by infrared spectroscopy

    Institute of Scientific and Technical Information of China (English)

    C.Z.Tan

    2005-01-01

    The surface structure and properties are different from those of the bulk, depending on the substrate materials and deposition condition, and playing an important role in precise optical components. The conventional spectroscopic methods to monitor the surface structure are restricted only in several layers of molecules. It is known that the penetration depth of the incident light increases with its wavelength and decreases with the angle of incidence. Thus infrared spectroscopy provides a powerful means for determination of surface structure and the depth profile up to micrometers. By recording the reflection spectra at different angles of incidence, the surface structure and its depth profile can be monitored successively. Further, the incident field has the subcomponents parallel and perpendicular to the surface, which excite the transverse and longitudinal optic modes, respectively. Change of the polarization direction of the incident light provides a practical function to study anisotropic property of the surface and the interaction between the transverse and longitudinal optic modes. In this work, infrared spectrophotometer was applied to investigate the depth profile in microstructure of silica glass. Combining with the glass fiber system, this technique can be used for in-situ control of the deposition process. In comparing with ellipsometry, this method reveals both structural and constitutional information.

  17. Compact surface structures for the efficient excitation of surface plasmon-polaritons

    Energy Technology Data Exchange (ETDEWEB)

    De la Cruz, S.; Mendez, E.R. [Division de Fisica Applicada, Centro de Investigacion Cientifica y de Educacion Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Ensenada 22860, BC (Mexico); Macias, D.; Salas-Montiel, R.; Adam, P.M. [Laboratoire de Nanotechnologie et d' Instrumentation Optique, Universite de Technologie de Troyes, 12 rue Marie Curie, BP-2060, 10010 Troyes Cedex (France)

    2012-06-15

    We present calculations of the efficiency of excitation of surface plasmon-polaritons (SPPs) with surface structures illuminated by focussed beams. First, it is shown that the low reflectivity observed with broad highly directional beams and periodic gratings does not necessarily imply an efficient coupling to SPPs. We then consider the coupling through surface features like steps, grooves and angled steps, and calculate efficiency maps for these structures as functions of the parameters that define them. Finally, we explore the possibilities of improving the coupling efficiency using periodic structures consisting of a small number of rectangular grooves. We find that a surface section with a length of about four wavelengths can couple as much as 45% of the incident light into a directional SPP. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Sulfur-induced structural motifs on copper and gold surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Walen, Holly [Iowa State Univ., Ames, IA (United States)

    2016-01-01

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  19. Robust biomimetic-structural superhydrophobic surface on aluminum alloy.

    Science.gov (United States)

    Li, Lingjie; Huang, Tao; Lei, Jinglei; He, Jianxin; Qu, Linfeng; Huang, Peiling; Zhou, Wei; Li, Nianbing; Pan, Fusheng

    2015-01-28

    The following facile approach has been developed to prepare a biomimetic-structural superhydrophobic surface with high stabilities and strong resistances on 2024 Al alloy that are robust to harsh environments. First, a simple hydrothermal treatment in a La(NO3)3 aqueous solution was used to fabricate ginkgo-leaf like nanostructures, resulting in a superhydrophilic surface on 2024 Al. Then a low-surface-energy compound, dodecafluoroheptyl-propyl-trimethoxylsilane (Actyflon-G502), was used to modify the superhydrophilic 2024 Al, changing the surface character from superhydrophilicity to superhydrophobicity. The water contact angle (WCA) of such a superhydrophobic surface reaches up to 160°, demonstrating excellent superhydrophobicity. Moreover, the as-prepared superhydrophobic surface shows high stabilities in air-storage, chemical and thermal environments, and has strong resistances to UV irradiation, corrosion, and abrasion. The WCAs of such a surface almost remain unchanged (160°) after storage in air for 80 days, exposure in 250 °C atmosphere for 24 h, and being exposed under UV irradiation for 24 h, are more than 144° whether in acidic or alkali medium, and are more than 150° after 48 h corrosion and after abrasion under 0.98 kPa for 1000 mm length. The remarkable durability of the as-prepared superhydrophobic surface can be attributed to its stable structure and composition, which are due to the existence of lanthanum (hydr)oxides in surface layer. The robustness of the as-prepared superhydrophobic surface to harsh environments will open their much wider applications. The fabricating approach for such robust superhydrophobic surface can be easily extended to other metals and alloys.

  20. Dimers on surface graphs and spin structures. II

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai

    2009-01-01

    In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function of the di......In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function...... of the dimer model on Γ. In the present article, we generalize these results to the case of compact oriented surfaces with boundary. We also show how the operations of cutting and gluing act on discrete spin structures and how they change the partition function. These operations allow to reformulate the dimer...

  1. Revealing the connectivity of groundwater and surface water using electromagnetic induction measurements

    Science.gov (United States)

    Binley, A. M.; McLachlan, P.; Chambers, J. E.; Uhlemann, S.

    2016-12-01

    It is now widely recognised that hydrological and biogeochemical processes that occur at the interface of groundwater (GW) and surface water (SW) can have a significant impact on catchment water quality and ecosystem health. Significant heterogeneity in the fabric of the subsurface at the GW-SW interface can lead to complex fluid flow pathways, both of which can exert a strong control on biogeochemical cycling. Revealing such heterogeneity remains a challenge because of the limitations of traditional field experimental processes. Such traditional techniques are often invasive, which often prevents their use in ecologically sensitive environments. Furthermore, they are often limited to localised characterisation. Studies to date have thus focussed on relatively small (easily accessible) stream environments, at short reach, or plot, scales. There is a clear demand for techniques that can capture the heterogeneity of sediments and pore fluids over larger scales. Geophysical methods may offer valuable information at such scales, particularly when used in combination with traditional sampling approaches. The value of electrical methods for revealing detailed information about the heterogeneity of sediments at the GW-SW interface has been demonstrated, and in a few studies such methods have assisted tracer tests in mapping the solute pathways. However, most investigations have been confined to relatively small scale (tens of metres). There is growing (and renewed) interest in the use of frequency domain electromagnetic induction (EMI) techniques in hydrogeophysics. At the GW-SW interface these methods allow rapid, non-invasive exploration of the top few metres. Relatively recent technological developments have provided multi-coil instrumentation, permitting rapid assessment of electrical conductivity at multiple depths of investigation. Here, we demonstrate the effectiveness of EMI for revealing the heterogeneity of sediments and flow pathways at the GW-SW interface. We

  2. Independent and collective roles of surface structures at different length scales on pool boiling heat transfer

    Science.gov (United States)

    Li, Calvin H.; Rioux, Russell P.

    2016-01-01

    Spherical Cu nanocavity surfaces are synthesized to examine the individual role of contact angles in connecting lateral Rayleigh-Taylor wavelength to vertical Kevin-Helmholtz wavelength on hydrodynamic instability for the onset of pool boiling Critical Heat Flux (CHF). Solid and porous Cu pillar surfaces are sintered to investigate the individual role of pillar structure pitch at millimeter scale, named as module wavelength, on hydrodynamic instability at CHF. Last, spherical Cu nanocavities are coated on the porous Cu pillars to create a multiscale Cu structure, which is studied to examine the collective role and relative significance of contact angles and module wavelength on hydrodynamic instability at CHF, and the results indicate that module wavelength plays the dominant role on hydrodynamic instability at CHF when the height of surface structures is equal or above ¼ Kelvin-Helmholtz wavelength. Pool boiling Heat Transfer Coefficient (HTC) enhancements on spherical Cu nanocavity surfaces, solid and porous Cu pillar surfaces, and the integrated multiscale structure have been investigated, too. The experimental results reveal that the nanostructures and porous pillar structures can be combined together to achieve even higher enhancement of HTC than that of individual structures. PMID:27841322

  3. Independent and collective roles of surface structures at different length scales on pool boiling heat transfer.

    Science.gov (United States)

    Li, Calvin H; Rioux, Russell P

    2016-11-14

    Spherical Cu nanocavity surfaces are synthesized to examine the individual role of contact angles in connecting lateral Rayleigh-Taylor wavelength to vertical Kevin-Helmholtz wavelength on hydrodynamic instability for the onset of pool boiling Critical Heat Flux (CHF). Solid and porous Cu pillar surfaces are sintered to investigate the individual role of pillar structure pitch at millimeter scale, named as module wavelength, on hydrodynamic instability at CHF. Last, spherical Cu nanocavities are coated on the porous Cu pillars to create a multiscale Cu structure, which is studied to examine the collective role and relative significance of contact angles and module wavelength on hydrodynamic instability at CHF, and the results indicate that module wavelength plays the dominant role on hydrodynamic instability at CHF when the height of surface structures is equal or above ¼ Kelvin-Helmholtz wavelength. Pool boiling Heat Transfer Coefficient (HTC) enhancements on spherical Cu nanocavity surfaces, solid and porous Cu pillar surfaces, and the integrated multiscale structure have been investigated, too. The experimental results reveal that the nanostructures and porous pillar structures can be combined together to achieve even higher enhancement of HTC than that of individual structures.

  4. Surface plasmon polariton amplification in metal-semiconductor structures.

    Science.gov (United States)

    Fedyanin, Dmitry Yu; Arsenin, Aleksey V

    2011-06-20

    We propose a novel scheme of surface plasmon polariton (SPP) amplification that is based on a minority carrier injection in a Schottky diode. This scheme uses compact electrical pumping instead of bulky optical pumping. Compact size and a planar structure of the proposed amplifier allow one to utilize it in integrated plasmonic circuits and couple it easily to passive plasmonic devices. Moreover, this technique can be used to obtain surface plasmon lasing.

  5. Fractal analysis of the hierarchic structure of fossil coal surface

    Energy Technology Data Exchange (ETDEWEB)

    Alekseev, A.D.; Vasilenko, T.A.; Kirillov, A.K. [National Academy of Sciences, Donetsk (Ukraine)

    2008-05-15

    The fractal analysis is described as method of studying images of surface of fossil coal, one of the natural sorbent, with the aim of determining its structural surface heterogeneity. The deformation effect as a reduction in the dimensions of heterogeneity boundaries is considered. It is shown that the theory of nonequilibrium dynamic systems permits to assess a formation level of heterogeneities involved into a sorbent composition by means of the Hurst factor.

  6. Structure and properties of GMA surfaced armour plates

    OpenAIRE

    A. Klimpel; K. Luksa; M. Burda

    2010-01-01

    Purpose: In the combat vehicles many materials can be used for the armour. Application of the monolithic armour plates in light combat vehicles is limited by the high armour weigh. Introduction of the layered armour plates is a way to limit the vehicle weight. In the paper test results of graded and nanostructural GMA surfaced armour plates are presented.Design/methodology/approach: Metallographic structure, chemical composition and hardness of surfaced layers were investigated in order to ex...

  7. Positron studies of surfaces, structure and electronic properties of nanocrystals

    OpenAIRE

    Eijt, S. W. H.; Barbiellini, B.; Houtepen, A.J.; Vanmaekelbergh, D.; Mijnarends, P. E.; Bansil, A.

    2007-01-01

    A brief review is given of recent positron studies of metal and semiconductor nanocrystals. The prospects offered by positron annihilation as a sensitive method to access nanocrystal (NC) properties are described and compared with other experimental methods. The tunability of the electronic structure of nanocrystals underlies their great potential for application in many areas. Owing to their large surface-to-volume ratio, the surfaces and interfaces of NCs play a crucial role in determining ...

  8. Modeling liquid crystal bilayer structures with minimal surfaces.

    Science.gov (United States)

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  9. STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability.

    Science.gov (United States)

    Gres, Anna T; Kirby, Karen A; KewalRamani, Vineet N; Tanner, John J; Pornillos, Owen; Sarafianos, Stefan G

    2015-07-03

    The detailed molecular interactions between native HIV-1 capsid protein (CA) hexamers that shield the viral genome and proteins have been elusive. We report crystal structures describing interactions between CA monomers related by sixfold symmetry within hexamers (intrahexamer) and threefold and twofold symmetry between neighboring hexamers (interhexamer). The structures describe how CA builds hexagonal lattices, the foundation of mature capsids. Lattice structure depends on an adaptable hydration layer modulating interactions among CA molecules. Disruption of this layer alters interhexamer interfaces, highlighting an inherent structural variability. A CA-targeting antiviral affects capsid stability by binding across CA molecules and subtly altering interhexamer interfaces remote to the ligand-binding site. Inherent structural plasticity, hydration layer rearrangement, and effector binding affect capsid stability and have functional implications for the retroviral life cycle. Copyright © 2015, American Association for the Advancement of Science.

  10. Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.

    Science.gov (United States)

    Clark, Howard W; Mackay, Rose-Marie; Deadman, Mary E; Hood, Derek W; Madsen, Jens; Moxon, E Richard; Townsend, J Paul; Reid, Kenneth B M; Ahmed, Abdul; Shaw, Amy J; Greenhough, Trevor J; Shrive, Annette K

    2016-05-01

    The carbohydrate recognition domains (CRDs) of lung collectin surfactant protein D (SP-D) recognize sugar patterns on the surface of lung pathogens and promote phagocytosis. Using Haemophilus influenzae Eagan strains expressing well-characterized lipopolysaccharide (LPS) surface structures of various levels of complexity, we show that bacterial recognition and binding by SP-D is inversely related to LPS chain extent and complexity. The crystal structure of a biologically active recombinant trimeric SP-D CRD complexed with a delipidated Eagan 4A LPS suggests that efficient LPS recognition by SP-D requires multiple binding interactions utilizing the three major ligand-binding determinants in the SP-D binding pocket, with Ca-dependent binding of inner-core heptose accompanied by interaction of anhydro-Kdo (4,7-anhydro-3-deoxy-d-manno-oct-2-ulosonic acid) with Arg343 and Asp325. Combined with enzyme-linked immunosorbent assays (ELISAs) and fluorescence-activated cell sorter (FACS) binding analyses, our results show that extended LPS structures previously thought to be targets for collectins are important in shielding the more vulnerable sites in the LPS core, revealing a mechanism by which pathogens with complex LPS extensions efficiently evade a first-line mucosal innate immune defense. The structure also reveals for the first time the dominant form of anhydro-Kdo.

  11. Optimal Design of Surface Structure of a Magnetic Head

    Institute of Scientific and Technical Information of China (English)

    WANG Yazhen; NIU Rongjun; HUANG Ping

    2009-01-01

    Currently, the surface structure of a magnetic head has been transferred from a positive to a negative model. In order to increase magnetic storage density and to decrease the flight height, the surface structure of a head needs to be optimized continually. In the present paper, the influence of surface structure of a negative magnetic head on its flight attitude is analyzed in brief by both theoretical analysis and numerical simulation. Firstly, based on theoretical analysis, one-dimensional model of optimal design is built whose results play an important role in guiding for the two-dimensional model. Secondly, to analyze the impacts of different structures of negative pressure heads, the original head structure is divided into five zones;the impacts of different zones on both pressure distribution and load carrying capacity were detailed analyzed by numerical analysis. Thirdly, remain the leading-head structure of the negative head, and optimized tail-end structure can be gained by the regional planning strategy to control the gas film pressure distribution. With layout strategy, three kinds of structures of the head were designed. The results show that the tail-end structure impacts on the flight performances significantly and the middle boss plays a major role on positive pressure, while the bilateral bosses lying in either side play assistant regulating role. The structures of bilateral bosses have slightly impact on pressure distribution. The results also show that an optimum tail structure can meet the needs of a lower flight height and a larger magnetic storage density.

  12. Fluorescence mapping of mitochondrial TIM23 complex reveals a water-facing, substrate-interacting helix surface.

    Science.gov (United States)

    Alder, Nathan N; Jensen, Robert E; Johnson, Arthur E

    2008-08-08

    Protein translocation across the mitochondrial inner membrane is mediated by the TIM23 complex. While its central component, Tim23, is believed to form a protein-conducting channel, the regions of this subunit that face the imported protein are unknown. To examine Tim23 structure and environment in intact membranes at high resolution, various derivatives, each with a single, environment-sensitive fluorescent probe positioned at a specific site, were assembled into functional TIM23 complexes in active mitochondria and analyzed by multiple spectral techniques. Probes placed sequentially throughout a transmembrane region that was identified by crosslinking as part of the protein-conducting channel revealed an alpha helix in an amphipathic environment. Probes on the aqueous-facing helical surface specifically underwent spectral changes during protein import, and their accessibility to hydrophilic quenching agents is considered in terms of channel gating. This approach has therefore provided an unprecedented view of a translocon channel structure in an intact, fully operational, membrane-embedded complex.

  13. Investigation of surface magnetostatic wave propagation in ferrite superconductor structure

    CERN Document Server

    Semenov, A A; Melkov, A A; Bobyl', A V; Suris, R A; Gal'perin, Y M; Iokhansen, T K

    2001-01-01

    Electrodynamic model describing dispersion properties of surface magnetostatic wave in ferrite/superconductor structure was suggested. On the basis of the model a new method of ascertaining superhigh frequency surface resistance R sub s of superconducting films in magnetic fields was developed. The calculated values agree with the results obtained by the Tauber method, making up R sub s =0.20-1.96 m Ohm. A regulated incursion of wave phase amounting to about 1.5 pi with the change in penetration depth 2.0-0.8 mu m for YBCO film was attained for YIG/YBCO structures

  14. Surface plasmon polariton amplification in semiconductor-graphene-dielectric structure

    Energy Technology Data Exchange (ETDEWEB)

    Dadoenkova, Yuliya S. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Novgorod State University, Veliky Novgorod (Russian Federation); Donetsk Institute for Physics and Technology, Donetsk (Ukraine); Moiseev, Sergey G. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Ulyanovsk (Russian Federation); Abramov, Aleksei S. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Kadochkin, Aleksei S.; Zolotovskii, Igor O. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32A Leninskiy Prosp., 119991, Moscow (Russian Federation); Fotiadi, Andrei A. [Ulyanovsk State University, Ulyanovsk (Russian Federation); Universite de Mons (Belgium)

    2017-05-15

    A mechanism of amplification of surface plasmon polaritons due to the transfer of electromagnetic energy from a drift current wave into a far-infrared surface wave propagating along a semiconductor-dielectric boundary in waveguide geometry is proposed. A necessary condition of the interaction of these waves is phase matching condition, i. e., when the phase velocity of the surface wave approaches the drift velocity of charge carriers. It is shown that in the spectral region of the surface plasmon polariton slowing-down its amplification coefficient can reach values substantially exceeding the ohmic loss coefficient of the surface wave in the structure. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  15. Waveguiding in surface plasmon polariton band gap structures

    DEFF Research Database (Denmark)

    Bozhevolnyi, S.I.; Østergaard, John Erland; Leosson, Kristjan

    2001-01-01

    Using near-held optical microscopy, we investigate propagation and scattering of surface plasmon polaritons (SPP's) excited in the wavelength range of 780-820 nm at nanostructured gold-film surfaces with areas of 200-nm-wide scatterers arranged in a 400-nm-period triangular lattice containing line...... defects. We observe the SPP reflection by such an area and SPP guiding along line defects at 782 nm, as well as significant deterioration of these effects is 815 nm, thereby directly demonstrating the SPP band gap effect and showing first examples of SPP channel waveguides in surface band gap structures....

  16. Crystal structure of human prion protein fragment reveals a motif for oligomer formation

    Science.gov (United States)

    Apostol, Marcin I.; Perry, Kay; Surewicz, Witold K.

    2013-01-01

    The structural transition of the prion protein from α-helical to β-sheet rich underlies its conversion into infectious and disease-associated isoforms. Here we describe the crystal structure of a fragment from human prion protein consisting of the disulfide bond linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into an β-sheet rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates, and suggests a possible mechanism for self-propagation of misfolded conformations by such non-amyloid oligomers. PMID:23808589

  17. Crystal structure of a human prion protein fragment reveals a motif for oligomer formation.

    Science.gov (United States)

    Apostol, Marcin I; Perry, Kay; Surewicz, Witold K

    2013-07-17

    The structural transition of the prion protein from α-helical- to β-sheet-rich underlies its conversion into infectious and disease-associated isoforms. Here we describe the crystal structure of a fragment from human prion protein consisting of the disulfide-bond-linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into a β-sheet-rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates and suggests a possible mechanism for self-propagation of misfolded conformations by such nonamyloid oligomers.

  18. Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information.

    Science.gov (United States)

    Siwek, M; Finocchiaro, R; Curik, I; Portolano, B

    2011-02-01

    Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amovaФ(ST) estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amovaФ(SC) estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure.

  19. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rong [Yale Univ., New Haven, CT (United States); Li, Xiaofeng [Yale Univ., New Haven, CT (United States); Boggon, Titus J. [Yale Univ., New Haven, CT (United States)

    2015-10-14

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/ TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is also an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD–FERM module. It resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD–FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  20. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.

    Science.gov (United States)

    Zhang, Rong; Li, Xiaofeng; Boggon, Titus J

    2015-12-01

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD-FERM module. This resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD-FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  1. Mutagenesis of tGCN5 core region reveals two critical surface residues F90 and R140

    Energy Technology Data Exchange (ETDEWEB)

    Mehta, Kinjal Rajesh; Chan, Yan M.; Lee, Man X.; Yang, Ching Yao; Voloshchuk, Natalya [Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201 (United States); Montclare, Jin Kim, E-mail: jmontcla@poly.edu [Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201 (United States); Department of Biochemistry, SUNY-Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203 (United States)

    2010-09-24

    Research highlights: {yields} Mutagenesis of the tGCN5 core region reveals two residues important for function. {yields} Developed a fluorescent lysate-based activity assay to assess mutants. {yields} Surface-exposed residues F90 and R140 of tGCN5 are critical for H3 acetylation. -- Abstract: Tetrahymena General Control Non-Derepressor 5 (tGCN5) is a critical regulator of gene transcription via acetylation of histones. Since the acetylation ability has been attributed to the 'core region', we perform mutagenesis of residues within the tGCN5 'core region' in order to identify those critical for function and stability. Residues that do not participate in catalysis are identified, mutated and characterized for activity, structure and thermodynamic stability. Variants I107V, Q114L, A121T and A130S maintain the acetylation function relative to wild-type tGCN5, while variants F90Y, F112R and R140H completely abolish function. Of the three non-functional variants, since F112 is mutated into a non-homologous charged residue, a loss in function is expected. However, the remaining two variants are mutated into homologous residues, suggesting that F90 and R140 are critical for the activity of tGCN5. While mutation to homologous residue maintains acetylation of histone H3 for the majority of the variants, the two surface-exposed residues, F90 and R140, appear to be essential for tGCN5 function, structure or stability.

  2. Surface Structure and Growth Mode of Pd Deposited on Mo(110) Surface

    Science.gov (United States)

    Maehara, Y.; Kawanowa, H.; Gotoh, Y.

    The surface structure and growth mode of Pd/Mo(110) have been studied using reflection high energy electron diffraction (RHEED). The surface diagram of Pd on the Mo(110) substrate for deposition thickness versus substrate temperature was obtained. Four kinds of surface structures, namely α1, α2, β and γ, were observed. At less than 1 ML, α2 appeared in temperatures ranging from 400 to 1050°C and α1 appeared from RT to 400°C. α2 has a structure intermediate between those of Pd(111) and Mo(110), in which the dense direction of the layer is parallel to the [111]Mo orientation and their atomic row distances are coincident, resulting in formation of a long-period structure with a Mo surface, namely a coincident site lattice. The α1 structure is similar to the 1 × 1 structure. At more than 1.0 ML, β and γ structures appeared simultaneously in the temperature region from 500 to 950°C. However, at a high temperature region from 950 to 1050°C, the α2 structure was observed. β shows a one-dimensional ordered structure, in which Pd atoms line along [111]Mo. γ exhibits a 3 × 1 structure with the same atomic arrangement as the Mo(110) plane rotated at 70.5°. At greater than 2.0 ML, the Pd film grows in the Frank van der Merwe growth mode at a low temperature with accumulation of a Pd(111) layer, and in the Stranski Krastanov growth mode at a high temperature with two-dimensional growth of the γ structure followed by formation of flat crystallites.

  3. Studies on electronic structure of GaN(0001) surface

    CERN Document Server

    Xie Chang Kun; Xu Fa Qiang; Deng Rui; Liu Feng; Yibulaxin, K

    2002-01-01

    An electronic structure investigation on GaN(0001) is reported. The authors employ a full-potential linearized augmented plane-wave (FPLAPW) approach to calculate the partial density of state, which is in agreement with previous experimental results. The effects of the Ga3d semi-core levels on the electronic structure of GaN are discussed. The valence-electronic structure of the wurtzite GaN(0001) surface is investigated using synchrotron radiation excited angle-resolved photoemission spectroscopy. The bulk bands dispersion along GAMMA A direction in the Brillouin zones is measured using normal-emission spectra by changing photon-energy. The band structure derived from authors' experimental data is compared well with the results of authors' FPLAPW calculation. Furthermore, off-normal emission spectra are also measured along the GAMMA K and GAMMA M directions. Two surface states are identified, and their dispersions are characterized

  4. MHD simulations reveal crucial differences between solar and very-cool star magnetic structures

    CERN Document Server

    Beeck, Benjamin; Reiners, Ansgar

    2011-01-01

    We carried out 3D radiative magnetohydrodynamic simulations of the convective and magnetic structure in the surface layers (uppermost part of the convection zone and photosphere) of main-sequence stars of spectral types F3 to M2. The simulation results were analyzed in terms of sizes and properties of the convection cells (granules) and magnetic flux concentrations as well as velocity, pressure, density, and temperature profiles. Our numerical simulations show for the first time a qualitative difference in the magneto-convection between solar-like stars and M dwarfs. Owing to higher surface gravity, lower opacity (resulting in higher density at optical depth unity), and more stable downflows, small-scale magnetic structures concentrate into pore-like configurations of reduced intensity. This implies that in very cool stars magnetic surface structures like plage regions and starspots significantly differ from the solar example. Such a difference would have major impact on the interpretation of Doppler imaging ...

  5. Surface potential domains on lamellar P3OT structures

    Energy Technology Data Exchange (ETDEWEB)

    Perez-GarcIa, B [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Abad, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Urbina, A [Departamento Electronica, TecnologIa de Computadoras y Proyectos, Universidad Politecnica de Cartagena, E-30202 Cartagena (Spain); Colchero, J [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain); Palacios-Lidon, E [Departamento Fisica, Facultad de Quimica (Campus Espinardo), Universidad de Murcia, E-30100 Murcia (Spain)

    2008-02-13

    In this work the electrostatic properties of poly(3-octylthiophene) thin films have been studied on a nanometer scale by means of electrostatic force microscopy and Kelvin probe microscopy (KPM). The KPM images reveal that different surface contact potential domains coexist on the polymer surface. This result, together with additional capacitance measurements, indicates that the potential domains are related to the existence of dipoles due to different molecular arrangements. Finally, capacitance measurements as a function of the tip-sample bias voltage show that in all regions large band bending effects take place.

  6. Structural Integrity Assessment Using Laser Measured Surface Vibration

    Science.gov (United States)

    2009-04-01

    structures. Figure 2. (Left) Experimental arrangement for plaster wall assessments at the U.S. Capitol Building showing the SLDV monitoring system, a... termite -like damage to the wood. Broadband SLDV scans were obtained across the available surface of the structure providing dynamic displacement...Figure 2. (Left) Experimental arrangement for plaster wall assessments at the U.S. Capitol Building showing the SLDV monitoring system, a shaker

  7. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further......, because of the complex composition of HDL, understanding the impact of its structure and dynamics on the function of HDL in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled...... essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...

  8. Interactions of arsenic with calcite surfaces revealed by in situ nanoscale imaging

    Science.gov (United States)

    Renard, François; Putnis, Christine V.; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hovelmann, Jörn; Sarret, Géraldine

    2015-06-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in situ study of the evolution of the (10-14) calcite cleavage surface morphology during dissolution and growth in the presence of solutions with various amounts of As(III) or As(V) at room temperature and pH range 6-11 using a flow-through cell connected to an atomic force microscope (AFM). Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  9. Interactions of arsenic with calcite surfaces revealed by in-situ nanoscale imaging

    Science.gov (United States)

    Renard, Francois; Putnis, Christine; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hövelmann, Jörn; Sarret, Géraldine

    2015-04-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in-situ study of calcite dissolution and growth in the presence of solutions with various amounts of As(III) or As(V). This was performed at room temperature and pH range 6-9 using a flow through cell connected to an atomic force microscope (AFM), to study the evolution of the (10-14) calcite cleavage surface morphology. Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  10. Conductivity anisotropy helps to reveal the microscopic structure of a density wave at imperfect nesting

    Science.gov (United States)

    Grigoriev, P. D.; Kostenko, S. S.

    2015-03-01

    Superconductivity or metallic state may coexist with density wave ordering at imperfect nesting of the Fermi surface. In addition to the macroscopic spatial phase separation, there are, at least, two possible microscopic structures of such coexistence: (i) the soliton-wall phase and (ii) the ungapped Fermi-surface pockets. We show that the conductivity anisotropy allows us to distinguish these two microscopic density-wave structures. The results obtained may help to analyze the experimental observations in layered organic metals (TMTSF)2PF6, (TMTSF)2ClO4, α-(BEDT-TTF)2KHg(SCN)4 and in other compounds.

  11. Conductivity anisotropy helps to reveal the microscopic structure of a density wave at imperfect nesting

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, P.D., E-mail: grigorev@itp.ac.ru [L.D. Landau Institute for Theoretical Physics, Chernogolovka 142432 (Russian Federation); Institut Laue-Langevin, Grenoble (France); Kostenko, S.S. [Institute of Problems of Chemical Physics, 142432 Chernogolovka (Russian Federation)

    2015-03-01

    Superconductivity or metallic state may coexist with density wave ordering at imperfect nesting of the Fermi surface. In addition to the macroscopic spatial phase separation, there are, at least, two possible microscopic structures of such coexistence: (i) the soliton-wall phase and (ii) the ungapped Fermi-surface pockets. We show that the conductivity anisotropy allows us to distinguish these two microscopic density-wave structures. The results obtained may help to analyze the experimental observations in layered organic metals (TMTSF){sub 2}PF{sub 6}, (TMTSF){sub 2}ClO{sub 4}, α-(BEDT-TTF){sub 2}KHg(SCN){sub 4} and in other compounds.

  12. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis.

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-09-21

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts.

  13. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    Science.gov (United States)

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  14. Refining femtosecond laser induced periodical surface structures with liquid assist

    Energy Technology Data Exchange (ETDEWEB)

    Jiao, L.S. [School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore (Singapore); Ng, E.Y.K., E-mail: mykng@ntu.edu.sg [School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore (Singapore); Zheng, H.Y. [Singapore Institute of Manufacturing Technology, 71 Nanyang Drive, 638075 Singapore (Singapore)

    2013-01-01

    Highlights: Black-Right-Pointing-Pointer LIPSS on silicon wafer was made in air and in ethanol environment. Black-Right-Pointing-Pointer Ethanol environment produce cleaner surface ripples. Black-Right-Pointing-Pointer Ethanol environment decrease spatial wavelength of the LIPSS by 30%. Black-Right-Pointing-Pointer More number of pulses produce smaller spatial wavelength in air. Black-Right-Pointing-Pointer Number of pulses do not influence spatial wavelength in ethanol environment. - Abstract: Laser induced periodic surface structures were generated on silicon wafer using femtosecond laser. The medium used in this study is both air and ethanol. The laser process parameters such as wavelength, number of pulse, laser fluence were kept constant for both the mediums. The focus of the study is to analyze spatial wavelength. When generating surface structures with air as a medium and same process parameter of the laser, spatial wavelength results showed a 30% increase compared to ethanol. The cleanliness of the surface generated using ethanol showed considerably less debris than in air. The results observed from the above investigation showed that the medium plays a predominant role in the generation of surface structures.

  15. Microphase separated structure and surface properties of fluorinated polyurethane resin

    Energy Technology Data Exchange (ETDEWEB)

    Sudaryanto; Nishino, T.; Hori, Y.; Nakamae, K. [Dept. Chem. Sci. and Eng., Faculty of Engineering, Kobe University, Kobe (Japan)

    2000-10-01

    The effect of fluorination on microphase separation and surface properties of segmented polyurethane (PU) resin were investigated. A series of fluorinated polyurethane resin (FPU) was synthesized by reacting a fluorinated diol with aromatic diisocyanate. The microphase separated structure of FPU was studied by thermal analysis, and small angle X-ray scattering (SAXS) as well as wide angle X-ray diffraction (WAXD). The surface structure and properties were characterized by X-ray photoelectron spectroscopy (XPS) and dynamic contact angle measurement. The incorporation of fluorine into hard segment brings the FPU to have a higher hard domain cohesion and increase the phase separation, however localization of fluorine on the surface could not be observed. On the other hands, localization of fluorine on the surface could be achieved for soft segment fluorinated PU without any significant change in microphase separated structure. The result from this study give an important basic information for designing PU coating material with a low surface energy and strong adhesion as well as for development of release film on pressure sensitive adhesive tape. (author)

  16. Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

    Science.gov (United States)

    Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

    2015-05-01

    Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer.

  17. Correlation of geothermal springs with sub-surface fault terminations revealed by high-resolution, UAV-acquired magnetic data

    Science.gov (United States)

    Glen, Jonathan; A.E. Egger,; C. Ippolito,; N.Athens,

    2013-01-01

    There is widespread agreement that geothermal springs in extensional geothermal systems are concentrated at fault tips and in fault interaction zones where porosity and permeability are dynamically maintained (Curewitz and Karson, 1997; Faulds et al., 2010). Making these spatial correlations typically involves geological and geophysical studies in order to map structures and their relationship to springs at the surface. Geophysical studies include gravity and magnetic surveys, which are useful for identifying buried, intra-basin structures, especially in areas where highly magnetic, dense mafic volcanic rocks are interbedded with, and faulted against less magnetic, less dense sedimentary rock. High-resolution magnetic data can also be collected from the air in order to provide continuous coverage. Unmanned aerial systems (UAS) are well-suited for conducting these surveys as they can provide uniform, low-altitude, high-resolution coverage of an area without endangering crew. In addition, they are more easily adaptable to changes in flight plans as data are collected, and improve efficiency. We have developed and tested a new system to collect magnetic data using small-platform UAS. We deployed this new system in Surprise Valley, CA, in September, 2012, on NASA's SIERRA UAS to perform a reconnaissance survey of the entire valley as well as detailed surveys in key transition zones. This survey has enabled us to trace magnetic anomalies seen in ground-based profiles along their length. Most prominent of these is an intra-basin magnetic high that we interpret as a buried, faulted mafic dike that runs a significant length of the valley. Though this feature lacks surface expression, it appears to control the location of geothermal springs. All of the major hot springs on the east side of the valley lie along the edge of the high, and more specifically, at structural transitions where the high undergoes steps, bends, or breaks. The close relationship between the springs

  18. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels.

  19. Fracture Resistance, Surface Defects and Structural Strength of Glass

    NARCIS (Netherlands)

    Rodichev, Y.M.; Veer, F.A.

    2010-01-01

    This paper poses the theory that the fracture resistance of basic float glass is dependent on it physicochemical properties and the surface defects fonned under the float glass production, glass processing and handling at the service conditions compose the aggregate basis for structural glass

  20. Probing surface structures of Shewanella spp. by microelectrophoresis

    NARCIS (Netherlands)

    Dague, E.; Duval, J.F.L.; Jorand, R.; Thomas, F.; Gaboriaud, F.

    2006-01-01

    Long-range electrostatic forces substantially influence bacterial interactions and bacterial adhesion during the preliminary steps of biofilm formation. The strength of these forces depends strongly on the structure of the bacterium surfaces investigated. The latter may be addressed from appropriate

  1. Moduli spaces of convex projective structures on surfaces

    DEFF Research Database (Denmark)

    Fock, V. V.; Goncharov, A. B.

    2007-01-01

    We introduce explicit parametrisations of the moduli space of convex projective structures on surfaces, and show that the latter moduli space is identified with the higher Teichmüller space for defined in [V.V. Fock, A.B. Goncharov, Moduli spaces of local systems and higher Teichmüller theory, ma...

  2. Functional oxide structures on a surface of metals and alloys

    Institute of Scientific and Technical Information of China (English)

    Rudnev; V.; S.; Yarovaya; T.; P.; Boguta; D.; L.; Lukiyanchuk; I.; V.; Tyrina; L.; M.; Morozova; V.; P.; Nedozorov; P.; M.; Vasilyeva; M.; S.; Kondrikov; N.; B.

    2005-01-01

    The investigations of the plasma electrolytic processes in our laboratory are aimed to the development of conditions of formation of oxide layers with determined composition, structure and functional properties on the surface of valve metals (Al, Ti) and their alloys.……

  3. Towards Friction Control using laser-induced periodic Surface Structures

    NARCIS (Netherlands)

    Eichstädt, J.; Römer, G.R.B.E.; Huis in 't Veld, A.J.

    2011-01-01

    This paper aims at contributing to the study of laser-induced periodic surface structures (LIPSS) and the description of their tribological properties in order to facilitate the knowledge for contact mechanical applications. To obtain laser parameters for LIPSS formation, we propose to execute two D

  4. Protein-induced surface structuring in myelin membrane monolayers.

    Science.gov (United States)

    Rosetti, Carla M; Maggio, Bruno

    2007-12-15

    Monolayers prepared from myelin conserve all the compositional complexity of the natural membrane when spread at the air-water interface. They show a complex pressure-dependent surface pattern that, on compression, changes from the coexistence of two liquid phases to a viscous fractal phase embedded in a liquid phase. We dissected the role of major myelin protein components, myelin basic protein (MBP), and Folch-Lees proteolipid protein (PLP) as crucial factors determining the structural dynamics of the interface. By analyzing mixtures of a single protein with the myelin lipids we found that MBP and PLP have different surface pressure-dependent behaviors. MBP stabilizes the segregation of two liquid phases at low pressures and becomes excluded from the film under compression, remaining adjacent to the interface. PLP, on the contrary, organizes a fractal-like pattern at all surface pressures when included in a monolayer of the protein-free myelin lipids but it remains mixed in the MBP-induced liquid phase. The resultant surface topography and dynamics is regulated by combined near to equilibrium and out-of-equilibrium effects. PLP appears to act as a surface skeleton for the whole components whereas MBP couples the structuring to surface pressure-dependent extrusion and adsorption processes.

  5. Bio-Inspired Functional Surfaces Based on Laser-Induced Periodic Surface Structures

    OpenAIRE

    Müller, Frank A.; Clemens Kunz; Stephan Gräf

    2016-01-01

    Nature developed numerous solutions to solve various technical problems related to material surfaces by combining the physico-chemical properties of a material with periodically aligned micro/nanostructures in a sophisticated manner. The utilization of ultra-short pulsed lasers allows mimicking numerous of these features by generating laser-induced periodic surface structures (LIPSS). In this review paper, we describe the physical background of LIPSS generation as well as the physical princip...

  6. Structural and surface changes of copper modified manganese oxides

    Energy Technology Data Exchange (ETDEWEB)

    Gac, Wojciech, E-mail: wojciech.gac@umcs.lublin.pl; Słowik, Grzegorz; Zawadzki, Witold

    2016-05-01

    Highlights: • Formation of MnO with regular rippled-like surface patterns. • Synthesis of copper nanorods supported on MnO nanoparticles. • Hydrogen production in steam methanol reforming over supported copper nanorods. - Abstract: The structural and surface properties of manganese and copper–manganese oxides were investigated. The oxides were prepared by the redox-precipitation method. X-ray diffraction and electron microscopy studies evidenced transformation of cryptomelane-type nanoparticles with 1-D channel structure into the large MnO crystallites with regular rippled-like surface patterns under reduction conditions. The development of Cu/CuO nanorods from strongly dispersed species was evidenced. Coper-modified manganese oxides showed good catalytic performance in methanol steam reforming reaction for hydrogen production. Low selectivity to CO was observed in the wide range of temperatures.

  7. In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop.

    Science.gov (United States)

    Shivhare, Devendra; Mueller-Cajar, Oliver

    2017-07-01

    To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice (Oryza sativa) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca Further mutational analysis suggested that Glu-217 restricts the flexibility of the α4-β4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function. © 2017 American Society of Plant Biologists. All Rights Reserved.

  8. Phase contrast imaging reveals low lung volumes and surface areas in the developing marsupial.

    Directory of Open Access Journals (Sweden)

    Shannon J Simpson

    Full Text Available Marsupials are born with immature lungs when compared to eutherian mammals and rely, to various extents, on cutaneous gas exchange in order to meet metabolic requirements. Indeed, the fat-tailed dunnart is born with lungs in the canalicular stage of development and relies almost entirely on the skin for gas exchange at birth; consequently undergoing the majority of lung development in air. Plane radiographs and computed tomography data sets were acquired using phase contrast imaging with a synchrotron radiation source for two marsupial species, the fat-tailed dunnart and the larger tammar wallaby, during the first weeks of postnatal life. Phase contrast imaging revealed that only two lung sacs contain air after the first hour of life in the fat-tailed dunnart. While the lung of the tammar wallaby was comparatively more developed, both species demonstrated massive increases in air sac number and architectural complexity during the postnatal period. In addition, both the tammar wallaby and fat-tailed dunnart had lower lung volumes and parenchymal surface areas than were expected from morphometrically determined allometric equations relating these variables to body mass during the neonatal period. However, lung volume is predicted to scale with mass as expected after the neonatal marsupial reaches a body mass of ∼1 g and no longer relies on the skin for gas exchange. Decreased lung volume in the marsupial neonate further supports the maxim that cutaneous gas exchange occurs in the marsupial neonate because the respiratory apparatus is not yet capable of meeting the gas exchange requirements of the newborn.

  9. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1 Reveals Features of Its Chitin Binding Domain.

    Directory of Open Access Journals (Sweden)

    Firas Fadel

    Full Text Available Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1 is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD. This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1 structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.

  10. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain

    Science.gov (United States)

    Fadel, Firas; Zhao, Yuguang; Cousido-Siah, Alexandra; Ruiz, Francesc X.; Mitschler, André; Podjarny, Alberto

    2016-01-01

    Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain. PMID:27111557

  11. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Directory of Open Access Journals (Sweden)

    Ivana Nemčovičová

    2013-03-01

    Full Text Available The TRAIL (TNF-related apoptosis inducing ligand death receptors (DRs of the tumor necrosis factor receptor superfamily (TNFRSF can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  12. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Science.gov (United States)

    Nemčovičová, Ivana; Benedict, Chris A; Zajonc, Dirk M

    2013-03-01

    The TRAIL (TNF-related apoptosis inducing ligand) death receptors (DRs) of the tumor necrosis factor receptor superfamily (TNFRSF) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV) expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER) and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  13. Osteogenic activity of titanium surfaces with nanonetwork structures

    Directory of Open Access Journals (Sweden)

    Xing H

    2014-04-01

    Full Text Available Helin Xing,1,2 Satoshi Komasa,3 Yoichiro Taguchi,4 Tohru Sekino,5 Joji Okazaki3 1Department of Prosthetic Dentistry, School of Stomatology, The Fourth Military Medical University, Xi’an, People’s Republic of China; 2Graduate School of Dentistry (Removable Prosthodontics and Occlusion, 3Department of Removable Prosthodontics and Occlusion, 4Department of Periodontology, Osaka Dental University, Hirakata, Osaka, Japan; 5Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai, Japan Background: Titanium surfaces play an important role in affecting osseointegration of dental implants. Previous studies have shown that the titania nanotube promotes osseointegration by enhancing osteogenic differentiation. Only relatively recently have the effects of titanium surfaces with other nanostructures on osteogenic differentiation been investigated. Methods: In this study, we used NaOH solutions with concentrations of 2.5, 5.0, 7.5, 10.0, and 12.5 M to develop a simple and useful titanium surface modification that introduces the nanonetwork structures with titania nanosheet (TNS nanofeatures to the surface of titanium disks. The effects of such a modified nanonetwork structure, with different alkaline concentrations on the osteogenic differentiation of rat bone marrow mesenchymal stem cells (BMMSCs, were evaluated. Results: The nanonetwork structures with TNS nanofeatures induced by alkali etching markedly enhanced BMMSC functions of cell adhesion and osteogenesis-related gene expression, and other cell behaviors such as proliferation, alkaline phosphatase activity, extracellular matrix deposition, and mineralization were also significantly increased. These effects were most pronounced when the concentration of NaOH was 10.0 M. Conclusion: The results suggest that nanonetwork structures with TNS nanofeatures improved BMMSC proliferation and induced BMMSC osteogenic differentiation. In addition, the surfaces formed

  14. Eye Movements Reveal the Influence of Event Structure on Reading Behavior

    Science.gov (United States)

    Swets, Benjamin; Kurby, Christopher A.

    2016-01-01

    When we read narrative texts such as novels and newspaper articles, we segment information presented in such texts into discrete events, with distinct boundaries between those events. But do our eyes reflect this event structure while reading? This study examines whether eye movements during the reading of discourse reveal how readers respond…

  15. Surface structure and relaxation during the oxidation of carbon monoxide on Pt Pd bimetallic surfaces

    Science.gov (United States)

    Lucas, C. A.; Markovic, N. M.; Ball, M.; Stamenkovic, V.; Climent, V.; Ross, P. N.

    2001-05-01

    The atomic structure and surface relaxation of Pd monolayer on Pt(1 1 1) has been studied by surface X-ray scattering, in an aqueous environment under electrostatic potential control, during the adsorption and oxidation of carbon monoxide. The results show that the Pd-Pt layer spacing contracts at the onset of CO oxidation before the Pd adlayer forms an oxide structure that is incommensurate with the Pt lattice. Both the oxide formation and the lattice contraction are fully reversible over many cycles of the applied electrode potential.

  16. Bio-Inspired Functional Surfaces Based on Laser-Induced Periodic Surface Structures

    Directory of Open Access Journals (Sweden)

    Frank A. Müller

    2016-06-01

    Full Text Available Nature developed numerous solutions to solve various technical problems related to material surfaces by combining the physico-chemical properties of a material with periodically aligned micro/nanostructures in a sophisticated manner. The utilization of ultra-short pulsed lasers allows mimicking numerous of these features by generating laser-induced periodic surface structures (LIPSS. In this review paper, we describe the physical background of LIPSS generation as well as the physical principles of surface related phenomena like wettability, reflectivity, and friction. Then we introduce several biological examples including e.g., lotus leafs, springtails, dessert beetles, moth eyes, butterfly wings, weevils, sharks, pangolins, and snakes to illustrate how nature solves technical problems, and we give a comprehensive overview of recent achievements related to the utilization of LIPSS to generate superhydrophobic, anti-reflective, colored, and drag resistant surfaces. Finally, we conclude with some future developments and perspectives related to forthcoming applications of LIPSS-based surfaces.

  17. Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

    Science.gov (United States)

    Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

    2014-07-22

    Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

  18. Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

    Energy Technology Data Exchange (ETDEWEB)

    Bond, Tiziana C; Miles, Robin; Davidson, James; Liu, Gang Logan

    2015-11-03

    Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

  19. The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation.

    Science.gov (United States)

    Yurtsever, Zeynep; Scheaffer, Suzanne M; Romero, Arthur G; Holtzman, Michael J; Brett, Tom J

    2015-04-01

    The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are therefore involved in specific diseases. Detailed structural studies of all p38 MAPK family members are crucial for the design of specific inhibitors. In order to facilitate such ventures, the structure of MAPK13 was determined in both the inactive (unphosphorylated; MAPK13) and active (dual phosphorylated; MAPK13/pTpY) forms. Here, the first preparation, crystallization and structure determination of MAPK13/pTpY are presented and the structure is compared with the previously reported structure of MAPK13 in order to facilitate studies for structure-based drug design. A comprehensive analysis of inactive versus active structures for the p38 MAPK family is also presented. It is found that MAPK13 undergoes a larger interlobe configurational rearrangement upon activation compared with MAPK14. Surprisingly, the analysis of activated p38 MAPK structures (MAP12/pTpY, MAPK13/pTpY and MAPK14/pTpY) reveals that, despite a high degree of sequence similarity, different side chains are used to coordinate the phosphorylated residues. There are also differences in the rearrangement of the hinge region that occur in MAPK14 compared with MAPK13 which would affect inhibitor binding. A thorough examination of all of the active (phosphorylated) and inactive (unphosphorylated) p38 MAPK family member structures was performed to reveal a common structural basis of activation for the p38 MAP kinase family and to identify structural differences that may be exploited for developing family member-specific inhibitors.

  20. On Surface Structure and Friction Regulation in Reptilian Limbless Locomotion

    CERN Document Server

    Abdel-Aal, Hisham A

    2012-01-01

    One way of controlling friction and associated energy losses is to engineer a deterministic structural pattern on the surface of the rubbing parts (i.e., texture engineering). Custom texturing enhances the quality of lubrication, reduces friction, and allows the use of lubricants of lower viscosity. To date, a standardized procedure to generate deterministic texture constructs is virtually non-existent. Many engineers, therefore, study natural species to explore surface construction and to probe the role surface topography assumes in friction control. Snakes offer rich examples of surfaces where topological features allow the optimization and control of frictional behavior. In this paper, we investigate the frictional behavior of a constrictor type reptile, Python regius. The study employed a specially designed tribo-acoustic probe capable of measuring the coefficient of friction and detecting the acoustical behavior of the skin in vivo. The results confirm the anisotropy of the frictional response of snakesk...

  1. Electrical mapping of microtubular structures by surface potential microscopy

    Science.gov (United States)

    Zhang, Peng; Cantiello, Horacio F.

    2009-09-01

    Microtubules (MTs) are important cytoskeletal polymers that play an essential role in cell division and transport in all eukaryotes and information processing in neurons. MTs are highly charged polyelectrolytes, composed of hollow cylindrical arrangements of αβ-tubulin dimers. To date, there is little information about electrical properties of MTs. Here, we deposited and dried MTs onto a gold-plated surface to image their topology by atomic force microscopy (AFM), and determined their electrical mapping with surface potential microscopy (SPM). We found a strong linear correlation between the magnitude of relative surface potential and MT parameters, including diameter and height. AFM images confirmed the cylindrical topology of microtubular structures, and the presence of topological discontinuities along their surface, which may contribute to their unique electrical properties.

  2. Electronic structure tuning via surface modification in semimetallic nanowires

    Science.gov (United States)

    Sanchez-Soares, Alfonso; O'Donnell, Conor; Greer, James C.

    2016-12-01

    Electronic structure properties of nanowires (NWs) with diameters of 1.5 and 3 nm based on semimetallic α -Sn are investigated by employing density functional theory and perturbative GW methods. We explore the dependence of electron affinity, band structure, and band-gap values with crystallographic orientation, NW cross-sectional size, and surface passivants of varying electronegativity. We consider four chemical terminations in our study: methyl (CH3), hydrogen (H ), hydroxyl (OH ), and fluorine (F ). Results suggest a high degree of elasticity of Sn-Sn bonds within the Sn NWs' cores with no significant structural variations for nanowires with different surface passivants. Direct band gaps at Brillouin-zone centers are found for most studied structures with quasiparticle corrected band-gap magnitudes ranging from 0.25 to 3.54 eV in 1.5-nm-diameter structures, indicating an exceptional range of properties for semimetal NWs below the semimetal-to-semiconductor transition. Band-gap variations induced by changes in surface passivants indicate the possibility of realizing semimetal-semiconductor interfaces in NWs with constant cross-section and crystallographic orientation, allowing the design of novel dopant-free NW-based electronic devices.

  3. Fabrication of laser induced periodic surface structure for geometrical engineering

    Energy Technology Data Exchange (ETDEWEB)

    Tsutsumi, Naoto [Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo, Kyoto 606-8585 (Japan)], E-mail: tsutsumi@kit.jp; Fujihara, Arata; Nagata, Kazuya [Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo, Kyoto 606-8585 (Japan)

    2008-12-31

    The paper presents the highly ordered geometrical structures of laser induced periodic surface structure (LIPSS) in azobenzene urethane polymer (DR19 polymer) from 4-(N,N-dihydroxyethylamino)-4'-nitroazobenzene (Disperse red 19) with tolylene-2,4-diisocyanate (TDI). One or two regulated striped LIPSS was formed in confined spaces between surface relief gratings (SRG) induced by the s-polarized interfered beams. The pitch of LIPSS was one-half or one-third of SRG pitch. Standing wave with some selected mode between SRG in the surface waveguide is responsible for the formation of the regulated striped LIPSS. The crossed illumination of the interfered beams showed the waffle-like structure for s-polarization beam and the egg crate-like (ECL) structure for p-polarized beam. Photoinduced microscopic molecular ordering was also investigated. The linear polarized beam gave the large optical anisotropy in the polymer and the circularly polarized beam produced the chiral structure. The circular dichroism spectra showed the sharp peak due to the circular Bragg reflection from which the chiral pitch was evaluated.

  4. Crystal structure of enhanced green fluorescent protein to 1.35 A resolution reveals alternative conformations for Glu222.

    Directory of Open Access Journals (Sweden)

    James A J Arpino

    Full Text Available Enhanced Green Fluorescent Protein (EGFP is one of the most widely used engineered variants of the original wild-type Green Fluorescent Protein. Here, we report the high resolution (1.35 Å structure of EGFP crystallised in its untagged sequence form that reveals the combined impact of the F64L and S65T, that give rise to improved folding and spectral characteristics. The overall structure of EGFP is very similar to wt GFP, forming the classical β-barrel fold with the chromophore containing helix running through the core of the structure. Replacement of Phe64 with Leu in EGFP results in subtle rearrangement of hydrophobic core packing close to the chromophore including the reduction in surface exposure of two hydrophobic residues. Replacement of Ser65 with Thr has a significant impact on the local hydrogen bond network in the vicinity of the chromophore. Detailed analysis of electron density reveals that several residues close to the chromophore occupy at least two distinct conformations. This includes Glu222 that defines the charged state on the chromophore, with the two conformations having slightly different effects on the hydrogen bond network surrounding the chromophore. Hence, the reported high-resolution structure of EGFP has provided a long overdue molecular description of one of the most important fluorescent protein variants currently in general use.

  5. Frequency selective surface structure optimized by genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    Lu Jun; Wang Jian-Bo; Sun Guan-Cheng

    2009-01-01

    Frequency selective surface(FSS)is a two-dimensional periodic structure which has prominent characteristics of bandpass or bandblock when interacting with electromagnetic waves.In this paper,the thickness,the dielectric constant,the element graph and the arrangement periodicity of an FSS medium are investigated by Genetic Algorithm(GA)when an electromagnetic wave is incident on the FSS at a wide angle,and an optimized FSS structure and transmission characteristics are obtained.The results show that the optimized structure has better stability in relation to incident angle of electromagnetic wave and preserves the stability of centre frequency even at an incident angle as large as 80°,thereby laying the foundation for the application of FSS to curved surfaces at wide angles.

  6. Electronic structure of graphene on Ni surfaces with different orientation

    Energy Technology Data Exchange (ETDEWEB)

    Pudikov, D.A., E-mail: gelbry@gmail.com; Zhizhin, E.V.; Rybkin, A.G.; Rybkina, A.A.; Zhukov, Y.M.; Vilkov, O. Yu.; Shikin, A.M.

    2016-08-15

    An experimental study of the graphene, synthesized by propylene cracking on Ni surfaces with different orientation: (100) and (111), using angle-resolved photoemission, has been performed. It has been shown that graphene on Ni(111) had a perfect lateral structure due to consistency of their lattices, whereas graphene/Ni(100) consisted of a lot of domains. For both systems electronic structure was quite similar and demonstrated a strong bonding of graphene to the underlying Ni surface. After Au intercalation the electronic structure of graphene in both systems was shifted to the Fermi level and became linear in the vicinity of the K point of the Brillouin zone. - Highlights: • Graphene on Ni(111) is well-ordered, whereas on Ni(100) – multi-domain. • Graphene on Ni(111) and Ni(100) is strongly bonded with substrate. • Intercalation of Au atoms restores the linearity in dispersion and makes graphene quasi-free on both Ni(100) and Ni(111).

  7. UV spectral filtering by surface structured multilayer mirrors.

    Science.gov (United States)

    Huang, Qiushi; Paardekooper, Daniel Mathijs; Zoethout, Erwin; Medvedev, V V; van de Kruijs, Robbert; Bosgra, Jeroen; Louis, Eric; Bijkerk, Fred

    2014-03-01

    A surface structured extreme ultraviolet multilayer mirror was developed showing full band suppression of UV (λ=100-400  nm) and simultaneously a high reflectance of EUV light (λ=13.5  nm). The surface structure consists of Si pyramids, which are substantially transparent for EUV but reflective for UV light. The reflected UV is filtered out by blazed diffraction, interference, and absorption. A first demonstration pyramid structure was fabricated on a multilayer by using a straightforward deposition technique. It shows an average suppression of 14 times over the whole UV range and an EUV reflectance of 56.2% at 13.5 nm. This robust scheme can be used as a spectral purity solution for all XUV sources that emit longer wavelength radiation as well.

  8. Local structural ordering in surface-confined liquid crystals

    Science.gov (United States)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  9. Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

    Science.gov (United States)

    Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

    2013-01-01

    Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

  10. Plant Surfaces: Structures and Functions for Biomimetic Innovations

    Science.gov (United States)

    Barthlott, Wilhelm; Mail, Matthias; Bhushan, Bharat; Koch, Kerstin

    2017-04-01

    An overview of plant surface structures and their evolution is presented. It combines surface chemistry and architecture with their functions and refers to possible biomimetic applications. Within some 3.5 billion years biological species evolved highly complex multifunctional surfaces for interacting with their environments: some 10 million living prototypes (i.e., estimated number of existing plants and animals) for engineers. The complexity of the hierarchical structures and their functionality in biological organisms surpasses all abiotic natural surfaces: even superhydrophobicity is restricted in nature to living organisms and was probably a key evolutionary step with the invasion of terrestrial habitats some 350-450 million years ago in plants and insects. Special attention should be paid to the fact that global environmental change implies a dramatic loss of species and with it the biological role models. Plants, the dominating group of organisms on our planet, are sessile organisms with large multifunctional surfaces and thus exhibit particular intriguing features. Superhydrophilicity and superhydrophobicity are focal points in this work. We estimate that superhydrophobic plant leaves (e.g., grasses) comprise in total an area of around 250 million km2, which is about 50% of the total surface of our planet. A survey of structures and functions based on own examinations of almost 20,000 species is provided, for further references we refer to Barthlott et al. (Philos. Trans. R. Soc. A 374: 20160191, 1). A basic difference exists between aquatic non-vascular and land-living vascular plants; the latter exhibit a particular intriguing surface chemistry and architecture. The diversity of features is described in detail according to their hierarchical structural order. The first underlying and essential feature is the polymer cuticle superimposed by epicuticular wax and the curvature of single cells up to complex multicellular structures. A descriptive terminology

  11. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  12. Structures of Cryptococcus neoformans protein farnesyltransferase reveal strategies for developing inhibitors that target fungal pathogens.

    Science.gov (United States)

    Hast, Michael A; Nichols, Connie B; Armstrong, Stephanie M; Kelly, Shannon M; Hellinga, Homme W; Alspaugh, J Andrew; Beese, Lorena S

    2011-10-07

    Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

  13. Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Hast, Michael A.; Nichols, Connie B.; Armstrong, Stephanie M.; Kelly, Shannon M.; Hellinga, Homme W.; Alspaugh, J. Andrew; Beese, Lorena S. (Duke)

    2012-09-17

    Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

  14. Novel genetic algorithm search procedure for LEED surface structure determination.

    Science.gov (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  15. The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, Jiapeng [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Mouveaux, Thomas [Université Lille Nord de France, (France); Light, Samuel H.; Minasov, George; Anderson, Wayne F. [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Tomavo, Stanislas [Université Lille Nord de France, (France); Ngô, Huân M., E-mail: h-ngo@northwestern.edu [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511 (United States)

    2015-03-01

    The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

  16. Morphology control of laser-induced periodic surface structure on the surface of nickel by femtosecond laser

    Institute of Scientific and Technical Information of China (English)

    Fantong Meng; Jie Hu; Weina Han; Penjun Liu; Qingsong Wang

    2015-01-01

    An interesting transition between low spatial frequency laser-induced periodic surface structure (LIPSS) and high spatial frequency LIPSS (HSFL) on the surface of nickel is revealed by changing the scanning speed and the laser fluence.The experimental results show the proportion of HSFL area in the overall LIPSS (i.e.,K) presents a quasi-parabola function trend with the polarization orientation under a femtosecond (fs) laser single-pulse train.Moreover,an obvious fluctuation dependence of K on the pulse delay is observed under a fs laser dual-pulse train.The peak value of the fluctuation is found to be determined by the polarization orientation of the dual-pulse train.

  17. Surface and Structure: Transcribing Intonation within and across Languages

    Directory of Open Access Journals (Sweden)

    Sónia Frota

    2016-06-01

    Full Text Available Intonation is the phonologically structured variation in phonetic features, primarily pitch, to express phrase-level meanings. As in other speech sound domains, analyzing intonation involves mapping continuously variable physical parameters to categories. The categories of intonation are organized in a set of relations and rule-governed distributions that define the intonation system of a language. From physical realizations, as shown by pitch tracks, surface or phonetic tonal patterns can be identified in terms of tonal targets. Whether surface patterns correspond or not to categories within a given intonation system requires looking at their distributions and contrastiveness. In this paper, I assume the view that a transcription is an analysis of the intonation system, which ultimately aims to identify the contrastive intonation categories of a given language and establish how they signal meaning. Under this view, it is crucial to discuss the ways surface pitch patterns and structural pitch patterns (or phonological categories are related. Given that intonational analysis is driven by system-internal considerations and that cues to a given category can vary across languages, it is also important to address the issue of how a language-specific transcription can be reconciled with the need and ability to do cross-language comparison of intonation. Bearing on these two issues, I discuss surface and structure in intonational analysis, drawing on mismatches between (dissimilarities in the phonetics and phonology of pitch contours, across languages and language varieties.

  18. Can atom-surface potential measurements test atomic structure models?

    Science.gov (United States)

    Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D

    2011-06-30

    van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.

  19. Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.

    Science.gov (United States)

    Chang, Aram; Singh, Shanteri; Helmich, Kate E; Goff, Randal D; Bingman, Craig A; Thorson, Jon S; Phillips, George N

    2011-10-25

    Glycosyltransferases are useful synthetic catalysts for generating natural products with sugar moieties. Although several natural product glycosyltransferase structures have been reported, design principles of glycosyltransferase engineering for the generation of glycodiversified natural products has fallen short of its promise, partly due to a lack of understanding of the relationship between structure and function. Here, we report structures of all four calicheamicin glycosyltransferases (CalG1, CalG2, CalG3, and CalG4), whose catalytic functions are clearly regiospecific. Comparison of these four structures reveals a conserved sugar donor binding motif and the principles of acceptor binding region reshaping. Among them, CalG2 possesses a unique catalytic motif for glycosylation of hydroxylamine. Multiple glycosyltransferase structures in a single natural product biosynthetic pathway are a valuable resource for understanding regiospecific reactions and substrate selectivities and will help future glycosyltransferase engineering.

  20. Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Aram; Singh, Shanteri; Helmich, Kate E.; Goff, Randal D.; Bingman, Craig A.; Thorson, Jon S.; Phillips, Jr., George N. (UW)

    2012-03-15

    Glycosyltransferases are useful synthetic catalysts for generating natural products with sugar moieties. Although several natural product glycosyltransferase structures have been reported, design principles of glycosyltransferase engineering for the generation of glycodiversified natural products has fallen short of its promise, partly due to a lack of understanding of the relationship between structure and function. Here, we report structures of all four calicheamicin glycosyltransferases (CalG1, CalG2, CalG3, and CalG4), whose catalytic functions are clearly regiospecific. Comparison of these four structures reveals a conserved sugar donor binding motif and the principles of acceptor binding region reshaping. Among them, CalG2 possesses a unique catalytic motif for glycosylation of hydroxylamine. Multiple glycosyltransferase structures in a single natural product biosynthetic pathway are a valuable resource for understanding regiospecific reactions and substrate selectivities and will help future glycosyltransferase engineering.

  1. Scalably Revealing the Dynamics of Soft Community Structure in Complex Networks

    Institute of Scientific and Technical Information of China (English)

    LI Huijia; LI Huiying

    2016-01-01

    Revealing the dynamics of community structure is of great concern for scientists from many fields.Specifically,how to quantify the dynamic details of soft community structure is a very interesting topic.In this paper,the authors propose a novel framework to study the scalable dynamic behavior of the soft community structure.First,the authors model the Potts dynamics to detect community structure using a "soft" Markov process.Then the soft stability of in a multiscale view is proposed to naturally uncover the local uniform behavior of spin values across multiple hierarchical levels.Finally,a new partition index is developed to detect fuzzy communities based on the stability and the dynamical information.Experiments on the both synthetically generated and real-world networks verify that the framework can be used to uncover hierarchical community structures effectively and efficiently.

  2. Cutting Edge: Il-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features And Multiple Conformations

    Energy Technology Data Exchange (ETDEWEB)

    Kuglstatter, A.; Villasenor, A.G.; Shaw, D.; Lee, S.W.; Tsing, S.; Niu, L.; Song, K.W.; Barnett, J.W.; Browner, M.F.

    2007-07-09

    L-1R-associated kinase (IRAK)4 plays a central role in innate and adaptive immunity, and is a crucial component in IL-1/TLR signaling. We have determined the crystal structures of the apo and ligand-bound forms of human IRAK4 kinase domain. These structures reveal several features that provide opportunities for the design of selective IRAK4 inhibitors. The N-terminal lobe of the IRAK4 kinase domain is structurally distinctive due to a loop insertion after an extended N-terminal helix. The gatekeeper residue is a tyrosine, a unique feature of the IRAK family. The IRAK4 structures also provide insights into the regulation of its activity. In the apo structure, two conformations coexist, differing in the relative orientation of the two kinase lobes and the position of helix C. In the presence of an ATP analog only one conformation is observed, indicating that this is the active conformation.

  3. Revealing the compact structure of lactic acid bacterial hetero-exopolysaccharides by SAXS and DLS

    DEFF Research Database (Denmark)

    Khan, Sanaullah; Birch, Johnny; Harris, Pernille

    2017-01-01

    a compact coil-like rather than an extended conformation. Constrained molecular modeling of 15,000 randomised HePS-1 conformers resulted in five best-fit structures with R factor of 3.94.6% revealing random coil-like structure. Φ and Ψ angle analysis of glycosidic linkages in HePS-1 structures suggests......Molecular structures of exopolysaccharides are required to understand their functions and the relationships between the structure and physical and rheological properties. Small-angle X-ray scattering and dynamic light scattering were used in conjunction with molecular modeling to characterize...... Galf residues significantly influence the conformation. Ab initio scattering modeling of HePS-2 and HePS-3 gave excellent curve fittings with χ2 of 0.43 and 0.34 for best-fit models, respectively, compatible with coil-like conformation. The findings disclose solution behaviour of HePS relevant...

  4. Crystal Structures of Lys-63-linked tri- and di-ubiquitin Reveal a Highly Extended Chain Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Weeks, S.; Grasty, K; Hernandez-Cuebas, L; Loll, P

    2009-01-01

    The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 {angstrom}, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of {approx}110 {angstrom}. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.

  5. Language learners privilege structured meaning over surface frequency.

    Science.gov (United States)

    Culbertson, Jennifer; Adger, David

    2014-04-22

    Although it is widely agreed that learning the syntax of natural languages involves acquiring structure-dependent rules, recent work on acquisition has nevertheless attempted to characterize the outcome of learning primarily in terms of statistical generalizations about surface distributional information. In this paper we investigate whether surface statistical knowledge or structural knowledge of English is used to infer properties of a novel language under conditions of impoverished input. We expose learners to artificial-language patterns that are equally consistent with two possible underlying grammars--one more similar to English in terms of the linear ordering of words, the other more similar on abstract structural grounds. We show that learners' grammatical inferences overwhelmingly favor structural similarity over preservation of superficial order. Importantly, the relevant shared structure can be characterized in terms of a universal preference for isomorphism in the mapping from meanings to utterances. Whereas previous empirical support for this universal has been based entirely on data from cross-linguistic language samples, our results suggest it may reflect a deep property of the human cognitive system--a property that, together with other structure-sensitive principles, constrains the acquisition of linguistic knowledge.

  6. Biomimetic surface structuring using cylindrical vector femtosecond laser beams

    Science.gov (United States)

    Skoulas, Evangelos; Manousaki, Alexandra; Fotakis, Costas; Stratakis, Emmanuel

    2017-03-01

    We report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications.

  7. Surface Structure of Thin Films of Multifunctional Ionizable Copolymers

    Science.gov (United States)

    Wickramasinghe, Anuradhi; Perahia, Dvora

    Phase segregation results in a rich variety of structures in co-polymers where interfacial forces often dominate the structure of thin films. Introduction of ionizable segments often drives the formation of compounded structures with multiple blocks residing at the interfaces. Here we probe thin films, 40-50nm, of an A-B-C-B-A co-polymer where C is a randomly sulfonated polystyrene with sulfonation fractions of 0, 26 and 52 mole %, B is poly (ethylene-r-propylene), and A is poly (t-butyl styrene) as the sulfonation level and temperature are varied using Neutron Reflectivity AFM, and surface tension measurements. As cast films form layers with both hydrophobic blocks dominating the solid and air interfaces and the ionizable block segregating to the center. Following annealing at 1700C, above Tg of styrene sulfonate, the films coarsen, with surface aggregation dominating the structure, though interfacial regions remain dominated by the hydrophobic segments. We show that in contrast to non-ionic co-polymers, formation of micelles dominated the structure of these ionic structured films. Supported in part by DOE Grant No. DE-SC007908.

  8. Surface-plasmons lasing in double-graphene-layer structures

    Energy Technology Data Exchange (ETDEWEB)

    Dubinov, A. A. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan); Institute for Physics of Microstructures of Russian Academy of Sciences, and Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603950 (Russian Federation); Aleshkin, V. Ya. [Institute for Physics of Microstructures of Russian Academy of Sciences, and Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603950 (Russian Federation); Ryzhii, V. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan); Center for Photonics and Infrared Engineering, Bauman Moscow State Technical University, Moscow 105005 (Russian Federation); Shur, M. S. [Department of Electrical, Electronics, and System Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States); Otsuji, T. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan)

    2014-01-28

    We consider the concept of injection terahertz lasers based on double-graphene-layer (double-GL) structures with metal surface-plasmon waveguide and study the conditions of their operation. The laser under consideration exploits the resonant radiative transitions between GLs. This enables the double-GL laser room temperature operation and the possibility of voltage tuning of the emission spectrum. We compare the characteristics of the double-GL lasers with the metal surface-plasmon waveguides with those of such laser with the metal-metal waveguides.

  9. Enhancing the chroma of pigmented polymers using antireflective surface structures

    DEFF Research Database (Denmark)

    Clausen, Jeppe Sandvik; Christiansen, Alexander Bruun; Kristensen, Anders;

    2013-01-01

    In this paper we investigate how the color of a pigmented polymer is affected by reduction of the reflectance at the air-polymer interface. Both theoretical and experimental investigations show modified diffuse-direct reflectance spectra when the reflectance of the surface is lowered. Specifically...... it is found that the color change is manifested as an increase in chroma, leading to a clearer color experience. The experimental implementation is done using random tapered surface structures replicated in polymer from silicon masters using hot embossing....

  10. Surface Monitoring of CFRP Structures for Adhesive Bonding

    Science.gov (United States)

    Ledesma, Rodolfo; Palmieri, Frank L.; Yost, William T.; Connell, John W.; Fitz-Gerald, James M.

    2017-01-01

    Adhesive bonding of composite materials requires reliable monitoring and detection of surface contaminants to assure robust and durable bonded structures. Surface treatment and effective monitoring prior to bonding is essential in order to obtain a surface free from contaminants that may degrade structural performance. Two techniques which monitor the effectiveness of the laser surface treatment of carbon fiber reinforced polymer (CFRP) materials are being investigated: laser induced breakdown spectroscopy (LIBS) and optically stimulated electron emission (OSEE). The applicability of LIBS to detect silicone contaminants on CFRP composites is studied using 35 ns Nd:YAG laser pulses at 355 nm with a pulse energy of 45 mJ. The LIBS regime in which pulse energies are < 100 mJ is referred to as mLIBS. CFRP surfaces were contaminated with polydimethylsiloxane (PDMS), a major component of silicone based mold release agents. The presence of PDMS is found by inspecting the Si I emission line at 288.2 nm. Untreated CFRP samples and CFRP contaminated with PDMS were tested. The PDMS areal density ranged from 0.36 Â+/- 0.04 to 0.51 Â+/- 0.16 mg/cm2. The results demonstrate the successful detection of PDMS on CFRP using mLIBS. In addition, OSEE was used to measure CFRP surface cleanliness pre- and post-treatment by laser ablation on specimens contaminated with PDMS coatings from 8 nm to 1311 nm in thickness. The results showed a significant increase in the OSEE photocurrent after laser surface treatment.

  11. Polarisation-dependent generation of fs-laser induced periodic surface structures

    Energy Technology Data Exchange (ETDEWEB)

    Gräf, Stephan, E-mail: stephan.graef@uni-jena.de; Müller, Frank A.

    2015-03-15

    Highlights: • LIPSS formation was studied under static and dynamic alteration of laser polarisation. • The dynamic polarisation is based on a continuously rotating E-field vector. • LIPSS generated with static linear polarisation reveal a period of 925 nm. • LIPSS orientation follows the direction of the rotating E-field vector. • The approach facilitates the formation of disordered structures for optical applications. - Abstract: The formation of laser induced periodic surface structures (LIPPS) was investigated on polished stainless steel surfaces under irradiation with fs-laser pulses characterised by a pulse duration τ = 300 fs, a laser wavelength λ = 1025 nm, a repetition frequency f{sub rep} = 250 Hz and a laser fluence F = 1 J/cm{sup 2}. For this purpose line scans with a scanning velocity v = 0.5 mm/s were performed in air environment at normal incidence utilising a well-defined temporal control of the electrical field vector. The generated surface structures were characterised by optical microscopy, by scanning electron microscopy and by atomic force microscopy in combination with Fourier transformation. The results reveal the formation of a homogenous and highly periodic surface pattern of ripples with a period Λ{sub exp} ≈ 925 nm aligned perpendicular to the incident electric field vector for static linear polarisation states. Utilising a motor-driven rotation device it was demonstrated that a continuously rotating electric field vector allows to transfer the originally well-ordered periodic ripples into tailored disordered surface structures that could be of particular interest for e.g. absorbing surfaces, plasmonic enhanced optoelectronic devices and biomedical applications.

  12. Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus*♦

    Science.gov (United States)

    Dickson, Claire F.; Kumar, Kaavya Krishna; Jacques, David A.; Malmirchegini, G. Reza; Spirig, Thomas; Mackay, Joel P.; Clubb, Robert T.; Guss, J. Mitchell; Gell, David A.

    2014-01-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins. PMID:24425866

  13. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus.

    Science.gov (United States)

    Dickson, Claire F; Kumar, Kaavya Krishna; Jacques, David A; Malmirchegini, G Reza; Spirig, Thomas; Mackay, Joel P; Clubb, Robert T; Guss, J Mitchell; Gell, David A

    2014-03-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins.

  14. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    Science.gov (United States)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  15. Femtosecond laser-induced periodic surface structures on steel and titanium alloy for tribological applications

    Science.gov (United States)

    Bonse, J.; Koter, R.; Hartelt, M.; Spaltmann, D.; Pentzien, S.; Höhm, S.; Rosenfeld, A.; Krüger, J.

    2014-10-01

    Laser-induced periodic surface structures (LIPSS, ripples) were generated on stainless steel (100Cr6) and titanium alloy (Ti6Al4V) surfaces upon irradiation with multiple femtosecond laser pulses (pulse duration 30 fs, central wavelength 790 nm). The experimental conditions (laser fluence, spatial spot overlap) were optimized in a sample-scanning geometry for the processing of large surface areas (5 × 5 mm2) covered homogeneously by the nanostructures. The irradiated surface regions were subjected to white light interference microscopy and scanning electron microscopy revealing spatial periods around 600 nm. The tribological performance of the nanostructured surface was characterized by reciprocal sliding against a ball of hardened steel in paraffin oil and in commercial engine oil as lubricants, followed by subsequent inspection of the wear tracks. For specific conditions, on the titanium alloy a significant reduction of the friction coefficient by a factor of more than two was observed on the laser-irradiated (LIPSS-covered) surface when compared to the non-irradiated one, indicating the potential benefit of laser surface structuring for tribological applications.

  16. Dissecting the structure of surface stabilizer on the dispersion of inorganic nanoparticles in aqueous medium

    Science.gov (United States)

    Ding, Yong; Yu, Zongzhi; Zheng, Junping

    2017-03-01

    Dispersing inorganic nanoparticles in aqueous solutions is a key requirement for a great variety of products and processes, including carriers in drug delivery or fillers in polymers. To be highly functional in the final product, inorganic particles are required to be finely dispersed in nanoscale. In this study, silica was selected as a representative inorganic particle. Surface stabilizers with different chain length and charged group were designed to reveal the influence of electrostatic and van der Waals forces between silica and stabilizer on the dispersion of silica particles in aqueous medium. Results showed surface stabilizer with longer alkyl chain and charged group exerted best ability to deaggregate silica, leading to a hydrodynamic size of 51.1 nm. Surface stabilizer designing with rational structure is a promising solution for deagglomerating and reducing process time and energy. Giving the designability and adaptability of surface stabilizer, this method is of potential for dispersion of other inorganic nanoparticles.

  17. Nanochemistry at the atomic scale revealed in hydrogen-induced semiconductor surface metallization

    Science.gov (United States)

    Derycke, Vincent; Soukiassian, Patrick G.; Amy, Fabrice; Chabal, Yves J.; D'Angelo, Marie D.; Enriquez, Hanna B.; Silly, Mathieu G.

    2003-04-01

    Passivation of semiconductor surfaces against chemical attack can be achieved by terminating the surface-dangling bonds with a monovalent atom such as hydrogen. Such passivation invariably leads to the removal of all surface states in the bandgap, and thus to the termination of non-metallic surfaces. Here we report the first observation of semiconductor surface metallization induced by atomic hydrogen. This result, established by using photo-electron and photo-absorption spectroscopies and scanning tunnelling techniques, is achieved on a Si-terminated cubic silicon carbide (SiC) surface. It results from competition between hydrogen termination of surface-dangling bonds and hydrogen-generated steric hindrance below the surface. Understanding the ingredient for hydrogen-stabilized metallization directly impacts the ability to eliminate electronic defects at semiconductor interfaces critical for microelectronics, provides a means to develop electrical contacts on high-bandgap chemically passive materials, particularly for interfacing with biological systems, and gives control of surfaces for lubrication, for example of nanomechanical devices.

  18. Fitting C² continuous parametric surfaces to frontiers delimiting physiologic structures.

    Science.gov (United States)

    Bayer, Jason D; Epstein, Matthew; Beaumont, Jacques

    2014-01-01

    We present a technique to fit C(2) continuous parametric surfaces to scattered geometric data points forming frontiers delimiting physiologic structures in segmented images. Such mathematical representation is interesting because it facilitates a large number of operations in modeling. While the fitting of C(2) continuous parametric curves to scattered geometric data points is quite trivial, the fitting of C(2) continuous parametric surfaces is not. The difficulty comes from the fact that each scattered data point should be assigned a unique parametric coordinate, and the fit is quite sensitive to their distribution on the parametric plane. We present a new approach where a polygonal (quadrilateral or triangular) surface is extracted from the segmented image. This surface is subsequently projected onto a parametric plane in a manner to ensure a one-to-one mapping. The resulting polygonal mesh is then regularized for area and edge length. Finally, from this point, surface fitting is relatively trivial. The novelty of our approach lies in the regularization of the polygonal mesh. Process performance is assessed with the reconstruction of a geometric model of mouse heart ventricles from a computerized tomography scan. Our results show an excellent reproduction of the geometric data with surfaces that are C(2) continuous.

  19. Cryogenic EBSD reveals structure of directionally solidified ice–polymer composite

    Energy Technology Data Exchange (ETDEWEB)

    Donius, Amalie E., E-mail: amalie.donius@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Obbard, Rachel W., E-mail: Rachel.W.Obbard@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Burger, Joan N., E-mail: ridge.of.the.ancients@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Hunger, Philipp M., E-mail: philipp.m.hunger@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Baker, Ian, E-mail: Ian.Baker@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Doherty, Roger D., E-mail: dohertrd@drexel.edu [Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Wegst, Ulrike G.K., E-mail: ulrike.wegst@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States)

    2014-07-01

    Despite considerable research efforts on directionally solidified or freeze-cast materials in recent years, little fundamental knowledge has been gained that links model with experiment. In this contribution, the cryogenic characterization of directionally solidified polymer solutions illustrates, how powerful cryo-scanning electron microscopy combined with electron backscatter diffraction is for the structural characterization of ice–polymer composite materials. Under controlled sublimation, the freeze-cast polymer scaffold structure is revealed and imaged with secondary electrons. Electron backscatter diffraction fabric analysis shows that the ice crystals, which template the polymer scaffold and create the lamellar structure, have a-axes oriented parallel to the direction of solidification and the c-axes perpendicular to it. These results indicate the great potential of both cryo-scanning electron microscopy and cryo-electron backscatter diffraction in gaining fundamental knowledge of structure–property–processing correlations. - Highlights: • Cryo-SEM of freeze-cast polymer solution reveals an ice-templated structure. • Cryo-EBSD reveals the ice crystal a-axis to parallel the solidification direction. • The honeycomb-like polymer phase favors columnar ridges only on one side. • Combining cryo-SEM with EBSD links solidification theory with experiment.

  20. Wireless structural sensor made with frequency selective surface antenna

    Science.gov (United States)

    Jang, Sang-Dong; Kim, Jaehwan

    2012-04-01

    Nondestructive Structural health monitoring (SHM) system using wireless sensor network is the one of important issue for aerospace and civil engineering. Chipless passive wireless sensor system is one of novel methods for SHM which uses the electromagnetic wave characteristic change by geometrical change of electromagnetic resonators or impedance change of functional material sensing part without RFID chip. In this paper, the chipless passive wireless SHM sensor using frequency selective surface (FSS) is investigated. Electromagnetic characteristic change of FSS by mechanical strain or structural damage is investigated by simulation and experiment.

  1. Structural phases of adsorption for flexible polymers on nanocylinder surfaces.

    Science.gov (United States)

    Gross, Jonathan; Vogel, Thomas; Bachmann, Michael

    2015-11-11

    By means of generalized-ensemble Monte Carlo simulations, we investigate the thermodynamic behavior of a flexible, elastic polymer model in the presence of an attractive nanocylinder. We systematically identify the structural phases that are formed by competing monomer-monomer and monomer-substrate interactions. The influence of the relative surface attraction strength on the structural phases in the hyperphase diagram, parameterized by cylinder radius and temperature, is discussed as well. In the limiting case of the infinitely large cylinder radius, our results coincide with previous outcomes of studies of polymer adsorption on planar substrates.

  2. Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition.

    Science.gov (United States)

    Batra, Monu; Sharma, Rajesh; Malik, Anjali; Dhindwal, Sonali; Kumar, Pravindra; Tomar, Shailly

    2016-12-01

    Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavorable ones. In this study, crystal structure of B. subtilis CheR (BsCheR) in complex with S-adenosyl-l-homocysteine (SAH) has been determined to 1.8Å resolution. This is the first report of crystal structure belonging to the pentapeptide-independent CheR (PICheR) class. Till date, only one crystal structure of CheR from S. typhimurium (StCheR) belonging to pentapeptide-dependent CheR (PDCheR) class is available. Structural analysis of BsCheR reveals a helix-X-helix motif (HXH) with Asp53 as the linker residue in the N-terminal domain. The key structural features of the PDCheR β-subdomain involved in the formation of a tight complex with the pentapeptide binding motif in MCPRs were found to be absent in the structure of BsCheR. Additionally, isothermal titration calorimetry (ITC) experiments were performed to investigate S-adenosyl-(l)-methionine (SAM) binding affinity and KD was determined to be 0.32mM. The structure of BsCheR reveals that mostly residues of the large C-terminal domain contribute to SAH binding, with contributions of few residues from the linker region and the N-terminal domain. Structural investigations and sequence analysis carried out in this study provide critical insights into the distinct receptor recognition mechanism of the PDCheR and PICheR methyltransferase classes.

  3. Laser-induced periodic surface structuring of biopolymers

    Science.gov (United States)

    Pérez, Susana; Rebollar, Esther; Oujja, Mohamed; Martín, Margarita; Castillejo, Marta

    2013-03-01

    We report here on a systematic study about the formation of laser-induced periodic surface structures (LIPSS) on biopolymers. Self-standing films of the biopolymers chitosan, starch and the blend of chitosan with the synthetic polymer poly (vinyl pyrrolidone), PVP, were irradiated in air with linearly polarized laser beams at 193, 213 and 266 nm, with pulse durations in the range of 6-17 ns. The laser-induced periodic surface structures were topographically characterized by atomic force microscopy and the chemical modifications induced by laser irradiation were inspected via Raman spectroscopy. Formation of LIPSS parallel to the laser polarization direction, with periods similar to the laser wavelength, was observed at efficiently absorbed wavelengths in the case of the amorphous biopolymer chitosan and its blend with PVP, while formation of LIPSS is prevented in the crystalline starch biopolymer.

  4. Femtosecond laser-induced surface structures on carbon fibers.

    Science.gov (United States)

    Sajzew, Roman; Schröder, Jan; Kunz, Clemens; Engel, Sebastian; Müller, Frank A; Gräf, Stephan

    2015-12-15

    The influence of different polarization states during the generation of periodic nanostructures on the surface of carbon fibers was investigated using a femtosecond laser with a pulse duration τ=300  fs, a wavelength λ=1025  nm, and a peak fluence F=4  J/cm². It was shown that linear polarization results in a well-aligned periodic pattern with different orders of magnitude concerning their period and an alignment parallel and perpendicular to fiber direction, respectively. For circular polarization, both types of uniform laser-induced periodic surface structures (LIPSS) patterns appear simultaneously with different dominance in dependence on the position at the fiber surface. Their orientation was explained by the polarization-dependent absorptivity and the geometrical anisotropy of the carbon fibers.

  5. Atomic and electronic structure of surfaces theoretical foundations

    CERN Document Server

    Lannoo, Michel

    1991-01-01

    Surfaces and interfaces play an increasingly important role in today's solid state devices. In this book the reader is introduced, in a didactic manner, to the essential theoretical aspects of the atomic and electronic structure of surfaces and interfaces. The book does not pretend to give a complete overview of contemporary problems and methods. Instead, the authors strive to provide simple but qualitatively useful arguments that apply to a wide variety of cases. The emphasis of the book is on semiconductor surfaces and interfaces but it also includes a thorough treatment of transition metals, a general discussion of phonon dispersion curves, and examples of large computational calculations. The exercises accompanying every chapter will be of great benefit to the student.

  6. Atomic and electronic structure of molybdenum carbide phases: bulk and low Miller-index surfaces.

    Science.gov (United States)

    Politi, José Roberto dos Santos; Viñes, Francesc; Rodriguez, Jose A; Illas, Francesc

    2013-08-14

    The geometric and electronic structure of catalytically relevant molybdenum carbide phases (cubic δ-MoC, hexagonal α-MoC, and orthorhombic β-Mo2C) and their low Miller-index surfaces have been investigated by means of periodic density functional theory (DFT) based calculations with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. Comparison to available experimental data indicates that this functional is particularly well suited to study these materials. The calculations reveal that β-Mo2C has a stronger metallic character than the other two polymorphs, both β-Mo2C and δ-MoC have a large ionic contribution, and δ- and α-MoC exhibit the strongest covalent character. Among the various surfaces explored, the calculations reveal the high stability of the δ-MoC(001) nonpolar surface, Mo- and C-terminated (001) polar surfaces of α-MoC, and the nonpolar (011) surface of β-Mo2C. A substantially low work function of only 3.4 eV is predicted for β-Mo2C(011), suggesting that this system is particularly well suited for (electro)catalytic processes where surface → adsorbate electron transfer is essential. The overall implications for heterogeneously catalysed reactions by these molybdenum carbide nanoparticles are also discussed.

  7. Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

    Directory of Open Access Journals (Sweden)

    Elizabeth R Sprague

    2006-06-01

    Full Text Available Herpes simplex virus type-1 expresses a heterodimeric Fc receptor, gE-gI, on the surfaces of virions and infected cells that binds the Fc region of host immunoglobulin G and is implicated in the cell-to-cell spread of virus. gE-gI binds immunoglobulin G at the basic pH of the cell surface and releases it at the acidic pH of lysosomes, consistent with a role in facilitating the degradation of antiviral antibodies. Here we identify the C-terminal domain of the gE ectodomain (CgE as the minimal Fc-binding domain and present a 1.78-angstroms CgE structure. A 5-angstroms gE-gI/Fc crystal structure, which was independently verified by a theoretical prediction method, reveals that CgE binds Fc at the C(H2-C(H3 interface, the binding site for several mammalian and bacterial Fc-binding proteins. The structure identifies interface histidines that may confer pH-dependent binding and regions of CgE implicated in cell-to-cell spread of virus. The ternary organization of the gE-gI/Fc complex is compatible with antibody bipolar bridging, which can interfere with the antiviral immune response.

  8. Curved hierarchically micro-micro structured polypropylene surfaces by injection molding

    Science.gov (United States)

    Mielonen, K.; Suvanto, M.; Pakkanen, T. A.

    2017-01-01

    Structural hierarchy of polymer surfaces has been of central interest due to its diverse surface functionalities. However, the research on hierarchically structured polymer surfaces has been focused on planar surfaces even though applications may also be variously curved. This study demonstrates the fabrication of curved rigid polymer surfaces with precisely controlled hierarchical microstructures. The surface structuration was made on an aluminum foil with a microworking robot, and polypropylene replicas were produced by injection molding. Depending on the mold structuration procedure, the curved mold can have either radially or vertically oriented structures. Both convex and concave curvatures were here applied to spherically and cylindrically curved surfaces. A simple structure protection technique was applied to support the structures during mechanical bending of the foil. The planar hierarchically microstructured polypropylene surfaces were characterized to exhibit superhydrophobicity, and similar structures were obtained on the curved surfaces. Introducing the curvature to the hierarchically structured surfaces may further widen the applicability of functionalized polymer surfaces.

  9. Study on Dielectric Function Models for Surface Plasmon Resonance Structure

    Directory of Open Access Journals (Sweden)

    Peyman Jahanshahi

    2014-01-01

    Full Text Available The most common permittivity function models are compared and identifying the best model for further studies is desired. For this study, simulations using several different models and an analytical analysis on a practical surface Plasmon structure were done with an accuracy of ∼94.4% with respect to experimental data. Finite element method, combined with dielectric properties extracted from the Brendel-Bormann function model, was utilized, the latter being chosen from a comparative study on four available models.

  10. Towards Friction Control using laser-induced periodic Surface Structures

    OpenAIRE

    Eichstädt, J.; Römer, G.R.B.E.; Huis in 't Veld, A.J.

    2011-01-01

    This paper aims at contributing to the study of laser-induced periodic surface structures (LIPSS) and the description of their tribological properties in order to facilitate the knowledge for contact mechanical applications. To obtain laser parameters for LIPSS formation, we propose to execute two D2-Experiments. For the transfer of results from static experiments to areas of LIPSS we propose the discrete accumulation of fluences. Areas covered by homogeneously distributed LIPSS were machined...

  11. Structural dynamics of potassium-channel gating revealed by single-molecule FRET.

    Science.gov (United States)

    Wang, Shizhen; Vafabakhsh, Reza; Borschel, William F; Ha, Taekjip; Nichols, Colin G

    2016-01-01

    Crystallography has provided invaluable insights regarding ion-channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites and then examined structural dynamics within lipid membranes by single-molecule fluorescence resonance energy transfer (FRET). We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states, both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and in cation channels in general.

  12. Structural dynamics of potassium channel gating revealed by single molecule FRET

    Science.gov (United States)

    Borschel, William F.; Ha, Taekjip; Nichols, Colin G.

    2016-01-01

    Crystallography has provided invaluable insights to ion channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites, and examined structural dynamics within lipid membranes by single molecule FRET. We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and for cation channels in general. PMID:26641713

  13. Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases

    Energy Technology Data Exchange (ETDEWEB)

    Taneja, Bhupesh; Patel, Asmita; Slesarev, Alexei; Mondragon, Alfonso (NWU); (FSI)

    2010-09-02

    Topoisomerases are involved in controlling and maintaining the topology of DNA and are present in all kingdoms of life. Unlike all other types of topoisomerases, similar type IB enzymes have only been identified in bacteria and eukarya. The only putative type IB topoisomerase in archaea is represented by Methanopyrus kandleri topoisomerase V. Despite several common functional characteristics, topoisomerase V shows no sequence similarity to other members of the same type. The structure of the 61 kDa N-terminal fragment of topoisomerase V reveals no structural similarity to other topoisomerases. Furthermore, the structure of the active site region is different, suggesting no conservation in the cleavage and religation mechanism. Additionally, the active site is buried, indicating the need of a conformational change for activity. The presence of a topoisomerase in archaea with a unique structure suggests the evolution of a separate mechanism to alter DNA.

  14. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    Science.gov (United States)

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. Copyright 1998 Academic Press.

  15. Adenovirus Structure as Revealed by X-Ray Crystallography, Electron Microscopy, and Difference Imaging

    Science.gov (United States)

    Stewart, Phoebe L.; Burnett, Roger M.

    1993-03-01

    The three-dimensional structure of human type 2 adenovirus was studied by combining X-ray crystallography and electron microscopy in a novel way. The 2.9 Å crystal structure of the major capsid protein, hexon, was positioned into a three-dimensional image reconstruction of the intact virus that was derived from cryo-electron micrographs. A three-dimensional difference map was generated by subtracting 240 copies of the crystallographic hexon from the density of the intact virus. This map revealed several minor structural proteins acting as “cement” to stabilize the assembly. The current state of structural knowledge concerning the location of the polypeptide components and the viral DNA is presented.

  16. X-ray CT Scanning Reveals Long-Term Copper Pollution Effects on Functional Soil Structure

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Homstrup, Martin

    Soil structure plays the main role in the ability of the soil to fulfill essential soil functions such as the root growth, rate of water infiltration and retention, transport of gaseous and chemicals/pollutants through the soil. Soil structure is a dynamic soil property and affected by various...... factors such as soil type, land use, and soil contamination. In this study, we quantified the soil structure using X-ray CT scanning and revealed the effect of a long history of Copper (Cu) pollution on it. A fallow field at Hygum Denmark provides this opportunity as it had a long history of Copper...... columns, macroporosity showed a significant decrease along the column depth. The results suggest that Cu contamination has a strong impact on soil structure and hence on all soil physical and biological processes....

  17. Mutual information reveals multiple structural relaxation mechanisms in a model glass former.

    Science.gov (United States)

    Dunleavy, Andrew J; Wiesner, Karoline; Yamamoto, Ryoichi; Royall, C Patrick

    2015-01-22

    Among the key challenges to our understanding of solidification in the glass transition is that it is accompanied by little apparent change in structure. Recently, geometric motifs have been identified in glassy liquids, but a causal link between these motifs and solidification remains elusive. One 'smoking gun' for such a link would be identical scaling of structural and dynamic lengthscales on approaching the glass transition, but this is highly controversial. Here we introduce an information theoretic approach to determine correlations in displacement for particle relaxation encoded in the initial configuration of a glass-forming liquid. We uncover two populations of particles, one inclined to relax quickly, the other slowly. Each population is correlated with local density and geometric motifs. Our analysis further reveals a dynamic lengthscale similar to that associated with structural properties, which may resolve the discrepancy between structural and dynamic lengthscales.

  18. Antireflective surface structures on infrared optics (Conference Presentation)

    Science.gov (United States)

    Busse, Lynda E.; Frantz, Jesse A.; Shaw, L. Brandon; Bayya, Shyam; Villalobos, Guillermo; Aggarwal, Ishwar D.; Sanghera, Jas S.

    2017-06-01

    Infrared-transmitting optics used in imaging systems have high refractive indices (n=1.4 to n > 3) that require antireflective (AR) coatings. These coatings have limitations in that they can delaminate in operational environments, which is a problem particularly for broadband coatings that consist of multiple layers of dissimilar materials. In addition, residual reflections within an imaging system can cause ghost reflections, degrading performance. Recently, new methods have been developed for fabrication of anti-reflective surface structures (ARSS) on optics that significantly reduce reflection losses at the surface. The ARSS approach provides a more robust solution by using surface structures built directly into the actual surface of the optics, without the need for a coating with extraneous materials. We present recent results that demonstrate superior ARSS performance on a variety of optics for use in the infrared spectral region. These materials have been successfully patterned with ARSS using reactive ion etching (RIE) or using photolithography and etching. We report on reflection losses as low as 0.02% for fused silica at 1.06 microns, and have also demonstrated low reflection losses for ARSS on germanium, spinel ceramic, and sapphire, all of which are important for mid- to long-wave infrared imaging applications.

  19. Intelligent sampling for the measurement of structured surfaces

    Science.gov (United States)

    Wang, J.; Jiang, X.; Blunt, L. A.; Leach, R. K.; Scott, P. J.

    2012-08-01

    Uniform sampling in metrology has known drawbacks such as coherent spectral aliasing and a lack of efficiency in terms of measuring time and data storage. The requirement for intelligent sampling strategies has been outlined over recent years, particularly where the measurement of structured surfaces is concerned. Most of the present research on intelligent sampling has focused on dimensional metrology using coordinate-measuring machines with little reported on the area of surface metrology. In the research reported here, potential intelligent sampling strategies for surface topography measurement of structured surfaces are investigated by using numerical simulation and experimental verification. The methods include the jittered uniform method, low-discrepancy pattern sampling and several adaptive methods which originate from computer graphics, coordinate metrology and previous research by the authors. By combining the use of advanced reconstruction methods and feature-based characterization techniques, the measurement performance of the sampling methods is studied using case studies. The advantages, stability and feasibility of these techniques for practical measurements are discussed.

  20. Mapping cardiac surface mechanics with structured light imaging.

    Science.gov (United States)

    Laughner, Jacob I; Zhang, Song; Li, Hao; Shao, Connie C; Efimov, Igor R

    2012-09-15

    Cardiovascular disease often manifests as a combination of pathological electrical and structural heart remodeling. The relationship between mechanics and electrophysiology is crucial to our understanding of mechanisms of cardiac arrhythmias and the treatment of cardiac disease. While several technologies exist for describing whole heart electrophysiology, studies of cardiac mechanics are often limited to rhythmic patterns or small sections of tissue. Here, we present a comprehensive system based on ultrafast three-dimensional (3-D) structured light imaging to map surface dynamics of whole heart cardiac motion. Additionally, we introduce a novel nonrigid motion-tracking algorithm based on an isometry-maximizing optimization framework that forms correspondences between consecutive 3-D frames without the use of any fiducial markers. By combining our 3-D imaging system with nonrigid surface registration, we are able to measure cardiac surface mechanics at unprecedented spatial and temporal resolution. In conclusion, we demonstrate accurate cardiac deformation at over 200,000 surface points of a rabbit heart recorded at 200 frames/s and validate our results on highly contrasting heart motions during normal sinus rhythm, ventricular pacing, and ventricular fibrillation.

  1. Coherence in ultrafast laser-induced periodic surface structures

    Science.gov (United States)

    Zhang, Hao; Colombier, Jean-Philippe; Li, Chen; Faure, Nicolas; Cheng, Guanghua; Stoian, Razvan

    2015-11-01

    Ultrafast laser irradiation can trigger anisotropically structured nanoscaled gratinglike arrangements of matter, the laser-induced periodic surface structures (LIPSSs). We demonstrate here that the formation of LIPSS is intrinsically related to the coherence of the laser field. Employing several test materials that allow large optical excursions, we observe the effect of randomizing spatial phase in generating finite domains of ripples. Using three-dimensional finite-difference time-domain methods, we evaluate energy deposition patterns below a material's rough surface and show that modulated pattern, i.e., a spatially ordered electromagnetic solution, results from the coherent superposition of waves. By separating the field scattered from a surface rough topography from the total field, the inhomogeneous energy absorption problem is reduced to a simple interference equation. We further distinguish the contribution of the scattered near field and scattered far field on various types of inhomogeneous energy absorption features. It is found that the inhomogeneous energy absorption which could trigger the low-spatial-frequency LIPSSs (LSFLs) and high-spatial-frequency LIPSSs (HSFLs) of periodicity Λ >λ /Re(n ˜) are due to coherent superposition between the scattered far field (propagation) and the refracted field, while HSFLs of Λ λ ) related to a feedback-driven topography evolution. Those results strongly suggest the electromagnetic interpretation of LIPSSs in interplay with an evolving surface topography.

  2. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N. (NIH)

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  3. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Xueling; Zhou, Tongqing; Zhu, Jiang; Zhang, Baoshan; Georgiev, Ivelin; Wang, Charlene; Chen, Xuejun; Longo, Nancy S.; Louder, Mark; McKee, Krisha; O’Dell, Sijy; Perfetto, Stephen; Schmidt, Stephen D.; Shi, Wei; Wu, Lan; Yang, Yongping; Yang, Zhi-Yong; Yang, Zhongjia; Zhang, Zhenhai; Bonsignori, Mattia; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Haynes, Barton F.; Simek, Melissa; Burton, Dennis R.; Koff, Wayne C.; Doria-Rose, Nicole A.; Connors, Mark; Mullikin, James C.; Nabel, Gary J.; Roederer, Mario; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R. (Tumaini); (NIH); (Duke); (Kilimanjaro Repro.); (IAVI)

    2013-03-04

    Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

  4. Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.

    Science.gov (United States)

    Törnroth-Horsefield, Susanna; Gourdon, Pontus; Horsefield, Rob; Brive, Lars; Yamamoto, Natsuko; Mori, Hirotada; Snijder, Arjan; Neutze, Richard

    2007-12-01

    Bacterial drug resistance is a serious concern for human health. Multidrug efflux pumps export a broad variety of substrates out of the cell and thereby convey resistance to the host. In Escherichia coli, the AcrB:AcrA:TolC efflux complex forms a principal transporter for which structures of the individual component proteins have been determined in isolation. Here, we present the X-ray structure of AcrB in complex with a single transmembrane protein, assigned by mass spectrometry as YajC. A specific rotation of the periplasmic porter domain of AcrB is also revealed, consistent with the hypothesized "twist-to-open" mechanism for TolC activation. Growth experiments with yajc-deleted E. coli reveal a modest increase in the organism's susceptibility to beta-lactam antibiotics, but this effect could not conclusively be attributed to the loss of interactions between YajC and AcrB.

  5. Spot--like Structures of Neutron Star Surface Magnetic Fields

    CERN Document Server

    Geppert, U; Gil, J

    2003-01-01

    There is growing evidence, based on both X-ray and radio observations of isolated neutron stars, that besides the large--scale (dipolar) magnetic field, which determines the pulsar spin--down behaviour, small--scale poloidal field components are present, which have surface strengths one to two orders of magnitude larger than the dipolar component. We argue in this paper that the Hall--effect can be an efficient process in producing such small--scale field structures just above the neutron star surface. It is shown that due to a Hall--drift induced instability, poloidal magnetic field structures can be generated from strong subsurface toroidal fields, which are the result of either a dynamo or a thermoelectric instability acting at early times of a neutron star's life. The geometrical structure of these small--scale surface anomalies of the magnetic field resembles that of some types of ``star--spots''. The magnetic field strength and the length--scales are comparable with values that can be derived from vario...

  6. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  7. Biomimetic electroactive polyimide with rose petal-like surface structure for anticorrosive coating application

    Directory of Open Access Journals (Sweden)

    W. F. Ji

    2017-08-01

    Full Text Available In this work, an electroactive polyimide (EPI coating with biomimetic surface structure of rose petal used in anticorrosion application was first presented. First of all, amino-capped aniline trimer (ACAT was synthesized by oxidative coupling reaction, followed by characterized through Fourier transform infrared spectroscooy (FTIR, liquid chromatography – mass spcerometry (LC-MS and proton nuclear magnetic resonance (1H-NMR spectroscopy. Subsequently, as-prepared ACAT was reacted with isopropylidenediphenoxy-bis(phthalic anhydride (BPADA to give electroactive poly(amic acid (EPAA. Moreover, poly(dimethylsiloxane (PDMS was used to be the soft negative template for pattern transfer from the surface of rose petal to the surface of polymer coating. The EPI coating with biomimetic structure was obtained by programmed heating the EPAA slurry casting onto the negative PDMS template. The anticorrosive performance of as-prepared biomimetic EPI coating was demonstrated by performing a series of electrochemical measurements (Tafel, Nyquist, and Bode plots upon cold-rolled steel (CRS electrode in a NaCl aqueous solution. It should be noted that the biomimetic EPI coating with rose petal-like structure was found to exhibit better anticorrosion than that of EPI without biomimetic structure. Moreover, the surface contact angle of water droplets for biomimetic EPI coating was found to be ~150°, which is significantly higher than that of EPI coating with smooth structure (~87°, indicating that the EPI coating with biomimetic structure reveals better hydrophobicity. The apparent mechanism for improved anticorrosive properties is twofold: (1 the biomimetic structure of EPI coating can repel water droplets. (2 electroactivity of EPI coating promotes the formation of densely passive layer of metal oxide on metallic surface.

  8. Resistance given by tiling grain surface with micro surface structures in polycrystalline metal oxide

    Science.gov (United States)

    Moriyama, T.; Yamasaki, T.; Ohno, T.; Kishida, S.; Kinoshita, K.

    2016-12-01

    Practical use of Resistive Random Access Memory (ReRAM) depends on thorough understanding of the resistive switching (RS) mechanism in transition metal oxides. Although most of ReRAM samples have polycrystalline structures, both experimental studies and theoretical calculations do not often consider the effects that grain boundaries have on the RS mechanism. This paper discusses what determines resistance values in a Pt/polycrystalline NiO/Pt ReRAM structures by using both experiments and first-principles calculations. Electrical measurements suggest that the RS is caused in the grain boundaries of NiO films. First-principles calculations indicate that slight displacements of atoms with a small energy change of 0.04 eV per atom on the surfaces exposed in the grain boundaries can drastically change conductivities. We propose the tiling model, in which grain surfaces are composed by insulating and conductive micro surface structures, and the surface resistances are determined by the tiling patterns.

  9. Clinoptilolite and heulandite structural differences as revealed by multinuclear nuclear magnetic resonance spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ward, R.L.; McKague, H.L. (Lawrence Livermore National Lab., CA (United States))

    1994-01-27

    Wide-line proton NMR has revealed differences in the water environment in two zeolitic isomorphs: clinoptilolite and heulandite. The proton spectrum of clinoptilolite is Gaussian in shape, while that of heulandite is a (reduced splitting) Pake doublet. Studies of clinoptilolite from five different locations and heulandite from nine different sites agree with this observation. These results suggest a simple nondestructive NMR method for distinguishing heulandite from clinoptilolite. Dehydration experiments are particularly informative. Proton line widths of clinoptilolite as a function of the dehydration temperature reveal three types of water binding, none being absorbed water. Similar studies with heulandite reveal a change from the Pake doublet to a Gaussian, which is probably associated with the heulandite to heulandite B transformation. [sup 27]Al and [sup 29]Si NMR studies of clinoptilolite indicate a change in framework structure and/or cation binding with dehydration. [sup 27]Al NMR of heulandite exhibits an increase in line width with dehydration temperature to 175[degrees]C. At this temperature the increase stops and the line width remains constant to 215[degrees]C, the maximum temperature studied. This agrees with the proton studies and is attributed to the heulandite to heulandite B transformation. [sup 29]Si NMR of heulandite reveals a framework structural change and/or cation binding with dehydration. All of these observations are reversible upon rehydration. 21 refs., 9 figs.

  10. Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building

    Directory of Open Access Journals (Sweden)

    Chen Shaotian

    2012-04-01

    Full Text Available Abstract Background Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM in 705 individuals from 47 localities. Results A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST = 0.975, P  Conclusions The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.

  11. Fine Structure of Hydrogen Bond in Cholic Acid Revealed by 2DIR Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on cryogenic FT-IR spectroscopic studies of hydrogen bonds in cholic acid, two-dimensional FT-IR spectroscopy was applied to enhance our understanding of the hydrogen bonds of cholic acid. Fine spectral structures were revealed by asynchronous 2D FT-IR spectra. The co-relationship among various bands was discussed according to the synchronous 2D FT-IR spectrum.

  12. Allelic diversity and population structure of Bacillus sphaericus as revealed by multilocus sequence typing.

    Science.gov (United States)

    Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming

    2011-08-01

    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains.

  13. Krebs cycle metabolon: structural evidence of substrate channeling revealed by cross-linking and mass spectrometry.

    Science.gov (United States)

    Wu, Fei; Minteer, Shelley

    2015-02-02

    It has been hypothesized that the high metabolic flux in the mitochondria is due to the self-assembly of enzyme supercomplexes (called metabolons) that channel substrates from one enzyme to another, but there has been no experimental confirmation of this structure or the channeling. A structural investigation of enzyme organization within the Krebs cycle metabolon was accomplished by in vivo cross-linking and mass spectrometry. Eight Krebs cycle enzyme components were isolated upon chemical fixation, and interfacial residues between mitochondrial malate dehydrogenase, citrate synthase, and aconitase were identified. Using constraint protein docking, a low-resolution structure for the three-enzyme complex was achieved, as well as the two-fold symmetric octamer. Surface analysis showed formation of electrostatic channeling upon protein-protein association, which is the first structural evidence of substrate channeling in the Krebs cycle metabolon.

  14. Structure of Ge(100) surfaces for high-efficiency photovoltaic applications

    Energy Technology Data Exchange (ETDEWEB)

    Olson, J.M.; McMahon, W.E. [National Renewable Energy Lab., Golden, CO (United States)

    1998-09-01

    While much is known about the Ge(100) surface in a UHV/MBE environment, little has been published about this surface in an MOCVD environment. The main objective of this study is to determine the structure of the surface of Ge substrates in the typical MOCVD reactor immediately prior to and following the heteronucleation of GaAs and other lattice-matched III-V alloys, and to determine the conditions necessary for the growth of device-quality epilayers. In this paper the authors present the first STM images of the MOCVD-prepared Ge surfaces. Although many of the observed features are very similar to UHV- or MBE-prepared surfaces, there are distinct and important differences. For example, while the As-terminated surfaces for MBE-Ge and MOCVD-Ge are virtually identical, the AsH{sub 3}-treated surfaces in an MOCVD reactor are quite different. The terrace reconstruction is rotated by {pi}/2, and significant step bunching or faceting is also observed. Time-dependent RD kinetic studies also reveal, for the first time, several interesting features: the transition rate from an As-terminated (1 x 2) terrace reconstruction to a stable AsH{sub 3}-annealed surface is a function of the substrate temperature, substrate miscut from (100) and AsH{sub 3} partial pressure, and, for typical prenucleation conditions, is relatively slow. These results explain many of the empirically derived nucleation conditions that have been devised by numerous groups.

  15. Scanning probe microscopy investigation of self-organized perylenetetracarboxdiimide nanostructures at surfaces: structural and electronic properties.

    Science.gov (United States)

    Palermo, Vincenzo; Liscio, Andrea; Gentilini, Desirée; Nolde, Fabian; Müllen, Klaus; Samorì, Paolo

    2007-01-01

    A scanning probe microscopy investigation of the self-organization and local electronic properties of spin-coated ultrathin films of N-alkyl substituted perylenetetracarboxdiimide (PDI) is described. By carefully balancing the interplay between molecule-molecule and molecule-substrate interactions, PDI is able to form highly ordered supramolecular architectures on flat surfaces from solution. On an electrically insulating yet highly polar surface (mica) PDI forms strongly anisotropic architectures with needlelike structures with lengths of up to a few micrometers. On a conductive yet apolar surface (highly oriented pyrolytic graphite), the competition between the strong molecule-substrate interactions and the intermolecular forces leads to the generation of more disordered structures. The local electronic properties of these architectures are studied by Kelvin probe force microscopy by estimating their surface potential (SP). Quantitative measurements of the SP are obtained by analyzing the experimentally estimated SP data with a computational model, which discriminates between the intrinsic SP and the effect of long-range tip-surface interactions. The SP of PDI aggregates depends on the structural order at the supramolecular level. Narrow needles of constant width reveal identical SPs independent of length. Wider needles with a polydisperse width distribution exhibit a greater SP.

  16. Structures and surface tensions of fluids near solid surfaces: an integral equation theory study.

    Science.gov (United States)

    Xu, Mengjin; Zhang, Chen; Du, Zhongjie; Mi, Jianguo

    2012-06-07

    In this work, integral equation theory is extended to describe the structures and surface tensions of confined fluids. To improve the accuracy of the equation, a bridge function based on the fundamental measure theory is introduced. The density profiles of the confined Lennard-Jones fluids and water are calculated, which are in good agreement with simulation data. On the basis of these density profiles, the grand potentials are then calculated using the density functional approach, and the corresponding surface tensions are predicted, which reproduce the simulation data well. In particular, the contact angles of water in contact with both hydrophilic and hydrophobic walls are evaluated.

  17. TEM investigation of laser-induced periodic surface structures on polymer surfaces

    Science.gov (United States)

    Prendergast, Úna; Kudzma, Sylwester; Sherlock, Richard; O'Connell, Claire; Glynn, Thomas

    2007-02-01

    Laser Induced Periodic Surface Structures (LIPSS) may have numerous applications, ranging from biomaterial applications to LCDs, microelectronic fabrication and photonics. However, in order to control the development of these structures for their particular application, it is necessary to understand how they are generated. We report our work on investigating the melting that occurs during LIPSS formation. LIPSS were generated on three polymer surfaces - polyethylene terephthalate (PET), amorphous polycarbonate (APC) and oriented crystalline polycarbonate (OPC) - which were irradiated with a polarized ArF excimer laser (193 nm) beam with fluences between 3 and 5 mJ/cm2. The structures were imaged using a Transmission Electron Microscope (TEM), which facilitated investigation of changes in the polymer structures and consequently the depth of the melt zone that accompanies LIPSS generation. We also present theoretical calculations of the temperature-depth profile due to the interaction of the low fluence 193 nm laser beam with the polymer surfaces and compare these calculations with our experimental results.

  18. Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds.

    Directory of Open Access Journals (Sweden)

    Mads Gabrielsen

    Full Text Available Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis (ypTpx in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for "forced" reduced states using the C61S mutant. In addition, by investigating the solution structure of ypTpx using small angle X-ray scattering (SAXS, we have confirmed that reduced state ypTpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of ypTpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to ypTpx, aiding our long-term strategy to understand the mode of action of this class of compounds.

  19. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates

    Directory of Open Access Journals (Sweden)

    Mariya Tarazanova

    2017-09-01

    Full Text Available Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.

  20. Cell Surface Properties of Lactococcus lactis Reveal Milk Protein Binding Specifically Evolved in Dairy Isolates.

    Science.gov (United States)

    Tarazanova, Mariya; Huppertz, Thom; Beerthuyzen, Marke; van Schalkwijk, Saskia; Janssen, Patrick; Wels, Michiel; Kok, Jan; Bachmann, Herwig

    2017-01-01

    Surface properties of bacteria are determined by the molecular composition of the cell wall and they are important for interactions of cells with their environment. Well-known examples of bacterial interactions with surfaces are biofilm formation and the fermentation of solid materials like food and feed. Lactococcus lactis is broadly used for the fermentation of cheese and buttermilk and it is primarily isolated from either plant material or the dairy environment. In this study, we characterized surface hydrophobicity, charge, emulsification properties, and the attachment to milk proteins of 55 L. lactis strains in stationary and exponential growth phases. The attachment to milk protein was assessed through a newly developed flow cytometry-based protocol. Besides finding a high degree of biodiversity, phenotype-genotype matching allowed the identification of candidate genes involved in the modification of the cell surface. Overexpression and gene deletion analysis allowed to verify the predictions for three identified proteins that altered surface hydrophobicity and attachment of milk proteins. The data also showed that lactococci isolated from a dairy environment bind higher amounts of milk proteins when compared to plant isolates. It remains to be determined whether the alteration of surface properties also has potential to alter starter culture functionalities.

  1. Structural and electronic properties of bulk and low-index surfaces of zincblende PtC

    Science.gov (United States)

    Gokhan Sensoy, Mehmet; Toffoli, Daniele; Ustunel, Hande

    2017-03-01

    Transition metal carbides have been extensively used in diverse applications over the past decade. Their versatility is in part thanks to their unique bonding, which displays a mixture of ionic, metallic and covalent character. While the bulk structure of zincblende (ZB) PtC has been investigated several times, a detailed understanding of the electronic and structural properties of its low-index surfaces is lacking. In this work, we present an ab initio investigation of the properties of five crystallographic ZB PtC surfaces (Pt/C-terminated PtC(1 0 0), PtC(1 1 0) and Pt/C-terminated PtC(1 1 1)). Upon geometry optimization, both polar and nonpolar surfaces undergo a mild interlayer relaxation, without extensive reconstructions. Calculated vacancy formation energies indicate facile C removal on the (1 1 1) surface while Pt-vacancy formation is endothermic. Finally, atomic O adsorption energies on all surfaces reveal a high affinity of the C-terminated surfaces towards this species.

  2. Structural and electronic properties of bulk and low-index surfaces of zincblende PtC.

    Science.gov (United States)

    Sensoy, Mehmet Gokhan; Toffoli, Daniele; Ustunel, Hande

    2017-03-29

    Transition metal carbides have been extensively used in diverse applications over the past decade. Their versatility is in part thanks to their unique bonding, which displays a mixture of ionic, metallic and covalent character. While the bulk structure of zincblende (ZB) PtC has been investigated several times, a detailed understanding of the electronic and structural properties of its low-index surfaces is lacking. In this work, we present an ab initio investigation of the properties of five crystallographic ZB PtC surfaces (Pt/C-terminated PtC(1 0 0), PtC(1 1 0) and Pt/C-terminated PtC(1 1 1)). Upon geometry optimization, both polar and nonpolar surfaces undergo a mild interlayer relaxation, without extensive reconstructions. Calculated vacancy formation energies indicate facile C removal on the (1 1 1) surface while Pt-vacancy formation is endothermic. Finally, atomic O adsorption energies on all surfaces reveal a high affinity of the C-terminated surfaces towards this species.

  3. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

    Directory of Open Access Journals (Sweden)

    Oleg M Ganichkin

    Full Text Available BACKGROUND: Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood. METHODOLOGY/PRINCIPAL FINDINGS: We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec. CONCLUSIONS/SIGNIFICANCE: We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  4. Ultrafast laser induced periodic sub-wavelength aluminum surface structures and nanoparticles in air and liquids

    Energy Technology Data Exchange (ETDEWEB)

    Kuladeep, Rajamudili; Dar, Mudasir H.; Rao, D. Narayana, E-mail: dnrsp@uohyd.ac.in, E-mail: dnr-laserlab@yahoo.com [School of Physics, University of Hyderabad, Hyderabad 500046 (India); Deepak, K. L. N. [Department of Physics and Center for Research in Photonics, University of Ottawa, 150 Louis Pasteur, Ottawa K1N6N5, Ontario (Canada)

    2014-09-21

    In this communication, we demonstrate the generation of laser-induced periodic sub-wavelength surface structures (LIPSS) or ripples on a bulk aluminum (Al) and Al nanoparticles (NPs) by femtosecond (fs) laser direct writing technique. Laser irradiation was performed on Al surface at normal incidence in air and by immersing in ethanol (C₂H₅OH) and water (H₂O) using linearly polarized Ti:sapphire fs laser pulses of ~110 fs pulse duration and ~800 nm wavelength. Field emission scanning electron microscope is utilized for imaging surface morphology of laser written structures and it reveals that the spatial periodicity as well as the surface morphology of the LIPSS depends on the surrounding dielectric medium and also on the various laser irradiation parameters. The observed LIPSS have been classified as low spatial frequency LIPSS which are perpendicularly oriented to the laser polarization with a periodicity from 460 to 620 nm and high spatial frequency LIPSS which spectacles a periodicity less than 100 nm with the orientation parallel to the polarization of the incident laser beam. Fabricated colloidal solutions, which contain the Al NPs, were characterized by UV-Vis absorption spectroscopy and transmission electron microscopy (TEM). TEM results reveal the formation of internal cavities in Al NPs both in ethanol and water. Formation mechanism of LIPSS and cavities inside the nanoparticles are discussed in detail.

  5. Ultrafast laser induced periodic sub-wavelength aluminum surface structures and nanoparticles in air and liquids

    Science.gov (United States)

    Kuladeep, Rajamudili; Dar, Mudasir H.; Deepak, K. L. N.; Rao, D. Narayana

    2014-09-01

    In this communication, we demonstrate the generation of laser-induced periodic sub-wavelength surface structures (LIPSS) or ripples on a bulk aluminum (Al) and Al nanoparticles (NPs) by femtosecond (fs) laser direct writing technique. Laser irradiation was performed on Al surface at normal incidence in air and by immersing in ethanol (C2H5OH) and water (H2O) using linearly polarized Ti:sapphire fs laser pulses of ˜110 fs pulse duration and ˜800 nm wavelength. Field emission scanning electron microscope is utilized for imaging surface morphology of laser written structures and it reveals that the spatial periodicity as well as the surface morphology of the LIPSS depends on the surrounding dielectric medium and also on the various laser irradiation parameters. The observed LIPSS have been classified as low spatial frequency LIPSS which are perpendicularly oriented to the laser polarization with a periodicity from 460 to 620 nm and high spatial frequency LIPSS which spectacles a periodicity less than 100 nm with the orientation parallel to the polarization of the incident laser beam. Fabricated colloidal solutions, which contain the Al NPs, were characterized by UV-Vis absorption spectroscopy and transmission electron microscopy (TEM). TEM results reveal the formation of internal cavities in Al NPs both in ethanol and water. Formation mechanism of LIPSS and cavities inside the nanoparticles are discussed in detail.

  6. Surface and Internal Structure of Pristine Presolar Silicon Carbide

    Science.gov (United States)

    Stroud, Rhonda, M.; Bernatowicz, Thomas J.

    2005-01-01

    Silicon carbide is the most well-studied type of presolar grain. Isotope measurements of thousands [1,2] and structural data from over 500 individual grains have been reported [3]. The isotope data indicate that approximately 98% originated in asymptotic giant branch stars and 2% in supernovae. Although tens of different polytypes of SiC are known to form synthetically, only two polytypes have been reported for presolar grains. Daulton et al. [3] found that for SiC grains isolated from Murchison by acid treatments, 79.4% are 3C cubic beta-SiC, 2.7% are 2H hexagonal alpha-SiC, 17.1% are intergrowths of and , and 0.9% are heavily disordered. They report that the occurrence of only the and polytypes is consistent with the observed range of condensation temperatures of circumstellar dust for carbon stars. Further constraint on the formation and subsequent alteration of the grains can be obtained from studies of the surfaces and interior structure of grains in pristine form, i.e., prepared without acid treatments [4,5]. The acid treatments remove surface coatings, produce etch pits around defect sites and could remove some subgrains. Surface oxides have been predicted by theoretical modeling as a survival mechanism for SiC grains exposed to the hot oxidizing solar nebula [6]. Scanning electron microscopy studies of pristine SiC shows some evidence for the existence of oxide and organic coatings [4]. We report herein on transmission electron microscopy studies of the surface and internal structure of two pristine SiC grains, including definitive evidence of an oxide rim on one grain, and the presence of internal TiC and AlN grains.

  7. Direct ambient noise tomography for 3-D near surface shear velocity structure: methodology and applications

    Science.gov (United States)

    Yao, H.; Fang, H.; Li, C.; Liu, Y.; Zhang, H.; van der Hilst, R. D.; Huang, Y. C.

    2014-12-01

    Ambient noise tomography has provided essential constraints on crustal and uppermost mantle shear velocity structure in global seismology. Recent studies demonstrate that high frequency (e.g., ~ 1 Hz) surface waves between receivers at short distances can be successfully retrieved from ambient noise cross-correlation and then be used for imaging near surface or shallow crustal shear velocity structures. This approach provides important information for strong ground motion prediction in seismically active area and overburden structure characterization in oil and gas fields. Here we propose a new tomographic method to invert all surface wave dispersion data for 3-D variations of shear wavespeed without the intermediate step of phase or group velocity maps.The method uses frequency-dependent propagation paths and a wavelet-based sparsity-constrained tomographic inversion. A fast marching method is used to compute, at each period, surface wave traveltimes and ray paths between sources and receivers. This avoids the assumption of great-circle propagation that is used in most surface wave tomographic studies, but which is not appropriate in complex media. The wavelet coefficients of the velocity model are estimated with an iteratively reweighted least squares (IRLS) algorithm, and upon iterations the surface wave ray paths and the data sensitivity matrix are updated from the newly obtained velocity model. We apply this new method to determine the 3-D near surface wavespeed variations in the Taipei basin of Taiwan, Hefei urban area and a shale and gas production field in China using the high-frequency interstation Rayleigh wave dispersion data extracted from ambient noisecross-correlation. The results reveal strong effects of off-great-circle propagation of high-frequency surface waves in these regions with above 30% shear wavespeed variations. The proposed approach is more efficient and robust than the traditional two-step surface wave tomography for imaging complex

  8. Effect of ion irradiation on the surface, structural and mechanical properties of brass

    Energy Technology Data Exchange (ETDEWEB)

    Ahmad, Shahbaz; Bashir, Shazia, E-mail: shaziabashir@gcu.edu.pk; Ali, Nisar; Umm-i-Kalsoom,; Yousaf, Daniel; Faizan-ul-Haq,; Naeem, Athar; Ahmad, Riaz; Khlaeeq-ur-Rahman, M.

    2014-04-01

    Highlights: • Brass targets were exposed to carbon ions of energy 2 MeV. • The effect of ion dose has been investigated. • The surface morphology is investigated by SEM analysis. • XRD analysis is performed to reveal structural modification. • Mechanical properties were investigated by tensile testing and microhardness testing. - Abstract: Modifications to the surface, structural and mechanical properties of brass after ion irradiation have been investigated. Brass targets were bombarded by carbon ions of 2 MeV energy from a Pelletron linear accelerator for various fluences ranging from 56 × 10{sup 12} to 26 × 10{sup 13} ions/cm{sup 2}. A scanning electron microscope and X-ray diffractometer were utilized to analyze the surface morphology and crystallographic structure respectively. To explore the mechanical properties e.g., yield stress, ultimate tensile strength and microhardness of irradiated brass, an universal tensile testing machine and Vickers microhardness tester were used. Scanning electron microscopy results revealed an irregular and randomly distributed sputter morphology for a lower ion fluence. With increasing ion fluence, the incoherently shaped structures were transformed into dendritic structures. Nano/micro sized craters and voids, along with the appearance of pits, were observed at the maximum ion fluence. From X-ray diffraction results, no new phases were observed to be formed in the brass upon irradiation. However, a change in the peak intensity and higher and lower angle shifting were observed, which represents the generation of ion-induced defects and stresses. Analyses confirmed modifications in the mechanical properties of irradiated brass. The yield stress, ultimate tensile strength and hardness initially decreased and then increased with increasing ion fluence. The changes in the mechanical properties of irradiated brass are well correlated with surface and crystallographic modifications and are attributed to the generation

  9. Structural and surface properties of semitransparent and antibacterial (Cu,Ti,Nb)Ox coating

    Science.gov (United States)

    Wojcieszak, D.; Mazur, M.; Kaczmarek, D.; Szponar, B.; Grobelny, M.; Kalisz, M.; Pelczarska, A.; Szczygiel, I.; Poniedzialek, A.; Osekowska, M.

    2016-09-01

    In this work structural and surface properties of oxide thin-film coating based on Cu, Ti and Nb prepared by reactive magnetron sputtering have been described. During the deposition process metallic Cu, Ti and Nb targets were sputtered in oxygen plasma. Structural characterization of the film microstructure has revealed that as-prepared coating was amorphous. Due to such structure and the content of Ti and Nb the hardness of the oxide film was about 3.6 GPa, which is 40% higher as compared to metallic Cu film. Moreover, the surface roughness was below 1 nm, what resulted in receiving of hydrophobic properties. The multioxide film was transparent at the level of 40%, but due to high Cu-content its optical absorption edge was about 450 nm and had bright orange color. Optical investigation has revealed that the energy band-gap of this film was 1.41 eV, which indicates on the presence of CuO form. Moreover, the studies of antimicrobial activity showed that as-prepared film had a strong bactericidal effect for Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis and Enterococcus hirae, while fungicidal effect for Candida albicans was not observed. The biological activity was related to the amount of copper ions released from the surface of (Cu,Ti Nb)Ox coating, which was equal to 0.041 ppm per day.

  10. Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hui; Klein, Michael G.; Snell, Gyorgy; Lane, Weston; Zou, Hua; Levin, Irena; Li, Ke; Sang, Bi-Ching (Takeda Cali)

    2016-07-01

    Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. The GIVD cPLA2 (cPLA2δ) is a potential drug target for developing a selective therapeutic agent for the treatment of psoriasis. Here, we present two X-ray structures of human cPLA2δ, capturing an apo state, and in complex with a substrate-like inhibitor. Comparison of the apo and inhibitor-bound structures reveals conformational changes in a flexible cap that allows the substrate to access the relatively buried active site, providing new insight into the mechanism for substrate recognition. The cPLA2δ structure reveals an unexpected second C2 domain that was previously unrecognized from sequence alignments, placing cPLA2δ into the class of membrane-associated proteins that contain a tandem pair of C2 domains. Furthermore, our structures elucidate novel inter-domain interactions and define three potential calcium-binding sites that are likely important for regulation and activation of enzymatic activity. These findings provide novel insights into the molecular mechanisms governing cPLA2's function in signal transduction.

  11. Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members

    Energy Technology Data Exchange (ETDEWEB)

    Porebski, Przemyslaw J.; Klimecka, Maria; Chruszcz, Maksymilian; Nicholls, Robert A.; Murzyn, Krzysztof; Cuff, Marianne E.; Xu, Xiaohui; Cymborowski, Marcin; Murshudov, Garib N.; Savchenko, Alexei; Edwards, Aled; Minor, Wladek (MCSG); (UV); (MRC)

    2012-07-11

    Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS-ATP and hpDTBS-GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway.

  12. The Asymmetrical Structure of Golgi Apparatus Membranes Revealed by In situ Atomic Force Microscope

    Science.gov (United States)

    Xu, Haijiao; Su, Weiheng; Cai, Mingjun; Jiang, Junguang; Zeng, Xianlu; Wang, Hongda

    2013-01-01

    The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm –200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level. PMID:23613878

  13. The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

    Science.gov (United States)

    Xu, Haijiao; Su, Weiheng; Cai, Mingjun; Jiang, Junguang; Zeng, Xianlu; Wang, Hongda

    2013-01-01

    The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

  14. The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

    Directory of Open Access Journals (Sweden)

    Haijiao Xu

    Full Text Available The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

  15. Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations.

    Science.gov (United States)

    Yu, Lu; Lee, Seung-Joo; Yee, Vivien C

    2015-06-16

    The pathogenesis of prion diseases is associated with the conformational conversion of normal, predominantly α-helical prion protein (PrP(C)) into a pathogenic form that is enriched with β-sheets (PrP(Sc)). Several PrP(C) crystal structures have revealed β1-mediated intermolecular sheets, suggesting that the β1 strand may contribute to a possible initiation site for β-sheet-mediated PrP(Sc) propagation. This β1 strand contains the polymorphic residue 129 that influences disease susceptibility and phenotype. To investigate the effect of the residue 129 polymorphism on the conformation of amyloid-like continuous β-sheets formed by β1, crystal structures of β1 peptides containing each of the polymorphic residues were determined. To probe the conformational influence of the peptide construct design, four different lengths of β1 peptides were studied. From the 12 peptides studied, 11 yielded crystal structures ranging in resolution from 0.9 to 1.4 Å. This ensemble of β1 crystal structures reveals conformational differences that are influenced by both the nature of the polymorphic residue and the extent of the peptide construct, indicating that comprehensive studies in which peptide constructs vary are a more rigorous approach to surveying conformational possibilities.

  16. Surface Structures of the Metal-Oxide Materials Strontium Titanate and Lanthanum Aluminate

    Science.gov (United States)

    Kienzle, Danielle M.

    A wide array of techniques were applied in this research to investigate the perovskite materials SrTiO3 and LaAlO3 with the goal of furthering the understanding of oxide surfaces. Specifically, a combination of transmission electron diffraction, direct methods and density functional theory was used to determine the structure of the SrTiO3 (001) (√13x√13)R33.7° surface reconstruction. It has a TiO 2-rich surface with a 2D tiling of edge or corner-sharing TiO5 octahedra. By tiling these units and forming network surface structures ranging from ordered, like the 2x1 and c(4x2), to pseudo-ordered, like the c(6x2), to a disordered glass-like surface layer made up of TiOx units, dictated by local bond valence sums. The LaAlO3 (110) 3x1 surface reconstruction, here reported for the first time, was found to have a hydroxylated Al-rich surface with X-ray photoelectron spectroscopy. Transmission electron diffraction data and direct methods revealed a high resemblance to the previously solved SrTiO3 (110) 3x1 reconstruction leading to a hydrated version that fits the for LaAlO3 3x1 structure. The hydroxyl groups are necessary to balance the surface polarity, an issue arising from the difference in cationic valences between La/Sr and Al/Ti. Also reported and investigated here for the first time is a LaAlO3 (100) 5x2 reconstruction. A direct methods analysis was done for several sets of recorded diffraction pattern; however the results have yet to lead to an atomic surface structure solution. X-ray photoelectron spectra were collected over a range of detector-to-surface-normal angles elucidating an Al-rich surface layer. X-ray photoelectron intensities were calculated for a model of alternating Al and La layers over a range of grazing angles and varying amounts of Al in the top surface layer. An Al concentration of 0.5 was found to give the best fit to experimental results.

  17. Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Y.; Huang, H; Zhou, B; Wang, S; Hu, Y; Li, X; Liu, J; Niu, L; Wu, J; et. al.

    2010-01-01

    Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 {angstrom} crystal structure of the core domain of Rtt106p, which adopts an unusual 'double pleckstrin homology' domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

  18. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

    Science.gov (United States)

    Schur, Florian K M; Obr, Martin; Hagen, Wim J H; Wan, William; Jakobi, Arjen J; Kirkpatrick, Joanna M; Sachse, Carsten; Kräusslich, Hans-Georg; Briggs, John A G

    2016-07-29

    Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.

  19. Revealing daily travel patterns and city structure with taxi trip data

    CERN Document Server

    Liu, Xi; Gong, Yongxi; Liu, Yu

    2013-01-01

    Detecting regional spatial structures based on spatial interactions is crucial in applications ranging from urban planning to traffic control. In the big data era, various movement trajectories are available for studying spatial structures. This research uses large scale Shanghai taxi trip data extracted from GPS-enabled taxi trajectories to reveal traffic flow patterns and urban structure of the city. Using the network science methods, 15 temporally stable regions reflecting the scope of people's daily travels are found using community detection method on the network built from short trips, which represent residents' daily intra-urban travels and exhibit a clear pattern. In each region, taxi traffic flows are dominated by a few 'hubs' and 'hubs' in suburbs impact more trips than 'hubs' in urban areas. Land use conditions in urban regions are different from those in suburban areas. Additionally, 'hubs' in urban area associate with office buildings and commercial areas more, whereas residential land use is mor...

  20. Structure of a bacterial cell surface decaheme electron conduit.

    Science.gov (United States)

    Clarke, Thomas A; Edwards, Marcus J; Gates, Andrew J; Hall, Andrea; White, Gaye F; Bradley, Justin; Reardon, Catherine L; Shi, Liang; Beliaev, Alexander S; Marshall, Matthew J; Wang, Zheming; Watmough, Nicholas J; Fredrickson, James K; Zachara, John M; Butt, Julea N; Richardson, David J

    2011-06-07

    Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along "nanowire" appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split β-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface.

  1. Simultaneous measurements of top surface and its underlying film surfaces in multilayer film structure.

    Science.gov (United States)

    Ghim, Young-Sik; Rhee, Hyug-Gyo; Davies, Angela

    2017-09-19

    With the growth of 3D packaging technology and the development of flexible, transparent electrodes, the use of multilayer thin-films is steadily increasing throughout high-tech industries including semiconductor, flat panel display, and solar photovoltaic industries. Also, this in turn leads to an increase in industrial demands for inspection of internal analysis. However, there still remain many technical limitations to overcome for measurement of the internal structure of the specimen without damage. In this paper, we propose an innovative optical inspection technique for simultaneous measurements of the surface and film thickness corresponding to each layer of multilayer film structures by computing the phase and reflectance over a wide range of wavelengths. For verification of our proposed method, the sample specimen of multilayer films was fabricated via photolithography process, and the surface profile and film thickness of each layer were measured by two different techniques of a stylus profilometer and an ellipsometer, respectively. Comparison results shows that our proposed technique enables simultaneous measurements of the top surface and its underlying film surfaces with high precision, which could not be measured by conventional non-destructive methods.

  2. Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

    Energy Technology Data Exchange (ETDEWEB)

    Bertonati, C.; Punta, M; Fischer, M; Yachdav, G; Forouhar, F; Hunt, J; Tong, L; Montelione, G; Rost, B; et. al.

    2008-01-01

    We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.

  3. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions

    Science.gov (United States)

    Matsunami, Hideyuki; Barker, Clive S.; Yoon, Young-Ho; Wolf, Matthias; Samatey, Fadel A.

    2016-01-01

    The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook. PMID:27811912

  4. Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

    Science.gov (United States)

    Welin, Martin; Wang, Liya; Eriksson, Staffan; Eklund, Hans

    2007-03-01

    Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.

  5. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    Science.gov (United States)

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. © 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.

  6. Atmospheric Drivers of Greenland Surface Melt Revealed by Self-Organizing Maps

    Science.gov (United States)

    Mioduszewski, J. R.; Rennermalm, A. K.; Hammann, A.; Tedesco, M.; Noble, E. U.; Stroeve, J. C.; Mote, T. L.

    2016-01-01

    Recent acceleration in surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous atmospheric circulation patterns over Greenland. To identify synoptic setups favoring enhanced GrIS surface melt and their decadal changes, we develop a summer Arctic synoptic climatology by employing self-organizing maps. These are applied to daily 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications reanalysis, 1979-2014. Particular circulation regimes are related to meteorological conditions and GrIS surface melt estimated with outputs from the Modèle Atmosphérique Régional. Our results demonstrate that the largest positive melt anomalies occur in concert with positive height anomalies near Greenland associated with wind, temperature, and humidity patterns indicative of strong meridional transport of heat and moisture. We find an increased frequency in a 500 hPa ridge over Greenland coinciding with a 63% increase in GrIS melt between the 1979-1988 and 2005-2014 periods, with 75.0% of surface melt changes attributed to thermodynamics, 17% to dynamics, and 8.0% to a combination. We also confirm that the 2007-2012 time period has the largest dynamic forcing relative of any period but also demonstrate that increased surface energy fluxes, temperature, and moisture separate from dynamic changes contributed more to melt even during this period. This implies that GrIS surface melt is likely to continue to increase in response to an ever warmer future Arctic, regardless of future atmospheric circulation patterns.

  7. Polymer masks for structured surface and plasma etching

    Energy Technology Data Exchange (ETDEWEB)

    Vital, Alexane [Centre de Recherche sur la Matière Divisée (CRMD), 1b rue de la Férollerie, F45071 Orléans Cedex (France); Groupe de Recherches sur l’Énergétique des Milieux Ionisés (GREMI), Polytech’Orléans, 14 rue d’Issoudun, B.P. 6744, F45067 Orléans Cedex 2 (France); Vayer, Marylène, E-mail: marylene.vayer@univ-orleans.fr [Centre de Recherche sur la Matière Divisée (CRMD), 1b rue de la Férollerie, F45071 Orléans Cedex (France); Sinturel, Christophe [Centre de Recherche sur la Matière Divisée (CRMD), 1b rue de la Férollerie, F45071 Orléans Cedex (France); Tillocher, Thomas; Lefaucheux, Philippe; Dussart, Rémi [Groupe de Recherches sur l’Énergétique des Milieux Ionisés (GREMI), Polytech’Orléans, 14 rue d’Issoudun, B.P. 6744, F45067 Orléans Cedex 2 (France)

    2015-03-30

    Graphical abstract: - Highlights: • Sub-micrometric silicon structures were prepared by cryogenic plasma etching. • Polymer templates based on phase-separated films of PS/PLA were used. • Silica structured masks were prepared by filling the polymer templates. • Etching of underlying silicon through silica templates gave original structures. - Abstract: Silica and silicon structures have been prepared at the sub-micrometer length-scale, using laterally phase-separated thin films of poly(styrene) (PS) and poly(lactic acid) (PLA) homopolymer blends. The selective removal of one polymer and the filling of the released space by silica precursor solution led, after calcination, to silica structures on silicon such as arrays of bowl-shape features or pillars, layers with through or non-through cylindrical holes, which has not been observed for some of them. The control of the morphology of the initial polymer film was a key point to achieve such type of structures. Particularly relevant was the use of solvent vapor annealing (vs thermal annealing) of the initial spin-coated films that favored and stabilized laterally phase-separated morphologies. Characteristic dimension of the domains were shown to be coupled with the thickness of the film, thinner films giving smaller domain sizes. Despite a relatively high incompatibility of the two polymers, a macro-phase separation was prevented in all the studied conditions. Sub-micrometric domains were formed, and for the thinner films, nanometric domains as small as 74 nm in size can be obtained. The silica structures formed by the infiltration of the polymer templates were used as hard masks for the cryogenic etching of underlying silicon. New structured surfaces, arrays of silicon pillars which can be plain or hollow at the upper part or arrays of cylindrical holes were formed. A selectivity as high as 21 was obtained using this type of mask for 1.5 μm deep holes having a typical diameter of 200 nm.

  8. Structure of aqueous electrolyte solutions near a hydrophobic surface

    Directory of Open Access Journals (Sweden)

    M.Kinoshita

    2007-09-01

    Full Text Available The structure of aqueous solutions of 1:1 salts (KCl, NaCl, KF,and CsI near a hydrophobic surface is analysed using the angle-dependent integral equation theory. Water molecules are taken to be hard spheres imbedded with multipolar moments including terms up to octupole order, and hard spherical ions are immersed in this model water. The many-body interactions associated with molecular polarizability are treated at the self-consistent mean field level. The effects of cationic and anionic sizes and salt concentration in the bulk are discussed in detail. As the salt concentration increases, the layer of water molecules next to the surface becomes denser but its orientational order remains almost unchanged. The concentration of each ion at the surface can be drastically different from that in the bulk. Asa striking example, at sufficiently low salt concentrations, the concentration of I- is about 500 times higher than that of F- at the surface.

  9. Structural Reorganization and Fibrinogen Adsorption Behaviors on the Polyrotaxane Surfaces Investigated by Sum Frequency Generation Spectroscopy.

    Science.gov (United States)

    Ge, Aimin; Seo, Ji-Hun; Qiao, Lin; Yui, Nobuhiko; Ye, Shen

    2015-10-14

    Polyrotaxanes, such as supramolecular assemblies with methylated α-cyclodextrins (α-CDs) as host molecules noncovalently threaded on the linear polymer backbone, are promising materials for biomedical applications because they allow adsorbed proteins possessing a high surface flexibility as well as control of the cellular morphology and adhesion. To provide a general design principle for biomedical materials, we examined the surface reorganization behaviors and adsorption conformations of fibrinogen on the polyrotaxane surfaces with comparison to several random copolymers by sum frequency generation (SFG) vibrational spectroscopy. We showed that the polyrotaxane (OMe-PRX-PMB) with methylated α-CDs as the host molecule exhibited unique surface structures in an aqueous environment. The hydrophobic interaction between the methoxy groups of the methylated α-CD molecules and methyl groups of the n-butyl methacrylate (BMA) side chains may dominate the surface restructuring behavior of the OMe-PRX-PMB. The orientation analysis revealed that the orientation of the fibrinogen adsorbed on the OMe-PRX-PMB surface is close to a single distribution, which is different from the adsorption behaviors of fibrinogen on other polyrotaxane or random copolymer surfaces.

  10. Preservation of Archaeal Surface Layer Structure During Mineralization.

    Science.gov (United States)

    Kish, Adrienne; Miot, Jennyfer; Lombard, Carine; Guigner, Jean-Michel; Bernard, Sylvain; Zirah, Séverine; Guyot, François

    2016-05-25

    Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer "ghosts" during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.

  11. Preservation of Archaeal Surface Layer Structure During Mineralization

    Science.gov (United States)

    Kish, Adrienne; Miot, Jennyfer; Lombard, Carine; Guigner, Jean-Michel; Bernard, Sylvain; Zirah, Séverine; Guyot, François

    2016-05-01

    Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer “ghosts” during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.

  12. Structures and Functions of Pestivirus Glycoproteins: Not Simply Surface Matters

    Directory of Open Access Journals (Sweden)

    Fun-In Wang

    2015-06-01

    Full Text Available Pestiviruses, which include economically important animal pathogens such as bovine viral diarrhea virus and classical swine fever virus, possess three envelope glycoproteins, namely Erns, E1, and E2. This article discusses the structures and functions of these glycoproteins and their effects on viral pathogenicity in cells in culture and in animal hosts. E2 is the most important structural protein as it interacts with cell surface receptors that determine cell tropism and induces neutralizing antibody and cytotoxic T-lymphocyte responses. All three glycoproteins are involved in virus attachment and entry into target cells. E1-E2 heterodimers are essential for viral entry and infectivity. Erns is unique because it possesses intrinsic ribonuclease (RNase activity that can inhibit the production of type I interferons and assist in the development of persistent infections. These glycoproteins are localized to the virion surface; however, variations in amino acids and antigenic structures, disulfide bond formation, glycosylation, and RNase activity can ultimately affect the virulence of pestiviruses in animals. Along with mutations that are driven by selection pressure, antigenic differences in glycoproteins influence the efficacy of vaccines and determine the appropriateness of the vaccines that are currently being used in the field.

  13. Tunable Omnidirectional Surface Plasmon Resonance in Cylindrical Plasmonic Structure

    Institute of Scientific and Technical Information of China (English)

    WANG Yi; WANG Bing; ZHOU Zhi-Ping

    2008-01-01

    @@ The tunable omnidirectional surface plasmon resonance in the optical range is theoretically demonstrated in a cylindrical plasmonic crystal by using rigorous coupled-wave analysis.The cylindrical plasmonic crystal consists of an infinite chain of two-dimensional cylindrical metal-dielectric-dielectric-metal structures.The dispersion relation of the cylindrical plasmonic crystal is obtained by calculating the absorptance as a function of a TM-polarized incident plane wave and its in-plane wave vector.The omnidirectional surface plasmon resonance can be tuned from UV region to visible region by adjusting the thickness of the cylindrical dielectric layers.The absorption spectrum of the infinite chain of nanocylinders is also investigated for comparison.

  14. Using Pattern Search Methods for Surface Structure Determinationof Nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Zhengji; Meza, Juan; Van Hove, Michel

    2006-06-09

    Atomic scale surface structure plays an important roleindescribing many properties of materials, especially in the case ofnanomaterials. One of the most effective techniques for surface structuredetermination is low-energy electron diffraction (LEED), which can beused in conjunction with optimization to fit simulated LEED intensitiesto experimental data. This optimization problem has a number ofcharacteristics that make it challenging: it has many local minima, theoptimization variables can be either continuous or categorical, theobjective function can be discontinuous, there are no exact analyticderivatives (and no derivatives at all for categorical variables), andfunction evaluations are expensive. In this study, we show how to apply aparticular class of optimization methods known as pattern search methodsto address these challenges. These methods donot explicitly usederivatives, and are particularly appropriate when categorical variablesare present, an important feature that has not been addressed in previousLEED studies. We have found that pattern search methods can produceexcellent results, compared to previously used methods, both in terms ofperformance and locating optimal results.

  15. Surface structure and stability of MoSx model clusters.

    Science.gov (United States)

    Wen, Xiao-Dong; Zeng, Tao; Li, Yong-Wang; Wang, Jianguo; Jiao, Haijun

    2005-10-01

    Density functional theory (DFT) computations have been carried out to study the structure and stability of MoSx clusters with the change of sulfur coverage at both Mo and S edges. DFT shows that adding sulfur to the Mo edge is always exothermic. However, deleting corner sulfur from the S edge is exothermic for 67 and 50% sulfur coverages, while deleting edge sulfur from the S edge is endothermic for 33 and 0% sulfur coverages. On the basis of the computed free energies along a wide range of H2S/H2 ratios, it is found that there are two stable structures with 33 and 50% sulfur coverages on the Mo edge by having 100% sulfur coverage on the S edge and one stable structure with 67% sulfur coverage on the S edge by having 0% sulfur coverage on the Mo edge. Under fully sulfiding atmosphere or at a very high H2S/H2 ratio, triangle MoSx structures with 100% sulfur coverage on the Mo edge are computed to be more stable than those with 100% sulfur coverage on the S edge, in agreement with the observation of scanning tunneling microscopy. In addition, the effects of cluster sizes on the surface structures are discussed.

  16. Response surface reconciliation method of bolted joints structure

    Directory of Open Access Journals (Sweden)

    Yunus Mohd Azmi

    2017-01-01

    Full Text Available Structural joining methods such as bolted joints are commonly used for the assembly of structural components due to their simplicity and easy maintenance. Understandably, the dynamic characteristic of bolted joined structure is mainly influenced by the properties of their joints such as preload on the bolts and joints stiffness which alter the measured dynamics response of the structure. Therefore, the need to include the local effect of the bolted joints into the numerical model of the bolted joined structure is vitally important in order to represent the model accurately. In this paper, a few types of connector elements that can be used to represent the bolted joints such as CBAR, CBEAM and CELAS have been investigated numerically and experimentally. The initial numerical results of these element connectors are compared with the experimental results in term of natural frequencies and mode shapes. The comparative evaluation of numerical and the experimental data are performed in order to provide some insights of inaccuracies in the numerical model due to invalid assumption in the numerical modelling such as geometry, material properties, and boundary conditions. The discrepancies between both results (numerical and experimental data are then corrected using the response surface reconciliation method (RSRM through which the finite element model is altered in order to provide closer agreement with the measured data so that it can be used for subsequence analysis.

  17. Revealing the role of catechol moieties in the interactions between peptides and inorganic surfaces.

    Science.gov (United States)

    Das, Priyadip; Reches, Meital

    2016-08-18

    Catechol (1,2-dihydroxy benzene) moieties are being widely used today in new adhesive technologies. Understanding their mechanism of action is therefore of high importance for developing their applications in materials science. This paper describes a single-molecule study of the interactions between catechol-related amino acid residues and a well-defined titanium dioxide (TiO2) surface. It is the first quantified measurement of the adhesion of these residues with a well-defined TiO2 surface. Single-molecule force spectroscopy measurements with AFM determined the role of different substitutions of the catechol moiety on the aromatic ring in the adhesion to the surface. These results shed light on the nature of interactions between these residues and inorganic metal oxide surfaces. This information is important for the design and fabrication of catechol-based materials such as hydrogels, coatings, and composites. Specifically, the interaction with TiO2 is important for the development of solar cells.

  18. The surface and interior evolution of Ceres revealed by fractures and secondary crater chains

    Science.gov (United States)

    Scully, Jennifer E. C.; Buczkowski, Debra; Schmedemann, Nico; King, Scott; O'Brien, David P.; Castillo-Rogez, Julie; Raymond, Carol; Marchi, Simone; Russell, Christopher T.; Mitri, Giuseppe; Bland, Michael T.

    2016-10-01

    Dawn became the first spacecraft to visit and orbit Ceres, a dwarf planet and the largest body in the asteroid belt (radius ~470 km) (Russell et al., 2016). Before Dawn's arrival, telescopic observations and thermal evolution modeling indicated Ceres was differentiated, with an average density of 2,100 kg/m3 (e.g. McCord & Sotin, 2005; Castillo-Rogez & McCord, 2010). Moreover, pervasive viscous relaxation in a water-ice-rich outer layer was predicted to erase most features on Ceres' surface (Bland, 2013). However, a full understanding of Ceres' surface and interior evolution remained elusive. On the basis of global geologic mapping, we identify prevalent ≥1 km wide linear features that formed: 1) as the surface expression of subsurface fractures, and 2) as material ejected during impact-crater formation impacted and scoured the surface, forming secondary crater chains. The formation and preservation of these linear features indicates Ceres' outer layer is relatively strong, and is not dominated by viscous relaxation as predicted. The fractures also give us insights into Ceres' interior: their spacing indicates the fractured layer is ~30 km thick, and we interpret the fractures formed because of uplift and extension induced by an upwelling region, which is consistent with geodynamic modeling (King et al., 2016). In addition, we find that some secondary crater chains do not form radial patterns around their source impact craters, and are located in a different hemisphere from their source impact craters, because of Ceres' fast rotation (period of ~9 hours) and relatively small radius. Our results show Ceres has a surface and outer layer with characteristics that are different than predicted, and underwent complex surface and interior evolution. Our fuller understanding of Ceres, based on Dawn data, gives us important insights into the evolution of bodies in the asteroid belt, and provides unique constraints that can be used to evaluate predictions of the surface

  19. Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function.

    Science.gov (United States)

    Wells, Stephen A; Crennell, Susan J; Danson, Michael J

    2014-10-01

    Citrate synthase (CS) catalyses the entry of carbon into the citric acid cycle and is highly-conserved structurally across the tree of life. Crystal structures of dimeric CSs are known in both "open" and "closed" forms, which differ by a substantial domain motion that closes the substrate-binding clefts. We explore both the static rigidity and the dynamic flexibility of CS structures from mesophilic and extremophilic organisms from all three evolutionary domains. The computational expense of this wide-ranging exploration is kept to a minimum by the use of rigidity analysis and rapid all-atom simulations of flexible motion, combining geometric simulation and elastic network modeling. CS structures from thermophiles display increased structural rigidity compared with the mesophilic enzyme. A CS structure from a psychrophile, stabilized by strong ionic interactions, appears to display likewise increased rigidity in conventional rigidity analysis; however, a novel modified analysis, taking into account the weakening of the hydrophobic effect at low temperatures, shows a more appropriate decreased rigidity. These rigidity variations do not, however, affect the character of the flexible dynamics, which are well conserved across all the structures studied. Simulation trajectories not only duplicate the crystallographically observed symmetric open-to-closed transitions, but also identify motions describing a previously unidentified antisymmetric functional motion. This antisymmetric motion would not be directly observed in crystallography but is revealed as an intrinsic property of the CS structure by modeling of flexible motion. This suggests that the functional motion closing the binding clefts in CS may be independent rather than symmetric and cooperative.

  20. The structure and surface energy of Ni{sub 80}Fe{sub 20} thin films

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yuan-Tsung, E-mail: ytchen@yuntech.edu.tw; Chen, Chin-Wu; Wu, Te-Ho

    2015-10-01

    Highlights: • X-ray diffraction patterns indicated NiFe thin films exhibited a face-centred cubic (FCC) structural. • NiFe films were more crystalline after postannealing treatment than they were after RT treatment. • NiFe films formed a contact angle of <90°, which indicated that the NiFe films were hydrophilic. • The surface energy was associated with the crystallinity of the thin films. • NiFe thin films exhibit low surface-energy characteristics that can produce a self-cleaning effect. - Abstract: In this study, NiFe thin films were deposited on a glass substrate at room temperature (RT) or postannealed at 150 and 250 °C for 1 h; the Ni{sub 80}Fe{sub 20} films were 300–1500 Å thick. The structure, surface energy, and average contact angle properties of the NiFe thin films were investigated. X-ray diffraction (XRD) results demonstrated that the NiFe thin films exhibited a face-centred cubic (FCC) structural state. The XRD results also revealed that the NiFe films were more crystalline after post-annealing treatment than they were after RT treatment alone, suggesting that the NiFe crystalline structure exhibited FCC (1 1 1) texturing. The NiFe films formed a contact angle of <90° with the test liquids water and diiodomethane, which indicated that the NiFe films were hydrophilic. The surface energy of the NiFe thin films decreased when post-annealing treatment was used and their thickness was increased from 60.4 to 47.9 mJ/mm{sup 2}, suggesting that the surface energy was associated with the crystallinity of the thin films. Therefore, these NiFe thin films exhibit low surface-energy characteristics that can produce a self-cleaning effect.

  1. Maps of sparse Markov chains efficiently reveal community structure in network flows with memory

    CERN Document Server

    Persson, Christian; Edler, Daniel; Rosvall, Martin

    2016-01-01

    To better understand the flows of ideas or information through social and biological systems, researchers develop maps that reveal important patterns in network flows. In practice, network flow models have implied memoryless first-order Markov chains, but recently researchers have introduced higher-order Markov chain models with memory to capture patterns in multi-step pathways. Higher-order models are particularly important for effectively revealing actual, overlapping community structure, but higher-order Markov chain models suffer from the curse of dimensionality: their vast parameter spaces require exponentially increasing data to avoid overfitting and therefore make mapping inefficient already for moderate-sized systems. To overcome this problem, we introduce an efficient cross-validated mapping approach based on network flows modeled by sparse Markov chains. To illustrate our approach, we present a map of citation flows in science with research fields that overlap in multidisciplinary journals. Compared...

  2. Evaluation of multilayered pavement structures from measurements of surface waves

    Science.gov (United States)

    Ryden, N.; Lowe, M.J.S.; Cawley, P.; Park, C.B.

    2006-01-01

    A method is presented for evaluating the thickness and stiffness of multilayered pavement structures from guided waves measured at the surface. Data is collected with a light hammer as the source and an accelerometer as receiver, generating a synthetic receiver array. The top layer properties are evaluated with a Lamb wave analysis. Multiple layers are evaluated by matching a theoretical phase velocity spectrum to the measured spectrum. So far the method has been applied to the testing of pavements, but it may also be applicable in other fields such as ultrasonic testing of coated materials. ?? 2006 American Institute of Physics.

  3. Variable structure guidance law for attacking surface maneuver targets

    Institute of Scientific and Technical Information of China (English)

    Han Yanhua; Xu Bo

    2008-01-01

    The characteristics of surface maneuver targets are analyzed and a 3-D relative motion model for missiles and targets is established. A variable structure guidance law is designed considering the characteristics of targets. In the guidance law, the distance between missiles and targets as well as the missile-target relative velocity are all substituted by estimation values. The estimation errors, the target's velocity, and the maneuver acceleration are all treated as bounded disturbance. The guidance law proposed can be implemented conveniently in engineering with little target information. The performance of the guidance system is analyzed theoretically and the numerical simulation result shows the effectiveness of the guidance law.

  4. Surface flaw detection in structural ceramics by scanning photoacoustic spectroscopy

    Science.gov (United States)

    Khandelwal, P. K.; Heitman, P. W.; Wakefield, T. D.; Silversmith, A. J.

    1980-01-01

    Laser-scanned photoacoustic spectroscopy has been used to detect tightly closed surface cracks in three structural ceramic materials: sintered silicon nitride, reaction-bonded silicon nitride, and sintered silicon carbide. It is found that the amplitude of the photoacoustic signal from the flaws is greater for the silicon nitrides than for silicon carbide, which is attributed to the lower thermal diffusivity of silicon nitride as well as differences in the grain size distribution and chemical composition. Signal amplitude, reproducibility, and signal-to-noise ratio are acceptable for effective flaw detection

  5. Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation

    Science.gov (United States)

    Madhuprakash, Jogi; Singh, Avinash; Kumar, Sanjit; Sinha, Mau; Kaur, Punit; Sharma, Sujata; Podile, Appa R; Singh, Tej P

    2013-01-01

    Chitinases are known to hydrolyze chitin polymers into smaller chitooligosaccharides. Chitinase from bacterium Serratia proteamaculans (SpChiD) is found to exhibit both hydrolysis and transglycosylation activities. SpChiD belongs to family 18 of glycosyl hydrolases (GH-18). The recombinant SpChiD was crystallized and its three-dimensional structure was determined at 1.49 Å resolution. The structure was refined to an R-factor of 16.2%. SpChiD consists of 406 amino acid residues. The polypeptide chain of SpChiD adopts a (β/α)8 triosephosphate isomerase (TIM) barrel structure. SpChiD contains three acidic residues, Asp149, Asp151 and Glu153 as part of its catalytic scheme. While both Asp149 and Glu153 adopt single conformations, Asp151 is observed in two conformations. The substrate binding cleft is partially obstructed by a protruding loop, Asn30 - Asp42 causing a considerable reduction in the number of available subsites in the substrate binding site. The positioning of loop, Asn30 - Asp42 appears to be responsible for the transglycosylation activity. The structure determination indicated the presence of sulfone Met89 (SMet89). The sulfone methionine residue is located on the surface of the protein at a site where extra domain is attached in other chitinases. This is the first structure of a single domain chitinase with hydrolytic and transglycosylation activities. PMID:24380021

  6. Enhanced field emission from nanosecond laser based surface micro-structured stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Singh, A.K., E-mail: anilks@barc.gov.in [Laser & Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai 400085< p/ostalC> (India); Shinde, Deodatta; More, Mahendra A. [Department of Physics, Savitribai Phule Pune University, Pune 411007 (India); Sinha, Sucharita [Laser & Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai 400085< p/ostalC> (India)

    2015-12-01

    Highlights: • Stainless steel (SS) sheets have been surface treated using a frequency doubled nanosecond pulsed Nd:YAG laser at laser fluence level ∼0.7 J/cm{sup 2} resulting in formation of micro protrusions. • In regions near periphery of the laser treated spot showed formation of micro-protrusions with density as high as ∼4.5 × 10{sup 7} cones/cm{sup 2}. • Energy dispersive X-ray spectroscopy (EDS) analysis of untreated and laser treated samples reveals trend in change of elemental composition of the sample on laser treatment. • Grazing incidence X-ray diffraction analysis of untreated and laser treated samples shows formation of oxides and nitrides of iron upon laser treatment. • Field emission study on the laser micro-structured (SS) sample has shown low turn on field in comparison to untreated stainless steel. • Parameters characterizing large area field emitters such as turn ON field, macroscopic field enhancement factor and pre exponential factor corresponding to the laser micro-structured steel surface have been estimated. • Field emission current has shown good stability when tested over a period of 140 min at a preset level of 4 μA. - Abstract: This paper presents results of field emission study of laser based surface micro-structured stainless steel (SS). Surface micro-structuring of SS samples has been performed by direct irradiation of sample surface with a frequency doubled Nd:YAG nanosecond (ns) laser in atmospheric ambience. Laser treated samples have been characterized in terms of their surface morphology, elemental composition and field emission properties. Our results reveal formation of micro-protrusions of varying height and tip diameter depending on incident laser fluence. Within the laser irradiated spot, regions near periphery showed formation of micro-protrusions with number density as high as 4.5 × 10{sup 7} protrusions/cm{sup 2}. Such laser micro-structured samples have shown much lower turn on electric field (7.5 V

  7. Structural determinants for protein adsorption/non-adsorption to silica surface.

    Directory of Open Access Journals (Sweden)

    Christelle Mathé

    Full Text Available The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.

  8. Rapid regional surface uplift of the northern Altiplano plateau revealed by multiproxy paleoclimate reconstruction

    Science.gov (United States)

    Kar, Nandini; Garzione, Carmala N.; Jaramillo, Carlos; Shanahan, Timothy; Carlotto, Victor; Pullen, Alex; Moreno, Federico; Anderson, Veronica; Moreno, Enrique; Eiler, John

    2016-08-01

    The central Altiplano is inferred to have experienced ∼ 2.5 ± 1km surface uplift between ∼10 and 6 Ma, while the southern Altiplano experienced a similar magnitude of surface uplift that began earlier, between ∼16 and 9 Ma. To properly constrain the along strike timing of the Altiplano plateau surface uplift, it is necessary to know how and when the northernmost part of the Altiplano plateau evolved. We reconstruct the paleoclimate and infer the corresponding paleoelevation from the Miocene-Pliocene deposits of the Descanso-Yauri basin (14-15°S) in the northernmost part of the Altiplano plateau using 4 different proxies, including carbonate clumped isotope composition (i.e., Δ47 values), carbonate δ18Oc, leaf wax δDwax and pollen assemblages from paleosol, lacustrine and palustrine carbonates and organic-rich sediments. The isotopic signatures reflect past climate conditions of mean annual air temperature (Δ47) and meteoric water isotope values (δ18Oc, δDwax). Our results show that the northernmost plateau remained at low elevation (0.9 ± 0.8 to 2.1 ± 0.9km) until late Miocene time (∼9 Ma) characterized by ∼15 °C warmer than modern temperature (mean annual air temperature of 23 ± 4 °C, 2σ), low elevation vegetation and precipitation signature with reconstructed □ δ18Omw (VSMOW) of - 8.3 ± 2.0 ‰ (2 σ) from carbonate (δ18Oc) and - 8.6 ± 1.8 ‰ (2 σ) from leaf wax (δDwax). Modern elevations of 4 km were not reached until 5.4 ± 1.0Ma, as indicated by a negative shift in δDwax (VSMOW) from - 143.4 ± 12.8 ‰ (2 σ) to - 209.2 ± 21.1 ‰ (2 σ) between 9.1 ± 0.7 and 5.4 ± 1.0Ma. The timing of surface uplift of the northernmost Altiplano is consistent with the evidence for late Miocene surface uplift of the central Altiplano (16-19°S) between 10 and 6 Ma, and indicates that regional scale uplift in the northern-central plateau significantly postdates the onset of surface uplift in the southern Altiplano (19-22°S) between ∼16

  9. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.

    Science.gov (United States)

    Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang

    2015-04-01

    Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

  10. Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction.

    Science.gov (United States)

    Teramoto, Takamasa; Fujikawa, Yukari; Kawaguchi, Yoshirou; Kurogi, Katsuhisa; Soejima, Masayuki; Adachi, Rumi; Nakanishi, Yuichi; Mishiro-Sato, Emi; Liu, Ming-Cheh; Sakakibara, Yoichi; Suiko, Masahito; Kimura, Makoto; Kakuta, Yoshimitsu

    2013-01-01

    Post-translational protein modification by tyrosine sulfation has an important role in extracellular protein-protein interactions. The protein tyrosine sulfation reaction is catalysed by the Golgi enzyme called the tyrosylprotein sulfotransferase. To date, no crystal structure is available for tyrosylprotein sulfotransferase. Detailed mechanism of protein tyrosine sulfation reaction has thus remained unclear. Here we present the first crystal structure of the human tyrosylprotein sulfotransferase isoform 2 complexed with a substrate peptide (C4P5Y3) derived from complement C4 and 3'-phosphoadenosine-5'-phosphate at 1.9 Å resolution. Structural and complementary mutational analyses revealed the molecular basis for catalysis being an SN2-like in-line displacement mechanism. Tyrosylprotein sulfotransferase isoform 2 appeared to recognize the C4 peptide in a deep cleft by using a short parallel β-sheet type interaction, and the bound C4P5Y3 forms an L-shaped structure. Surprisingly, the mode of substrate peptide recognition observed in the tyrosylprotein sulfotransferase isoform 2 structure resembles that observed for the receptor type tyrosine kinases.

  11. Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association

    Science.gov (United States)

    Sprink, Thiemo; Ramrath, David J. F.; Yamamoto, Hiroshi; Yamamoto, Kaori; Loerke, Justus; Ismer, Jochen; Hildebrand, Peter W.; Scheerer, Patrick; Bürger, Jörg; Mielke, Thorsten; Spahn, Christian M. T.

    2016-01-01

    Throughout the four phases of protein biosynthesis—initiation, elongation, termination, and recycling—the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAiMet in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation. PMID:26973877

  12. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  13. Structures and construction of nuclear power plants on lunar surface

    Science.gov (United States)

    Shimizu, Katsunori; Kobatake, Masuhiko; Ogawa, Sachio; Kanamori, Hiroshi; Okada, Yasuhiko; Mano, Hideyuki; Takagi, Kenji

    1991-07-01

    The best structure and construction techniques of nuclear power plants in the severe environments on the lunar surface are studied. Facility construction types (functional conditions such as stable structure, shield thickness, maintainability, safety distances, and service life), construction conditions (such as construction methods, construction equipment, number of personnel, time required for construction, external power supply, and required transportation) and construction feasibility (construction method, reactor transportation between the moon and the earth, ground excavation for installation, loading and unloading, transportation, and installation, filling up the ground, electric power supply of plant S (300 kW class) and plant L (3000 kW class)) are outlined. Items to pay attention to in construction are (1) automation and robotization of construction; (2) cost reduction by multi functional robots; and (3) methods of supplying power to robots. A precast concrete block manufacturing plant is also outlined.

  14. Structure of a passivated Ge surface prepared from aqueous solution.

    Energy Technology Data Exchange (ETDEWEB)

    Lyman, P. F.; Sakata, O.; Marasco, D, L.; Lee, T.-L.; Breneman, K. D.; Keane, D. T.; Bedzyk, M. J.; Materials Science Division; Northwestern Univ.; Univ. of Wisconsin at Milwaukee

    2000-08-10

    The structure of a passivating sulfide layer on Ge(001) was studied using X-ray standing waves and X-ray fluorescence. The sulfide layer was formed by reacting clean Ge substrates in (NH{sub 4}){sub 2}S solutions of various concentrations at 80{sup o}C. For each treatment, a sulfide layer containing approximately two to three monolayers (ML) of S was formed on the surface, and an ordered structure was found at the interface that contained approximately 0.4 ML of S. Our results suggest the rapid formation of a glassy GeS{sub x} layer containing 1.5-2.5 ML S residing atop a partially ordered interfacial layer of bridge-bonded S. The passivating reaction appears to be self-limited to 2-3 ML at this reaction temperature.

  15. Investigations of surface structural, dynamical, and magnetic properties of systems exhibiting multiferroicity, and topological phases by helium scattering spectroscopies

    Energy Technology Data Exchange (ETDEWEB)

    El-Batanouny, Maged

    2015-08-03

    We propose to investigate the surface structural, dynamics and magnetic properties of the novel class of topological insulator crystals, as well as crystals that exhibit multiferroicity, magnetoelectricity and thermoelectricity. Topological insulators (TIs) are a new class of insulators in which a bulk gap for electronic excitations is generated because of the strong spin-orbit coupling inherent to these systems. These materials are distinguished from ordinary insulators by the presence of gapless metallic surface states, resembling chiral edge modes in quantum Hall systems, but with unconventional spin textures. These exotic metallic states are formed by topological conditions that also render the electrons travelling on such surfaces insensitive to scattering by impurities. The electronic quasi-particles populating the topological surface state are Dirac fermions; they have a linear dispersion and thus are massless just like photons. We propose to investigate the interaction of these massless Dirac fermions with the massive lattice in the newly discovered crystals, Bi2Se3, Bi2Te3 and Sb2Te3. We shall use inelastic helium beam scattering from surfaces to search for related signatures in surface phonon dispersions mappings that cover the entire surface Brillouin zone of these materials. Our recent investigations of the (001) surface of the multiferroic crystals (Li/Na)Cu2O2 revealed an anomalous surface structural behavior where surface Cu$^{2+}$ row rise above the surface plane as the crystal was cooled. Subsequent worming revealed the onset of a thermally activated incommensurate surface phase, driven by the elevated rows. We are currently investigating the structure of the magnetic phases in these quasi-one-dimensional magnetic rows. Multiferroics are excellent candidates for large magnetoelectric response. We propose to extend this investigation to the class of delafossites which are also multiferroics and have been investigated as good candidates for

  16. The role of surface pigmentation for recognition revealed by contrast reversal in faces and Greebles.

    Science.gov (United States)

    Vuong, Quoc C; Peissig, Jessie J; Harrison, Marianne C; Tarr, Michael J

    2005-05-01

    Faces are difficult to recognize when viewed as negatives [Galper (1970). Recognition of faces in photographic negative. Psychonomic Science, 19, 207]. Here we examined the contribution of surface properties to this contrast effect, and whether it is modulated by object category. We tested observers in a matching task using faces or Greebles, presented with or without pigmentation. When stimulus pairs were shown with mismatched contrast (e.g., positive-negative), there was a decrement in performance. This decrement was larger when the stimuli were shown with pigmentation, and this difference was more pronounced with faces than with Greebles. Overall, contrast reversal disrupts the recognition of both faces and objects to a greater degree in the presence of pigmentation, suggesting that surface properties are important components of the object representation.

  17. Correlation in the sequential evolutionary pattern of influenza hemagglutinin reveals its immunogenic and structural characters

    Science.gov (United States)

    Pan, Keyao; Deem, Michael

    2010-03-01

    The immune system recognizes the hemagglutinin (HA) protein on the surface of the influenza virus. It is this protein that evolves to escape immune recognition. Correlation analysis is performed for all pairs of positions in the alignment of HA sequences collected in history. Spectral decomposition of the resulting matrix yields several independent eigenvectors that clusters those positions into several sectors, each of which corresponds to a subset of the positions and follows a relatively independent evolutionary pattern. Some of the obtained sectors match well with the five experimentally and statistically (using Shannon entropy) determined epitopes that are the sites of antibody binding. This result implies that different immunogenic epitopes of HA have characteristic patterns of escape mutation, arguably due to the distinct structures of the epitopes and properties of corresponding antibodies. In the three dimensional structure of HA, each sector is located in a compact surface region, thus the correlations in the evolution pattern occur locally in the tertiary structure. Novel sectors found, beyond the five known HA epitopes, may also possess certain biophysical functions.

  18. Femtosecond laser structuring of silver-containing glass: Silver redistribution, selective etching, and surface topology engineering

    Energy Technology Data Exchange (ETDEWEB)

    Desmoulin, Jean-Charles; Petit, Yannick; Cardinal, Thierry, E-mail: thierry.cardinal@icmcb.cnrs.fr [CNRS, ICMCB, UPR 9048, F-33600 Pessac, France and Univ. Bordeaux, ICMCB, UPR 9048, F-33600 Pessac (France); Canioni, Lionel [Université Bordeaux, Centre Lasers Intenses et Applications–UMR 5107 CNRS, 351 cours de la Libération, 33405 Talence Cedex (France); Dussauze, Marc [Université de Bordeaux, Institut des Sciences Moléculaires, CNRS UMR 5255, 351 cours de la Libération, 33405 Talence Cedex (France); Lahaye, Michel [Université de Bordeaux, Placamat, avenue Docteur Albert Schweitzer, 33608 Pessac Cedex (France); Gonzalez, Hernando Magallanes; Brasselet, Etienne [Université Bordeaux, Laboratoire Ondes et Matière d' Aquitaine–UMR 5798, CNRS, 351 cours de la Libération, 33405 Talence Cedex (France)

    2015-12-07

    Femtosecond direct laser writing in silver-containing phosphate glasses allows for the three-dimensional (3D) implementation of complex photonic structures. Sample translation along or perpendicular to the direction of the beam propagation has been performed, which led to the permanent formation of fluorescent structures, either corresponding to a tubular shape or to two parallel planes at the vicinity of the interaction voxel, respectively. These optical features are related to significant modifications of the local material chemistry. Indeed, silver depletion areas with a diameter below 200 nm were evidenced at the center of the photo-produced structures while photo-produced luminescence properties are attributed to the formation of silver clusters around the multiphoton interaction voxel. The laser-triggered oxidation-reduction processes and the associated photo-induced silver redistribution are proposed to be at the origin of the observed original 3D luminescent structures. Thanks to such material structuring, surface engineering has been also demonstrated. Selective surface chemical etching of the glass has been obtained subsequently to laser writing at the location of the photo-produced structures, revealing features with nanometric depth profiles and radial dimensions strongly related to the spatial distributions of the silver clusters.

  19. Revealing the fate of cell surface human P-glycoprotein (ABCB1): The lysosomal degradation pathway.

    Science.gov (United States)

    Katayama, Kazuhiro; Kapoor, Khyati; Ohnuma, Shinobu; Patel, Atish; Swaim, William; Ambudkar, Indu S; Ambudkar, Suresh V

    2015-10-01

    P-glycoprotein (P-gp) transports a variety of chemically dissimilar amphipathic compounds including anticancer drugs. Although mechanisms of P-gp drug transport are widely studied, the pathways involving its internalization are poorly understood. The present study is aimed at elucidating the pathways involved in degradation of cell surface P-gp. The fate of P-gp at the cell surface was determined by biotinylating cell surface proteins followed by flow cytometry and Western blotting. Our data shows that the half-life of endogenously expressed P-gp is 26.7±1.1 h in human colorectal cancer HCT-15 cells. Treatment of cells with Bafilomycin A1 (BafA1) a vacuolar H+ ATPase inhibitor increased the half-life of P-gp at the cell surface to 36.1±0.5 h. Interestingly, treatment with the proteasomal inhibitors MG132, MG115 or lactacystin alone did not alter the half-life of the protein. When cells were treated with both lysosomal and proteasomal inhibitors (BafA1 and MG132), the half-life was further prolonged to 39-50 h. Functional assays done with rhodamine 123 or calcein-AM, fluorescent substrates of P-gp, indicated that the transport function of P-gp was not affected by either biotinylation or treatment with BafA1 or proteasomal inhibitors. Immunofluorescence studies done with the antibody against lysosomal marker LAMP1 and the P-gp-specific antibody UIC2 in permeabilized cells indicated that intracellular P-gp is primarily localized in the lysosomal compartment. Our results suggest that the lysosomal degradation system could be targeted to increase the sensitivity of P-gp- expressing cancer cells towards chemotherapeutic drugs.

  20. Revealing the fate of cell surface human P-glycoprotein (ABCB1): The Lysosomal Degradation Pathway

    Science.gov (United States)

    Katayama, Kazuhiro; Kapoor, Khyati; Ohnuma, Shinobu; Patel, Atish; Swaim, William; Ambudkar, Indu S.; Ambudkar, Suresh V.

    2015-01-01

    P-glycoprotein (P-gp) transports a variety of chemically dissimilar amphipathic compounds including anticancer drugs. Although mechanisms of P-gp drug transport are widely studied, the pathways involving its internalization are poorly understood. The present study is aimed at elucidating the pathways involved in degradation of cell surface P-gp. The fate of P-gp at the cell surface was determined by biotinylating cell surface proteins followed by flow cytometry and Western blotting. Our data shows that the half-life of endogenously expressed P-gp is 26.7 ± 1.1 h in human colorectal cancer HCT-15 cells. Treatment of cells with Bafilomycin A1 (BafA1) a vacuolar H+ ATPase inhibitor increased the half-life of P-gp at the cell surface to 36.1± 0.5 h. Interestingly, treatment with the proteasomal inhibitors MG132, MG115 or lactacystin alone did not alter the half-life of the protein. When cells were treated with both lysosomal and proteasomal inhibitors (BafA1 and MG132), the half-life was further prolonged to 39-50 h. Functional assays done with rhodamine 123 or calcein-AM, fluorescent substrates of P-gp, indicated that the transport function of P-gp was not affected by either biotinylation or treatment with BafA1 or proteasomal inhibitors. Immunofluorescence studies done with the antibody against lysosomal marker LAMP1 and the P-gp-specific antibody UIC2 in permeabilized cells indicated that intracellular P-gp is primarily localized in the lysosomal compartment. Our results suggest that the lysosomal degradation system could be targeted to increase the sensitivity of P-gp expressing cancer cells towards chemotherapeutic drugs. PMID:26057472

  1. Surface structure of anatase TiO{sub 2}(001): Reconstruction, atomic steps, and domains

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yong; Gan, Shupan; Chambers, Scott A.; Altman, Eric I.

    2001-06-15

    The surface structure of anatase TiO{sub 2}(001) was investigated using scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), reflection high-energy electron diffraction (RHEED), and low-energy electron diffraction (LEED). A two-domain (1{times}4)/(4{times}1) reconstruction, similar to those previously reported in LEED and ion scattering studies, was observed by STM and RHEED. This reconstruction was found to be stable not only from room temperature to 850{degree}C in ultrahigh vacuum and oxygen-rich environments, but also during the anatase film growth. High-resolution STM images obtained at positive sample biases revealed two types of atomic row within each surface unit cell, indicating different Ti-derived states at the surface. At the same time, XPS of the reconstructed surfaces showed no evidence of Ti{sup 3+}. Based on the STM, XPS, RHEED, and LEED results, an {open_quotes}added{close_quotes}-and-{open_quotes}missing{close_quotes}-row model is proposed to account for the (1{times}4) reconstruction. Atomic steps and their relationship to the population of (1{times}4) and (4{times}1) domains were also investigated. The results showed that for vicinal surfaces the domain population depended strongly on the overall surface step orientation. While populations of the (1{times}4) and the (4{times}1) domains were nearly equal on flat (001) surfaces, they became significantly lopsided on a surface with its normal 2{degree} away from the (001) direction, demonstrating a strong correlation between surface steps and domain population on vicinal surfaces.

  2. Surface Structure of Anatase TiO{sub 2}(001): Reconstruction, Atomic Steps, and Domains

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yong; Gan, Shupan; Chambers, Scott A.; Altman, Eric I.

    2001-06-15

    The surface structure of anatase TiO{sub 2}(001) was investigated using scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), reflection high energy electron diffraction (RHEED), and low energy electron diffraction (LEED). A two-domain (1 x 4)/(4 x 1) reconstruction, similar to those previously reported in LEED and ion scattering studies, was observed by STM and RHEED. This reconstruction was found to be stable not only from room temperature to 850 C in ultra-high vacuum and oxygen rich environments, but also during the anatase film growth. High-resolution STM images obtained at positive sample biases revealed two types of atomic rows within each surface unit cell, indicating different Ti-derived states at the surface. At the same time, XPS of the reconstructed surfaces showed no evidence of Ti{sup 3+}. Based on the STM, XPS, RHEED, and LEED results, an ''added''-and-''missing''-row model is proposed to account for the (1 x 4) reconstruction. Atomic steps and their relationship to the population of (1 x 4) and (4 x 1) domains were also investigated. Results showed that for vicinal surfaces, the domain population depended strongly on the overall surface step orientation. While populations of the (1 x 4) and the (4 x 1) domains were nearly equal on the flat (001) surfaces, they became significantly lopsided on the surface with its normal 2{sup o} away from the (001) direction, demonstrating a strong correlation between surface steps and domain population on vicinal surfaces.

  3. Chemical Modification: an Effective Way of Avoiding the Collapse of SWNTs on Al Surface Revealed by Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Xie, J.; Xue, Q. Z.; Yan, K. Y.

    2009-01-01

    The rapid collapse of intrinsic single-walled carbon nanotube (SWNT) on the aluminum surface is observed using molecular dynamics simulation. The collapsing threshold is similar to 10 angstrom, and the length has no influence on its collapse. Furthermore, we report that the structural stability...

  4. Protein structural dynamics revealed by time-resolved X-ray solution scattering.

    Science.gov (United States)

    Kim, Jong Goo; Kim, Tae Wu; Kim, Jeongho; Ihee, Hyotcherl

    2015-08-18

    One of the most important questions in biological science is how a protein functions. When a protein performs its function, it undergoes regulated structural transitions. In this regard, to better understand the underlying principle of a protein function, it is desirable to monitor the dynamic evolution of the protein structure in real time. To probe fast and subtle motions of a protein in physiological conditions demands an experimental tool that is not only equipped with superb spatiotemporal resolution but also applicable to samples in solution phase. Time-resolved X-ray solution scattering (TRXSS), discussed in this Account, fits all of those requirements needed for probing the movements of proteins in aqueous solution. The technique utilizes a pump-probe scheme employing an optical pump pulse to initiate photoreactions of proteins and an X-ray probe pulse to monitor ensuing structural changes. The technical advances in ultrafast lasers and X-ray sources allow us to achieve superb temporal resolution down to femtoseconds. Because X-rays scatter off all atomic pairs in a protein, an X-ray scattering pattern provides information on the global structure of the protein with subangstrom spatial resolution. Importantly, TRXSS is readily applicable to aqueous solution samples of proteins with the aid of theoretical models and therefore is well suited for investigating structural dynamics of protein transitions in physiological conditions. In this Account, we demonstrate that TRXSS can be used to probe real-time structural dynamics of proteins in solution ranging from subtle helix movement to global conformational change. Specifically, we discuss the photoreactions of photoactive yellow protein (PYP) and homodimeric hemoglobin (HbI). For PYP, we revealed the kinetics of structural transitions among four transient intermediates comprising a photocycle and, by applying structural analysis based on ab initio shape reconstruction, showed that the signaling of PYP involves

  5. Analysis of surface structures of Cladonia mitis podetia in historic and recent collections from Greenland

    DEFF Research Database (Denmark)

    Heide-Jørgensen, Henning; Johnsen, Ib

    1995-01-01

    Field observations in Greenland combined with a scanning electron microscopical survey have revealed a hitherto undescribed correspondence in the distribution of a brownish colour and a crust-like surface structure formed by hyphae at exposed parts of the shoot tips of podetia of Cladonia mitis. ...

  6. Effect of ion irradiation on the surface, structural and mechanical properties of brass

    Science.gov (United States)

    Ahmad, Shahbaz; Bashir, Shazia; Ali, Nisar; Umm-i-Kalsoom; Yousaf, Daniel; Faizan-ul-Haq; Naeem, Athar; Ahmad, Riaz; Khlaeeq-ur-Rahman, M.

    2014-04-01

    Modifications to the surface, structural and mechanical properties of brass after ion irradiation have been investigated. Brass targets were bombarded by carbon ions of 2 MeV energy from a Pelletron linear accelerator for various fluences ranging from 56 × 1012 to 26 × 1013 ions/cm2. A scanning electron microscope and X-ray diffractometer were utilized to analyze the surface morphology and crystallographic structure respectively. To explore the mechanical properties e.g., yield stress, ultimate tensile strength and microhardness of irradiated brass, an universal tensile testing machine and Vickers microhardness tester were used. Scanning electron microscopy results revealed an irregular and randomly distributed sputter morphology for a lower ion fluence. With increasing ion fluence, the incoherently shaped structures were transformed into dendritic structures. Nano/micro sized craters and voids, along with the appearance of pits, were observed at the maximum ion fluence. From X-ray diffraction results, no new phases were observed to be formed in the brass upon irradiation. However, a change in the peak intensity and higher and lower angle shifting were observed, which represents the generation of ion-induced defects and stresses. Analyses confirmed modifications in the mechanical properties of irradiated brass. The yield stress, ultimate tensile strength and hardness initially decreased and then increased with increasing ion fluence. The changes in the mechanical properties of irradiated brass are well correlated with surface and crystallographic modifications and are attributed to the generation, augmentation, recombination and annihilation of the ion-induced defects.

  7. Front surface structured targets for enhancing laser-plasma interactions

    Science.gov (United States)

    Snyder, Joseph; George, Kevin; Ji, Liangliang; Yalamanchili, Sasir; Simonoff, Ethan; Cochran, Ginevra; Daskalova, Rebecca; Poole, Patrick; Willis, Christopher; Lewis, Nathan; Schumacher, Douglass

    2016-10-01

    We present recent progress made using front surface structured interfaces for enhancing ultrashort, relativistic laser-plasma interactions. Structured targets can increase laser absorption and enhance ion acceleration through a number of mechanisms such as direct laser acceleration and laser guiding. We detail experimental results obtained at the Scarlet laser facility on hollow, micron-scale plasma channels for enhancing electron acceleration. These targets show a greater than three times enhancement in the electron cutoff energy as well as an increased slope temperature for the electron distribution when compared to a flat interface. Using three-dimensional particle-in-cell (PIC) simulations, we have modeled the interaction to give insight into the physical processes responsible for the enhancement. Furthermore, we have used PIC simulations to design structures that are more advantageous for ion acceleration. Such targets necessitate advanced target fabrication methods and we describe techniques used to manufacture optimized structures, including vapor-liquid-solid growth, cryogenic etching, and 3D printing using two-photon-polymerization. This material is based upon work supported by the Air Force Office of Scientific Research under Award Number FA9550-14-1-0085.

  8. Microscopically derived potential energy surfaces from mostly structural considerations

    Energy Technology Data Exchange (ETDEWEB)

    Ermamatov, M.J. [Instituto de Física, Universidade Federal Fluminense, 24210-340, Niterói, Rio de Janeiro (Brazil); Institute of Nuclear Physics, Ulughbek, Tashkent 100214 (Uzbekistan); Hess, Peter O., E-mail: hess@nucleares.unam.mx [Instituto de Ciencias Nucleares, UNAM, Circuito Exterior, C.U., A.P. 70-543, 04510, Mexico D.F. (Mexico)

    2016-08-15

    A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. We will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.

  9. The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics

    Energy Technology Data Exchange (ETDEWEB)

    Auerbach, Tamar; Mermershtain, Inbal; Davidovich, Chen; Bashan, Anat; Belousoff, Matthew; Wekselman, Itai; Zimmerman, Ella; Xiong, Liqun; Klepacki, Dorota; Arakawa, Kenji; Kinashi, Haruyasu; Mankin, Alexander S.; Yonath, Ada (Hiroshima); (WIS-I); (UIC)

    2010-04-26

    Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacid