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Sample records for analysis structural evolution

  1. Structural evolution

    SciTech Connect

    Burr, M.T.

    1993-03-01

    In this special report, financial executives discuss key trends in power project finance, new funding sources and evolving project structures. Industry wide, financial firms and developers are striving to improve the cost-effectiveness and efficiency of project financing, for projects in both greenfield development and the growing secondary market.

  2. An Analysis of the Structure and Evolution of Networks

    ERIC Educational Resources Information Center

    Hua, Guangying

    2011-01-01

    As network research receives more and more attention from both academic researchers and practitioners, network analysis has become a fast growing field attracting many researchers from diverse fields such as physics, computer science, and sociology. This dissertation provides a review of theory and research on different real data sets from the…

  3. Differential evolution: Global search problem in LEED-IV surface structural analysis

    SciTech Connect

    Nascimento, V.B.; Plummer, E.W.

    2015-02-15

    The search process associated with the quantitative theory–experiment comparison in Low Energy Electron Diffraction surface structural analysis can be very time consuming, especially in the case of complex materials with many atoms in the unit cell. Global search algorithms need to be employed to locate the global minimum of the reliability factor in the multi-dimensional structural parameter space. In this study we investigate the use of the Differential Evolution algorithm in Low Energy Electron Diffraction structural analysis. Despite the simplicity of its mechanism the Differential Evolution algorithm presents an impressive performance when applied to ultra-thin films of BaTiO{sub 3}(001) in a theory–theory comparison. A scaling relation of N{sup (1.47} {sup ±} {sup 0.08)} was obtained, where N is the total number of parameters to be optimized. - Highlights: • We investigated the use of the Differential Evolution algorithm (DE) for the LEED search problem. • The DE method was applied to the optimization of the surface structure of the BaTiO{sub 3}(001) ultra-thin films. • A very favorable scaling relation of N{sup 1.47} was obtained, where N is the total number of parameters to be optimized.

  4. Structural evolution of Ga-Ge-Te glasses by combined EXAFS and XPS analysis

    SciTech Connect

    Golovchak, R.; Calvez, L.; Bureau, B.; Jain, H.

    2013-08-07

    The structural evolution of Ga{sub x}Ge{sub y}Te{sub 100−x−y} glasses in the vicinity of GeTe{sub 4}-GaTe{sub 3} pseudo-binary tie-line is determined with high-resolution X-ray photoelectron (XPS) and extended X-ray absorption fine structure (EXAFS) spectroscopies. The analysis of XPS data is complicated by similar electronegativity values for the constituent chemical elements, but then the interpretation is facilitated by information from complementary EXAFS analysis of the structure around each element independently. The results show 4/4/2 coordination for Ga/Ge/Te atoms and absence of Ga(Ge)-Ge(Ga) bonds or extended Te clusters in significant concentrations within the whole range of studied composition. The observed structural features correlate well with the measured basic physical properties of Ga-containing germanium telluride glasses.

  5. Genre Analysis: Structural and Linguistic Evolution of the English-Medium Medical Research Article (1985-2004)

    ERIC Educational Resources Information Center

    Li, Li-Juan; Ge, Guang-Chun

    2009-01-01

    This paper reports a corpus-based genre analysis of the structural and linguistic evolution of medical research articles (RAs) written in English. Towards that end, we analyzed the frequency of occurrence of the 11 moves identified by Nwogu (1997), of the three most frequently used verb tenses (simple past, simple present and present perfect) and…

  6. Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.

    PubMed

    Bukhari, Syed Abbas; Caetano-Anollés, Gustavo

    2013-01-01

    The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable. PMID:23555236

  7. Lagrangian analysis of formation, structure, evolution and splitting of anticyclonic Kuril eddies

    NASA Astrophysics Data System (ADS)

    Prants, S. V.; Lobanov, V. B.; Budyansky, M. V.; Uleysky, M. Yu.

    2016-03-01

    We studied in detail a mesoscale anticylonic eddy that has been sampled in the R/V Professor Gagarinskiy cruise (June-July 2012) in the area east of the Kuril Islands in the northwestern subarctic Pacific. Lagrangian approach was applied to study formation, structure and evolution of this feature called the eddy A and of its parent eddy B using a simulation with synthetic tracers advected by the AVISO velocity field. We used different Lagrangian methods and techniques to identify those eddies and their boundaries, to know their structure and to document their deformation, metamorphoses and splitting. It has been found that the eddy A was born as a result of splitting of the eddy B with the core water to be borrowed from the eddy B which, in turn, was influenced by the Okhotsk Sea water flowing into the ocean through the Kuril straits. The periphery of the eddy A was formed mainly by East Kamchatka Current water in the process of its winding onto the eddy A core by portions. All these processes have been documented in detail with the help of drift and tracking Lagrangian maps computed forward and backward in time with a large number of synthetic tracers distributed over the studied area. We have found a Lagrangian structure of those eddies and the ways how they have gained and released water. Simulated and measured locations of the center of the eddy A and its boundary have been be estimated to coincide with the accuracy of ≈ 7-10 and ≈ 15-20 km, respectively. Our simulations were validated in part by tracks of available surface drifters and Argo floats. We presented CTD hydrographic observations of the Kuril eddy A from the surface to deep waters and compared observed and simulated results in order to establish origin and properties of water masses constituting that eddy.

  8. Asteroseismic Analysis of the Internal Structure and Evolution of Red Giant Branch Bump Stars

    NASA Astrophysics Data System (ADS)

    Gai, Ning; Tang, Yanke

    2015-05-01

    The “bump” is a prominent feature of the red giant branch (RGB) luminosity function of stellar clusters. Through constructing a grid of models with different masses and metallicities to study the feature of the RGB bump luminosity we find that the luminosity increases almost monotonically with increasing mass for a given metallicity and decreases monotonically with increasing metallicity. Moreover, different stars have different shapes of the RGB bump. It is correlated with the sharpness of the H discontinuity, which is left over by the convection envelope during the first dredge-up. Using the periodicity in the small separations d01, d10 to probe the internal structure, we find that, at about half the acoustic radius, the sound speed has a sharp variation that is caused by a local depression of the first adiabatic exponent {{{Γ }}1} in the second helium ionization zone. It induces an oscillation modulation in d01, d10 with a period of 6.4 μ Hz. Meanwhile, in the same model, the base of the convective envelope is located at a relatively small acoustic radius {{t}envp}/T, which is about 10-1. It is too deep to detect the exact location of the bottom of the outer convective envelope. In order to discriminate the evolutionary status of different stars, we calculate the asymptotic g-mode period spacing {Δ }{{{\\Pi }}1}. We find that {Δ }{{{\\Pi }}1} decreases monotonically with evolution. It is a reliable parameter for distinguishing stars in different positions of the RGB bump.

  9. Metagenomic analysis of microbiota structure evolution in phytoremediation of a swine lagoon wastewater.

    PubMed

    Ye, Jianfeng; Song, Zhaofeng; Wang, Liang; Zhu, Jun

    2016-11-01

    Pytoremediation was studied in this project to treat swine manure lagoon wastewater characteristic of high concentrations of organic carbon, ammonium (N) and phosphorus (P). The impacts of introducing exogenous microalgae Chlorella into the lagoon wastewater on the removal of major nutrients and the transformation of the native wastewater microbiota structure were explored under two phytoremediation modes (shake flask and CO2-air bubbling). The results showed that the inoculation of microalgae could significantly enhance N and P removal. Metagenomic analysis of the native microbiota composition in the wastewater affected by algae inoculation revealed that a substantial population of algicidal bacteria was developed in the shake flask system, while in the CO2-air bubbling system, a niche for more mutualistic bacteria was created, which benefited the maximal algal growth with the simultaneous optimal N and P removal. To our knowledge, this study presents, the first reported case of applying metagenomic approach to a phytoremediation system treating real swine lagoon wastewater. PMID:27518033

  10. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution

    PubMed Central

    Vitte, Clémentine; Bennetzen, Jeffrey L.

    2006-01-01

    Analysis of LTR retrotransposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with >10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with >1,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were >1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat Triticum monococcum and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages. PMID:17101966

  11. Planetary Origin Evolution and Structure

    NASA Technical Reports Server (NTRS)

    Stevenson, David J.

    2005-01-01

    This wide-ranging grant supported theoretical modeling on many aspects of the formation, evolution and structure of planets and satellites. Many topics were studied during this grant period, including the evolution of icy bodies; the origin of magnetic fields in Ganymede; the thermal histories of terrestrial planets; the nature of flow inside giant planets (especially the coupling to the magnetic field) and the dynamics of silicate/iron mixing during giant impacts and terrestrial planet core formation. Many of these activities are ongoing and have not reached completion. This is the nature of this kind of research.

  12. Functional evolution of nuclear structure

    PubMed Central

    Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis. PMID:22006947

  13. Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

    PubMed

    Díez, Beatriz; Nylander, Johan A A; Ininbergs, Karolina; Dupont, Christopher L; Allen, Andrew E; Yooseph, Shibu; Rusch, Douglas B; Bergman, Birgitta

    2016-01-01

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important. PMID:27196065

  14. Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

    PubMed Central

    Díez, Beatriz; Nylander, Johan A. A.; Ininbergs, Karolina; Dupont, Christopher L.; Allen, Andrew E.; Yooseph, Shibu; Rusch, Douglas B.; Bergman, Birgitta

    2016-01-01

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0–20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important. PMID:27196065

  15. Shallow structure and recent evolution of the Aegean Sea deduced from the seismic reflection analysis

    SciTech Connect

    Laure, M.; Mascle, J.

    1988-08-01

    Together with the Tyrrhenian Sea, the Aegean Sea represents one of two marine basins still developing as a consequence of the subduction of the African lithosphere beneath Europe. Despite many geophysical similarities with the Tyrrhenian Sea, the Aegean displays a specific structural segmentation characterized by two distinct domains separated by the central Aegean. To the north of the basin, the so-called North Aegean trough likely represents the western marine extension of the transtensive Anatolian transform fault zone. The northern margin of this area contains a series of disconnected, often thickly sedimented small basins that probably initiated during the late Miocene as a consequence of a dominantly north-south extension; typical uppermost Miocene (Messinian) formations can be observed on seismic grounds. To the south, the Cretan Sea shows clear evidence of important distensive events occurring during two main episodes and following two main trends; a dominantly north-south-directed extension is responsibile for most of the structural features detected along both the Cretan and southern Cyclades margins.

  16. Kin structure, ecology and the evolution of social organization in shrimp: a comparative analysis

    PubMed Central

    Duffy, J. Emmett; Macdonald, Kenneth S.

    2010-01-01

    Eusocial societies present a Darwinian paradox, yet they have evolved independently in insects, mole-rats and symbiotic shrimp. Historically, eusociality has been thought to arise as a response to ecological challenges, mediated by kin selection, but the role of kin selection has recently been questioned. Here we use phylogenetically independent contrasts to test the association of eusociality with ecological performance and genetic structure (via life history) among 20 species of sponge-dwelling shrimp (Synalpheus) in Belize. Consistent with hypotheses that cooperative groups enjoy an advantage in challenging habitats, we show that eusocial species are more abundant, occupy more sponges and have broader host ranges than non-social sister species, and that these patterns are robust to correction for the generally smaller body sizes of eusocial species. In contrast, body size explains less or no variation after accounting for sociality. Despite strong ecological pressures on most sponge-dwellers, however, eusociality arose only in species with non-dispersing larvae, which form family groups subject to kin selection. Thus, superior ability to hold valuable resources may favour eusociality in shrimp but close genetic relatedness is nevertheless key to its origin, as in other eusocial animals. PMID:19889706

  17. Kin structure, ecology and the evolution of social organization in shrimp: a comparative analysis.

    PubMed

    Duffy, J Emmett; Macdonald, Kenneth S

    2010-02-22

    Eusocial societies present a Darwinian paradox, yet they have evolved independently in insects, mole-rats and symbiotic shrimp. Historically, eusociality has been thought to arise as a response to ecological challenges, mediated by kin selection, but the role of kin selection has recently been questioned. Here we use phylogenetically independent contrasts to test the association of eusociality with ecological performance and genetic structure (via life history) among 20 species of sponge-dwelling shrimp (Synalpheus) in Belize. Consistent with hypotheses that cooperative groups enjoy an advantage in challenging habitats, we show that eusocial species are more abundant, occupy more sponges and have broader host ranges than non-social sister species, and that these patterns are robust to correction for the generally smaller body sizes of eusocial species. In contrast, body size explains less or no variation after accounting for sociality. Despite strong ecological pressures on most sponge-dwellers, however, eusociality arose only in species with non-dispersing larvae, which form family groups subject to kin selection. Thus, superior ability to hold valuable resources may favour eusociality in shrimp but close genetic relatedness is nevertheless key to its origin, as in other eusocial animals. PMID:19889706

  18. Multidimensional operando analysis of macroscopic structure evolution in lithium sulfur cells by X-ray radiography.

    PubMed

    Risse, S; Jafta, C J; Yang, Y; Kardjilov, N; Hilger, A; Manke, I; Ballauff, M

    2016-04-21

    Lithium sulfur cells are the most promising candidate for the post lithium-ion battery era. Their major drawback is rapid capacity fading attributed to the complex electrochemical processes during charge and discharge which are not known precisely. Here we present for the first time a multidimensional operando measurement by combining X-ray radiography with impedance spectroscopy while galvanostatically charging and discharging a lithium sulfur cell. The formation of macroscopic sulfur crystals at the end of charge can be seen directly by X-ray radiography. These crystals can be assigned to stable α-sulfur (rhombic) and metastable β-sulfur (monoclinic) by their characteristic crystal habit. These crystal structures with a length of more than 1 mm form and dissolve rapidly during cycling. Their appearance is accompanied by characteristic signals in impedance spectroscopy. Macroscopic crystals of Li2S cannot be observed in full agreement with earlier studies by operando X-ray diffraction. In addition, X-ray radiography reveals non-wetted areas on the carbon cathode. These regions grow during discharge and are reduced during charge. The area of these electrochemically inactive spots is inversely proportional to discharge capacity. PMID:27035926

  19. Structural evolution of the Brazilian airport network

    NASA Astrophysics Data System (ADS)

    da Rocha, Luis E. C.

    2009-04-01

    The aviation sector is profitable, but sensitive to economic fluctuations, geopolitical constraints and governmental regulations. As for other means of transportation, the relation between origin and destination results in a complex map of routes, which can be complemented with information associated with the routes themselves, for instance, frequency, traffic load and distance. The theory of networks provides a natural framework for investigating the dynamics on the resulting structure. Here, we investigate the structure and evolution of the Brazilian airport network (BAN) as regards several quantities: routes, connections, passengers and cargo. Some structural features are in accordance with previous results for other airport networks. The analysis of the evolution of the BAN shows that its structure is dynamic, with changes in the relative relevance of some airports and routes. The results indicate that the connections converge to specific routes. The network shrinks at the route level but grows in number of passengers and amount of cargo, which more than doubled during the period studied.

  20. An analysis of the structure and evolution of the scientific collaboration network of computer intelligence in games

    NASA Astrophysics Data System (ADS)

    Lara-Cabrera, R.; Cotta, C.; Fernández-Leiva, A. J.

    2014-02-01

    Games constitute a research domain that is attracting the interest of scientists from numerous disciplines. This is particularly true from the perspective of computational intelligence. In order to examine the growing importance of this area in the gaming domain, we present an analysis of the scientific collaboration network of researchers working on computational intelligence in games (CIG). This network has been constructed from bibliographical data obtained from the Digital Bibliography & Library Project (DBLP). We have analyzed from a temporal perspective several properties of the CIG network at the macroscopic, mesoscopic and microscopic levels, studying the large-scale structure, the growth mechanics, and collaboration patterns among other features. Overall, computational intelligence in games exhibits similarities with other collaboration networks such as for example a log-normal degree distribution and sub-linear preferential attachment for new authors. It also has distinctive features, e.g. the number of papers co-authored is exponentially distributed, the internal preferential attachment (new collaborations among existing authors) is linear, and fidelity rates (measured as the relative preference for publishing with previous collaborators) grow super-linearly. The macroscopic and mesoscopic evolution of the network indicates the field is very active and vibrant, but it is still at an early developmental stage. We have also analyzed communities and central nodes and how these are reflected in research topics, thus identifying active research subareas.

  1. A structural perspective of compensatory evolution

    PubMed Central

    Ivankov, Dmitry N; Finkelstein, Alexei V; Kondrashov, Fyodor A

    2014-01-01

    The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution. PMID:24981969

  2. [Raman spectroscopy analysis of carbon structural evolution of diesel particulate matters with the treatment of nonthermal plasma].

    PubMed

    Han, Wen-he; Cai, Yi-xi; Li, Xiao-hua; Wang, Jun; Wang, Jing; Li, Kang-hua; Wei, Xing

    2012-08-01

    Original and nonthermal plasma treated particulate matters (PM) samples of a diesel were obtained and characterized by Raman spectroscopy. A five-bands model was adopted for Raman spectrum curve fitting. As parameters involving most information about carbon structure, variation of FWHM of D1 band and D3 relative intensity were analyzed. It was found that original PM presented higher graphical structural order and lower chemical heterogeneity with the increase in the diesel load. After the treatment of NTP, the graphical structural order and chemical heterogeneity of PM kept at a relative stable level, affected very slightly by diesel load. Meanwhile, the amount of molecular carbon in PM increased. Further study for relation between structural evolution and chemical reactivity of PM with chemical kinetics would make Raman spectroscopy of great promise to become an important method for PM characterization, which could provide basis for more effective removal. PMID:23156771

  3. Structural Analysis

    NASA Technical Reports Server (NTRS)

    1991-01-01

    After an 800-foot-tall offshore oil recovery platform collapsed, the engineers at Engineering Dynamics, Inc., Kenner, LA, needed to learn the cause of the collapse, and analyze the proposed repairs. They used STAGSC-1, a NASA structural analysis program with geometric and nonlinear buckling analysis. The program allowed engineers to determine the deflected and buckling shapes of the structural elements. They could then view the proposed repairs under the pressure that caused the original collapse.

  4. Evolution of the Northeast German Basin — inferences from a 3D structural model and subsidence analysis

    NASA Astrophysics Data System (ADS)

    Scheck, M.; Bayer, U.

    1999-11-01

    A 3D structural model of the Northeast German Basin was evaluated with special emphasis on its evolution as an intracontinental depression. The study includes investigations on subsidence history and structural setting of the basin. Thickness evolution and calculated tectonic subsidence volumes of Permian to Quaternary sediments in the Northeast German Basin indicate that the subsidence history was related to five stages of basin evolution which differ in their subsidence mechanisms. For the initial rift phase in the Late Carboniferous to Early Permian, a dominant thermal event and subordinate horizontal stresses were indicated by thickness variation evolution and by structural evidence. The main part of basin subsidence occurred in a NW-SE-oriented basin in the subsequent phase of thermal relaxation with maximum subsidence from Early Permian (Rotliegend) to Middle Triassic (Muschelkalk). From Middle Triassic the thermal subsidence pattern was superposed by further tectonic events. In the Middle Triassic regional extension led to a reconfiguration of the southern part of the basin, where new NNE-SSW-trending troughs (Rheinsberg and Gifhorn Troughs) developed. In the Jurassic the northwestern part of the basin was uplifted while in the south the Keuper subsiding areas continued to sink and NW-SE-trending depressions, related to salt margins, became important. Differentiation continued into Cretaceous times when regional compression caused uplift of the southeastern part of the basin and basin margins. A final subsidence phase occurred in the Cenozoic. This was accompanied by intensive salt movement. Recent basin configuration reflects the superposition of structural elements resulting from different evolution stages. The main structural characteristics of the basin are: (1) a vertical tectonic zonation in a pre-Zechstein succession, which lacks significant internal structures, and a strongly deformed post-Zechstein succession, which was decoupled due to the thick

  5. Substorm evolution of auroral structures

    NASA Astrophysics Data System (ADS)

    Partamies, N.; Juusola, L.; Whiter, D.; Kauristie, K.

    2015-07-01

    Auroral arcs are often associated with magnetically quiet time and substorm growth phases. We have studied the evolution of auroral structures during global and local magnetic activity to investigate the occurrence rate of auroral arcs during different levels of magnetic activity. The ground-magnetic and auroral conditions are described by the magnetometer and auroral camera data from five Magnetometers — Ionospheric radars — All-sky cameras Large Experiment stations in Finnish and Swedish Lapland. We identified substorm growth, expansion, and recovery phases from the local electrojet index (IL) in 1996-2007 and analyzed the auroral structures during the different phases. Auroral structures were also analyzed during different global magnetic activity levels, as described by the planetary Kp index. The distribution of auroral structures for all substorm phases and Kp levels is of similar shape. About one third of all detected structures are auroral arcs. This suggests that auroral arcs occur in all conditions as the main element of the aurora. The most arc-dominated substorm phases occur in the premidnight sector, while the least arc-dominated substorm phases take place in the dawn sector. Arc event lifetimes and expectation times calculated for different substorm phases show that the longest arc-dominated periods are found during growth phases, while the longest arc waiting times occur during expansion phases. Most of the arc events end when arcs evolve to more complex structures. This is true for all substorm phases. Based on the number of images of auroral arcs and the durations of substorm phases, we conclude that a randomly selected auroral arc most likely belongs to a substorm expansion phase. A small time delay, of the order of a minute, is observed between the magnetic signature of the substorm onset (i.e., the beginning of the negative bay) and the auroral breakup (i.e., the growth phase arc changing into a dynamic display). The magnetic onset was

  6. Analysis on the Filament Structure Evolution in Reset Transition of Cu/HfO2/Pt RRAM Device

    NASA Astrophysics Data System (ADS)

    Zhang, Meiyun; Long, Shibing; Li, Yang; Liu, Qi; Lv, Hangbing; Miranda, Enrique; Suñé, Jordi; Liu, Ming

    2016-05-01

    The resistive switching (RS) process of resistive random access memory (RRAM) is dynamically correlated with the evolution process of conductive path or conductive filament (CF) during its breakdown (rupture) and recovery (reformation). In this study, a statistical evaluation method is developed to analyze the filament structure evolution process in the reset operation of Cu/HfO2/Pt RRAM device. This method is based on a specific functional relationship between the Weibull slopes of reset parameters' distributions and the CF resistance ( R on). The CF of the Cu/HfO2/Pt device is demonstrated to be ruptured abruptly, and the CF structure of the device has completely degraded in the reset point. Since no intermediate states are generated in the abrupt reset process, it is quite favorable for the reliable and stable one-bit operation in RRAM device. Finally, on the basis of the cell-based analytical thermal dissolution model, a Monte Carlo (MC) simulation is implemented to further verify the experimental results. This work provides inspiration for RRAM reliability and performance design to put RRAM into practical application.

  7. Analysis on the Filament Structure Evolution in Reset Transition of Cu/HfO2/Pt RRAM Device.

    PubMed

    Zhang, Meiyun; Long, Shibing; Li, Yang; Liu, Qi; Lv, Hangbing; Miranda, Enrique; Suñé, Jordi; Liu, Ming

    2016-12-01

    The resistive switching (RS) process of resistive random access memory (RRAM) is dynamically correlated with the evolution process of conductive path or conductive filament (CF) during its breakdown (rupture) and recovery (reformation). In this study, a statistical evaluation method is developed to analyze the filament structure evolution process in the reset operation of Cu/HfO2/Pt RRAM device. This method is based on a specific functional relationship between the Weibull slopes of reset parameters' distributions and the CF resistance (R on). The CF of the Cu/HfO2/Pt device is demonstrated to be ruptured abruptly, and the CF structure of the device has completely degraded in the reset point. Since no intermediate states are generated in the abrupt reset process, it is quite favorable for the reliable and stable one-bit operation in RRAM device. Finally, on the basis of the cell-based analytical thermal dissolution model, a Monte Carlo (MC) simulation is implemented to further verify the experimental results. This work provides inspiration for RRAM reliability and performance design to put RRAM into practical application. PMID:27389343

  8. Structural evolution of proteinlike heteropolymers

    NASA Astrophysics Data System (ADS)

    Nelson, Erik D.; Grishin, Nick V.

    2014-12-01

    The biological function of a protein often depends on the formation of an ordered structure in order to support a smaller, chemically active configuration of amino acids against thermal fluctuations. Here we explore the development of proteins evolving to satisfy this requirement using an off-lattice polymer model in which monomers interact as low resolution amino acids. To evolve the model, we construct a Markov process in which sequences are subjected to random replacements, insertions, and deletions and are selected to recover a predefined minimum number of solid-ordered monomers using the Lindemann melting criterion. We show that polymers generated by this process consistently fold into soluble, ordered globules of similar length and complexity to small protein motifs. To compare the evolution of the globules with proteins, we analyze the statistics of amino acid replacements, the dependence of site mutation rates on solvent exposure, and the dependence of structural distance on sequence distance for homologous alignments. Despite the simplicity of the model, the results display a surprisingly close correspondence with protein data.

  9. Chloroplast evolution, structure and functions

    PubMed Central

    Jensen, Poul Erik

    2014-01-01

    In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism. PMID:24991417

  10. Structural Evolution of Carbon During Oxidation

    SciTech Connect

    Adel F. Sarofim; Angelo Kandas

    1998-10-28

    The examination of the structural evolution of carbon during oxidation has proven to be of scientific interest. Early modeling work of fluidized bed combustion showed that most of the reactions of interest occurs iOn the micropores, and this work has concentrated on these pores. This work has concentrated on evolution of macroporosity and rnicroporosity of carbons during kinetic controlled oxidation using SAXS, C02 and TEM analysis. Simple studies of fluidized bed combustion of coal chars has shown that many of the events considered fragmentation events previously may in fact be "hidden" or nonaccessible porosity. This makes the study of the microporous combustion characteristics of carbon even more important. The generation of a combustion resistant grid, coupled with measurements of the SAXS and C02 surface areas, fractal analysis and TEM studies has confined that soot particles shrink during their oxidation, as previously suspected. However, this shrinkage results in an overall change in structure. This structure becomes, on a radial basis, much more ordered near the edges, while the center itself becomes transparent to the TEM beam, implying a total lack of structure in this region. Although complex, this carbon structure is probably burning as to keep the density of the soot particles nearly the same. The TEM techniques developed for examination of soots has also been applied to Spherocarb. The Spherocarb during oxidation also increases its ordering,. This ordering, by present theories, would imply that the reactivity would go. However, the reactivity goes up, implying that structure of carbon is secondary in importance to catalytic effects.

  11. Evolution in Stage-Structured Populations

    PubMed Central

    Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

    2016-01-01

    For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

  12. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

    PubMed Central

    2014-01-01

    Background A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described. Results Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons. Conclusion Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles. PMID:24734980

  13. Analysis of very-high-resolution Galileo images of Europa: Implications for small-scale structure and surface evolution

    NASA Astrophysics Data System (ADS)

    Leonard, E. J.; Pappalardo, R. T.; Yin, A.; Prockter, L. M.; Patthoff, D. A.

    2014-12-01

    The Galileo Solid State Imager (SSI) recorded nine very high-resolution frames (8 at 12 m/pixel and 1 at 6 m/pixel) during the E12 flyby of Europa in Dec. 1997. To understand the implications for the small-scale structure and evolution of Europa, we mosaicked these frames (observations 12ESMOTTLE01 and 02, incidence ≈18°, emission ≈77°) into their regional context (part of observation 11ESREGMAP01, 220 m/pixel, incidence ≈74°, emission ≈23°), despite their very different viewing and lighting conditions. We created a map of geological units based on morphology, structure, and albedo along with stereoscopic images where the frames overlapped. The highly diverse units range from: high albedo sub-parallel ridge and grooved terrain; to variegated-albedo hummocky terrain; to low albedo and relatively smooth terrain. We classified and analyzed the diverse units solely based on the high-resolution image mosaic, prior to comparison to the context image, to obtain an in-depth look at possible surface evolution and underlying formational processes. We infer that some of these units represent different stages and forms of resurfacing, including cryovolcanic and tectonic resurfacing. However, significant morphological variation among units in the region indicates that there are different degrees of resurfacing at work. We have created candidate morphological sequences that provide insight into the conversion of ridged plains to chaotic terrain—generally, a process of subduing formerly sharp features through tectonic modification and/or cryovolcanism. When the map of the high-resolution area is compared to the regional context, features that appear to be one unit at regional resolution are comprised of several distinct units at high resolution, and features that appear to be smooth in the context image are found to show distinct textures. Moreover, in the context image, transitions from ridged units to disrupted units appear to be gradual; however the high

  14. Observational Analysis of Tropical Cyclogenesis in the Western North Pacific. Part I: Structural Evolution of Cloud Clusters.

    NASA Astrophysics Data System (ADS)

    Lee, Cheng Shang

    1989-08-01

    This paper is the first of a two-part series summarizing recent attempts to advance omit understanding of the physical processes associated with tropical cyclone formation in the western North Pacific. A combination of rawinsonde composite and individual case analyses are shown for both pre-cyclone tropical cloud clusters (genesis) and those-prominent cloud cluster that do not develop into tropical cyclones (nongenesis). This research is an extension of previous works at Colorado State University by McBride, Zehr, and Love.The first part of the study concerns the structural evolution of the genesis cloud clusters and nongenesis cloud clusters. Results show that nongenesis cloud clusters have about the same mean vertical motion and cumulus activity as the genesis cloud clusters. However, genesis cloud clusters are found to have much stronger middle-to low-level cyclonic circulation extending over a radius 2°-8° outward from the center. The buildup of this strong precyclogenesis circulation is associated with varying combinations of a stronger than normal monsoon trough and large-scale, low-level tradewind and/or monsoon wind surges.

  15. Tectonic evolution of the eastern margin of the Thaumasia Plateau (Mars) as inferred from detailed structural mapping and analysis

    NASA Astrophysics Data System (ADS)

    Borraccini, F.; Di Achille, G.; Ori, G. G.; Wezel, F. C.

    2007-05-01

    The eastern margin of the Thaumasia Plateau (EMTP) is characterized by a diversity of tectonic features, which recorded its complex, and still controversial, tectonic history. A detailed structural survey and analyses have been carried out in order to assess the kinematics and relative age of the main deformational events. Combining results from statistics of lineament orientations and density of fault length for each geologic unit and taking into account crosscutting relationships among tectonic structures, three main deformational events have been recognized. The early stage of the tectonic evolution of EMTP is recorded by Noachian units at the southern edge of Melas Dorsa and is represented by N-S oriented grabens sutured by Early Hesperian formations. Starting from Late Noachian, the extensional stress field became NE-SW oriented and resulted in the formation of NW-SE striking sets of grabens. At the boundary between Noachian and Hesperian, the most important change in tectonic regime occurred. The Hesperian tectonics are characterized by an E-W shortening possibly related to an eastward motion of the Thaumasia Plateau. This tectonic phase likely produced a N-S-oriented wrinkle ridges as well as regional folds and thrust faults. E-W-oriented preexisting tectonic lineaments could have been reactivated forming regional transfer zones. In this scenario, Coprates Rise, Melas Dorsa, and Thaumasia Ridge could be interpreted as mountain belts resulting from buckling and thrust faulting of the eastern and southern margins of the Thaumasia plateau. The proto-Valles Marineris could have experienced a left-lateral component of displacement and played a role of a transfer shear zone.

  16. Phylogeny and evolution of RNA structure.

    PubMed

    Gesell, Tanja; Schuster, Peter

    2014-01-01

    Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution. PMID:24639167

  17. The structure and evolution of story networks.

    PubMed

    Karsdorp, Folgert; van den Bosch, Antal

    2016-06-01

    With this study, we advance the understanding about the processes through which stories are retold. A collection of story retellings can be considered as a network of stories, in which links between stories represent pre-textual (or ancestral) relationships. This study provides a mechanistic understanding of the structure and evolution of such story networks: we construct a story network for a large diachronic collection of Dutch literary retellings of Red Riding Hood, and compare this network to one derived from a corpus of paper chain letters. In the analysis, we first provide empirical evidence that the formation of these story networks is subject to age-dependent selection processes with a strong lopsidedness towards shorter time-spans between stories and their pre-texts (i.e. 'young' story versions are preferred in producing new versions). Subsequently, we systematically compare these findings with and among predictions of various formal models of network growth to determine more precisely which kinds of attractiveness are also at play or might even be preferred as explicatory models. By carefully studying the structure and evolution of the two story networks, then, we show that existing stories are differentially preferred to function as a new version's pre-text given three types of attractiveness: (i) frequency-based and (ii) model-based attractiveness which (iii) decays in time. PMID:27429767

  18. The structure and evolution of story networks

    PubMed Central

    Karsdorp, Folgert; van den Bosch, Antal

    2016-01-01

    With this study, we advance the understanding about the processes through which stories are retold. A collection of story retellings can be considered as a network of stories, in which links between stories represent pre-textual (or ancestral) relationships. This study provides a mechanistic understanding of the structure and evolution of such story networks: we construct a story network for a large diachronic collection of Dutch literary retellings of Red Riding Hood, and compare this network to one derived from a corpus of paper chain letters. In the analysis, we first provide empirical evidence that the formation of these story networks is subject to age-dependent selection processes with a strong lopsidedness towards shorter time-spans between stories and their pre-texts (i.e. ‘young’ story versions are preferred in producing new versions). Subsequently, we systematically compare these findings with and among predictions of various formal models of network growth to determine more precisely which kinds of attractiveness are also at play or might even be preferred as explicatory models. By carefully studying the structure and evolution of the two story networks, then, we show that existing stories are differentially preferred to function as a new version's pre-text given three types of attractiveness: (i) frequency-based and (ii) model-based attractiveness which (iii) decays in time. PMID:27429767

  19. A Preliminary Analysis of the Structure of a Northeast cold vortex and the Mechanism for its Evolution

    NASA Astrophysics Data System (ADS)

    Liu, Y.

    2012-04-01

    mutual migration of updrafts and downdrafts by the warm and cold air, respectively, and that the downward extension of the upper cold air plays a key role in the development of the cold vortex. Crossing through the isobaric surfaces, the upper dry cold currents intrude downward, along the isentropic surface, into the area near the cold vortex centre, which is able to cause the cold vortex to develop and maintain its structure of cold core. The mechanism responsible for dry intrusion can, in nature, expressed as the intrusion and downward extension of high potential vorticity. This demonstrates an important indicative implication in forecasting the development and evolution of a cold vortex.

  20. Structural evolution across the insulator-metal transition in oxygen-deficient BaTiO3-δ studied using neutron total scattering and Rietveld analysis

    DOE PAGESBeta

    Jeong, I.-K.; Lee, Seunghun; Jeong, Se-Young; Won, C. J.; Hur, N.; Llobet, A.

    2011-08-29

    Oxygen-deficient BaTiO3-δ exhibits an insulator-metal transition with increasing δ. We performed neutron total scattering measurements to study structural evolution across an insulator-metal transition in BaTiO3-δ. Despite its significant impact on resistivity, slight oxygen reduction (δ=0.09) caused only a small disturbance on the local doublet splitting of Ti-O bond. This finding implies that local polarization is well preserved under marginal electric conduction. In the highly oxygen-deficient metallic state (δ=0.25), however, doublet splitting of the Ti-O bond became smeared. The smearing of the local Ti-O doublet is complemented with long-range structural analysis and demonstrates that the metallic conduction in the highly oxygen-reducedmore » BaTiO3-δ is due to the appearance of nonferroelectric cubic lattice.« less

  1. An investigation of lithospheric structure and evolution in convergent orogenic systems using seismic receiver functions and surface wave analysis

    NASA Astrophysics Data System (ADS)

    Calkins, Joshua A.

    Whether by accretion, magmatic addition, or refinement of more mafic lithologies, continental arcs are likely zones for the creation of "average" continental crust with intermediate silica content. This dissertation contains the results of broadband seismic studies carried out in two field areas, an active subduction zone and the remnants of an extinct arc, with the aim of understanding lithospheric evolution at convergent margins. The analytical techniques of receiver function calculation and surface wave tomography are applied to data sets collected above the Andean subduction zone in Chile and western Argentina and in the Coast Mountains Batholith of central British Columbia. We present the first in-depth comparison of receiver functions calculated using the high frequencies available in records of intermediate-depth local earthquakes with those calculated from the lower frequency data in records of larger teleseismic events. The comparison reveals that the lower crust beneath the Western Sierras Pampeanas contains a gradational velocity increase over ˜20km above a small velocity step at the Moho. Surface wave tomography confirms the existence of an unusually high velocity anomaly in the mantle above the slab and yields estimates of slab thickness on the order of 50 km. To the south of the flat slab region, we see evidence of active mantle wedge convection above the steep slab, but no evidence of the lithosphere-asthenosphere boundary beneath the subducting Nazca plate. In the Coast Mountains Batholith (CMB), receiver functions image a bright, continuous Moho throughout the study region. Combined with petrologic modeling, the receiver function data point toward convective removal of any ultramafic root that formed beneath the CMB. Low absolute shear wave velocities in the upper mantle resolved via surface wave analysis strengthen the case for root removal beneath the eastern section of the CMB. On the far western edge of the CMB, we find evidence of a partially

  2. Evolution of dinosaur epidermal structures.

    PubMed

    Barrett, Paul M; Evans, David C; Campione, Nicolás E

    2015-06-01

    Spectacularly preserved non-avian dinosaurs with integumentary filaments/feathers have revolutionized dinosaur studies and fostered the suggestion that the dinosaur common ancestor possessed complex integumentary structures homologous to feathers. This hypothesis has major implications for interpreting dinosaur biology, but has not been tested rigorously. Using a comprehensive database of dinosaur skin traces, we apply maximum-likelihood methods to reconstruct the phylogenetic distribution of epidermal structures and interpret their evolutionary history. Most of these analyses find no compelling evidence for the appearance of protofeathers in the dinosaur common ancestor and scales are usually recovered as the plesiomorphic state, but results are sensitive to the outgroup condition in pterosaurs. Rare occurrences of ornithischian filamentous integument might represent independent acquisitions of novel epidermal structures that are not homologous with theropod feathers. PMID:26041865

  3. Evolution of dinosaur epidermal structures

    PubMed Central

    Barrett, Paul M.; Evans, David C.; Campione, Nicolás E.

    2015-01-01

    Spectacularly preserved non-avian dinosaurs with integumentary filaments/feathers have revolutionized dinosaur studies and fostered the suggestion that the dinosaur common ancestor possessed complex integumentary structures homologous to feathers. This hypothesis has major implications for interpreting dinosaur biology, but has not been tested rigorously. Using a comprehensive database of dinosaur skin traces, we apply maximum-likelihood methods to reconstruct the phylogenetic distribution of epidermal structures and interpret their evolutionary history. Most of these analyses find no compelling evidence for the appearance of protofeathers in the dinosaur common ancestor and scales are usually recovered as the plesiomorphic state, but results are sensitive to the outgroup condition in pterosaurs. Rare occurrences of ornithischian filamentous integument might represent independent acquisitions of novel epidermal structures that are not homologous with theropod feathers. PMID:26041865

  4. Evolution of the Chos Malal and Agrio fold and thrust belts, Andes of Neuquén: Insights from structural analysis and apatite fission track dating

    NASA Astrophysics Data System (ADS)

    Rojas Vera, E. A.; Mescua, J.; Folguera, A.; Becker, T. P.; Sagripanti, L.; Fennell, L.; Orts, D.; Ramos, V. A.

    2015-12-01

    The Chos Malal and Agrio fold and thrust belts are located in the western part of the Neuquén basin, an Andean retroarc basin of central-western Argentina. Both belts show evidence of tectonic inversion at the western part during Late Cretaceous times. The eastern part is dominated by late Miocene deformation which also partially reactivated the western structures. This work focuses on the study of the regional structure and the deformational event that shaped the relief of this part of the Andes. Based on new field work and structural data and previously published works a detailed map of the central part of the Neuquén basin is presented. Three regional structural cross sections were surveyed and balanced using the 2d Move™ software. In order to define a more accurate uplift history, new apatite fission track analyses were carried on selected structures. These data was used for new thermal history modeling of the inner part of the Agrio and Chos Malal fold and thrust belts. The results of the fission track analyses improve the knowledge of how these fold and thrust belts have grown trough time. Two main deformational events are defined in Late Cretaceous to Paleocene and Late Miocene times. Based on this regional structural analysis and the fission track data the precise location of the orogenic front for the Late Cretaceous-Paleocene times is reconstructed and it is proposed a structural evolution of this segment of the Andes. This new exhumation data show how the Late Cretaceous to Paleocene event was a continuous and uninterrupted deformational event.

  5. Evolution of avian eggshell structure.

    PubMed

    Osterström, Ola; Lilja, Clas

    2012-03-01

    Data are presented suggesting that birds have evolved eggs with shells containing different structures (numbers of mammillae per unit of inner eggshell surface area, i.e., mammillary densities) to cope up with different calcium requirements imposed by different growth rates and modes of development. Precocial bird species grow slowly, but have high mammillary density, while altricial bird species grow rapidly, but have low mammillary density. These results suggest an adaptation associated with growth rate and mode of development and show, moreover, that the mammillary layer is indicative of the breeding biology of the bird. PMID:21987469

  6. Evolution of the Himalayan structures

    SciTech Connect

    Bhatt, K. )

    1990-05-01

    Sedimentologically, the Himalayan sediments were deposited in the Tethyan Sea and represent rocks from the Paleozoic to the Holocene. During the early Paleozoic, localized movements divided the Tethyan Sea into two geosynclines separated by a geoanticline of Precambrian central crystallines. The northern deep basin which contains euogeosynclinal sediments, is known as the Tethyan zone, and the southern shallow basin which has miogeosynclinal sediments, represents the rocks of the Himalayan zone. Structurally, three major zones of tectonic movement have been recognized, all of which show similar structural trend: (1) along the Indus suture zone (ISZ), (2) along the Main Central thrust (MCT), and (3) along the Main Boundary thrust (MBT). The ISZ represents the subduction zone between the Indian and Asian plate. The origin of the MCT is related to initial subduction along the trench area and may have been formed during the Late Cretaceous-early Paleocene due to offscrapping of sediments in the subduction zone. Further compression between the two plates caused southward migration of the subduction zone and formed the MBT, during or after the Pliocene, which brought old Paleozoic rocks of lesser Himalaya in contact with younger Tertiary rocks (Siwaliks) of Sub-Himalaya. Both the MCT and MBT are parts of an imbricated system formed in the subduction zone representing different geological time periods. The present position of the subduction zone indicates that future subduction of Indian plate into the Asian plate and will cause tectonic activation of the MBT and movement along the MCT will diminish.

  7. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    NASA Astrophysics Data System (ADS)

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

  8. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    PubMed Central

    He, Yi-Ming; Ma, Bin-Guang

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

  9. Cross-linked structure of network evolution

    NASA Astrophysics Data System (ADS)

    Bassett, Danielle S.; Wymbs, Nicholas F.; Porter, Mason A.; Mucha, Peter J.; Grafton, Scott T.

    2014-03-01

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  10. Cosmic evolution of Quasar radio structure

    NASA Technical Reports Server (NTRS)

    Hutchings, J. B.; Neff, S. G.

    1991-01-01

    We discuss the results of a survey of Quasar radio structures over redshifts from 0.6 to 3.7. There are clear evolutionary trends in size and luminosity, which suggest that the duty cycle of individual Quasars has increased over cosmic time. This affects source count statistics and gives clues on the evolution of Quasar environments.

  11. Object Recognition and Random Image Structure Evolution

    ERIC Educational Resources Information Center

    Sadr, Jvid; Sinha, Pawan

    2004-01-01

    We present a technique called Random Image Structure Evolution (RISE) for use in experimental investigations of high-level visual perception. Potential applications of RISE include the quantitative measurement of perceptual hysteresis and priming, the study of the neural substrates of object perception, and the assessment and detection of subtle…

  12. Cross-linked structure of network evolution

    SciTech Connect

    Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Porter, Mason A.; Mucha, Peter J.

    2014-03-15

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  13. Shaping galaxy evolution with galaxy structure

    NASA Astrophysics Data System (ADS)

    Cheung, Edmond

    A fundamental pursuit of astronomy is to understand galaxy evolution. The enormous scales and complex physics involved in this endeavor guarantees a never-ending journey that has enamored both astronomers and laymen alike. But despite the difficulty of this task, astronomers have still attempted to further this goal. Among of these astronomers is Edwin Hubble. His work, which includes the famous Hubble sequence, has immeasurably influenced our understanding of galaxy evolution. In this thesis, we present three works that continues Hubble's line of study by using galaxy structure to learn about galaxy evolution. First, we examine the dependence of galaxy quiescence on inner galactic structure with the AEGIS/ DEEP2 survey at 0.5In this thesis, we present three works that continues Hubble's line of study by using galaxy structure to learn about galaxy evolution. First, we examine the dependence of galaxy quiescence on inner galactic structure with the AEGIS/ DEEP2 survey at 0.5structure. Second, we explore the relationship between galactic bars and their host galaxies with Galaxy Zoo 2 at z˜0. The correlations of bar properties and galaxy properties are consistent with simulations of bar formation and evolution, indicating that bars affect their host galaxies. Finally, we investigate whether bars can drive supermassive black hole growth with data from Chandra and Galaxy Zoo: Hubble at 0.2

  14. Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals.

    PubMed

    Xiao, Shan; Zhang, Jia-Yu; Zheng, Ke-Wei; Hao, Yu-Hua; Tan, Zheng

    2013-12-01

    Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand. PMID:23999096

  15. The nonsinglet structure function evolution by Laplace method

    SciTech Connect

    Boroun, G. R. E-mail: boroun@razi.ac.ir; Zarrin, S.

    2015-12-15

    We derive a general scheme for the evolution of the nonsinglet structure function at the leadingorder (LO) and next-to-leading-order (NLO) by using the Laplace-transform technique. Results for the nonsinglet structure function are compared with MSTW2008, GRV, and CKMT parameterizations and also EMC experimental data in the LO and NLO analysis. The results are in good agreement with the experimental data and other parameterizations in the low- and large-x regions.

  16. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

    PubMed Central

    Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; Gonzalez, Jose M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigó, Roderic

    2012-01-01

    The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs. PMID:22955988

  17. Evolution on folding landscapes in combinatorial structures

    SciTech Connect

    Fraser, S.M.; Reidys, C.M.

    1997-11-01

    In this paper the authors investigate the evolution of molecular structures by random point mutations. They will consider two types of molecular structures: (a) (RNA) secondary structures, and (b) random structures. In both cases structure consists of: (1) a contact graph, and (2) a family of relations imposed on its adjacent vertices. The vertex set of the contact graph is simply the set of all indices of a sequence, and its edges are the bonds. The corresponding relations associated with the edges are viewed as secondary base pairing rules and tertiary interaction rules respectively. Mapping of sequences into secondary and random structures are modeled and analyzed. Here, the set of all sequences that map into a particular structure is modeled as a random graph in the sequence space, the so called neutral network and they study how neutral networks are embedded in sequence space. A basic replication of deletion experiment reveals how effective secondary and random structures can be searched by random point mutations and to what extent the structure effects the dynamics of this optimization process. In particular the authors can report a nonlinear relation between the fraction of tertiary interactions in random structures, and the times taken for a population of sequences to find a high fitness target random structure.

  18. Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

    PubMed Central

    2008-01-01

    Background The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes. Results We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU r

  19. Biophysical constraints on the evolution of tissue structure and function

    PubMed Central

    Hunter, P J; de Bono, B

    2014-01-01

    Phylogenetic analyses based on models of molecular sequence evolution have driven to industrial scale the generation, cataloguing and modelling of nucleic acid and polypeptide structure. The recent application of these techniques to study the evolution of protein interaction networks extends this analytical rigour to the study of nucleic acid and protein function. Can we further extend phylogenetic analysis of protein networks to the study of tissue structure and function? If the study of tissue phylogeny is to join up with mainstream efforts in the molecular evolution domain, the continuum field description of tissue biophysics must be linked to discrete descriptions of molecular biochemistry. In support of this goal we discuss tissue units, and biophysical constraints to molecular function associated with these units, to present a rationale with which to model tissue evolution. Our rationale combines a multiscale hierarchy of functional tissue units (FTUs) with the corresponding application of physical laws to describe molecular interaction networks and flow processes over continuum fields within these units. Non-dimensional numbers, derived from the equations governing biophysical processes in FTUs, are proposed as metrics for comparative studies across individuals, species or evolutionary time. We also outline the challenges inherent to the systematic cataloguing and phylogenetic analysis of tissue features relevant to the maintenance and regulation of molecular interaction networks. These features are key to understanding the core biophysical constraints on tissue evolution. PMID:24882821

  20. Evolution of structure during phase transitions

    SciTech Connect

    Martin, J.E.; Wilcoxon, J.P.; Anderson, R.A.

    1996-03-01

    Nanostructured materials can be synthesized by utilizing the domain growth that accompanies first-order phase separation. Structural control can be achieved by appropriately selecting the quench depth and the quench time, but in order to do this in a mindful fashion one must understand the kinetics of domain growth. The authors have completed detailed light scattering studies of the evolution of structure in both temperature- and field-quenched phase transitions in two and three dimensional systems. They have studied these systems in the quiescent state and in shear and have developed theoretical models that account for the experimental results.

  1. Geometry and evolution of structural traps formed by inversion structures

    SciTech Connect

    Mitra, S. )

    1994-07-01

    Inversion structures form by compressional reactivation of preexisting extensional structures. Experimental models and observations of natural structures are used to develop quantitative models for the geometry and kinematic evolution of inversion structures. Two main mechanisms of formation of inversion structures are analyzed: (1) fault-propagation folding on planar faults, and (2) fault-bend folding on listric faults. Inversion structures formed by fault-propagation folding are characterized by the upward termination of a basement fault into a tight fold and thickening of synextensional units into the basin. Inversion structures formed by fault-bend folding are characterized by open-fold geometries and thickening of synextensional units into the fault zone. Characteristic variations in fold geometry and bed thickness provide predictive models for interpreting the subsurface geometries of these two classes of inversion structures in areas with poor seismic data. Examples of both types of structures are described from the Taranaki basin, the southern North Sea, and the Kangean Basin.

  2. Macrodomains: Structure, Function, Evolution, and Catalytic Activities.

    PubMed

    Rack, Johannes Gregor Matthias; Perina, Dragutin; Ahel, Ivan

    2016-06-01

    Recent developments indicate that macrodomains, an ancient and diverse protein domain family, are key players in the recognition, interpretation, and turnover of ADP-ribose (ADPr) signaling. Crucial to this is the ability of macrodomains to recognize ADPr either directly, in the form of a metabolic derivative, or as a modification covalently bound to proteins. Thus, macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. Their importance is further indicated by the fact that dysregulation or mutation of a macrodomain is associated with several diseases, including cancer, developmental defects, and neurodegeneration. In this review, we summarize the current insights into macrodomain evolution and how this evolution influenced their structural and functional diversification. We highlight some aspects of macrodomain roles in pathobiology as well as their emerging potential as therapeutic targets. PMID:26844395

  3. Evolution of sensory structures in basal metazoa.

    PubMed

    Jacobs, Dave K; Nakanishi, Nagayasu; Yuan, David; Camara, Anthony; Nichols, Scott A; Hartenstein, Volker

    2007-11-01

    Cnidaria have traditionally been viewed as the most basal animals with complex, organ-like multicellular structures dedicated to sensory perception. However, sponges also have a surprising range of the genes required for sensory and neural functions in Bilateria. Here, we: (1) discuss "sense organ" regulatory genes, including; sine oculis, Brain 3, and eyes absent, that are expressed in cnidarian sense organs; (2) assess the sensory features of the planula, polyp, and medusa life-history stages of Cnidaria; and (3) discuss physiological and molecular data that suggest sensory and "neural" processes in sponges. We then develop arguments explaining the shared aspects of developmental regulation across sense organs and between sense organs and other structures. We focus on explanations involving divergent evolution from a common ancestral condition. In Bilateria, distinct sense-organ types share components of developmental-gene regulation. These regulators are also present in basal metazoans, suggesting evolution of multiple bilaterian organs from fewer antecedent sensory structures in a metazoan ancestor. More broadly, we hypothesize that developmental genetic similarities between sense organs and appendages may reflect descent from closely associated structures, or a composite organ, in the common ancestor of Cnidaria and Bilateria, and we argue that such similarities between bilaterian sense organs and kidneys may derive from a multifunctional aggregations of choanocyte-like cells in a metazoan ancestor. We hope these speculative arguments presented here will stimulate further discussion of these and related questions. PMID:21669752

  4. Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming

    PubMed Central

    Zhou, Cheng; Ye, Jintong; Xue, Yanfen

    2015-01-01

    Thermostable alkaline pectate lyases have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. In particular, the alkaline pectate lyase from Bacillus sp. strain N16-5 (BspPelA) has potential for enzymatic ramie degumming because of its high specific activity under extremely alkaline conditions without the requirement for additional Ca2+. However, BspPelA displays poor thermostability and is inactive after incubation at 50°C for only 30 min. Here, directed evolution was used to improve the thermostability of BspPelA for efficient and stable degumming. After two rounds of error-prone PCR and screening of >12,000 mutants, 10 mutants with improved thermostability were obtained. Sequence analysis and site-directed mutagenesis revealed that single E124I, T178A, and S271G substitutions were responsible for improving thermostability. Structural and molecular dynamic simulation analysis indicated that the formation of a hydrophobic cluster and new H-bond networks was the key factor contributing to the improvement in thermostability with these three substitutions. The most thermostable combined mutant, EAET, exhibited a 140-fold increase in the t50 (time at which the enzyme loses 50% of its initial activity) value at 50°C, accompanied by an 84.3% decrease in activity compared with that of wild-type BspPelA, while the most advantageous combined mutant, EA, exhibited a 24-fold increase in the t50 value at 50°C, with a 23.3% increase in activity. Ramie degumming with the EA mutant was more efficient than that with wild-type BspPelA. Collectively, our results suggest that the EA mutant, exhibiting remarkable improvements in thermostability and activity, has the potential for applications in ramie degumming in the textile industry. PMID:26070675

  5. Phylogenetic analysis of honey bee behavioral evolution.

    PubMed

    Raffiudin, Rika; Crozier, Ross H

    2007-05-01

    DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance. PMID:17123837

  6. Colloidal structural evolution of asphaltene studied by confocal microscopy

    NASA Astrophysics Data System (ADS)

    Hung, Jannett; Castillo, Jimmy A.; Reyes, A.

    2004-10-01

    In this work, a detail analysis of the flocculation kinetic of asphaltenes colloidal particles has been carried out usng confocal microscopy. The colloidal structural evolution of the asphaltene flocculated has had varies postulated; however, the aggregation process of asphaltene is still not fully understood. In a recent paper, using Confocal microscope (homemade), we reported high-resolution micrographic images of asphaltenes flocculated and the correlation between crude oil stability and flocculation process. This technique permitted visualizes directly the physical nature of asphaltene flocculated. In this work, a detail analysis of the flocculation kinetic of asphaltene colloidal particles has been carried out using confocal microscopy. The physical nature of asphaltene flocculated from different crude oils is showed through of high-resolution image micrographies and its colloidal structural evolution.

  7. Structural and palaeomagnetic Analysis of the Koolau Dyke Swarm Exposed in the Kapa'a Quarry, Oahu: Implications for the Structural Evolution of Kilauea - Type Volcanic Rift Zones.

    NASA Astrophysics Data System (ADS)

    Day, S. J.; Herrero-Bervera, E.; Knight, M. D.

    2003-12-01

    The Koolau dyke swarms, exposed within the Kailua embayment on the northeastern side of Oahu, have been interpreted as feeders to rift zones in the Koolau volcano, analagous to the rift zones of Kilauea volcano (Walker, 1987), that developed prior to the giant Nuuanu lateral collapse at about 2.0 Ma. Systematic determination of cross-cutting relationships between Koolau dykes has proved difficult because of dense vegetation and rapid weathering in the humid tropical climate of windward Oahu. For this study we have concentrated on exposures of the dykes in the large (450 m wide and 200m deep) Kapa'a quarry, about 3 km NE of the near vertical Nuuanu Pali escarpment. Kapa'a quarry was chosen for this study because it has large, freshly exposed sections nearly perpendicular to the dyke swarm trend in hydrothermally altered but largely unweathered rocks. The hydrothermal alteration indicates that the dykes exposed in the quarry were emplaced well below a high water table resulting from trapping of water between dykes: this high water table may have played a part in the eventual collapse. The excellent exposure at Kapa'a allows systematic, accurate determination of structural data and cross-cutting relationships for every dyke in the measured sections. These data were collected for 171 dykes, of which 10 dykes have so far been sampled for palaeomagnetic analysis (i.e remanence and petrofabrics). Most dykes at Kapa'a dip steeply, from around 70 degrees SW (away from the unstable flank of the volcano) through vertical to 50 degrees NE (towards the unstable flank). NE dipping dykes are more abundant overall. Groups of SW - dipping dykes alternate with groups of subvertical to NE - dipping dykes, suggesting a quasi-periodic alternation of the stress regime within the Koolau volcano. Dyke dilations were typically subhorizontal. A final group of dykes, cross-cutting all the others, dip from 50 degrees NE to as little as 35 degrees NE, and dilated in a steeply SW - plunging

  8. Crystallography, Evolution, and the Structure of Viruses

    PubMed Central

    Rossmann, Michael G.

    2012-01-01

    My undergraduate education in mathematics and physics was a good grounding for graduate studies in crystallographic studies of small organic molecules. As a postdoctoral fellow in Minnesota, I learned how to program an early electronic computer for crystallographic calculations. I then joined Max Perutz, excited to use my skills in the determination of the first protein structures. The results were even more fascinating than the development of techniques and provided inspiration for starting my own laboratory at Purdue University. My first studies on dehydrogenases established the conservation of nucleotide-binding structures. Having thus established myself as an independent scientist, I could start on my most cherished ambition of studying the structure of viruses. About a decade later, my laboratory had produced the structure of a small RNA plant virus and then, in another six years, the first structure of a human common cold virus. Many more virus structures followed, but soon it became essential to supplement crystallography with electron microscopy to investigate viral assembly, viral infection of cells, and neutralization of viruses by antibodies. A major guide in all these studies was the discovery of evolution at the molecular level. The conservation of three-dimensional structure has been a recurring theme, from my experiences with Max Perutz in the study of hemoglobin to the recognition of the conserved nucleotide-binding fold and to the recognition of the jelly roll fold in the capsid protein of a large variety of viruses. PMID:22318719

  9. Structure and evolution of Saturn's rings

    NASA Technical Reports Server (NTRS)

    Esposito, L. W.

    1986-01-01

    It is noted that many Voyager observations on the structure and evolution of Saturn's rings remain largely unexplained. The variation of ring thickness and particle size with composition may be partly explained by the input of density waves in the 'heating' of such rings as the outer A ring; in addition, the particles appear to resemble Weidenschilling et al.'s (1984) 'ephemeral bodies' rather than chunks of ice. It is suggested that many current difficulties may be resolved by positing that at least ring A is young, having been created by the destruction of one of the ring moons.

  10. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.

    PubMed

    Sun, Yanxia; Moore, Michael J; Zhang, Shoujun; Soltis, Pamela S; Soltis, Douglas E; Zhao, Tingting; Meng, Aiping; Li, Xiaodong; Li, Jianqiang; Wang, Hengchang

    2016-03-01

    The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was

  11. Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution

    SciTech Connect

    Shanker, Sreejesh; Choi, Jae-Mun; Sankaran, Banumathi; Atmar, Robert L.; Estes, Mary K.; Prasad, B.V. Venkataram

    2012-03-23

    Susceptibility to norovirus (NoV), a major pathogen of epidemic gastroenteritis, is associated with histo-blood group antigens (HBGAs), which are also cell attachment factors for this virus. GII.4 NoV strains are predominantly associated with worldwide NoV epidemics with a periodic emergence of new variants. The sequence variations in the surface-exposed P domain of the capsid protein resulting in differential HBGA binding patterns and antigenicity are suggested to drive GII.4 epochal evolution. To understand how temporal sequence variations affect the P domain structure and contribute to epochal evolution, we determined the P domain structure of a 2004 variant with ABH and secretor Lewis HBGAs and compared it with the previously determined structure of a 1996 variant. We show that temporal sequence variations do not affect the binding of monofucosyl ABH HBGAs but that they can modulate the binding strength of difucosyl Lewis HBGAs and thus could contribute to epochal evolution by the potentiated targeting of new variants to Lewis-positive, secretor-positive individuals. The temporal variations also result in significant differences in the electrostatic landscapes, likely reflecting antigenic variations. The proximity of some of these changes to the HBGA binding sites suggests the possibility of a coordinated interplay between antigenicity and HBGA binding in epochal evolution. From the observation that the regions involved in the formation of the HBGA binding sites can be conformationally flexible, we suggest a plausible mechanism for how norovirus disassociates from salivary mucin-linked HBGA before reassociating with HBGAs linked to intestinal epithelial cells during its passage through the gastrointestinal tract.

  12. Geometry and kinematic evolution of inversion structures

    SciTech Connect

    Mitra, S. )

    1993-07-01

    Positive inversion structures form by the compressional reactivation of preexisting extensional structures. Experimental models and observations of natural structures are used to develop quantitative models for the geometry and kinematic evolution of inversion structures. In this paper, I analyze two main formation mechanisms of inversion structures: (1) fault-propagation folding on planar faults, and (2) fault-bend folding on listric faults. Inversion structures formed by fault-propagation folding occur in the southern North Sea, the Central Montana platform, and the Kangean Basin. During extension, a broad fault-propagation (or drape) fold develops above the master fault, with the fault subsequently breaking through the fold. Synextensional growth units deposited in the hanging wall typically thicken into the basin. Compressional reactivation results in slip reversal on the master and secondary faults, their rotation to shallower dips, and the development of a compressional fault-propagation fold. Inversion structures formed by fault-bend folding on listric faults occur in the Taranaki Basin, and possibly in the southern North Sea. Rollover folding in the hanging wall occurs during extension, possibly accompanied by a small component of fault-propagation folding in the vicinity of the fault tip. Deformation is primarily along a system of antithetic faults. Synextensional growth sediments typically thicken into the fault, but also show thinning in the immediate vicinity of the fault. During compression, the extensional fold is first unfolded and then folded into a compressional fault-bend fold. The characteristic variations in bed geometry and thickness provide predictive models for interpreting the subsurface geometries of these two classes of inversion structures in areas with poor seismic data. These models are particularly useful in exploring for structural traps in the complex and relatively unexplored synextensional growth units. 31 refs., 29 figs.

  13. Planetary Boundary Layer (PBL) Structures and Evolution analysis by Combination of Fractal Dimension of 3 Wavelength Lidar Signal and Range Correct Signal of 1064nm

    NASA Astrophysics Data System (ADS)

    Lei, L.; McCormick, M. P.; Su, J.

    2015-12-01

    Detection of the PBL heights and the PBL structure is very important for understanding the dynamic of the PBL since heat, water vapor and pollutions which come from the surface must transport through the PBL before they can affect the upper atmosphere. Fractal dimension (FD) retrieved from the three wavelengths lidar signals and the range- corrected signal (RCS) of 1064nm were used to analyses the PBL height and structure in Hampton University (HU, 37.02° N, 76.33° W). And the result shows that the new method has the potential to determine the top of different layer at same time. Combination of the FD and RCS signal also can be used to derive the structure of the PBL. Also the PBL evolution and the long time variety of the PBL in Hampton were analyzed. Wavelet covariance transform (WCT) was used to objectively determine the top and structure of the PBL from the FD signal and RCS signal.

  14. Assembly and Structural Evolution of Micelleplexes

    NASA Astrophysics Data System (ADS)

    Jiang, Yaming; Sprouse, Dustin; Laaser, Jennifer; Reineke, Theresa; Lodge, Timothy

    Cationic micelles complex with DNA to form micelleplexes, which are attractive vehicles for gene delivery. We investigate the formation and structural evolution of micelleplexes in buffered solutions. The micelles are composed of poly((2-dimethylamino)ethyl methacrylate)-block-poly(n-butyl methacrylate). The formation of the micelleplexes is monitored via turbidimetric titration. With DNA oligomers, solutions of the complexes are homogeneous until near the charge neutral point, at which point the complexes precipitate. With plasmid DNA, more than a stoichiometric amount of DNA is needed to reach the inhomogeneous region, which suggests that binding is partially inhibited. This inhibition is not fully relieved when the plasmid DNA is linearized, suggesting that the stiffness of the DNA is the main source of the inhibition. With micelles in excess, the micelleplexes formed at low ionic strength exhibit bimodal size distributions and remain stable in solution. With DNA in excess, soluble micelleplexes aggregate over time and precipitate. We explain the structural evolution of the micelleplexes as an interplay between kinetic trapping and thermodynamic equilibrium, and compare the results for DNA with those for a flexible polyanion.

  15. Structural evolution and metallicity of lead clusters

    NASA Astrophysics Data System (ADS)

    Götz, Daniel A.; Shayeghi, Armin; Johnston, Roy L.; Schwerdtfeger, Peter; Schäfer, Rolf

    2016-05-01

    The evolution of the metallic state in lead clusters and its structural implications are subject to ongoing discussions. Here we present molecular beam electric deflection studies of neutral PbN (N = 19-25, 31, 36, 54) clusters. Many of them exhibit dipole moments or anomalies of the polarizability indicating a non-metallic state. In order to resolve their structures, the configurational space is searched using the Pool Birmingham Cluster Genetic algorithm based on density functional theory. Spin-orbit effects on the geometries and dipole moments are taken into account by further relaxing them with two-component density functional theory. Geometries and dielectric properties from quantum chemical calculations are then used to simulate beam deflection profiles. Structures are assigned by the comparison of measured and simulated beam profiles. Energy gaps are calculated using time-dependent density functional theory. They are compared to Kubo gaps, which are an indicator of the metallicity in finite particles. Both, experimental and theoretical data suggest that lead clusters are not metallic up to at least 36 atoms.The evolution of the metallic state in lead clusters and its structural implications are subject to ongoing discussions. Here we present molecular beam electric deflection studies of neutral PbN (N = 19-25, 31, 36, 54) clusters. Many of them exhibit dipole moments or anomalies of the polarizability indicating a non-metallic state. In order to resolve their structures, the configurational space is searched using the Pool Birmingham Cluster Genetic algorithm based on density functional theory. Spin-orbit effects on the geometries and dipole moments are taken into account by further relaxing them with two-component density functional theory. Geometries and dielectric properties from quantum chemical calculations are then used to simulate beam deflection profiles. Structures are assigned by the comparison of measured and simulated beam profiles. Energy gaps

  16. Evolution of genomic structures on Mammalian sex chromosomes.

    PubMed

    Katsura, Yukako; Iwase, Mineyo; Satta, Yoko

    2012-04-01

    Throughout mammalian evolution, recombination between the two sex chromosomes was suppressed in a stepwise manner. It is thought that the suppression of recombination led to an accumulation of deleterious mutations and frequent genomic rearrangements on the Y chromosome. In this article, we review three evolutionary aspects related to genomic rearrangements and structures, such as inverted repeats (IRs) and palindromes (PDs), on the mammalian sex chromosomes. First, we describe the stepwise manner in which recombination between the X and Y chromosomes was suppressed in placental mammals and discuss a genomic rearrangement that might have led to the formation of present pseudoautosomal boundaries (PAB). Second, we describe ectopic gene conversion between the X and Y chromosomes, and propose possible molecular causes. Third, we focus on the evolutionary mode and timing of PD formation on the X and Y chromosomes. The sequence of the chimpanzee Y chromosome was recently published by two groups. Both groups suggest that rapid evolution of genomic structure occurred on the Y chromosome. Our re-analysis of the sequences confirmed the species-specific mode of human and chimpanzee Y chromosomal evolution. Finally, we present a general outlook regarding the rapid evolution of mammalian sex chromosomes. PMID:23024603

  17. Fabric Analysis in the Koppal Granitoid (Southern India) using AMS and its significance in understanding the structural evolution of Dharwar Craton

    NASA Astrophysics Data System (ADS)

    Bhatt, Sandeep; Mamtani, Manish A.; Rana, Virendra

    2016-04-01

    fabric recorded in the gneisses is having an orientation varying from NW-NNW. In some parts of the Koppal Granitoid, a foliation with NE-NNE orientation is recorded; however several parts of this granitoid do not show a clear foliation. Therefore, to analyse the fabric in the granitoid, the authors have carried out AMS analysis, and it is found that the mean orientation of the magnetic foliation is NNE (20° /64° /110°). These initial results indicate that whilst the host rock (gneiss) has NW-SE fabric, the Koppal granitoid is dominated by NE-SW planar fabric. This indicates that the granitoid fabric developed during regional D3 deformation that was on account of NW-SE compression, which is in contrast to the granitoids of WDC (Mulgund Granitoid). It is envisaged that further integration of microstructural studies with the above information will enhance the existing knowledge of the accretionary processes and kinematic evolution of Dharwar craton. References Chadwick et al., 2003 B. Chadwick, V.N. Vasudev, G.V. Hedge The Chitradurga schist belt and its adjacent plutonic rocks NW of Tungabhadra: Karnataka: a duplex in the late Archean convergent setting of the Dharwar craton Journal of the Geological Society of India, v.61, pp. 611-613. Mondal, T.K., Mamtani, M.A. (2013). 3-D Mohr circle construction using vein orientation data from Gadag (southern India) Implications to recognize fluid pressure fluctuation. Journal of Structural Geology, v. 56, pp.45-56. Mondal, T.K. and Mamtani, M.A., 2014. Fabric analysis in rocks of the Gadag region (southern India) - Implications for time relationship between regional deformation and gold mineralization. Tectonophysics, v. 629, pp.238-249. Mondal, T.K. and Mamtani, M.A., 2016. Palaeostress analysis of normal faults in granite-implications for interpreting Riedel shearing related to regional deformation. Journal of the Geological Society, v.173 (1), pp.216-227.

  18. Evolution of groups with a hierarchical structure

    NASA Astrophysics Data System (ADS)

    Ohnishi, Teruaki

    2012-12-01

    The universal occurrence of a hierarchical structure and its dynamic behavior in various types of group, living or abstract, are discussed. Here the word “group” refers not only to tangible aggregation but also to invisible aggregation of social psychological and of geopolitical meaning. The evolution of these groups is simulated using a model of agents distributed on the lattices of cellular grids. It is assumed that agents, fearing isolation, interact asymmetrically with each other with regard to exchange of “power”. As an indicator of hierarchy, the Gini coefficient is introduced. Example calculations are made for the aggregation, fusion and fission of animal groups, and for the appearance of a powerful empire and the rise and fall of supremacy. It is shown that such abstract objects evolve with time in accordance with the universal rules of groups common to birds and fish.

  19. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

  20. Structure, dynamics, and evolution of centromeric nucleosomes

    PubMed Central

    Dalal, Yamini; Furuyama, Takehito; Vermaak, Danielle; Henikoff, Steven

    2007-01-01

    Centromeres are defining features of eukaryotic chromosomes, providing sites of attachment for segregation during mitosis and meiosis. The fundamental unit of centromere structure is the centromeric nucleosome, which differs from the conventional nucleosome by the presence of a centromere-specific histone variant (CenH3) in place of canonical H3. We have shown that the CenH3 nucleosome core found in interphase Drosophila cells is a heterotypic tetramer, a “hemisome” consisting of one molecule each of CenH3, H4, H2A, and H2B, rather than the octamer of canonical histones that is found in bulk nucleosomes. The surprising discovery of hemisomes at centromeres calls for a reevaluation of evidence that has long been interpreted in terms of a more conventional nucleosome. We describe how the hemisome structure of centromeric nucleosomes can account for enigmatic properties of centromeres, including kinetochore accessibility, epigenetic inheritance, rapid turnover of misincorporated CenH3, and transcriptional quiescence of pericentric heterochromatin. Structural differences mediated by loop 1 are proposed to account for the formation of stable tetramers containing CenH3 rather than stable octamers containing H3. Asymmetric CenH3 hemisomes might interrupt the global condensation of octameric H3 arrays and present an asymmetric surface for kinetochore formation. We suggest that this simple mechanism for differentiation between centromeric and packaging nucleosomes evolved from an archaea-like ancestor at the dawn of eukaryotic evolution. PMID:17893333

  1. Structural evolution and metallicity of lead clusters.

    PubMed

    Götz, Daniel A; Shayeghi, Armin; Johnston, Roy L; Schwerdtfeger, Peter; Schäfer, Rolf

    2016-06-01

    The evolution of the metallic state in lead clusters and its structural implications are subject to ongoing discussions. Here we present molecular beam electric deflection studies of neutral PbN (N = 19-25, 31, 36, 54) clusters. Many of them exhibit dipole moments or anomalies of the polarizability indicating a non-metallic state. In order to resolve their structures, the configurational space is searched using the Pool Birmingham Cluster Genetic algorithm based on density functional theory. Spin-orbit effects on the geometries and dipole moments are taken into account by further relaxing them with two-component density functional theory. Geometries and dielectric properties from quantum chemical calculations are then used to simulate beam deflection profiles. Structures are assigned by the comparison of measured and simulated beam profiles. Energy gaps are calculated using time-dependent density functional theory. They are compared to Kubo gaps, which are an indicator of the metallicity in finite particles. Both, experimental and theoretical data suggest that lead clusters are not metallic up to at least 36 atoms. PMID:27181365

  2. Nonlinear Structural Analysis

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Nonlinear structural analysis techniques for engine structures and components are addressed. The finite element method and boundary element method are discussed in terms of stress and structural analyses of shells, plates, and laminates.

  3. Structural evolution in the crystallization of rapid cooling silver melt

    SciTech Connect

    Tian, Z.A.; Dong, K.J.; Yu, A.B.

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  4. Evolution of Tertiary Structure of Viral RNA Dependent Polymerases

    PubMed Central

    Černý, Jiří; Černá Bolfíková, Barbora; Valdés, James J.; Grubhoffer, Libor; Růžek, Daniel

    2014-01-01

    Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution. PMID:24816789

  5. Models of protocellular structures, functions and evolution

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; New, Michael H.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The central step in the origin of life was the emergence of organized structures from organic molecules available on the early earth. These predecessors to modern cells, called 'proto-cells,' were simple, membrane bounded structures able to maintain themselves, grow, divide, and evolve. Since there is no fossil record of these earliest of life forms, it is a scientific challenge to discover plausible mechanisms for how these entities formed and functioned. To meet this challenge, it is essential to create laboratory models of protocells that capture the main attributes associated with living systems, while remaining consistent with known, or inferred, protobiological conditions. This report provides an overview of a project which has focused on protocellular metabolism and the coupling of metabolism to energy transduction. We have assumed that the emergence of systems endowed with genomes and capable of Darwinian evolution was preceded by a pre-genomic phase, in which protocells functioned and evolved using mostly proteins, without self-replicating nucleic acids such as RNA.

  6. Aspects of alternative network structure evolution

    NASA Astrophysics Data System (ADS)

    Singh, Naveen Kumar

    The focus of this prospectus is to study a new and simple process method to prepare and characterize elastomers and hydrogels. A prestressed double network thermoplastic elastomer and hydrogel is prepared by a two step curing process where first network is introduced in the unstrained state, while the second is introduced in the strained state, hence varying prestress after first curing step. The focus of this thesis is towards the understanding of the basic network mechanism governing the final physical, mechanical and thermo-mechanical properties of these prestressed double networks and relating them to their microstructure and morphology. Moreover, the major factors governing the final properties of these networks are being identified including the type of crosslinks, the extent of crosslinking in the two states of stresses/strains, mode of deformation and the behavior is compared with simple theoretical models. The network structure of swollen hydrogel networks has been studied and the effect of various topological constraints ranging from the crosslinks to entangled linear chains to stiff nanofillers have been studied. The study has been utilized to propose a filler reinforcing mechanism for elastomeric networks and also identify the competition between the effect of various constraints in the final steady state and relaxation properties of the swollen hydrogel networks. The final part of this thesis focuses towards the network evolution in ultra high molecular weight poly (tetrafluoroethylene) (PTFE) in its melt state. Initial studies on the viscoelastic properties of PTFE in its melt state has been discussed and later a method to alter the network evolution utilizing supercritical carbon dioxide has been discussed. The effect of supercritical carbon dioxide on the melt of PTFE has been observed by utilizing a new setup to understand the behavior of PTFE in-situ in presence of supercritical carbon dioxide.

  7. Clouds on Neptune: Motions, Evolution, and Structure

    NASA Technical Reports Server (NTRS)

    Sromovsky, Larry A.; Morgan, Thomas (Technical Monitor)

    2001-01-01

    The aims of our original proposal were these: (1) improving measurements of Neptune's circulation, (2) understanding the spatial distribution of cloud features, (3) discovery of new cloud features and understanding their evolutionary process, (4) understanding the vertical structure of zonal cloud patterns, (5) defining the structure of discrete cloud features, and (6) defining the near IR albedo and light curve of Triton. Towards these aims we proposed analysis of existing 1996 groundbased NSFCAM/IRTF observations and nearly simultaneous WFPC2 observations from the Hubble Space Telescope. We also proposed to acquire new observations from both HST and the IRTF.

  8. Structure-property evolution during polymer crystallization

    NASA Astrophysics Data System (ADS)

    Arora, Deepak

    The main theme of this research is to understand the structure-property evolution during crystallization of a semicrystalline thermoplastic polymer. A combination of techniques including rheology, small angle light scattering, differential scanning calorimetry and optical microscopy are applied to follow the mechanical and optical properties along with crystallinity and the morphology. Isothermal crystallization experiments on isotactic poly-1-butene at early stages of spherulite growth provide quantitative information about nucleation density, volume fraction of spherulites and their crystallinity, and the mechanism of connecting into a sample spanning structure. Optical microscopy near the fluid-to-solid transition suggests that the transition, as determined by time-resolved mechanical spectroscopy, is not caused by packing/jamming of spherulites but by the formation of a percolating network structure. The effect of strain, Weissenberg number (We ) and specific mechanical work (w) on rate of crystallization (nucleation followed by growth) and on growth of anisotropy was studied for shear-induced crystallization of isotactic poly-1-butene. The samples were sheared for a finite strain at the beginning of the experiment and then crystallized without further flow (Janeschitz-Kriegl protocol). Strain requirements to attain steady state/leveling off of the rate of crystallization were found to be much larger than the strain needed to achieve steady state of flow. The large strain and We>1 criteria were also observed for morphological transition from spherulitic growth to oriented growth. An apparatus for small angle light scattering (SALS) and light transmission measurements under shear was built and tested at the University of Massachusetts Amherst. As a new development, the polarization direction can be rotated by a liquid crystal polarization rotator (LCPR) with a short response time of 20 ms. The experiments were controlled and analyzed with a LabVIEW(TM) based

  9. Analysis of the geological structure and tectonic evolution of Xingning-Jinghai sag in deep water area, northern South China Sea

    NASA Astrophysics Data System (ADS)

    Han, Xiaoying; Ren, Jianye; Lin, Zi; Yang, Linlong

    2015-04-01

    Recent years, oil and gas exploration of the Pearl River Mouth Basin in the northern margin of South China Sea continuously achieved historic breakthroughs. The Xingning-Jinghai sag, which is located in southeast of the Pearl River Mouth Basin, is a deep-water sag with a great exploration potential. Its tectonic evolution is extremely complex. It experienced Mesozoic subduction to Cenozoic intra-continental rifting background, and finally evolved into a deep-water sag of the northern continental margin of South China Sea. The geological characteristics and the tectonic evolution of Xingning-Jinghai sag was closely related to the process of formation and evolution of the passive continental margin of the northern South China Sea. It is confirmed by many geophysical data that compared with adjacent Chaoshan depression, the crustal thickness of Xingning-Jinghai sag was rapidly thinning, and it developed detachment faults with later magmatic intrusion. The development of detachment faults have dynamic significance for the spreading of the South China Sea. Based on the seismic geological interpretation of 2D seismic data in the study area, the characteristics of detachment fault and supra-detachment basin have been proposed in this study. The characteristics of the detachment fault are low angle and high ratio between heave and throw. The geometry of the detachment fault is a typical lisric shape, with the dip of fault decreasing generally from the seismic profile. The detachment basin where sediments are not deposited over a tilting hanging-wall block but onto a tectonically exhumed footwall which is different from the typical half graben basin. Seismic profiles indicate two different structural styles in the east and west part of Xingning-Jinghai sag. In the west of the sag, there developed two large detachment faults, which control their detachment basin systems and the typical H block, and the two detachment faults are dipping landward and seaward, respectively. In

  10. Evolution and structure of sustainability science

    PubMed Central

    Bettencourt, Luís M. A.; Kaur, Jasleen

    2011-01-01

    The concepts of sustainable development have experienced extraordinary success since their advent in the 1980s. They are now an integral part of the agenda of governments and corporations, and their goals have become central to the mission of research laboratories and universities worldwide. However, it remains unclear how far the field has progressed as a scientific discipline, especially given its ambitious agenda of integrating theory, applied science, and policy, making it relevant for development globally and generating a new interdisciplinary synthesis across fields. To address these questions, we assembled a corpus of scholarly publications in the field and analyzed its temporal evolution, geographic distribution, disciplinary composition, and collaboration structure. We show that sustainability science has been growing explosively since the late 1980s when foundational publications in the field increased its pull on new authors and intensified their interactions. The field has an unusual geographic footprint combining contributions and connecting through collaboration cities and nations at very different levels of development. Its decomposition into traditional disciplines reveals its emphasis on the management of human, social, and ecological systems seen primarily from an engineering and policy perspective. Finally, we show that the integration of these perspectives has created a new field only in recent years as judged by the emergence of a giant component of scientific collaboration. These developments demonstrate the existence of a growing scientific field of sustainability science as an unusual, inclusive and ubiquitous scientific practice and bode well for its continued impact and longevity. PMID:22114186

  11. Evolution and structure of sustainability science.

    PubMed

    Bettencourt, Luís M A; Kaur, Jasleen

    2011-12-01

    The concepts of sustainable development have experienced extraordinary success since their advent in the 1980s. They are now an integral part of the agenda of governments and corporations, and their goals have become central to the mission of research laboratories and universities worldwide. However, it remains unclear how far the field has progressed as a scientific discipline, especially given its ambitious agenda of integrating theory, applied science, and policy, making it relevant for development globally and generating a new interdisciplinary synthesis across fields. To address these questions, we assembled a corpus of scholarly publications in the field and analyzed its temporal evolution, geographic distribution, disciplinary composition, and collaboration structure. We show that sustainability science has been growing explosively since the late 1980s when foundational publications in the field increased its pull on new authors and intensified their interactions. The field has an unusual geographic footprint combining contributions and connecting through collaboration cities and nations at very different levels of development. Its decomposition into traditional disciplines reveals its emphasis on the management of human, social, and ecological systems seen primarily from an engineering and policy perspective. Finally, we show that the integration of these perspectives has created a new field only in recent years as judged by the emergence of a giant component of scientific collaboration. These developments demonstrate the existence of a growing scientific field of sustainability science as an unusual, inclusive and ubiquitous scientific practice and bode well for its continued impact and longevity. PMID:22114186

  12. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

  13. Data Management System (DMS) Evolution Analysis

    NASA Technical Reports Server (NTRS)

    Douglas, Katherine

    1990-01-01

    The all encompassing goal for the Data Management System (DMS) Evolution Analysis task is to develop an advocacy for ensuring that growth and technology insertion issues are properly and adequately addressed during DMS requirements specification, design, and development. The most efficient methods of addressing those issues are via planned and graceful evolution, technology transparency, and system growth margins. It is necessary that provisions, such as those previously mentioned, are made to accommodate advanced missions requirements (e.g., Human Space Exploration Programs) in addition to evolving Space Station Freedom operations and user requirements .

  14. Structural evolution of carbon during oxidation. Final report

    SciTech Connect

    Sarofim, A.F.

    1998-04-01

    The examination of the structural evolution of carbon during oxidation has proven to be of scientific interest. Early modeling work of fluidized bed combustion showed that most of the reactions of interest occurs in the micropores, and this work has concentrated on these pores. This work has concentrated on evolution of macroporosity and microporosity of carbons during kinetic controlled oxidation using SAXS, CO{sub 2} and TEM analysis. Simple studies of fluidized bed combustion of coal chars has shown that many of the events considered fragmentation events previously may in fact be {open_quotes}hidden{close_quotes} or nonaccessible porosity. This makes the study of the microporous combustion characteristics of carbon even more important. The generation of a combustion resistant grid, coupled with measurements of the SAXS and CO{sub 2} surface areas, fractal analysis and TEM. Studies has confirmed that soot particles shrink during their oxidation, as previously suspected. However, this shrinkage results in an overall change in structure. This structure becomes, on a radial basis, much more ordered near the edges, while the center itself becomes transparent to the TEM beam, implying a total lack of structure in this region. Although complex, this carbon structure is probably burning as to keep the density of the soot particles nearly the same. The TEM techniques developed for examination of soots has also been applied to Spherocarb. The Spherocarb during oxidation also increases its ordering. This ordering, by present theories, would imply that the reactivity would go. However, the reactivity goes up, implying that structure of carbon is secondary in importance to catalytic effects.

  15. Molecular Evolution and Structural Features of IRAK Family Members

    PubMed Central

    Gosu, Vijayakumar; Basith, Shaherin; Durai, Prasannavenkatesh; Choi, Sangdun

    2012-01-01

    The interleukin-1 receptor-associated kinase (IRAK) family comprises critical signaling mediators of the TLR/IL-1R signaling pathways. IRAKs are Ser/Thr kinases. There are 4 members in the vertebrate genome (IRAK1, IRAK2, IRAKM, and IRAK4) and an IRAK homolog, Pelle, in insects. IRAK family members are highly conserved in vertebrates, but the evolutionary relationship between IRAKs in vertebrates and insects is not clear. To investigate the evolutionary history and functional divergence of IRAK members, we performed extensive bioinformatics analysis. The phylogenetic relationship between IRAK sequences suggests that gene duplication events occurred in the evolutionary lineage, leading to early vertebrates. A comparative phylogenetic analysis with insect homologs of IRAKs suggests that the Tube protein is a homolog of IRAK4, unlike the anticipated protein, Pelle. Furthermore, the analysis supports that an IRAK4-like kinase is an ancestral protein in the metazoan lineage of the IRAK family. Through functional analysis, several potentially diverged sites were identified in the common death domain and kinase domain. These sites have been constrained during evolution by strong purifying selection, suggesting their functional importance within IRAKs. In summary, our study highlighted the molecular evolution of the IRAK family, predicted the amino acids that contributed to functional divergence, and identified structural variations among the IRAK paralogs that may provide a starting point for further experimental investigations. PMID:23166766

  16. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  17. Analysis of methods. [information systems evolution environment

    NASA Technical Reports Server (NTRS)

    Mayer, Richard J. (Editor); Ackley, Keith A.; Wells, M. Sue; Mayer, Paula S. D.; Blinn, Thomas M.; Decker, Louis P.; Toland, Joel A.; Crump, J. Wesley; Menzel, Christopher P.; Bodenmiller, Charles A.

    1991-01-01

    Information is one of an organization's most important assets. For this reason the development and maintenance of an integrated information system environment is one of the most important functions within a large organization. The Integrated Information Systems Evolution Environment (IISEE) project has as one of its primary goals a computerized solution to the difficulties involved in the development of integrated information systems. To develop such an environment a thorough understanding of the enterprise's information needs and requirements is of paramount importance. This document is the current release of the research performed by the Integrated Development Support Environment (IDSE) Research Team in support of the IISEE project. Research indicates that an integral part of any information system environment would be multiple modeling methods to support the management of the organization's information. Automated tool support for these methods is necessary to facilitate their use in an integrated environment. An integrated environment makes it necessary to maintain an integrated database which contains the different kinds of models developed under the various methodologies. In addition, to speed the process of development of models, a procedure or technique is needed to allow automatic translation from one methodology's representation to another while maintaining the integrity of both. The purpose for the analysis of the modeling methods included in this document is to examine these methods with the goal being to include them in an integrated development support environment. To accomplish this and to develop a method for allowing intra-methodology and inter-methodology model element reuse, a thorough understanding of multiple modeling methodologies is necessary. Currently the IDSE Research Team is investigating the family of Integrated Computer Aided Manufacturing (ICAM) DEFinition (IDEF) languages IDEF(0), IDEF(1), and IDEF(1x), as well as ENALIM, Entity

  18. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

  19. Evolution of structural and functional diversification among plant Argonautes

    PubMed Central

    Singh, Ravi K; Pandey, Shree P

    2015-01-01

    Argonautes (AGOs) are the effector proteins of the RNA-induced silencing (RISC) complex, formed during the phenomena of small-RNA mediated post-transcriptional gene silencing. AGOs are a large family of proteins; their number varies from a few (4 in Chlamydomonas reinhardtii) to many (18 in Oryza sativa) in plants. Genetics-guided analysis have demonstrated the roles of some of the AGOs during growth and development of plants. Biochemical studies have further revealed differences in functional specificities among AGOs. How the AGO family expanded in different plant species during the course of evolution is starting to emerge. We hypothesized that 4 classes of AGOs evolved after divergence of unicellular green algae when an ancestral AGO underwent duplication events. Evolution of multicellularity may have coincided with the diversification of AGOs. A comparative sequence and structure analysis of the plant AGOs, including those from the mosses and the unicellular algae, show not only conformational differences between those from lower and higher plants, but also functional divergence of important sites. PMID:26237574

  20. Evolution of structural and functional diversification among plant Argonautes.

    PubMed

    Singh, Ravi K; Pandey, Shree P

    2015-01-01

    Argonautes (AGOs) are the effector proteins of the RNA-induced silencing (RISC) complex, formed during the phenomena of small-RNA mediated post-transcriptional gene silencing. AGOs are a large family of proteins; their number varies from a few (4 in Chlamydomonas reinhardtii) to many (18 in Oryza sativa) in plants. Genetics-guided analysis have demonstrated the roles of some of the AGOs during growth and development of plants. Biochemical studies have further revealed differences in functional specificities among AGOs. How the AGO family expanded in different plant species during the course of evolution is starting to emerge. We hypothesized that 4 classes of AGOs evolved after divergence of unicellular green algae when an ancestral AGO underwent duplication events. Evolution of multicellularity may have coincided with the diversification of AGOs. A comparative sequence and structure analysis of the plant AGOs, including those from the mosses and the unicellular algae, show not only conformational differences between those from lower and higher plants, but also functional divergence of important sites. PMID:26237574

  1. The relativistic equations of stellar structure and evolution

    NASA Technical Reports Server (NTRS)

    Thorne, K. S.

    1977-01-01

    The general-relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. Also, a general-relativistic version of the mixing-length formalism for convection is presented.

  2. Structural evolution across the insulator-metal transition in oxygen-deficient BaTiO3-δ studied using neutron total scattering and Rietveld analysis

    SciTech Connect

    Jeong, I.-K.; Lee, Seunghun; Jeong, Se-Young; Won, C. J.; Hur, N.; Llobet, A.

    2011-08-29

    Oxygen-deficient BaTiO3-δ exhibits an insulator-metal transition with increasing δ. We performed neutron total scattering measurements to study structural evolution across an insulator-metal transition in BaTiO3-δ. Despite its significant impact on resistivity, slight oxygen reduction (δ=0.09) caused only a small disturbance on the local doublet splitting of Ti-O bond. This finding implies that local polarization is well preserved under marginal electric conduction. In the highly oxygen-deficient metallic state (δ=0.25), however, doublet splitting of the Ti-O bond became smeared. The smearing of the local Ti-O doublet is complemented with long-range structural analysis and demonstrates that the metallic conduction in the highly oxygen-reduced BaTiO3-δ is due to the appearance of nonferroelectric cubic lattice.

  3. The Evolution of Baryons in Cosmic Large Scale Structure

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  4. Synthesis and analysis in chemical evolution.

    NASA Astrophysics Data System (ADS)

    Ponnamperuma, C.

    In the first part the author examines the synthesis of the fundamental complex molecules of life (aminoacids and their polymerization to proteins, lipids, sugars, purines and pyrimidines, and nucleic acids) from simple molecules (H2O, CH4, NH3, HCN, CO2, etc.) under a variety of natural and laboratory conditions and sources of energy. In the second part the author examines the analysis of the data that confirm the early appearance of life on Earth and the presence of complex organic compounds in a variety of environments (carbonaceous chondritic meteorites, the atmospheres of Jupiter and Titan, interstellar space, etc.). All these results confirm the universal effectiveness of chemical evolution.

  5. Generalized Structured Component Analysis

    ERIC Educational Resources Information Center

    Hwang, Heungsun; Takane, Yoshio

    2004-01-01

    We propose an alternative method to partial least squares for path analysis with components, called generalized structured component analysis. The proposed method replaces factors by exact linear combinations of observed variables. It employs a well-defined least squares criterion to estimate model parameters. As a result, the proposed method…

  6. Structural evolution of small ruthenium cluster anions

    SciTech Connect

    Waldt, Eugen; Hehn, Anna-Sophia; Ahlrichs, Reinhart; Kappes, Manfred M.; Schooss, Detlef

    2015-01-14

    The structures of ruthenium cluster anions have been investigated using a combination of trapped ion electron diffraction and density functional theory computations in the size range from eight to twenty atoms. In this size range, three different structural motifs are found: Ru{sub 8}{sup −}–Ru{sub 12}{sup −} have simple cubic structures, Ru{sub 13}{sup −}–Ru{sub 16}{sup −} form double layered hexagonal structures, and larger clusters form close packed motifs. For Ru{sub 17}{sup −}, we find hexagonal close packed stacking, whereas octahedral structures occur for Ru{sub 18}{sup −}–Ru{sub 20}{sup −}. Our calculations also predict simple cubic structures for the smaller clusters Ru{sub 4}{sup −}–Ru{sub 7}{sup −}, which were not accessible to electron diffraction measurements.

  7. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-10-01

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions. {copyright} {ital 1997} {ital The American Physical Society}

  8. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-05-07

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions.

  9. Trichome structure and evolution in Neotropical lianas

    PubMed Central

    Nogueira, Anselmo; El Ottra, Juliana Hanna Leite; Guimarães, Elza; Machado, Silvia Rodrigues; Lohmann, Lúcia G.

    2013-01-01

    Background and Aims Trichomes are epidermal outgrowths generally associated with protection against herbivores and/or desiccation that are widely distributed from ferns to angiosperms. Patterns of topological variation and morphological evolution of trichomes are still scarce in the literature, preventing valid comparisons across taxa. This study integrates detailed morphoanatomical data and the evolutionary history of the tribe Bignonieae (Bignoniaceae) in order to gain a better understanding of current diversity and evolution of trichome types. Methods Two sampling schemes were used to characterize trichome types: (1) macromorphological characterization of all 105 species currently included in Bignonieae; and (2) micromorphological characterization of 16 selected species. Individual trichome morphotypes were coded as binary in each vegetative plant part, and trichome density and size were coded as multistate. Ancestral character state reconstructions were conducted using maximum likelihood (ML) assumptions. Key Results Two main functional trichome categories were found: non-glandular and glandular. In glandular trichomes, three morphotypes were recognized: peltate (Pg), stipitate (Sg) and patelliform/cupular (P/Cg) trichomes. Non-glandular trichomes were uniseriate, uni- or multicellular and simple or branched. Pg and P/Cg trichomes were multicellular and non-vascularized with three clearly distinct cell layers. Sg trichomes were multicellular, uniseriate and long-stalked. ML ancestral character state reconstructions suggested that the most recent common ancestor (MRCA) of Bignonieae probably had non-glandular, Pg and P/Cg trichomes, with each trichome type presenting alternative histories of appearance on the different plant parts. For example, the MRCA of Bignonieae probably had non-glandular trichomes on the stems, prophylls, petiole, petiolule and leaflet veins while P/Cg trichomes were restricted to leaflet blades. Sg trichomes were not present in the MRCA

  10. Analysis of Geological Structures

    NASA Astrophysics Data System (ADS)

    Price, Neville J.; Cosgrove, John W.

    1990-08-01

    A knowledge of structural geology is fundamental to understanding the processes by which the earth's crust has evolved. It is a subject of fundamental importance to students of geology, experienced field geologists and academic researchers as well as to petroleum and mining engineers. In contrast to many structural textbooks which dwell upon geometrical descriptions of geological structures, this book emphasises mechanical principles and the way in which they can be used to understand how and why a wide range of geological structures develop. Structures on all scales are considered but the emphasis of the book is on those that can be seen on the scale of hand specimen or outcrop. Drawing on their considerable teaching experience the authors present a coherent and lucid analysis of geological structures which will be welcomed by a wide variety of earth scientists.

  11. Probabilistic Structural Analysis Program

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.; Murthy, Pappu L. N.; Stefko, George L.; Riha, David S.; Thacker, Ben H.; Nagpal, Vinod K.; Mital, Subodh K.

    2010-01-01

    NASA/NESSUS 6.2c is a general-purpose, probabilistic analysis program that computes probability of failure and probabilistic sensitivity measures of engineered systems. Because NASA/NESSUS uses highly computationally efficient and accurate analysis techniques, probabilistic solutions can be obtained even for extremely large and complex models. Once the probabilistic response is quantified, the results can be used to support risk-informed decisions regarding reliability for safety-critical and one-of-a-kind systems, as well as for maintaining a level of quality while reducing manufacturing costs for larger-quantity products. NASA/NESSUS has been successfully applied to a diverse range of problems in aerospace, gas turbine engines, biomechanics, pipelines, defense, weaponry, and infrastructure. This program combines state-of-the-art probabilistic algorithms with general-purpose structural analysis and lifting methods to compute the probabilistic response and reliability of engineered structures. Uncertainties in load, material properties, geometry, boundary conditions, and initial conditions can be simulated. The structural analysis methods include non-linear finite-element methods, heat-transfer analysis, polymer/ceramic matrix composite analysis, monolithic (conventional metallic) materials life-prediction methodologies, boundary element methods, and user-written subroutines. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. NASA/NESSUS 6.2c is structured in a modular format with 15 elements.

  12. Evolution of extortion in structured populations

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games.

  13. Directed evolution and structural analysis of N-carbamoyl-D-amino acid amidohydrolase provide insights into recombinant protein solubility in Escherichia coli

    SciTech Connect

    Jiang, Shimin; Li, Chunhong; Zhang, Weiwen; Cai, Yuanheng; Yang, Yunlin; Yang, Sheng; Jiang, Weihong

    2007-03-15

    One of the greatest bottlenecks in producing recombinant proteins in Escherichia coli is that over-expressed target proteins are mostly present in an insoluble form without any biological activity. N-carbamoyl-D-amino-acid amidohydrolase (DCase) is an important enzyme involved in semi-synthesis of β-lactam antibiotics in industry. In this study, in order to determine the amino acid sites responsible for solubility in DCase, error-prone PCR and DNA shuffling techniques are applied to randomly mutate its encoding sequence, followed by an efficient screening based on structural complementation. Several mutants of DCase with reduced aggregation are isolated. Solubility tests of these mutants and several other mutants generated by site-directed mutagenesis indicate that three amino acid residues of DCase (A18, Y30 and K34) are related to the protein solubility in DCase. In silico structural modeling analyses further suggest that hydrophilicity and/or negative charge at these three residues may be responsible for the increased solubility of DCase proteins in E. coli. Based on the information, multiple engineering designated mutants were constructed by site-directed mutagenesis; among them, a triple mutant A18T/Y30N/K34E (named as DCase-M3) can be over-expressed in E. coli with up to 80% of DCase-M3 protein as soluble. DCase-M3 is purified to homogeneity and a comparative analysis with WT DCase demonstrates that DCase-M3 enzyme is similar to the native DCase in terms of its kinetic and thermodynamic properties. The study provides new insights on recombinant protein solubility in E. coli.

  14. Beneath the surface of giant planets: Evolution, structure, and composition

    NASA Astrophysics Data System (ADS)

    Kelly Miller, Neil L.

    This thesis is focused on utilizing the combination of giant exoplanet mass via radial velocity observations and radius via transit observations to study their structure and evolution. In Chapter 2, Giant planet thermal evolution models are coupled to tidal evolution dynamics, including orbital evolution and planet interior heating. Viable tidal evolution histories are explored to explain inflated radii of hot Jupiters. Tidal evolution is demonstrated to be a viable heating mechanism in some cases, but for other cases it can not explain the large radii. The thesis continues in Chapter 3 by exhibiting cases when the tidal-thermal evolution model, including energy-limited mass loss, can be used to infer interior properties and demonstrate a possible evolution history. Specifically, I utilize the thermal evolution models to examine planets CoRoT-2b, CoRoT-7b, and the Kepler-11 system. In Chapter 4, planets with lower incident irradiation are examined to infer the heavy element composition inside a range of planets. These planets don't appear to be significantly inflated by the unknown radius inflation mechanism, thus the mysterious mechanism can be ignored. It is shown that the heavy element mass inside these planets correlates with the metallicity of the star. The heavy element mass also correlates with the mass of the planet. However, the heavy element enrichment is inversely related to the mass of the planet. In the final chapter, I develop a mixing equation of state code for the MESA stellar evolution project. This code is developed with the intention of studying inhomogeneous thermal evolution of planets.

  15. Rapid Modeling and Analysis Tools: Evolution, Status, Needs and Directions

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.; Stone, Thomas J.; Ransom, Jonathan B. (Technical Monitor)

    2002-01-01

    Advanced aerospace systems are becoming increasingly more complex, and customers are demanding lower cost, higher performance, and high reliability. Increased demands are placed on the design engineers to collaborate and integrate design needs and objectives early in the design process to minimize risks that may occur later in the design development stage. High performance systems require better understanding of system sensitivities much earlier in the design process to meet these goals. The knowledge, skills, intuition, and experience of an individual design engineer will need to be extended significantly for the next generation of aerospace system designs. Then a collaborative effort involving the designer, rapid and reliable analysis tools and virtual experts will result in advanced aerospace systems that are safe, reliable, and efficient. This paper discusses the evolution, status, needs and directions for rapid modeling and analysis tools for structural analysis. First, the evolution of computerized design and analysis tools is briefly described. Next, the status of representative design and analysis tools is described along with a brief statement on their functionality. Then technology advancements to achieve rapid modeling and analysis are identified. Finally, potential future directions including possible prototype configurations are proposed.

  16. [Petrological Analysis of Astrophysical Dust Analog Evolution

    NASA Technical Reports Server (NTRS)

    Rietmeijer, Frans J. M.

    1997-01-01

    This project "Petrological analysis of astrophysical dust analog evolution" was initiated to try to understand the vapor phase condensation, and the nature of the reaction products, in circumstellar environments, such as the solar nebula 4,500 Myrs ago, and in the interstellar medium. Telescope-based infrared [IR] spectroscopy offers a broad-scale inventory of the various types of dust in these environments but no details on small-scale variations in terms of chemistry and morphology and petrological phase relationships. Vapor phase condensation in these environments is almost certainly a non-equilibrium process. The main challenge to this research was to document the nature of this process that, based on astrophysical observations, seems to yield compositionally consistent materials. This observation may suggest a predictable character during non-equilibrium condensation. These astrophysical environments include two chemically distinct, that is, oxygen-rich and carbon-rich environments. The former is characterized by silicates the latter by carbon-bearing solids. According to cosmological models of stellar evolution circumstellar dust accreted into protoplanets wherein thermal and/or aqueous processes will alter the dust under initially, non-equilibrium conditions.

  17. Structural stages and evolution of the Urals

    NASA Astrophysics Data System (ADS)

    Puchkov, V. N.

    2013-02-01

    Five main structural and historical stages are established in the territory of the Urals: 1) Archean-Paleoproterozoic, a time of formation of the Volgo-Uralia subcontinent and its amalgamation with the other blocks of the craton of Baltica; 2) Riphean-Vendian (Meso- and Neoproterozoic), а stage that was finished with formation of Timanides; 3) Paleozoic-Early Mesozoic stage, corresponding to the development of the Uralides; 4) Mid-Jurassic-to Miocene platform stage; 5) Pliocene-Quaternary neo-orogenic stage. In this paper stratigraphic data are discussed, schemes of the structural zonation are presented, and the problems of the structural geology and geodynamics of sedimentary and magmatic complexes are discussed in a chronological order. Ideologically, the paper is based on plate and plume tectonics, in their modern versions.

  18. Evolution of extortion in structured populations.

    PubMed

    Szolnoki, Attila; Perc, Matjaž

    2014-02-01

    Extortion strategies can dominate any opponent in an iterated prisoner's dilemma game. But if players are able to adopt the strategies performing better, extortion becomes widespread and evolutionary unstable. It may sometimes act as a catalyst for the evolution of cooperation, and it can also emerge in interactions between two populations, yet it is not the evolutionarily stable outcome. Here we revisit these results in the realm of spatial games. We find that pairwise imitation and birth-death dynamics return known evolutionary outcomes. Myopic best response strategy updating, on the other hand, reveals counterintuitive solutions. Defectors and extortioners coarsen spontaneously, which allows cooperators to prevail even at prohibitively high temptations to defect. Here extortion strategies play the role of a Trojan horse. They may emerge among defectors by chance, and once they do, cooperators become viable as well. These results are independent of the interaction topology, and they highlight the importance of coarsening, checkerboard ordering, and best response updating in evolutionary games. PMID:25353531

  19. Structure and evolution of Uranus and Neptune

    SciTech Connect

    Hubbard, W.B.; MacFarlane, J.J.

    1980-01-10

    We present three-layer interior models of Uranus and Neptune with central rocky cores, mantles of water, methane, and ammonia (the 'ices'), and outer envelopes primarily composed of hydrogen and helium. The models incorporate a new H/sub 2/O equation of state based on experimental data which is considerably 'softer' than previous H/sub 2/O equations of state. Corrections for interior temperature approx.5000 /sup 0/K are included in the models, and the thermal evolution of both planets is investigated using recent heat flow measurements. We find that evolutionary considerations are consistent with gravitational field data in supporting models with approximately solar abundances of 'ice' and 'rock.' Models with very low abundances of water, methane, and ammonia can be excluded. Evolutionary considerations indicate that initial temperatures and luminosities for Uranus and Neptune were not substantially higher than the present value. Both planets apparently have relatively small (approx.1--2 earth masses) hydrogen-helium envelopes, with Neptune's envelope smaller than Uranus'. A monotonic trend is evident among the Jovian planets: all have central rock-ice cores of approx.15 earth masses, but with hydrogen-helium envelopes which decrease in mass from Jupiter to Saturn to Uranus to Neptune.

  20. Evolution of atomic structure during nanoparticle formation

    PubMed Central

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; Christensen, Mogens; Bøjesen, Espen D.; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J. L.; Iversen, Bo B.

    2014-01-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  1. Evolution of atomic structure during nanoparticle formation.

    PubMed

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M Ø; Christensen, Mogens; Bøjesen, Espen D; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J L; Iversen, Bo B

    2014-05-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  2. Investigating the Structural Evolution of the Western Baltic

    NASA Astrophysics Data System (ADS)

    Hübscher, C.; Lykke-Anderson, H.; Hansen, M. Bak; Reicherter, K.

    2004-03-01

    The western Baltic Sea, located along the northern margin of the Central European Basin System (CEBS), is a world-class site for investigating the dynamics and stratigraphic evolution of a continental basin with marine geophysical data acquisition techniques. The universities of Aarhus and Hamburg have joined forces to investigate the post-Permian-to-recent structural evolution of the western Baltic, with special emphasis on neotectonic re-activation along major structural lineaments. Deep crustal structures of the CEBS are well established from previous studies. However, no systematic and localized research has yet been carried out to investigate the neotectonic activity in this region. In fact, the limited seismic resolution of previously available data prevented detailed research on Mesozoic and Cenozoic evolution or neotectonics.

  3. Dynamic structure evolution of time-dependent network

    NASA Astrophysics Data System (ADS)

    Zhang, Beibei; Zhou, Yadong; Xu, Xiaoyan; Wang, Dai; Guan, Xiaohong

    2016-08-01

    In this paper, we research the long-voided problem of formulating the time-dependent network structure evolution scheme, it focus not only on finding new emerging vertices in evolving communities and new emerging communities over the specified time range but also formulating the complex network structure evolution schematic. Previous approaches basically applied to community detection on time static networks and thus failed to consider the potentially crucial and useful information latently embedded in the dynamic structure evolution process of time-dependent network. To address these problems and to tackle the network non-scalability dilemma, we propose the dynamic hierarchical method for detecting and revealing structure evolution schematic of the time-dependent network. In practice and specificity, we propose an explicit hierarchical network evolution uncovering algorithm framework originated from and widely expanded from time-dependent and dynamic spectral optimization theory. Our method yields preferable results compared with previous approaches on a vast variety of test network data, including both real on-line networks and computer generated complex networks.

  4. Design Evolution and Analysis of the ITER Cryostat Support System

    NASA Astrophysics Data System (ADS)

    Xie, Han; Song, Yuntao; Wang, Songke

    2015-12-01

    The cryostat is a vacuum tight container enveloping the entire basic systems of the ITER tokamak machine, including a vacuum vessel, a superconducting magnet and thermal shield etc. It is evacuated to a pressure of 10-4 Pa to limit the heat transfer via gas conduction and convection to the cryogenically cooled components. Another important function of cryostat is to support all the loads from the tokamak to the concrete floor of the pit by its support system during different operational regimes and accident scenarios. This paper briefly presents the design evolution and associated analysis of the cryostat support system and the structural interface with the building.

  5. Evolution and Structure of the Internet

    NASA Astrophysics Data System (ADS)

    Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2007-09-01

    Preface; List of abbreviations; 1. A brief history of the Internet; 2. How the Internet works; 3. Measuring the global Internet; 4. The Internet's large-scale topology; 5. Modeling the Internet; 6. Internet robustness; 7. Virtual and social networks in the Internet; 8. Searching and walking on the Internet; 9. Epidemics in the Internet; 10. Beyond the Internet's skeleton: traffic and global performance; 11. Outlook; Appendix I: graph theory applied to topology analysis; Appendix II: interface resolution and router topology; Appendix III: numerical analysis of heavy-tailed distributions; Appendix IV: degree correlations; Appendix V: scale-free networks: scaling relations; Appendix VI: the SIR model of virus propagation; References; Index.

  6. Evolution and Structure of the Internet

    NASA Astrophysics Data System (ADS)

    Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2004-02-01

    Preface; List of abbreviations; 1. A brief history of the Internet; 2. How the Internet works; 3. Measuring the global Internet; 4. The Internet's large-scale topology; 5. Modeling the Internet; 6. Internet robustness; 7. Virtual and social networks in the Internet; 8. Searching and walking on the Internet; 9. Epidemics in the Internet; 10. Beyond the Internet's skeleton: traffic and global performance; 11. Outlook; Appendix I: graph theory applied to topology analysis; Appendix II: interface resolution and router topology; Appendix III: numerical analysis of heavy-tailed distributions; Appendix IV: degree correlations; Appendix V: scale-free networks: scaling relations; Appendix VI: the SIR model of virus propagation; References; Index.

  7. The high temperature structural evolution of hafnia

    NASA Astrophysics Data System (ADS)

    Haggerty, Ryan Paul

    The transformations of HfO2 are often described as analogous with the transformations in ZrO2 because of the similar crystal structures; however the phase transformations in HfO2 occur at higher temperatures. Even though this phase transformation has been extensively studied in ZrO2, the respective transformation in HfO2 is relatively unstudied and the properties that are reported are inconsistent. Much of the difficulty associated with studying HfO2 is related to the high temperatures needed and the sensitivity of the crystal to the environmental partial pressure of O2. HfO2 is expected to be capable of producing the same level of transformation toughening as ZrO2 at temperatures beyond 1000°C, the thermodynamic limit for toughened ZrO2. Despite significant effort the toughening acquired has not met with expectation. By providing information on the structure of HfO2 as it undergoes transformation, this study makes a significant step towards solving this problem. Significant advancements in experimentation have enabled a systematic study of the structure of HfO2 in its monoclinic and tetragonal phases in air. Using a quadrupole lamp furnace and a novel curved image plate detector the structure of HfO2 and ZrO 2 have been characterized by high temperature x-ray diffraction. The structural information provided by these experiments allows the properties of the transformation to be further investigated. Using phenomenological theory of martensite crystallography, the strain associated with the transformation from the tetragonal to the monoclinic phase has been described and provides insight into the lack of transformation toughening found in HfO2. Further characterization includes determination of the transformation temperature in air, the change in volume associated with the transformation and the temperature hysteresis of the transformation. In addition to transformation properties, the thermal expansion of HfO2 and ZrO2 has been thoroughly described as a function

  8. Structural analysis of glucans

    PubMed Central

    Novak, Miroslav

    2014-01-01

    Glucans are most widespread polysaccharides in the nature. There is a large diversity in their molecular weight and configuration depending on the original source. According to the anomeric structure of glucose units it is possible to distinguish linear and branched α-, β- as well as mixed α,β-glucans with various glycoside bond positions and molecular masses. Isolation of glucans from raw sources needs removal of ballast compounds including proteins, lipids, polyphenols and other polysaccharides. Purity control of glucan fractions is necessary to evaluate the isolation and purification steps; more rigorous structural analyses of purified polysaccharides are required to clarify their structure. A set of spectroscopic, chemical and separation methods are used for this purpose. Among them, NMR spectroscopy is known as a powerful tool in structural analysis of glucans both in solution and in solid state. Along with chemolytic methods [methylation analysis (MA), periodate oxidation, partial chemical or enzymatic hydrolysis, etc.], correlation NMR experiments are able to determine the exact structure of tested polysaccharides. Vibration spectroscopic methods (FTIR, Raman) are sensitive to anomeric structure of glucans and can be used for purity control as well. Molecular weight distribution, homogeneity and branching of glucans can be estimated by size-exclusion chromatography (SEC), laser light scattering (LLS) and viscometry. PMID:25332993

  9. COI Structural Analysis Presentation

    NASA Technical Reports Server (NTRS)

    Cline, Todd; Stahl, H. Philip (Technical Monitor)

    2001-01-01

    This report discusses the structural analysis of the Next Generation Space Telescope Mirror System Demonstrator (NMSD) developed by Composite Optics Incorporated (COI) in support of the Next Generation Space Telescope (NGST) project. The mirror was submitted to Marshall Space Flight Center (MSFC) for cryogenic testing and evaluation. Once at MSFC, the mirror was lowered to approximately 40 K and the optical surface distortions were measured. Alongside this experiment, an analytical model was developed and used to compare to the test results. A NASTRAN finite element model was provided by COI and a thermal model was developed from it. Using the thermal model, steady state nodal temperatures were calculated based on the predicted environment of the large cryogenic test chamber at MSFC. This temperature distribution was applied in the structural analysis to solve for the deflections of the optical surface. Finally, these deflections were submitted for optical analysis and comparison to the interferometer test data.

  10. Retirement and the Evolution of Pension Structure

    ERIC Educational Resources Information Center

    Friedberg, Leora; Webb, Anthony

    2005-01-01

    A comparative analysis of defined benefit pension plans that were more common before 1980s and the defined contribution plans is presented. It is observed that defined benefit pension plans offered age related incentives thereby encouraging people to retire earlier. In contrast, defined contribution plans encourage people to continue with jobs…

  11. Late Paleozoic structural evolution of Permian basin

    SciTech Connect

    Ewing, T.E.

    1984-04-01

    The southern Permian basin is underlain by the NNW-trending Central Basin disturbed belt of Wolfcamp age (Lower Permian), the deep Delaware basin to its west, and the shallower Midland basin to its eat. The disturbed belt is highly segmented with zones of left-lateral offset. Major segments from south to north are: the Puckett-Grey Ranch zone; the Fort Stockton uplift; the Monahans transverse zone; the Andector ridges and the Eunice ridge; the Hobbs transverse zone; and the Tatum ridges, which abut the broad Roosevelt uplift to the north. The disturbed belt may have originated along rift zones of either Precambrian or Cambrian age. The extent of Lower and Middle Pennsylvanian deformation is unclear; much of the Val Verde basin-Ozona arch structure may have formed then. The main Wolfcamp deformation over thrust the West Texas crustal block against the Delaware block, with local denudation of the uplifted edge and eastward-directed backthrusting into the Midland basin. Latter in the Permian, the area was the center of a subcontinental bowl of subsidence - the Permian basin proper. The disturbed belt formed a pedestal for the carbonate accumulations which created the Central Basin platform. The major pre-Permian reservoirs of the Permian basin lie in large structural and unconformity-bounded traps on uplift ridges and domes. Further work on the regional structural style may help to predict fracture trends, to assess the timing of oil migration, and to evaluate intrareservoir variations in the overlying Permian giant oil fields.

  12. Modelling the Evolution of Social Structure

    PubMed Central

    Sutcliffe, A. G.; Dunbar, R. I. M.; Wang, D.

    2016-01-01

    Although simple social structures are more common in animal societies, some taxa (mainly mammals) have complex, multi-level social systems, in which the levels reflect differential association. We develop a simulation model to explore the conditions under which multi-level social systems of this kind evolve. Our model focuses on the evolutionary trade-offs between foraging and social interaction, and explores the impact of alternative strategies for distributing social interaction, with fitness criteria for wellbeing, alliance formation, risk, stress and access to food resources that reward social strategies differentially. The results suggest that multi-level social structures characterised by a few strong relationships, more medium ties and large numbers of weak ties emerge only in a small part of the overall fitness landscape, namely where there are significant fitness benefits from wellbeing and alliance formation and there are high levels of social interaction. In contrast, ‘favour-the-few’ strategies are more competitive under a wide range of fitness conditions, including those producing homogeneous, single-level societies of the kind found in many birds and mammals. The simulations suggest that the development of complex, multi-level social structures of the kind found in many primates (including humans) depends on a capacity for high investment in social time, preferential social interaction strategies, high mortality risk and/or differential reproduction. These conditions are characteristic of only a few mammalian taxa. PMID:27427758

  13. Modelling the Evolution of Social Structure.

    PubMed

    Sutcliffe, A G; Dunbar, R I M; Wang, D

    2016-01-01

    Although simple social structures are more common in animal societies, some taxa (mainly mammals) have complex, multi-level social systems, in which the levels reflect differential association. We develop a simulation model to explore the conditions under which multi-level social systems of this kind evolve. Our model focuses on the evolutionary trade-offs between foraging and social interaction, and explores the impact of alternative strategies for distributing social interaction, with fitness criteria for wellbeing, alliance formation, risk, stress and access to food resources that reward social strategies differentially. The results suggest that multi-level social structures characterised by a few strong relationships, more medium ties and large numbers of weak ties emerge only in a small part of the overall fitness landscape, namely where there are significant fitness benefits from wellbeing and alliance formation and there are high levels of social interaction. In contrast, 'favour-the-few' strategies are more competitive under a wide range of fitness conditions, including those producing homogeneous, single-level societies of the kind found in many birds and mammals. The simulations suggest that the development of complex, multi-level social structures of the kind found in many primates (including humans) depends on a capacity for high investment in social time, preferential social interaction strategies, high mortality risk and/or differential reproduction. These conditions are characteristic of only a few mammalian taxa. PMID:27427758

  14. Model of evolution of surface grain structure under ion bombardment

    SciTech Connect

    Knyazeva, Anna G.; Kryukova, Olga N.

    2014-11-14

    Diffusion and chemical reactions in multicomponent systems play an important role in numerous technology applications. For example, surface treatment of materials and coatings by particle beam leads to chemical composition and grain structure change. To investigate the thermal-diffusion and chemical processes affecting the evolution of surface structure, the mathematical modeling is efficient addition to experiment. In this paper two-dimensional model is discussed to describe the evolution of titanium nitride coating on the iron substrate under implantation of boron and carbon. The equation for diffusion fluxes and reaction rate are obtained using Gibbs energy expansion into series with respect to concentration and their gradients.

  15. Structural evolution in the electric utility industry

    SciTech Connect

    Kahn, E.P. )

    1990-01-04

    This article anticipates (and discusses) the changes in structure, planning, and operations that will be thrust upon the electric utility industry by the emergency of competition, which is assumed to have reached nearly irreversible momentum. Some of them present problems for solution. The significance of others is uncertain from a public interest standpoint, or that of cost and reliability of service for consumers. The author also considers the possibility that the decentralization which accompanies increased competition initially will ultimately eventuate in a greater degree of consolidation in this industry.

  16. Design oriented structural analysis

    NASA Technical Reports Server (NTRS)

    Giles, Gary L.

    1994-01-01

    Desirable characteristics and benefits of design oriented analysis methods are described and illustrated by presenting a synoptic description of the development and uses of the Equivalent Laminated Plate Solution (ELAPS) computer code. ELAPS is a design oriented structural analysis method which is intended for use in the early design of aircraft wing structures. Model preparation is minimized by using a few large plate segments to model the wing box structure. Computational efficiency is achieved by using a limited number of global displacement functions that encompass all segments over the wing planform. Coupling with other codes is facilitated since the output quantities such as deflections and stresses are calculated as continuous functions over the plate segments. Various aspects of the ELAPS development are discussed including the analytical formulation, verification of results by comparison with finite element analysis results, coupling with other codes, and calculation of sensitivity derivatives. The effectiveness of ELAPS for multidisciplinary design application is illustrated by describing its use in design studies of high speed civil transport wing structures.

  17. EVOLUTION OF FAST MAGNETOACOUSTIC PULSES IN RANDOMLY STRUCTURED CORONAL PLASMAS

    SciTech Connect

    Yuan, D.; Li, B.; Pascoe, D. J.; Nakariakov, V. M.; Keppens, R. E-mail: bbl@sdu.edu.cn

    2015-02-01

    We investigate the evolution of fast magnetoacoustic pulses in randomly structured plasmas, in the context of large-scale propagating waves in the solar atmosphere. We perform one-dimensional numerical simulations of fast wave pulses propagating perpendicular to a constant magnetic field in a low-β plasma with a random density profile across the field. Both linear and nonlinear regimes are considered. We study how the evolution of the pulse amplitude and width depends on their initial values and the parameters of the random structuring. Acting as a dispersive medium, a randomly structured plasma causes amplitude attenuation and width broadening of the fast wave pulses. After the passage of the main pulse, secondary propagating and standing fast waves appear. Width evolution of both linear and nonlinear pulses can be well approximated by linear functions; however, narrow pulses may have zero or negative broadening. This arises because narrow pulses are prone to splitting, while broad pulses usually deviate less from their initial Gaussian shape and form ripple structures on top of the main pulse. Linear pulses decay at an almost constant rate, while nonlinear pulses decay exponentially. A pulse interacts most efficiently with a random medium with a correlation length of about half of the initial pulse width. This detailed model of fast wave pulses propagating in highly structured media substantiates the interpretation of EIT waves as fast magnetoacoustic waves. Evolution of a fast pulse provides us with a novel method to diagnose the sub-resolution filamentation of the solar atmosphere.

  18. The structure of photosystem I and evolution of photosynthesis.

    PubMed

    Nelson, Nathan; Ben-Shem, Adam

    2005-09-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on earth. The primary step in this process--the conversion of sunlight into chemical energy--is driven by four multi-subunit membrane protein complexes named photosystem I, photosystem II, cytochrome b(6)f complex and F-ATPase. Photosystem I generates the most negative redox potential in nature and thus largely determines the global amount of enthalpy in living systems. The recent structural determination of PSI complexes from cyanobacteria and plants sheds light on the evolutionary forces that shaped oxygenic photosynthesis. The fortuitous formation of our solar system in a space plentiful of elements, our distance from the sun and the long time of uninterrupted evolution enabled the perfection of photosynthesis and the evolution of advanced organisms. The available structural information complements the knowledge gained from genomic and proteomic data to illustrate a more precise scenario for the evolution of life systems on earth. PMID:16108066

  19. Time-resolved evolution of coherent structures in turbulent channels

    NASA Astrophysics Data System (ADS)

    Lozano-Duran, Adrian; Jimenez, Javier

    2012-11-01

    The temporal evolution of vortex clusters and of the structures responsible for the momentum transfer in turbulent channels at Reτ = 950 , 2000 and 4000 are studied using DNS sequences with temporal separations among fields short enough for individual structures to be tracked. From the geometric intersection of structures in consecutive fields we build temporal connection graphs of all the objects and define main and secondary branches in a way that each branch represents the temporal evolution of one coherent structure. A family of evolutions is found with self-similar sizes and lifetimes that can be born at any height with respect to the wall, although the probability increases close to it. Especial attention is paid to the wall-normal displacement of the structures. Sweeps tend to go towards the wall whereas ejections move away from it. In all the cases, the vertical velocity is close to uτ and the wall-normal displacement is proportional to the lifetime of the structures and to their sizes. Finally, direct and inverse physical cascades are defined, associated with the process of splitting and merging among structures. The direct cascade predominates, but both directions are roughly comparable. Funded by ERC, CICYT and Spanish Ministry of Science.

  20. Structure, Function, and Evolution of Rice Centromeres

    SciTech Connect

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  1. Structural evolution of Colloidal Gels under Flow

    NASA Astrophysics Data System (ADS)

    Boromand, Arman; Maia, Joao; Jamali, Safa

    Colloidal suspensions are ubiquitous in different industrial applications ranging from cosmetic and food industries to soft robotics and aerospace. Owing to the fact that mechanical properties of colloidal gels are controlled by its microstructure and network topology, we trace the particles in the networks formed under different attraction potentials and try to find a universal behavior in yielding of colloidal gels. Many authors have implemented different simulation techniques such as molecular dynamics (MD) and Brownian dynamics (BD) to capture better picture during phase separation and yielding mechanism in colloidal system with short-ranged attractive force. However, BD neglects multi-body hydrodynamic interactions (HI) which are believed to be responsible for the second yielding of colloidal gels. We envision using dissipative particle dynamics (DPD) with modified depletion potential and hydrodynamic interactions, as a coarse-grain model, can provide a robust simulation package to address the gel formation process and yielding in short ranged-attractive colloidal systems. The behavior of colloidal gels with different attraction potentials under flow is examined and structural fingerprints of yielding in these systems will be discussed.

  2. Plant enolase: gene structure, expression, and evolution.

    PubMed Central

    Van der Straeten, D; Rodrigues-Pousada, R A; Goodman, H M; Van Montagu, M

    1991-01-01

    Enolase genes were cloned from tomato and Arabidopsis. Comparison of their primary structures with other enolases revealed a remarkable degree of conservation, except for the presence of an insertion of 5 amino acids unique to plant enolases. Expression of the enolase genes was studied under various conditions. Under normal growth conditions, steady-state messenger and enzyme activity levels were significantly higher in roots than in green tissue. Large inductions of mRNA, accompanied by a moderate increase in enzyme activity, were obtained by an artificial ripening treatment in tomato fruits. However, there was little effect of anaerobiosis on the abundance of enolase messenger. In heat shock conditions, no induction of enolase mRNA was observed. We also present evidence that, at least in Arabidopsis, the hypothesis that there exists a complete set of glycolytic enzymes in the chloroplast is not valid, and we propose instead the occurrence of a substrate shuttle in Arabidopsis chloroplasts for termination of the glycolytic cycle. PMID:1841726

  3. Computational engine structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Johns, R. H.

    1986-01-01

    A significant research activity at the NASA Lewis Research Center is the computational simulation of complex multidisciplinary engine structural problems. This simulation is performed using computational engine structural analysis (CESA) which consists of integrated multidisciplinary computer codes in conjunction with computer post-processing for problem-specific application. A variety of the computational simulations of specific cases are described in some detail in this paper. These case studies include: (1) aeroelastic behavior of bladed rotors, (2) high velocity impact of fan blades, (3) blade-loss transient response, (4) rotor/stator/squeeze-film/bearing interaction, (5) blade-fragment/rotor-burst containment, and (6) structural behavior of advanced swept turboprops. These representative case studies are selected to demonstrate the breath of the problems analyzed and the role of the computer including post-processing and graphical display of voluminous output data.

  4. The relativistic equations of stellar structure and evolution

    NASA Technical Reports Server (NTRS)

    Thorne, K. S.

    1975-01-01

    The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. A general relativistic version of the mixing-length formalism for convection is presented. It is argued that in work on spherical systems, general relativity theorists have identified the wrong quantity as total mass-energy inside radius r.

  5. Population structure and the rate of evolution.

    PubMed

    Wei, Xinzhu; Zhao, Lei; Lascoux, Martin; Waxman, David

    2015-01-21

    The way population size, population structure (with migration), and spatially dependent selection (where there is no globally optimal allele), combine to affect the substitution rate is poorly understood. Here, we consider a two patch model where mutant alleles are beneficial in one patch and deleterious in the other patch. We assume that the spatial average of selection on mutant alleles is zero. We take each patch to maintain a finite number of N adults each generation, hence random genetic drift can independently occur in each patch. We show that the principal way the population size, N, when large, affects the substitution rate, R∞, is through its dependence on two composite parameters. These are the scaled migration rate M (∝ population size × migration rate), and the scaled selection intensity S (∝population size × beneficial effect of a mutant). Any relation between S and M that arises for ecological/evolutionary reasons can strongly influence the way the substitution rate, R∞, depends on the population size, N. In the simplest situation, both M and S are proportional to N, and this is shown to lead to R∞ increasing with N when S is not large. The behaviour, that R∞ increases with N, is not inevitable; a more complex relation between S and M can lead to the opposite or other behaviours. In particular, let us assume that dM/dN is positive, as would occur if the migration rate were constant, S is not large, and S depends on M (i.e., S=S(M)). We then find that if S(M) satisfies S(M)>((1+M)/1+2M)S(0) then the substitution rate, R∞, increases with N, but if S(M)<((1+M)/1+2M)S(0) then R∞ decreases with N. PMID:25451534

  6. The structure and evolution of plankton communities

    NASA Astrophysics Data System (ADS)

    Longhurst, Alan R.

    New understanding of the circulation of ancient oceans is not yet matched by progress in our understanding of their pelagic ecology, though it was the planktonic ecosystems that generated our offshore oil and gas reserves. Can we assume that present-day models of ecosystem function are also valid for ancient seas? This question is addressed by a study of over 4000 plankton samples to derive a comprehensive, global description of zooplankton community structure in modern oceans: this shows that copepods form only 50% of the biomass of all plankton, ranging from 70% in polar to 35% in tropical seas. Comparable figures are derived from 14 other taxonomic categories of zooplankton. For trophic groupings, the data indicate globally: geletinous predators - 14%; gelatinous herbivores - 4%; raptorial predators - 33%; macrofiltering herbivores - 20%; macrofiltering omnivores - 25%; and detritivores - 3%. A simple, idealized model for the modern pelagic ecosystem is derived from these percentages which indicates that metazooplankton are not the most important consumers of pico- and nano-plankton production which itself probably constitutes 90% of primary production in warm oceans. This model is then compared with candidate life-forms available in Palaeozoic and Mesozoic oceans to determine to what extent it is also valid for ancient ecosystems: it is concluded that it is probably unnecessary to postulate models fundamentally differing from it in order to accommodate the life-forms, both protozoic and metazoic, known to have populated ancient seas. Remarkably few life-forms have existed which cannot be paralleled in the modern ocean, which contains remarkably few life-forms which cannot be paralleled in the Palaeozoic ocean. As a first assumption, then, it is reasonable to assume that energy pathways were similar in ancient oceans to those we study today.

  7. Transregional zones of concentrated deformation: Structure, evolution, and comparative geodynamics

    NASA Astrophysics Data System (ADS)

    Leonov, M. G.

    2016-03-01

    The comparative tectonic characterization of transregional linear structures (zones of concentrated deformations) is given for the Pieniny Klippen Belt, the Main Mongolian Lineament, and the transregional Alpine Fault Zone. They represent significant geodynamic elements of the Earth's crust, which separate large crustal segments and reflect their interaction in time and space. The main features of the structure, evolution, and geodynamics inherent to zones of concentrated deformations are described. It is shown that the similarity of their outlines, morphology, internal structure, and kinematic features is combined with a clearly distinct structural position, set of rock associations, formation mechanism, and their role in the origin of mobile belts.

  8. Structural analysis and evolution of the Hadong-Sancheong-Hwagae area in the Yeongnam massif, Korea: a NS-trend tectonic frame in the Korean Peninsula

    NASA Astrophysics Data System (ADS)

    Deok-Seon, Lee; Ji-Hoon, Kang

    2016-04-01

    The Hadong-Sancheong-Hwagae area in the Jirisan province of the Yeongnam massif, Korea, is mainly composed of Precambrian Hadong anorthosite complex (HAC), Precambrian Jirisan metamorphic rock complex (JMRC), Jurassic˜Triassic granitoids which intrude them, and Cretaceous sedimentary rocks which unconformably cover them. Lithofacies distribution and tectonic frame of the Precambrian constituent rocks mainly show a NS trend, unlike a general NE trend of those in the Korean Peninsula. To unravel the geological structures associated with the NS-trend tectonic frame which was built in the HAC and JMRC, we researched the structural characteristics of each deformation phase based on the geometric and kinematic features and the forming sequence of rock structures of the multi-deformed HAC and JMRC. The results indicate that the pre-Late Paleozoic geological structures of this area were formed at least through the following three times of ductile deformation phases. The D1 deformation happened due to the large-scale top-to-the SE shearing, and formed sheath or A-type folds and a regional NE trend of tectonic frame in the HAC and JMRC. The D2 deformation occurred under the EW-directed tectonic compression, and formed a regional NS trend of active and passive folds and Hadong ductile shear zone over 2.3˜1.4 km width, and transposed most of D1 tectonic frame into D1-2 composite tectonic frame. The extensive Hadong shear zone, which was formed in the mylonitization process accompanying the passive folding, was persistently developed along the eastern boundary of HAC and JMRC which corresponds to a limb of passive fold on a geological map scale. It produced a very strong mylonitic structure and stretching lineation. The NE-trend D1 structural elements were mainly reoriented into NS trend by the powerful active and passive folding. The D3 deformation occurred under the NS-trend tectonic compression environment, and formed EW-trend kink or open folds, and partially rearranged

  9. Structural Analysis Made 'NESSUSary'

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Everywhere you look, chances are something that was designed and tested by a computer will be in plain view. Computers are now utilized to design and test just about everything imaginable, from automobiles and airplanes to bridges and boats, and elevators and escalators to streets and skyscrapers. Computer-design engineering first emerged in the 1970s, in the automobile and aerospace industries. Since computers were in their infancy, however, architects and engineers during the time were limited to producing only designs similar to hand-drafted drawings. (At the end of 1970s, a typical computer-aided design system was a 16-bit minicomputer with a price tag of $125,000.) Eventually, computers became more affordable and related software became more sophisticated, offering designers the "bells and whistles" to go beyond the limits of basic drafting and rendering, and venture into more skillful applications. One of the major advancements was the ability to test the objects being designed for the probability of failure. This advancement was especially important for the aerospace industry, where complicated and expensive structures are designed. The ability to perform reliability and risk assessment without using extensive hardware testing is critical to design and certification. In 1984, NASA initiated the Probabilistic Structural Analysis Methods (PSAM) project at Glenn Research Center to develop analysis methods and computer programs for the probabilistic structural analysis of select engine components for current Space Shuttle and future space propulsion systems. NASA envisioned that these methods and computational tools would play a critical role in establishing increased system performance and durability, and assist in structural system qualification and certification. Not only was the PSAM project beneficial to aerospace, it paved the way for a commercial risk- probability tool that is evaluating risks in diverse, down- to-Earth application

  10. Evolution in vitro: analysis of a lineage of ribozymes

    NASA Technical Reports Server (NTRS)

    Lehman, N.; Joyce, G. F.

    1993-01-01

    Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.

  11. Fault Wear and Friction Evolution: Experimental Analysis

    NASA Astrophysics Data System (ADS)

    Boneh, Y.; Chang, J. C.; Lockner, D. A.; Reches, Z.

    2011-12-01

    -body' structure that acts to lubricate the fault (Reches & Lockner, 2010). The steady-state stage is characterized by (1) relatively low wear-rate (approximately 10% of running-in wear-rate) and (2) quasi-constant friction coefficient. These observations suggest only small changes in the gouge layer in term of thickness (100 to 200 microns) and strength in this final stage. The present study indicates that (1) wear by plowing and asperity failure initiate early, during the first few millimeters of slip; and (2) wear and associated gouge formation appear as the controlling factors of friction evolution and fault weakening.

  12. THE STRUCTURE, ORIGIN, AND EVOLUTION OF INTERSTELLAR HYDROCARBON GRAINS

    SciTech Connect

    Chiar, J. E.; Ricca, A.; Tielens, A. G. G. M.; Adamson, A. J. E-mail: Alessandra.Ricca@1.nasa.gov E-mail: aadamson@gemini.edu

    2013-06-10

    Many materials have been considered for the carrier of the hydrocarbon absorption bands observed in the diffuse interstellar medium (ISM). In order to refine the model for ISM hydrocarbon grains, we analyze the observed aromatic (3.28, 6.2 {mu}m) and aliphatic (3.4 {mu}m) hydrocarbon absorption features in the diffuse ISM along the line of sight toward the Galactic center Quintuplet Cluster. Observationally, sp {sup 2} bonds can be measured in astronomical spectra using the 6.2 {mu}m CC aromatic stretch feature, whereas the 3.4 {mu}m aliphatic feature can be used to quantify the fraction of sp {sup 3} bonds. The fractional abundance of these components allows us to place the Galactic diffuse ISM hydrocarbons on a ternary phase diagram. We conclude that the Galactic hydrocarbon dust has, on average, a low H/C ratio and sp {sup 3} content and is highly aromatic. We have placed the results of our analysis within the context of the evolution of carbon dust in the ISM. We argue that interstellar carbon dust consists of a large core of aromatic carbon surrounded by a thin mantle of hydrogenated amorphous carbon (a-C:H), a structure that is a natural consequence of the processing of stardust grains in the ISM.

  13. Structured Data in Structural Analysis Software

    NASA Technical Reports Server (NTRS)

    Kunz, Donald L.; Hopkins, Stewart

    1987-01-01

    This paper discusses the use of computer data structures in finite-element structural analysis programs. A number of data structure types that have been shown to be useful in such programs are introduced and described. A simple finite-element model is used to demonstrate how the given set of data structure types naturally lend themselves to developing software for the model. Different methods of implementing data structures in the context of a program are discussed.

  14. Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.

    PubMed

    van der Sluis, Eli O; Bauerschmitt, Heike; Becker, Thomas; Mielke, Thorsten; Frauenfeld, Jens; Berninghausen, Otto; Neupert, Walter; Herrmann, Johannes M; Beckmann, Roland

    2015-05-01

    The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic

  15. Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes

    PubMed Central

    van der Sluis, Eli O.; Bauerschmitt, Heike; Becker, Thomas; Mielke, Thorsten; Frauenfeld, Jens; Berninghausen, Otto; Neupert, Walter; Herrmann, Johannes M.; Beckmann, Roland

    2015-01-01

    The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic

  16. Time evolution of a single, quiet-Sun magnetic structure

    NASA Astrophysics Data System (ADS)

    Requerey, Iker S.; Bonet, José Antonio; Solanki, Sami K.; Bellot Rubio, L. R.; Del Toro Iniesta, Jose Carlos

    Isolated flux tubes are considered to be fundamental magnetic building blocks of the solar photosphere. Their formation is usually attributed to the concentration of magnetic field to kG strengths by the convective instability mechanism. However, the small size of the magnetic elements in quiet-Sun areas has prevented this scenario from being studied in fully resolved structures. Here we report on the formation and subsequent evolution of a photospheric magnetic flux tube, observed in the quiet Sun with unprecedented spatial resolution (0. ('') 15 - 0. ('') 18) and high temporal cadence (33 s). The observations were acquired by the Imaging Magnetograph Experiment (IMaX) aboard the textsc{Sunrise} balloon-borne solar observatory. The equipartition field strength magnetic element is reached from the merging of several magnetic flux patches in a mesogranule-sized sink. The magnetic structure is then further intensified to kG field strengths by convective collapse and granular compression. The fine structure found within the flux concentration reveal that the scenario is more complex than a canonical flux tube model. After a subsequent weakening process, the field is further intensified to kG strengths. Seen as a whole, the evolution of the magnetic structure is compatible with oscillations in all basic physical quantities. A discussion on whether this evolution fits to the current theoretical descriptions is also presented.

  17. Structural evolution and optoelectronic applications of multilayer silicene

    NASA Astrophysics Data System (ADS)

    Guo, Zhi-Xin; Zhang, Yue-Yu; Xiang, Hongjun; Gong, Xin-Gao; Oshiyama, Atsushi

    2015-11-01

    Despite the recent progress on two-dimensional multilayer materials (2DMMs) with weak interlayer interactions, the investigation of 2DMMs with strong interlayer interactions is far from sufficient. Here, we report on first-principles calculations that clarify the structural evolution and optoelectronic properties of such a 2DMM, multilayer silicene. With our global optimization algorithm, we discover the existence of rich dynamically stable multilayer silicene phases, whose stability is closely related to the extent of s p3 hybridization that can be evaluated by average bonds and effective bond angles. Stable Si(111) surface structures are obtained when the silicene thickness gets up to four, showing the critical thickness for a structural evolution. We also find that multilayer silicene with π -bonded surfaces presents outstanding optoelectronic properties for solar cells and optical fiber communications due to the incorporation of s p2 -type bonds in the s p3 -type bond dominated system. This study helps to complete the picture of the structure and related property evolution of 2DMMs with strong interlayer interactions.

  18. Structural Analysis of Biodiversity

    PubMed Central

    Sirovich, Lawrence; Stoeckle, Mark Y.; Zhang, Yu

    2010-01-01

    Large, recently-available genomic databases cover a wide range of life forms, suggesting opportunity for insights into genetic structure of biodiversity. In this study we refine our recently-described technique using indicator vectors to analyze and visualize nucleotide sequences. The indicator vector approach generates correlation matrices, dubbed Klee diagrams, which represent a novel way of assembling and viewing large genomic datasets. To explore its potential utility, here we apply the improved algorithm to a collection of almost 17000 DNA barcode sequences covering 12 widely-separated animal taxa, demonstrating that indicator vectors for classification gave correct assignment in all 11000 test cases. Indicator vector analysis revealed discontinuities corresponding to species- and higher-level taxonomic divisions, suggesting an efficient approach to classification of organisms from poorly-studied groups. As compared to standard distance metrics, indicator vectors preserve diagnostic character probabilities, enable automated classification of test sequences, and generate high-information density single-page displays. These results support application of indicator vectors for comparative analysis of large nucleotide data sets and raise prospect of gaining insight into broad-scale patterns in the genetic structure of biodiversity. PMID:20195371

  19. Effect of PE on the structural evolution of iPP : analysis of a series of iPP-PE copolymers

    NASA Astrophysics Data System (ADS)

    Tenneti, Kishore; Tso, Chung; Li, Christopher

    2005-03-01

    The three different morphological forms of isotactic polypropylene (iPP), namely alpha, beta, and gamma, are well established. Alpha is the most common crystal phase while beta is metastable. The gamma form of iPP often exists as the minor component, intermixed with the alpha phase, during crystallization of copolymers at atmospheric pressures. A series of iPP-Polyethylene (PE) copolymers with varying percentages of PE have been investigated. Thermal and x-ray analysis reveal that as the PE content increases from 0 to 5 percent, gamma became the dominant phase. Single crystal morphology of the iPP-PE copolymers have been studied using TEM, SEM and AFM. The signature of alpha phase, the cross-hatch morphology, was observed in all the samples. Gamma single crystals were clearly observed like a ribbon shape and the center of the ribbon consisted of alpha lath. Fractal-like growth was also observed, presumably due to the thermal degradation of the polymer.

  20. Data structures for parsimony correlation and biosequence co-evolution.

    PubMed

    Hochberg, Robert; Milam, Treena Larrew

    2014-04-01

    We give an algorithm for discovering co-evolution in biosequences from a dataset consisting of aligned data and a phylogeny. The method correlates vectors of parsimony scores on the edges of a graph, averaged over all optimally parsimonious reconstructions of the data. We describe an efficient data structure, and a preprocessing step that allows for rapid, interactive computation of many correlation scores, at the expense of storage space. PMID:19563266

  1. Modeling Structural and Genomic Constraints in the Evolution of Proteins

    NASA Astrophysics Data System (ADS)

    Bastolla, Ugo; Porto, Markus

    Macromolecules influence the phenotype of the organism where they are expressed through their function, and in particular through their interactions. Nevertheless, it is very difficult to computationally predict protein function and interactions. Moreover, only a few residues take part in them. For these reasons, models of molecular evolution usually represent folded macromolecules such as RNA or proteins and identify the function of the molecule with the folded structure, whose stability determines the modeled fitness.

  2. Protoplanetary Disk Structure with Grain Evolution: The ANDES Model

    NASA Astrophysics Data System (ADS)

    Akimkin, V.; Zhukovska, S.; Wiebe, D.; Semenov, D.; Pavlyuchenkov, Ya.; Vasyunin, A.; Birnstiel, T.; Henning, Th.

    2013-03-01

    We present a self-consistent model of a protoplanetary disk: "ANDES" ("AccretioN disk with Dust Evolution and Sedimentation"). ANDES is based on a flexible and extendable modular structure that includes (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains onto the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R <~ 50 AU) and lower in the outer disk (R >~ 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO2, NH2CN, HNO, H2O, HCOOH, HCN, and CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.

  3. PROTOPLANETARY DISK STRUCTURE WITH GRAIN EVOLUTION: THE ANDES MODEL

    SciTech Connect

    Akimkin, V.; Wiebe, D.; Pavlyuchenkov, Ya.; Zhukovska, S.; Semenov, D.; Henning, Th.; Vasyunin, A.; Birnstiel, T. E-mail: dwiebe@inasan.ru E-mail: zhukovska@mpia.de E-mail: henning@mpia.de E-mail: tbirnstiel@cfa.harvard.edu

    2013-03-20

    We present a self-consistent model of a protoplanetary disk: 'ANDES' ('AccretioN disk with Dust Evolution and Sedimentation'). ANDES is based on a flexible and extendable modular structure that includes (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains onto the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R {approx}< 50 AU) and lower in the outer disk (R {approx}> 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO{sub 2}, NH{sub 2}CN, HNO, H{sub 2}O, HCOOH, HCN, and CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.

  4. Structural evolution of the Kolar Schist Belt, South India

    NASA Technical Reports Server (NTRS)

    Mukhopahyay, Dilip K.

    1988-01-01

    The structural evolution of the Kolar Schist Belt was discussed. Evidence was described from structures in the ferrigenous quartzite within the schist belt for two periods of nearly coaxial isoclinal folding attributable to E-W compression. This folding was followed by collapse of the F sub 1/F sub 2 folds, forming open F sub 3 folds with NNE-SSW axes. Finally, a period of N-S shortening caused a broad warping of the earlier N-S trending fold axes. There is evidence within the gneisses for shearing produced by similar, nearly E-W compression.

  5. Influence of carbon nanotube on the structure evolution of Ni-Cu alloy nanorod

    NASA Astrophysics Data System (ADS)

    Guo, J.-Y.; Xu, C.-X.; Yang, C.; Dai, J.; Li, Z.-H.

    2011-02-01

    A Monte Carlo method has been performed to simulate the structure evolution of Ni-Cu alloy nanorods encapsulated in the carbon nanotube and removed from the carbon nanotube. The Sutton-Chen many-body potential and Lennard-Jones potential are used to describe the metal-metal and metal-carbon interactions, respectively. The studies show that all Ni-Cu atoms in carbon nanotube are arranged in a series of concentric cylindrical layers even they have different fractions, and Cu atoms are apt to stay at the surface layers. If the carbon nanotube was removed, Ni-Cu alloy nanorod would turn into a cluster with nickel core and copper shell. The physical origin for such structure formation and evolution toward core-shell motifs are discussed. The bond pair analysis shows that the nanorods and clusters are amorphous structures dominated by the rhombohedral structure and mixed up with some local short-range order.

  6. Polyhedra structures and the evolution of the insect viruses

    PubMed Central

    Ji, Xiaoyun; Axford, Danny; Owen, Robin; Evans, Gwyndaf; Ginn, Helen M.; Sutton, Geoff; Stuart, David I.

    2015-01-01

    Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each). Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%. These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability. The conservation of crystal contacts is maintained across most of the molecular surface, except for a dispensable virus recognition domain. By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes. Overall these unusual structural constraints seem to have skewed the molecule’s evolution so that surface residues are almost as conserved as the internal residues. PMID:26291392

  7. Evol and ProDy for bridging protein sequence evolution and structural dynamics

    PubMed Central

    Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet

    2014-01-01

    Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

  8. Speed of evolution with spatial structure and interacting mutations

    NASA Astrophysics Data System (ADS)

    Otwinowski, Jakub

    Perhaps the simplest question about long term evolutionary adaptation is how quickly do populations adapt to a new environment by incorporating mutations? This question is approached from several different angles. Chapter 1 investigates the speed of evolution when there is a large supply of beneficial mutations and the population has spatial structure. For large system sizes, a speed limit is found on the rate adaptation. The model is analyzed as a surface growth model in physics, which reveals universal properties of the model, such as the distribution of fitnesses. However, neglecting spatial structure, the speed of evolution also depends on how mutations interact with each other. This may be quantified by a fitness landscape, or a genotype-phenotype-fitness map. In chapter 2, the fitness landscape and genotype-phenotype map of an E. coli lac promoter is inferred from a large dataset with 100,000 sequences and fluorescence measurements. The interactions between mutations are quantified using a simple quadratic model, similar to a spin glass Hamiltonian. Chapter 3 describes a toy model based on an overdamped particle in a potential, which demonstrates how a fitness landscape with time dependent interactions between mutations determines the speed of evolution.

  9. Evolution of complex dynamics in spatially structured populations

    PubMed Central

    Johst, K.; Doebeli, M.; Brandl, R.

    1999-01-01

    Dynamics of populations depend on demographic parameters which may change during evolution. In simple ecological models given by one-dimensional difference equations, the evolution of demographic parameters generally leads to equilibrium population dynamics. Here we show that this is not true in spatially structured ecological models. Using a multi-patch metapopulation model, we study the evolutionary dynamics of phenotypes that differ both in their response to local crowding, i.e. in their competitive behaviour within a habitat, and in their rate of dispersal between habitats. Our simulation results show that evolution can favour phenotypes that have the intrinsic potential for very complex dynamics provided that the environment is spatially structured and temporally variable. These phenotypes owe their evolutionary persistence to their large dispersal rates. They typically coexist with phenotypes that have low dispersal rates and that exhibit equilibrium dynamics when alone. This coexistence is brought about through the phenomenon of evolutionary branching, during which an initially uniform population splits into the two phenotypic classes.

  10. Geometry and kinematic evolution of Riedel shear structures, Capitol Reef National Park, Utah

    NASA Astrophysics Data System (ADS)

    Katz, Yoram; Weinberger, Ram; Aydin, Atilla

    2004-03-01

    Riedel shear structures are common fault patterns identified within shear zones and related to the embryonic stages of fault formation. This study focuses on the geometry of outcrop-scale natural shear zones consisting of different generations of Riedel structures, exposed in the Jurassic Navajo sandstone, Capitol Reef National Park, Utah. Geometric analysis of different structures shows that the spacing of synthetic R-deformation bands increases with the spacing of antithetic R'-deformation bands. Systematic correlation is found between the R-band spacing and the angles formed between R- and R'-bands. Examination of young Riedel structures shows their tendency to localize along narrow, elongated domains sub-parallel to the shear direction and create denser Riedel networks. We suggest that the evolution of Riedel structures is dominated by two mechanisms: (1) discrete faulting in the form of conjugate deformation bands, generally complying with the Mohr-Coulomb criteria, and (2) granular flow, which rotates mainly the R'-deformation bands. Both mechanisms are intensified with progressive strain, decreasing the deformation-band spacing and increasing the R- to R'-angles. The tendency of young Riedel structures to organize in dense elongated networks is related to strain localization during the shear-zone evolution. We suggest a kinematic explanation for the evolution of Riedel-structure networks, which relates the network geometry to the progressive accumulation and localization of shear strain.

  11. Structural evolution of Alpine salt deposits, Austria and Bavaria

    NASA Astrophysics Data System (ADS)

    Leitner, Ch.; Neubauer, F.; Genser, H.; Borojevic Sostaric, S.

    2009-04-01

    Structural evolution of Alpine salt deposits, Austria and Bavaria Alpine salt deposits consist of a tectonic melange of rocksalt and shale called haselgebirge representing the Haselgebirge Formation of Permian to Early Triassic age and mainly exposed within the central and eastern Northern Calcareous Alps. The initial evaporitic sediments were transformed into a breccia (protocataclasite, mylonite) during Alpine orogeny. Residual rocks of shale, anhydrite, polyhalite, sandstone and limestone float as isolated bodies in the haselgebirge matrix. Field investigations of foliation, halite mineral lineation, fold axis, veins and the overall present slickensides in shale revealed an individual history for all investigated mines (Dürrnberg, Berchtesgaden, Altaussee, in part Hallstatt). Ar-Ar dating of various micostructural types of polyhalite yield several preliminary age groups: 235 Ma, 180 Ma, and 110 Ma. Fluid inclusion measurements on anhydrite together with vitrinite reflectance data showed that temperatures of 140-180 °C were reached in Berchtesgaden and around 250° C in Altaussee. Microstructural analysis of anhydrite reveals strong stretching structures with lobate grain boundaries and the fomation of large anhydrite crystals in polyhalite (locally called muriazite). Rock salt and Haselgebirge samples were gamma-irradiated to intensify contrasts in thin section analysis. No primary structures like fluid inclusion bands or chevrons were found. The oldest visible parts are innner cores of large residual grains. All other types of grains suffered grain size reduction during the subsequent deformation. Using subgrain piezometry, high differential stresses of around 5 MPa formed the present microstructure. The Alpine rock salt deposits suffered a complex deformation history. A first peak was the formation of polyhalite veins, 235 Ma ago. The overburden was around 800 m (Rantitsch & Russegger, 2005) and first differentiation of the sea floor occurred (Mandl, 1984

  12. NASA Structure and Evolution of the Universe Theme: Science Overview

    NASA Technical Reports Server (NTRS)

    White, Nicholas E.; Margon, Bruce

    2001-01-01

    The NASA Office of Space Science Structure and Evolution of the Universe (SEU) theme covers a wide variety of scientific investigations, from the nearest bodies to the farthest observable distances just after the time of the Big Bang. SEU supports experiments that sense radiation of all wavelengths, together with particle and gravitational wave detection. Recently completed road mapping and strategic planning exercises have identified a number of near- and medium-term space initiatives for the 2003-2023 time frame. Each of these experiments pushes the state of the art technically, but will return incredible new insights on the formation and evolution of the universe, as well as probe fundamental laws of physics in regimes never before tested. The scientific goals and technological highlights of each mission are described.

  13. Spectral evolution of pulse structures in gamma-ray bursts

    NASA Technical Reports Server (NTRS)

    Norris, J. P.; Share, G. H.; Messina, D. C.; Dennis, B. R.; Desai, U. D.; Cline, T. L.

    1986-01-01

    The Hard X-Ray Burst Spectrometer (HXRBS) and Gamma-Ray Spectrometer (GRS) data from the Solar Maximum Mission satellite have been searched for gamma-ray bursts with sufficient intensities and relatively simple time profiles such that their spectral behavior may be studied on a time scale of about 1 s. Ten such events were observed with the GRS experiment, and four of these were also detected within the HXRBS field of view. Details are presented for two moderately intense bursts with relatively simple structure. The spectral evolutions of the remaining events are summarized briefly. Results suggest a pattern in the spectral evolution within burst pulses: a tendency for the high-energy emission to lead the low-energy emission, in contrast to the correlation of intensity and spectral hardness reported by Golenetskii et al. (1983).

  14. The Structure and Evolution of Self-Gravitating Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Holliman, John Herbert, II

    1995-01-01

    We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative

  15. Structural Evolution in Nuclei: The Importance of a Systematic Perspective

    SciTech Connect

    Casten, R.F.

    2005-05-24

    One of the signature features of Raman's work was the love and exploitation of nuclear systematics as a tool to discern interesting structural phenomena and to understand better the evolution of structure with nucleon number. Such a tool, properly used, can be extremely powerful, especially when data are correlated with a physically meaningful variable that yields simple and compact trajectories. It can reveal trends that reflect basic elements of nucleonic interactions, it can reveal nuclei with special symmetries, or anomalous nuclei, and it can point to possibly incorrect measurements. We focus on several uses of correlations of nuclear data, illustrating the above ideas. Particular aspects are proton-neutron interactions, quadrupole collectivity, the search for phase transitional behavior and critical point nuclei, and a new mapping of collective nuclear structure across large parts of the nuclear chart, leading to a discovery of an 'arc of regularity' characterizing certain nuclei while others nearby in Z and N exhibit chaotic spectra.

  16. The thermal structure and thermal evolution of the continental lithosphere

    NASA Technical Reports Server (NTRS)

    Morgan, P.

    1984-01-01

    The thermal structure and evolution of the continental lithosphere are examined. Surface heat flow data and the factors which modify them are addressed, and the diversity of thermal phenomena in the lithosphere is discussed in the framework of plate interactions. The lithosphere is divided into three sections for the purposes of discussion. In the upper, near-surface zone, temperatures can be strongly affected by near-surface processes, which must be taken into account in the measurement and evaluation of surface heat flow. The thermal structure of the middle, internal zone of the lithosphere responds to the heat balance and thermal properties of the lithosphere, which define its steady state thermal structure. Internal deformation and magmatic intrusion within this zone, and interaction between the lithosphere and the asthenosphere in the lower boundary zone of the lithosphere cause transient thermal disturbances in the lithosphere. The criteria for defining the base of the thermal lithosphere are briefly discussed.

  17. The interface of protein structure, protein biophysics, and molecular evolution

    PubMed Central

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  18. Synthesis and textural evolution of alumina particles with mesoporous structures

    SciTech Connect

    Liu Xun; Peng Tianyou; Yao Jinchun; Lv Hongjin; Huang Cheng

    2010-06-15

    Alumina particles with mesostructures were synthesized through a chemical precipitation method by using different inorganic aluminum salts followed by a heterogeneous azeotropic distillation and calcination process. The obtained mesoporous {gamma}-alumina particles were systematically characterized by the X-ray diffraction, transmission electron microscopy and nitrogen adsorption-desorption measurement. Effects of the aluminum salt counter anion, pH value and the azeotropic distillation process on the structural or textural evolution of alumina particles were investigated. It is found that Cl{sup -} in the reaction solution can restrain the textural evolution of the resultant precipitates into two-dimensional crystallized pseudoboehmite lamellae during the heterogeneous azeotropic distillation, and then transformed into {gamma}-Al{sub 2}O{sub 3} particles with mesostructures after further calcination at 1173 K, whereas coexisting SO{sub 4}{sup 2-} can promote above morphology evolution and then transformed into {gamma}-Al{sub 2}O{sub 3} nanofibers after calcination at 1173 K. Moreover nearly all materials retain relatively high specific surface areas larger than 100 m{sup 2} g{sup -1} even after calcinations at 1173 K. - Graphical abstract: Co-existing Cl{sup -} is beneficial for the formation of {gamma}-alumina nanoparticles with mesostructures during the precipitation process. Interparticle and intraparticle mesopores can be derived from acidic solution and near neutral solution, respectively.

  19. egoSlider: Visual Analysis of Egocentric Network Evolution.

    PubMed

    Wu, Yanhong; Pitipornvivat, Naveen; Zhao, Jian; Yang, Sixiao; Huang, Guowei; Qu, Huamin

    2016-01-01

    Ego-network, which represents relationships between a specific individual, i.e., the ego, and people connected to it, i.e., alters, is a critical target to study in social network analysis. Evolutionary patterns of ego-networks along time provide huge insights to many domains such as sociology, anthropology, and psychology. However, the analysis of dynamic ego-networks remains challenging due to its complicated time-varying graph structures, for example: alters come and leave, ties grow stronger and fade away, and alter communities merge and split. Most of the existing dynamic graph visualization techniques mainly focus on topological changes of the entire network, which is not adequate for egocentric analytical tasks. In this paper, we present egoSlider, a visual analysis system for exploring and comparing dynamic ego-networks. egoSlider provides a holistic picture of the data through multiple interactively coordinated views, revealing ego-network evolutionary patterns at three different layers: a macroscopic level for summarizing the entire ego-network data, a mesoscopic level for overviewing specific individuals' ego-network evolutions, and a microscopic level for displaying detailed temporal information of egos and their alters. We demonstrate the effectiveness of egoSlider with a usage scenario with the DBLP publication records. Also, a controlled user study indicates that in general egoSlider outperforms a baseline visualization of dynamic networks for completing egocentric analytical tasks. PMID:26529706

  20. Evolution and structure of Mercury's interior from MESSENGER observations

    NASA Astrophysics Data System (ADS)

    Tosi, Nicola

    2015-04-01

    During the past four years, the MESSENGER mission (MErcury Surface, Space Environment, GEochemistry and Ranging) has delivered a wealth of information that has been dramatically advancing the understanding of the geological, chemical, and physical state of Mercury. Taking into account the latest constraints on the interior structure, surface composition, volcanic and tectonic history, we employed numerical models to simulate the thermo-chemical evolution of the planet's interior [1]. Typical evolution scenarios that allow the observational constraints to be satisfied consist of an initial phase of mantle heating accompanied by planetary expansion and the production of a substantial amount of partial melt. The evolution subsequent to 2 Ga is characterised by secular cooling that proceeds approximately at a constant rate and implies that contraction should be still ongoing. Most of the models also predict mantle convection to cease after 3-4 Ga, indicating that Mercury may be no longer dynamically active. In addition, the topography, measured by laser altimetry and the gravity field, obtained from radio-tracking, represent fundamental observations that can be interpreted in terms of the chemical and mechanical structure of the interior. The observed geoid-to-topography ratios at intermediate wavelengths are well explained by the isostatic compensation of the topography associated with lateral variations of the crustal thickness, whose mean value can be estimated to be ~35 km, broadly confirming the predictions of the evolution simulations [2]. Finally, we will show that the degree-2 and 4 of the topography and geoid spectra can be explained in terms of the long-wavelength deformation of the lithosphere resulting from deep thermal anomalies caused by the large latitudinal and longitudinal variations in temperature experienced by Mercury's surface. [1] Tosi N., M. Grott, A.-C. Plesa and D. Breuer (2013). Thermo-chemical evolution of Mercury's interior. Journal of

  1. Structure evolution and optimization in the fabrication of PVA-based activated carbon fibers.

    PubMed

    Zhang, Shu-Juan; Feng, Hui-Min; Wang, Jian-Ping; Yu, Han-Qing

    2008-05-01

    The structure and composition evolution of polyvinyl alcohol (PVA) fibers during the fabrication of activated carbon fibers (ACF) by a newly developed method were systematically elucidated. The pore structure of the fibers was significantly influenced by the carbonization and activation conditions. The elemental composition and chemical structure evolution of the fibers during the heat treatment processes were evaluated by elemental analysis, Fourier transform infrared spectrophotometry (FTIR), and X-ray photoelectron spectroscopy (XPS). Crystal structure evolution of the fibers during the heat treatment processes was elucidated by X-ray diffraction (XRD) analysis. Based on these understandings, the process conditions were optimized using an L(9)(3)(4) orthogonal array design matrix. Appropriate process parameters for the fabrication of PVA-ACFs were established as carbonizing the dehydrated fiber at 300 degrees C for 60 min, and then lifting the temperature to 900 degrees C with a heating speed of 10 degrees C/min in an inert atmosphere, thereafter keeping the fiber at 900 degrees C for 60 min in an oxidizing atmosphere. PMID:18261741

  2. Evolution of the structural and superconducting properties of FeSe crystals upon long-term storage

    NASA Astrophysics Data System (ADS)

    Gorina, J. I.; Kaljuzhnaia, G. A.; Golubkov, M. V.; Rodin, V. V.; Romanova, T. A.; Sentjurina, N. N.; Chernook, S. G.

    2016-03-01

    A comprehensive analysis of the evolution of the structural and superconducting properties of FeSe crystals stored in air for several years has been performed. It is established that the structure and phase composition of the samples remained invariable, while the superconducting parameters significantly degraded. These changes may be due to the stress relaxation or redistribution of defects in the samples.

  3. PIECE: A database for plant gene structure comparison and evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a com...

  4. Origin, Internal Structure and Evolution of 4 Vesta

    NASA Astrophysics Data System (ADS)

    Zuber, Maria T.; McSween, Harry Y.; Binzel, Richard P.; Elkins-Tanton, Linda T.; Konopliv, Alexander S.; Pieters, Carle M.; Smith, David E.

    2011-12-01

    Asteroid 4 Vesta is the only preserved intact example of a large, differentiated protoplanet like those believed to be the building blocks of terrestrial planet accretion. Vesta accreted rapidly from the solar nebula in the inner asteroid belt and likely melted due to heat released due to the decay of 26Al. Analyses of meteorites from the howardite-eucrite-diogenite (HED) suite, which have been both spectroscopically and dynamically linked to Vesta, lead to a model of the asteroid with a basaltic crust that overlies a depleted peridotitic mantle and an iron core. Vesta’s crust may become more mafic with depth and might have been intruded by plutons arising from mantle melting. Constraints on the asteroid’s moments of inertia from the long-wavelength gravity field, pole position and rotation, informed by bulk composition estimates, allow tradeoffs between mantle density and core size; cores of up to half the planetary radius can be consistent with plausible mantle compositions. The asteroid’s present surface is expected to consist of widespread volcanic terrain, modified extensively by impacts that exposed the underlying crust or possibly the mantle. Hemispheric heterogeneity has been observed by poorly resolved imaging of the surface that suggests the possibility of a physiographic dichotomy as occurs on other terrestrial planets. Vesta might have had an early magma ocean but details of the early thermal structure are far from clear owing to model uncertainties and paradoxical observations from the HEDs. Petrological analysis of the eucrites coupled with thermal evolution modeling recognizes two possible mechanisms of silicate-metal differentiation leading to the formation of the basaltic achondrites: equilibrium partial melting or crystallization of residual liquid from the cooling magma ocean. A firmer understanding the plethora of complex physical and chemical processes that contribute to melting and crystallization will ultimately be required to

  5. The structural and property evolution of cellulose during carbonization

    NASA Astrophysics Data System (ADS)

    Rhim, Yo-Rhin

    The understanding of the structure and related property evolution during carbonization is imperative in engineering carbon materials for specific functionalities. High purity cellulose was used as a model precursor to help understand the conversion of organic compounds to hard carbons. Several characterization techniques were employed to follow the structural, compositional and property changes during the thermal transformation of microcrystalline cellulose to carbon over the temperature range of 250°C to 2000°C. These studies revealed several stages of composition and microstructure evolution during carbonization supported by the observation of five distinct regions of electrical and thermal properties. In Region I, from 250°C to 400°C, depolymerisation of cellulose molecules caused the evolution of volatile gases and decrease in dipole polarization. This also led to the reduction of overall AC electrical conductivity and specific heat. In Region II, from 450°C to 500°C, the formation and growth of conducting sp 2 carbon clusters resulted in increases in overall AC electrical conductivity and thermal diffusivity with rising temperature. For heat treatment temperatures of 550°C and 600°C, Region III, carbon clusters grew into aggregates of curved carbon layers leading to interfacial polarization and onset of percolation. AC electrical and thermal conductivities are enhanced due to electron hopping and improved phonon transport among carbon clusters. With temperatures rising from 650°C to 1000°C, Region IV, DC conductivity began to emerge and increased sharply along with thermal conductivity with further percolation of carbon clusters as lateral growth of carbon layers continued. Lastly, from 1200°C to 2000°C, Region V, DC electrical conductivity remained constant due to a fully percolated system.

  6. Saturn layered structure and homogeneous evolution models with different EOSs

    NASA Astrophysics Data System (ADS)

    Nettelmann, Nadine; Püstow, Robert; Redmer, Ronald

    2013-07-01

    The core mass of Saturn is commonly assumed to be 10-25M⊕ as predicted by interior models with various equations of state (EOSs) and the Voyager gravity data, and hence larger than that of Jupiter (0-10M⊕). We here re-analyze Saturn's internal structure and evolution by using more recent gravity data from the Cassini mission and different physical equations of state: the ab initio LM-REOS which is rather soft in Saturn's outer regions but stiff at high pressures, the standard Sesame-EOS which shows the opposite behavior, and the commonly used SCvH-i EOS. For all three EOS we find similar core mass ranges, i.e. of 0-20M⊕ for SCvH-i and Sesame EOS and of 0-17M⊕ for LM-REOS. Assuming an atmospheric helium mass abundance of 18%, we find maximum atmospheric metallicities, Zatm of 7× solar for SCvH-i and Sesame-based models and a total mass of heavy elements, MZ of 25-30M⊕. Some models are Jupiter-like. With LM-REOS, we find MZ = 16-20M⊕, less than for Jupiter, and Zatm ≲ 3× solar. For Saturn, we compute moment of inertia values λ = 0.2355(5). Furthermore, we confirm that homogeneous evolution leads to cooling times of only ˜2.5 Gyr, independent on the applied EOS. Our results demonstrate the need for accurately measured atmospheric helium and oxygen abundances, and of the moment of inertia for a better understanding of Saturn's structure and evolution.

  7. Dynamic structural network evolution in compressed granular systems

    NASA Astrophysics Data System (ADS)

    Papadopoulos, Lia; Puckett, James; Daniels, Karen; Bassett, Danielle

    The heterogeneous dynamic behavior of granular packings under shear or compression is not well-understood. In this study, we use novel techniques from network science to investigate the structural evolution that occurs in compressed granular systems. Specifically, we treat particles as network nodes, and pressure-dependent forces between particles as layer-specific network edges. Then, we use a generalization of community detection methods to multilayer networks, and develop quantitative measures that characterize changes in the architecture of the force network as a function of pressure. We observe that branchlike domains reminiscent of force chains evolve differentially as pressure is applied: topological characteristics of these domains at rest predict their coalescence or dispersion under pressure. Our methods allow us to study the dynamics of mesoscale structure in granular systems, and provide a direct way to compare data from systems under different external conditions or with different physical makeup.

  8. Structural framework, stratigraphy, and evolution of Brazilian marginal basins

    SciTech Connect

    Ojeda, H.A.O.

    1982-06-01

    The structural framework of the Brazilian continental margin is basically composed of eight structural types: antithetic tilted step-fault blocks, synthetic untilted step-fault blocks, structural inversion axes, hinges with compensation grabens, homoclinal structures, growth faults with rollovers, diapirs, and igneous structures. The antithetic tilted and synthetic untilted step-fault blocks are considered as synchronous, complementary structural systems, separated by an inversion axis. Two evaporitic cycles (Paripueira and Ibura) were differentiated in the Sergipe-Alagoas type basin and tentatively correlated to the evaporitic section of other Brazilian marginal basis. Four phases are considered in the evolution of the Brazilian marginal basins: pre-rift, rift, transitional, and drift. During the pre-rift phase (Late Jurassic-Early Cretaceous), continental sediments were deposited in peripheral intracratonic basins. In the rift phase (Early Cretaceous), the breakup of the continental crust of the Gondwana continent gave rise to a central graben and rift valleys where lacustrine sediments were deposited. The transitional phase (Aptian) developed under relative tectonic stability, when evaporitic and clastic lacustrine sequences were being deposited. In the drift phase (Albian to Holocene), a regionl homoclinal structure developed, consisting of two distinct sedimentary sequences, a lower clastic-carbonate and an upper clastic. From the Albian to the Holocene Epoch, structures associated to plastic displacement of salt or shale developed in many Brazilian marginal basins. Two phases of major igneous activity occurred: one in the Early Cretaceous associated with the rift phase of the Gondwana continent, and the other in the Tertiary during the migration phase of the South American and African plates.

  9. Studying the Thermal and Structural Evolution of Planetary Bodies

    NASA Astrophysics Data System (ADS)

    Karimi, Mohammadali

    The focus of this research is to study the thermal and structural evolution of three planetary bodies, Mars, Venus and the asteroid Vesta. The almost uniform spatial distribution of craters on the surfaces of planets makes them excellent candidates to examine the evolution of planets as a whole. By modeling the viscoelastic deformation of craters at the surface and subsurface with the Finite Element Method (FEM), this study investigated the role of lower crustal flow in crater relaxation, and since lower crustal flow is sensitive to the thermal state, it serves as a probe into the thermal evolution of planets. The thermal history of Mars was explored by modeling the evolution of large craters and Quasi-Circular Depressions (QCDs) in the Southern Highlands and Northern Lowlands, respectively. Because of the spatial distribution of craters, this study yielded a thermal map for Mars that is more complete and less biased regionally relative to other studies. The results revealed a higher background heat flux for the Northern Lowlands relative to the Southern Highlands during the most ancient Noachian epoch, which suggests a thermal fingerprint to whatever process that formed the hemispherical crustal dichotomy, the oldest and most prominent geomorphic feature on Mars. Next, the largest crater on the surface of Venus, Mead, also appears to have undergone significant lower crustal flow. Modeling the viscoelastic deformation of Mead puts constraints on the thermal state of our sister planet in the vicinity of the basin. The background heat flux of Venus estimated here is higher than globally average values predicted by previous thermal models. Moreover, this study showed that Venus's crust and mantle seem to be dry relative to those of the Earth. Last, modeling the evolution of two large craters in the south polar region of Vesta (Rheasilvia and Veneneia) showed that the shallow topography and large central peak of these craters are likely the products of a planetary

  10. Structural damage evolution assessment using the regularised time step integration method

    NASA Astrophysics Data System (ADS)

    Chen, Hua-Peng; Maung, Than Soe

    2014-09-01

    This paper presents an approach to identify both the location and severity evolution of damage in engineering structures directly from measured dynamic response data. A relationship between the change in structural parameters such as stiffness caused by structural damage development and the measured dynamic response data such as accelerations is proposed, on the basis of the governing equations of motion for the original and damaged structural systems. Structural damage parameters associated with time are properly chosen to reflect both the location and severity development over time of damage in a structure. Basic equations are provided to solve the chosen time-dependent damage parameters, which are constructed by using the Newmark time step integration method without requiring a modal analysis procedure. The Tikhonov regularisation method incorporating the L-curve criterion for determining the regularisation parameter is then employed to reduce the influence of measurement errors in dynamic response data and then to produce stable solutions for structural damage parameters. Results for two numerical examples with various simulated damage scenarios show that the proposed method can accurately identify the locations of structural damage and correctly assess the evolution of damage severity from information on vibration measurements with uncertainties.

  11. The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution.

    PubMed

    Ahrens, Joseph; Dos Santos, Helena G; Siltberg-Liberles, Jessica

    2016-09-01

    Protein evolution often occurs at unequal rates in different sites along an amino acid chain. Site-specific evolutionary rates have been linked to several structural and functional properties of proteins. Previous analyses of this phenomenon have involved relatively small datasets and, in some cases, the interaction among multiple structural factors is not evaluated. Here, we present the results of a large-scale phylogenetic and statistical analysis, testing the effects and interactions of three structural properties on amino acid replacement rates. We used sequence-based computational methods to predict (i) intrinsic disorder propensity, (ii) secondary structure, and (iii) functional domain involvement across millions of amino acid sites in thousands of sequence alignments of metazoan proteins. Our results somewhat corroborate earlier findings that intrinsically disordered sites tend to be more variable than ordered sites, but there is considerable overlap among their rate distributions, and a significant confounding interaction exists between intrinsic disorder and secondary structure. Notably, protein sites that are consistently predicted to be both intrinsically disordered and involved in secondary structures tend to be the most conserved at the amino acid level, suggesting that they are highly constrained and functionally important. In addition, a significant interaction exists between functional domain involvement and secondary structure. These findings suggest that multiple structural drivers of protein evolution should be evaluated simultaneously in order to get a clear picture of their individual effects as well as any confounding interactions among them. PMID:27189555

  12. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  13. Structural basis for the divergent evolution of influenza B virus hemagglutinin

    PubMed Central

    Ni, Fengyun; Kondrashkina, Elena; Wang, Qinghua

    2013-01-01

    Influenza A and B viruses are responsible for the severe morbidity and mortality worldwide in annual influenza epidemics. Currently circulating influenza B virus belongs to the B/Victoria or B/Yamagata lineage that was diverged from each other about 30–40 years ago. However, a mechanistic understanding of their divergent evolution is still lacking. Here we report the crystal structures of influenza B/Yamanashi/166/1998 hemagglutinin (HA) belonging to B/Yamagata lineage and its complex with the avian-like receptor analogue. Comparison of these structures with those of undiverged and diverged influenza B virus HAs, in conjunction with sequence analysis, reveals the molecular basis for the divergent evolution of influenza B virus HAs. Furthermore, HAs of diverged influenza B virus strains display much stronger molecular interactions with terminal sialic acid of bound receptors, which may allow for a different tissue tropism for current influenza B viruses, for which further investigation is required. PMID:24074573

  14. Understanding the Global Structure and Evolution of Coronal Mass Ejections in the Solar Wind

    NASA Technical Reports Server (NTRS)

    Riley, Pete

    2004-01-01

    This report summarizes the technical progress made during the first six months of the second year of the NASA Living with a Star program contract Understanding the global structure and evolution of coronal mass ejections in the solar wind, between NASA and Science Applications International Corporation, and covers the period November 18, 2003 - May 17,2004. Under this contract SAIC has conducted numerical and data analysis related to fundamental issues concerning the origin, intrinsic properties, global structure, and evolution of coronal mass ejections in the solar wind. During this working period we have focused on a quantitative assessment of 5 flux rope fitting techniques. In the following sections we summarize the main aspects of this work and our proposed investigation plan for the next reporting period. Thus far, our investigation has resulted in 6 refereed scientific publications and we have presented the results at a number of scientific meetings and workshops.

  15. Directed Evolution and Structural Characterization of a Simvastatin Synthase

    SciTech Connect

    Gao, Xue; Xie, Xinkai; Pashkov, Inna; Sawaya, Michael R.; Laidman, Janel; Zhang, Wenjun; Cacho, Ralph; Yeates, Todd O.; Tang, Yi; UCLA

    2010-02-02

    Enzymes from natural product biosynthetic pathways are attractive candidates for creating tailored biocatalysts to produce semisynthetic pharmaceutical compounds. LovD is an acyltransferase that converts the inactive monacolin J acid (MJA) into the cholesterol-lowering lovastatin. LovD can also synthesize the blockbuster drug simvastatin using MJA and a synthetic {alpha}-dimethylbutyryl thioester, albeit with suboptimal properties as a biocatalyst. Here we used directed evolution to improve the properties of LovD toward semisynthesis of simvastatin. Mutants with improved catalytic efficiency, solubility, and thermal stability were obtained, with the best mutant displaying an {approx}11-fold increase in an Escherichia coli-based biocatalytic platform. To understand the structural basis of LovD enzymology, seven X-ray crystal structures were determined, including the parent LovD, an improved mutant G5, and G5 cocrystallized with ligands. Comparisons between the structures reveal that beneficial mutations stabilize the structure of G5 in a more compact conformation that is favorable for catalysis.

  16. Structural Evolution of Silica Gel and Silsesquioxane Using Thermal Curing.

    PubMed

    Hu, Nan; Rao, YuanQiao; Sun, Shengtong; Hou, Lei; Wu, Peiyi; Fan, Shaojuan; Ye, Bangjiao

    2016-08-01

    The curing of coatings of two types of siloxane containing materials, silica gel and silsesquioxane, at a modest temperature (<280℃) was studied with in situ heating Fourier transform infrared spectroscopy (FT-IR) in combination with perturbation correlation moving window (PCMW) and two-dimensional correlation spectroscopy (2D-COS) analyses. The result revealed detailed structural evolution of these two different gels. When the silica gel was heated, (Si-O)6 rings appeared from the random Si-O-Si network formed after sol gel reaction, followed by condensation of silanol groups. Upon further heating, the existing (Si-O)4 rings were broken down and converted into (Si-O)6 structures, and finally isolated silanols appeared. The transition from (Si-O)4 rings to (Si-O)6 rings was observed by IR and further confirmed with positron annihilation lifetime spectroscopy (PALS). In comparison, during the curing of hybrid silsesquioxane, the condensation of silanols happens immediately upon heating without the rearrangement of Si-O-Si network. Afterwards, the fraction of (Si-O)6 ring structure increased. (Si-O)4 structures exhibited higher stability in hybrid silsesquioxanes. In addition, the amount of silanols in silsesquioxane continued to reduce without the generation of isolated silanol in the end. The different curing behavior of silsesquioxanes from silica gel originates from the organic groups in silsesquioxanes, which lowers the cross-linking density and reduces the rigidity of siloxane network. PMID:27340213

  17. Structural evolution of the methane cation in subfemtosecond photodynamics.

    PubMed

    Mondal, T; Varandas, A J C

    2015-07-01

    An ab initio quantum dynamics study has been performed to explore the structural rearrangement of ground state CH4 (+) in subfemtosecond resolved photodynamics. The method utilizes time-dependent wave-packet propagation on the X˜(2)T2 electronic manifold of the title cation in full dimensionality, including nonadiabatic coupling of the three electronic sheets. Good agreement is obtained with recent experiments [Baker et al., Science 312, 424 (2006)] which use high-order harmonic generation to probe the attosecond proton dynamics. The novel results provide direct theoretical support of the observations while unravelling the underlying details. With the geometrical changes obtained by calculating the expectation values of the nuclear coordinates as a function of time, the structural evolution is predicted to begin through activation of the totally symmetric a1 and doubly degenerate e modes. While the former retains the original Td symmetry of the cation, the Jahn-Teller active e mode conducts it to a D2d structure. At ∼1.85 fs, the intermediate D2d structure is further predicted to rearrange to local C2v minimum geometry via Jahn-Teller active bending vibrations of t2 symmetry. PMID:26156480

  18. Structural evolution of the methane cation in subfemtosecond photodynamics

    NASA Astrophysics Data System (ADS)

    Mondal, T.; Varandas, A. J. C.

    2015-07-01

    An ab initio quantum dynamics study has been performed to explore the structural rearrangement of ground state CH 4+ in subfemtosecond resolved photodynamics. The method utilizes time-dependent wave-packet propagation on the X ˜ 2 T 2 electronic manifold of the title cation in full dimensionality, including nonadiabatic coupling of the three electronic sheets. Good agreement is obtained with recent experiments [Baker et al., Science 312, 424 (2006)] which use high-order harmonic generation to probe the attosecond proton dynamics. The novel results provide direct theoretical support of the observations while unravelling the underlying details. With the geometrical changes obtained by calculating the expectation values of the nuclear coordinates as a function of time, the structural evolution is predicted to begin through activation of the totally symmetric a1 and doubly degenerate e modes. While the former retains the original Td symmetry of the cation, the Jahn-Teller active e mode conducts it to a D2d structure. At ˜1.85 fs, the intermediate D2d structure is further predicted to rearrange to local C2v minimum geometry via Jahn-Teller active bending vibrations of t2 symmetry.

  19. Rheological structure in Mars and its time evolution

    NASA Astrophysics Data System (ADS)

    Azuma, S.; Katayama, I.

    2014-12-01

    Mars is one of the terrestrial planets which are composed of rock and metal such as the Earth. There is no water, no life, and no plate tectonics on Mars, suggesting that Mars and Earth followed different evolutionary paths. Rheological structure, which indicates the deformation behavior and the strength of planetary interior, plays an important role in the evolution of planets. The rheological behavior of planetary interiors is strongly sensitive to temperature, which may produce strong rheological layering. Rheological structure of Mars in past must be different from the current rheological structure. First, the evolutions of temperature profiles in Mars are inferred from the surface heat flow and the heat conduction equation. The surface heat flow of Mars every 1 billion years was calculated from present abundances of the radioactive isotopes (235U, 235U, 232Th, and 40K) and their half-lives (Hahn et al 2011). Based on the temperature profile, we calculate the rheological structure of Mars every 1 billion years using flow-law of plagioclase and olivine. Calculated rheological structure shows that the brittle-ductile transition of present Mars, which is transition of deformation behavior from brittle failure to viscous flow, is deeper as compared with that of past Mars, suggesting that current elastic thickness also becomes thicker than that of past Mars. Under water-saturated conditions, the rheological structure which simulates the northern lowlands shows the strength contrast between the crust and mantle, indicating that the decoupling might occur at the Moho from 4 Ga to present day. Under dry conditions, lithosphere of northern lowlands has no strength contrast at the Moho, implying that crust and mantle might be coupled from 3 Ga to present day. Viscosity contrast between the surface and planetary interior is key for the mantle convection style (Moresi and Solomatov 1995), and the calculated viscosity contrast at present Mars is ~10-5 (Pa), suggesting that

  20. Evolution Analysis of Simple Sequence Repeats in Plant Genome

    PubMed Central

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution. PMID:26630570

  1. Transverse zones controlling the structural evolution of the Zipaquira Anticline (Eastern Cordillera, Colombia): Regional implications

    NASA Astrophysics Data System (ADS)

    García, Helbert; Jiménez, Giovanny

    2016-08-01

    We report paleomagnetic, magnetic fabric and structural results from 21 sites collected in Cretaceous marine mudstones and Paleogene continental sandstones from the limbs, hinge and transverse zones of the Zipaquira Anticline (ZA). The ZA is an asymmetrical fold with one limb completely overturned by processes like gravity and salt tectonics, and marked by several axis curvatures. The ZA is controlled by at least two (2) transverse zones known as the Neusa and Zipaquira Transverse Zones (NTZ and ZTZ, respectively). Magnetic mineralogy methods were applied at different sites and the main carriers of the magnetic properties are paramagnetic components with some sites being controlled by hematite and magnetite. Magnetic fabric analysis shows rigid-body rotation for the back-limb in the ZA, while the forelimb is subjected to internal deformation. Structural and paleomagnetic data shows the influence of the NTZ and ZTZ in the evolution of the different structures like the ZA and the Zipaquira, Carupa, Rio Guandoque, Las Margaritas and Neusa faults, controlling several factors as vergence, extension, fold axis curvature and stratigraphic detatchment. Clockwise rotations unraveled a block segmentation following a discontinuos model caused by transverse zones and one site reported a counter clockwise rotation associated with a left-lateral strike slip component for transverse faults (e.g. the Neusa Fault). We propose that diverse transverse zones have been active since Paleogene times, playing an important role in the tectonic evolution of the Cundinamarca sub-basin and controlling the structural evolution of folds and faults with block segmentation and rotations.

  2. Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.

    PubMed

    Herrmann, Jonathan; Nathin, David; Lee, Soon Goo; Sun, Tony; Jez, Joseph M

    2015-10-01

    In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabidopsis thaliana (AtAPSK) identified a regulatory disulfide bond formed between the N-terminal domain (NTD) and a cysteine on the core scaffold. This thiol switch is unique to mosses, gymnosperms, and angiosperms. To understand the structural evolution of redox control of APSK, we investigated the redox-insensitive APSK from the cyanobacterium Synechocystis sp. PCC 6803 (SynAPSK). Crystallographic analysis of SynAPSK in complex with either APS and a non-hydrolyzable ATP analog or APS and sulfate revealed the overall structure of the enzyme, which lacks the NTD found in homologs from mosses and plants. A series of engineered SynAPSK variants reconstructed the structural evolution of the plant APSK. Biochemical analyses of SynAPSK, SynAPSK H23C mutant, SynAPSK fused to the AtAPSK NTD, and the fusion protein with the H23C mutation showed that the addition of the NTD and cysteines recapitulated thiol-based regulation. These results reveal the molecular basis for structural changes leading to the evolution of redox control of APSK in the green lineage from cyanobacteria to plants. PMID:26294763

  3. The spatial evolution of stellar structures in the LMC/SMC

    NASA Astrophysics Data System (ADS)

    Bastian, Nate; Gieles, Mark; Ercolano, Barbara; Gutermuth, Robert

    2009-03-01

    We present an analysis of the spatial distribution of various stellar populations within the Large and Small Magellanic Clouds. We use optically selected stellar samples with mean ages between ~9 and ~1000 Myr, and existing stellar cluster catalogues to investigate how stellar structures form and evolve within the LMC/SMC. We use two statistical techniques to study the evolution of structure within these galaxies, the Q-parameter and the two-point correlation function (TPCF). In both galaxies we find the stars are born with a high degree of substructure (i.e. are highly fractal) and that the stellar distribution approaches that of the “background” population on timescales similar to the crossing times of the galaxy (~ 80 Myr & ~ 150 Myr for the SMC/LMC respectively). By comparing our observations to simple models of structural evolution we find that “popping star clusters” do not significantly influence structural evolution in these galaxies. Instead we argue that general galactic dynamics are the main drivers, and that substructure will be erased in approximately the crossing time, regardless of spatial scale, from small clusters to whole galaxies. This can explain why many young Galactic clusters have high degrees of substructure, while others are smooth and centrally concentrated. We conclude with a general discussion on cluster “infant mortality”, in an attempt to clarify the time/spatial scales involved.

  4. Evolution, structure, and synthesis of vertebrate egg-coat proteins

    PubMed Central

    Litscher, Eveline S.; Wassarman, Paul M.

    2015-01-01

    All vertebrate eggs are surrounded by an extracellular coat that supports growth of oocytes, protects oocytes, eggs, and early embryos, and participates in the process of fertilization. In mammals (platypus to human beings) the coat is called a zona pellucida (ZP) and in non-mammals (molluscs to birds), a vitelline envelope (VE). The ZP and VE are composed of just a few proteins that are related to one another and possess a common motif, called the zona pellucida domain (ZPD). The ZPD arose more than ~600 million years ago, consists of ~260 amino acids, and has 8 conserved Cys residues that participate in 4 intramolecular disulfides. It is likely that egg-coat proteins are derived from a common ancestral gene. This gene duplicated several times during evolution and gave rise to 3–4 genes in fish, 5 genes in amphibians, 6 genes in birds, and 3–4 genes in mammals. Some highly divergent sequences, N- and C-terminal to the ZPD, have been identified in egg-coat proteins and some of these sequences may be under positive Darwinian selection that drives evolution of the proteins. These and other aspects of egg-coat proteins, including their structure and synthesis, are addressed in this review. PMID:26504367

  5. The origin and evolution of activity analysis.

    PubMed

    Creighton, C

    1992-01-01

    Practitioners of occupational therapy in the early 1900s selected therapeutic activities with an intuitive understanding of their characteristics and operations. The term activity analysis and the methodology for breaking down and examining tasks scientifically, however, were borrowed from industry during World War I. Methods originally used in time and motion study of jobs were applied to vocational retraining and therapeutic crafts; later, they were applied to a broader range of activities. The most systematic early use of activity analysis was in occupational therapy for physical dysfunction, particularly in military hospitals. Development of the concept was gradual until the 1970s, when the delineation of theoretical frames of reference for practice led to important changes. Today, activity analysis is viewed as a multifaceted process that involves both generic and specific components. PMID:1558138

  6. Investigation of the problems with using gas adsorption to probe catalyst pore structure evolution during coking.

    PubMed

    Gopinathan, Navin; Greaves, Malcolm; Wood, Joseph; Rigby, Sean P

    2013-03-01

    A common approach to try to understand the mechanism of coking in heterogeneous catalysts is to monitor the evolution of the pore structure using gas adsorption analysis of discharged pellets. However, the standard methods of analysis of gas adsorption data, to obtain pore-size distributions, make the key assumption of thermodynamically-independent pores. This assumption neglects the possibility of co-operative adsorption phenomena, which will shown to be a critical problem when looking at coking catalysts. In this work the serial adsorption technique has been used to detect and assess the extent of co-operative effects in adsorption within coking catalysts. The reaction of decane over a hydroprocessing catalyst was used as a case study. It has been shown that the conventional analysis method would lead to a flawed picture of the pore structure changes during the coking process. For the case-study considered in this work, it was found that co-operative adsorption effects meant that 26% of the measured adsorption was occurring in pores up to three times larger than the size conventional analysis would presume. The serial adsorption technique was thus shown to provide important additional information on pore structure evolution during coking. A study of the kinetics of adsorption has been used to infer information about the general spatial location of the coking process within a pellet. PMID:23141698

  7. Thermal and Structural Evolution of a Partially Differentiated Titan

    NASA Astrophysics Data System (ADS)

    Bland, Michael T.; McKinnon, W. B.

    2012-10-01

    Titan’s moment of inertia (C/MR2) has been measured by Cassini to be 0.34, indicating either partial differentiation, or full differentiation with a low-density (hydrated) silicate core. Fully differentiated models have been constructed [Castillo-Rogez and Lunine, 2010], but require specific geochemical assumptions (e.g., rapid accretion, minimal core dehydration). In contrast, the alternative, partially differentiated models have not yet been fully vetted. Here we investigate the thermal stability of such partially differentiated internal structures by evaluating whether complete differentiation can be avoided. Our model assumes an initial three-layer internal structure consisting of a pure ice layer, mixed ice-rock layer, and silicate core, and calculates the temperature of each layer following the numerical approach in Bland et al. (2008, 2009). The model allows melting in the pure ice and mixed layer, and dehydration of the initially hydrated silicate core (leading to densification and absorption of latent heat). Melting of the mixed layer liberates silicate material, which is assumed to sink to the top of the silicate layer over time scales short relative to simulation time scales (in reality some may mx back into the convecting mixed ice-rock layer). Simulations so far indicate that melting of Titan’s pure ice shell is common early in Solar System history, and that melting frequently extends into Titan’s nominal mixed ice-rock layer. Such melting leads to irreversible unmixing of some of the mixed ice-rock layer. Nearly complete dehydration of the silicate core occurs when condritic K is retained in the rock component. The structural evolution decreases Titan’s initial moment of inertia; however, long-lived radiogenic species are generally incapable of completely melting and separating Titan’s mixed layer. To date, thermally stable structural models with C/MR2 as large as 0.33 have been achieved. We continue to investigate how realistic ocean and

  8. Constraints on Composition, Structure and Evolution of the Lithosphere

    NASA Astrophysics Data System (ADS)

    Bianchini, Gianluca; Bonadiman, Costanza; Aulbach, Sonja; Schutt, Derek

    2015-05-01

    The idea for this special issue was triggered at the Goldschmidt Conference held in Florence (August 25-30, 2013), where we convened a session titled "Integrated Geophysical-Geochemical Constraints on Composition and Structure of the Lithosphere". The invitation to contribute was extended not only to the session participants but also to a wider spectrum of colleagues working on related topics. Consequently, a diverse group of Earth scientists encompassing geophysicists, geodynamicists, geochemists and petrologists contributed to this Volume, providing a comprehensive overview on the nature and evolution of lithospheric mantle by combining studies that exploit different types of data and interpretative approaches. The integration of geochemical and geodynamic datasets and their interpretation represents the state of the art in our knowledge of the lithosphere and beyond, and could serve as a blueprint for future strategies in concept and methodology to advance our knowledge of this and other terrestrial reservoirs.

  9. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  10. Microscopic derivation of IBM and structural evolution in nuclei

    SciTech Connect

    Nomura, Kosuke

    2011-05-06

    A Hamiltonian of the interacting boson model (IBM) is derived based on the mean-field calculations with nuclear energy density functionals (EDFs). The multi-nucleon dynamics of the surface deformation is simulated in terms of the boson degrees of freedom. The interaction strengths of the IBM Hamiltonian are determined by mapping the potential energy surfaces (PESs) of a given EDF with quadrupole degrees of freedom onto the corresponding PES of IBM. A fermion-to-boson mapping for a rotational nucleus is discussed in terms of the rotational response, which reflects a specific time-dependent feature. Ground-state correlation energy is evaluated as a signature of structural evolution. Some examples resulting from the present spectroscopic calculations are shown for neutron-rich Pt, Os and W isotopes including exotic ones.

  11. Diversity, structure and convergent evolution of the global sponge microbiome.

    PubMed

    Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B; Erwin, Patrick M; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W; Thacker, Robert W; Montoya, Jose M; Hentschel, Ute; Webster, Nicole S

    2016-01-01

    Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690

  12. The structure and evolution of boundary layers in stratified convection

    NASA Astrophysics Data System (ADS)

    Anders, Evan H.; Brown, Benjamin; Brandenburg, Axel; Rast, Mark

    2016-05-01

    Solar convection is highly stratified, and the density in the Sun increases by many orders of magnitude from the photosphere to the base of the convection zone. The photosphere is an important boundary layer, and interactions between the surface convection and deep convection may lie at the root of the solar convection conundrum, where observed large-scale velocities are much lower than predicted by full numerical simulations. Here, we study the structure and time evolution of boundary layers in numerical stratified convection. We study fully compressible convection within plane-parallel layers using the Dedalus pseudospectral framework. Within the context of polytropic stratification, we study flows from low (1e-3) to moderately high (0.1) Mach number, and at moderate to high Rayleigh number to study both laminar and turbulent convective transport. We aim to characterize the thickness and time variation of velocity and thermal (entropy) boundary layers at the top and bottom boundaries of the domain.

  13. Diversity, structure and convergent evolution of the global sponge microbiome

    PubMed Central

    Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.

    2016-01-01

    Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690

  14. Structure and Evolution of Internally Heated Hot Jupiters

    NASA Astrophysics Data System (ADS)

    Komacek, Thaddeus D.; Youdin, Andrew N.

    2015-11-01

    The transit radii of many close-in extrasolar giant planets, or "hot Jupiters," are systematically larger than those expected from models considering only cooling from an initial high-entropy state. Though these planets receive strong irradiation, with equilibrium temperatures of 1000-2500 Kelvin, the absorption of stellar incident flux in the upper atmosphere alone cannot explain these anomalous radii. More promising mechanisms involve irradiation-driven meteorological activity, which penetrates much deeper into the planet than direct stellar heating. This circulation can lead to large-scale mixing and downward transport of kinetic energy, both processes whereby a fraction of the stellar incident power is transported downwards to the interior of the planet. Here we consider how deposition of heat at different pressure levels or structural locations within a planet affects the resulting evolution. To do so, we run global gas giant evolutionary models with with the stellar structure code MESA including additional energy dissipation. We find that relatively shallow atmospheric heating alone can explain the transit radii of the hot Jupiter sample, but heating in the convective zone is an order of magnitude more efficient regardless of exact location. Additionally, a small difference in atmospheric heating location can have a significant effect on radius evolution, especially near the radiative-convective boundary. The most efficient location to heat the planet is at the radiative-convective boundary or deeper. We expect that shear instabilities at this interface may naturally explain energy dissipation at the radiative-convective boundary, which typically lies at a pressure of ~1 kilobar after 5 Gyr for a planet with the mass and incident stellar flux of HD 209458b. Hence, atmospheric processes are most efficient at explaining the bloated radii of hot Jupiters if they can transport incident stellar power downwards to the top of the inner convective zone.

  15. The influence of halo evolution on galaxy structure

    NASA Astrophysics Data System (ADS)

    White, Simon

    2015-03-01

    If Einstein-Newton gravity holds on galactic and larger scales, then current observations demonstrate that the stars and interstellar gas of a typical bright galaxy account for only a few percent of its total nonlinear mass. Dark matter makes up the rest and cannot be faint stars or any other baryonic form because it was already present and decoupled from the radiation plasma at z = 1000, long before any nonlinear object formed. The weak gravito-sonic waves so precisely measured by CMB observations are detected again at z = 4 as order unity fluctuations in intergalactic matter. These subsequently collapse to form today's galaxy/halo systems, whose mean mass profiles can be accurately determined through gravitational lensing. High-resolution simulations link the observed dark matter structures seen at all these epochs, demonstrating that they are consistent and providing detailed predictions for all aspects of halo structure and growth. Requiring consistency with the abundance and clustering of real galaxies strongly constrains the galaxy-halo relation, both today and at high redshift. This results in detailed predictions for galaxy assembly histories and for the gravitational arena in which galaxies live. Dark halos are not expected to be passive or symmetric but to have a rich and continually evolving structure which will drive evolution in the central galaxy over its full life, exciting warps, spiral patterns and tidal arms, thickening disks, producing rings, bars and bulges. Their growth is closely related to the provision of new gas for galaxy building.

  16. A Dynamic Model for the Evolution of Protein Structure.

    PubMed

    Tal, Guy; Boca, Simina Maria; Mittenthal, Jay; Caetano-Anollés, Gustavo

    2016-05-01

    Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) levels. We fit the models with data from phylogenomic trees of domain structures and evaluate the distributions of the resulting parameters and their implications. The trees were inferred from a census of domain structures in hundreds of genomes from all three superkingdoms of life. The models used birth-death differential equations with the global abundances of structures as state variables, with one set of equations for folds and another for FSFs. Only the transitions present in the tree are assumed possible. Each fold or FSF diversifies in variants, eventually producing a new fold or FSF. The parameters specify rates of generation of variants and of new folds or FSFs. The equations were solved for the parameters by simplifying the trees to a comb-like topology, treating branches as emerging directly from a trunk. We found that the rate constants for folds and FSFs evolved similarly. These parameters showed a sharp transient change at about 1.5 Gyrs ago. This time coincides with a period in which domains massively combined in proteins and their arrangements distributed in novel lineages during the rise of organismal diversification. Our simulations suggest that exploration of protein structure space occurs through coarse-grained discoveries that undergo fine-grained elaboration. PMID:27146880

  17. Deuterostome Evolution: Large Data Set Analysis

    NASA Technical Reports Server (NTRS)

    Janies, Daniel; Wheeler, Ward

    2004-01-01

    This award allowed us to develop novel hardware for phylogenetics, collect genomic data and produce several phylogenies of deuterostome organisms, communicate the results publicly, release software into the public domain, publish textbooks and papers, and prepare for the next research projects. There are no resulting subject inventions to report. We review these activities in three sections: 1) Hardware and software and development; 2) Evolutionary biology research; 3) Our proposed future direction, predictive analysis of pathogens in support of the NASA mission.

  18. Integrating Sequence Evolution into Probabilistic Orthology Analysis.

    PubMed

    Ullah, Ikram; Sjöstrand, Joel; Andersson, Peter; Sennblad, Bengt; Lagergren, Jens

    2015-11-01

    Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MrBayesMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts. PMID:26130236

  19. Halo formation and evolution: unifying physical properties with structure

    NASA Astrophysics Data System (ADS)

    Ernest, Alllan David; Collins, Matthew P.

    2015-08-01

    The assembly of matter in the universe proliferates a variety of structures with diverse properties. For example, massive halos of clusters of galaxies have temperatures often an order of magnitude or more higher than the individual galaxy halos within the cluster, or the temperatures of isolated galaxy halos. Giant spiral galaxies contain large quantities of both dark matter and hot gas while other structures like globular clusters appear to have little or no dark matter or gas. Still others, like the dwarf spheroidal galaxies have low gravity and little hot gas, but ironically contain some of the largest fractions of dark matter in the universe. Star forming rates (SFRs) also vary: compare for example the SFRs of giant elliptical galaxies, globular clusters, spiral and starburst galaxies. Furthermore there is evidence that the various structure types have existed over a large fraction of cosmic history. How can this array of variation in properties be reconciled with galaxy halo formation and evolution?We propose a model of halo formation [1] and evolution [2] that is consistent with both primordial nucleosynthesis (BBN) and the isotropies in the cosmic microwave background (CMB). The model uses two simple parameters, the total mass and size of a structure, to (1) explain why galaxies have the fractions of dark matter that they do (including why dwarf spheroidals are so dark matter dominated despite their weak gravity), (2) enable an understanding of the black hole-bulge/black hole-dark halo relations, (3) explain how fully formed massive galaxies can occur so early in cosmic history, (4) understand the connection between spiral and elliptical galaxies (5) unify the nature of globular clusters, dwarf spheroidal galaxies and bulges and (6) predict the temperatures of hot gas halos and understand how cool galaxy halos can remain stable in the hot environments of cluster-galaxy halos.[1] Ernest, A. D., 2012, in Prof. Ion Cotaescu (Ed) Advances in Quantum Theory, pp

  20. Markov chains or the game of structure and chance. From complex networks, to language evolution, to musical compositions

    NASA Astrophysics Data System (ADS)

    Blanchard, Ph.; Dawin, J. R.; Volchenkov, D.

    2010-06-01

    Markov chains provide us with a powerful tool for studying the structure of graphs and databases in details. We review the method of generalized inverses for Markov chains and apply it for the analysis of urban structures, evolution of languages, and musical compositions. We also discuss a generalization of Lévy flights over large complex networks and study the interplay between the nonlinearity of diffusion process and the topological structure of the network.

  1. Analysis of intratumor heterogeneity unravels lung cancer evolution.

    PubMed

    de Bruin, Elza C; McGranahan, Nicholas; Swanton, Charles

    2015-01-01

    Lung cancer is a disease with dismal outcome. We recently reported a detailed intratumor heterogeneity analysis in 7 non-small cell lung cancer samples, revealing spatially separated driver events as well as the temporal dynamics of mutational processes and demonstrating an important role for APOBEC-mediated heterogeneity later in disease evolution. PMID:27308463

  2. Analysis of intratumor heterogeneity unravels lung cancer evolution

    PubMed Central

    de Bruin, Elza C; McGranahan, Nicholas; Swanton, Charles

    2015-01-01

    Lung cancer is a disease with dismal outcome. We recently reported a detailed intratumor heterogeneity analysis in 7 non-small cell lung cancer samples, revealing spatially separated driver events as well as the temporal dynamics of mutational processes and demonstrating an important role for APOBEC-mediated heterogeneity later in disease evolution. PMID:27308463

  3. Lithosphere structure and subsidence evolution of the conjugate S-African and Argentine margins

    NASA Astrophysics Data System (ADS)

    Dressel, Ingo; Scheck-Wenderoth, Magdalena; Cacace, Mauro; Götze, Hans-Jürgen; Franke, Dieter

    2016-04-01

    The bathymetric evolution of the South Atlantic passive continental margins is a matter of debate. Though it is commonly accepted that passive margins experience thermal subsidence as a result of lithospheric cooling as well as load induced subsidence in response to sediment deposition it is disputed if the South Atlantic passive margins were affected by additional processes affecting the subsidence history after continental breakup. We present a subsidence analysis along the SW African margin and offshore Argentina and restore paleobathymetries to assess the subsidence evolution of the margin. These results are discussed with respect to mechanisms behind margin evolution. Therefore, we use available information about the lithosphere-scale present-day structural configuration of these margins as a starting point for the subsidence analysis. A multi 1D backward modelling method is applied to separate individual subsidence components such as the thermal- as well as the load induced subsidence and to restore paleobathymetries for the conjugate margins. The comparison of the restored paleobathymetries shows that the conjugate margins evolve differently: Continuous subsidence is obtained offshore Argentina whereas the subsidence history of the SW African margin is interrupted by phases of uplift. This differing results for both margins correlate also with different structural configurations of the subcrustal mantle. In the light of these results we discuss possible implications for uplift mechanisms.

  4. Thermal evolution of the crystal structure of the orthorhombic perovskite LaFeO{sub 3}

    SciTech Connect

    Dixon, Charlotte A.L.; Kavanagh, Christopher M.; Knight, Kevin S.; Kockelmann, Winfried; Morrison, Finlay D.; Lightfoot, Philip

    2015-10-15

    The thermal evolution of the crystal structure of the prototypical orthorhombic perovskite LaFeO{sub 3} has been studied in detail by powder neutron diffraction in the temperature range 25analysis, combined with an analysis in terms of symmetry-adapted modes, allows key aspects of the thermal behavior to be understood. In particular, the largest-amplitude symmetry modes (viz. in-phase and out-of-phase octahedral tilts, and A-site cation displacements) are shown to display relatively ‘normal’ behavior, increasing with decreasing temperature, which contrasts with the anomalous behavior previously shown by the derivative Bi{sub 0.5}La{sub 0.5}FeO{sub 3}. However, an unexpected behavior is seen in the nature of the intra-octahedral distortion, which is used to rationalize the unique occurrence of a temperature dependent crossover of the a and c unit cell metrics in this compound. - Graphical abstract: The unusual thermal evolution of lattice metrics in the perovskite LaFeO{sub 3} is rationalized from a detailed powder neutron diffraction study. - Highlights: • Crystal structure of the perovskite LaFeO{sub 3} studied in detail by powder neutron diffraction. • Unusual thermal evolution of lattice metrics rationalized. • Contrasting behavior to Bi-doped LaFeO{sub 3}. • Octahedral distortion/tilt parameters explain unusual a and c lattice parameter behavior.

  5. CODSTRAN - Composite durability structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Smith, G. T.

    1978-01-01

    CODSTRAN (COmposite Durability STRucture ANalysis) a NASA Lewis Center computer program for the prediction of defect growth and fracture of composite structures when subjected to service loads is presented. Organization, capabilities and present status are discussed. Organizational aspects include executive, input, output, analysis and composite mechanics modules. Capabilities include: durability assessment of large structures and complex structural parts from composites, structural response due to static, cyclic, transient impact and thermal loads, and criteria for static, cyclic, and dynamic fracture. At the present state of development some of CODSTRAN's analysis capabilities include composite mechanics, static failures, and lamination residual stresses. An application in which CODSTRAN is used to predict the defect growth in a flat specimen, with a center through-slit under tension is studied. When completed, CODSTRAN will account for geometry and material nonlinearities, environmental effects as well as static, cyclic and dynamic fracture.

  6. Structure and Molecular Evolution of CDGSH Iron-Sulfur Domains

    PubMed Central

    Lai, Shaomei; Ye, Keqiong

    2011-01-01

    The recently discovered CDGSH iron-sulfur domains (CISDs) are classified into seven major types with a wide distribution throughout the three domains of life. The type 1 protein mitoNEET has been shown to fold into a dimer with the signature CDGSH motif binding to a [2Fe-2S] cluster. However, the structures of all other types of CISDs were unknown. Here we report the crystal structures of type 3, 4, and 6 CISDs determined at 1.5 Å, 1.8 Å and 1.15 Å resolution, respectively. The type 3 and 4 CISD each contain one CDGSH motif and adopt a dimeric structure. Although similar to each other, the two structures have permutated topologies, and both are distinct from the type 1 structure. The type 6 CISD contains tandem CDGSH motifs and adopts a monomeric structure with an internal pseudo dyad symmetry. All currently known CISD structures share dual iron-sulfur binding modules and a β-sandwich for either intermolecular or intramolecular dimerization. The iron-sulfur binding module, the β-strand N-terminal to the module and a proline motif are conserved among different type structures, but the dimerization module and the interface and orientation between the two iron-sulfur binding modules are divergent. Sequence analysis further shows resemblance between CISD types 4 and 7 and between 1 and 2. Our findings suggest that all CISDs share common ancestry and diverged into three primary folds with a characteristic phylogenetic distribution: a eukaryote-specific fold adopted by types 1 and 2 proteins, a prokaryote-specific fold adopted by types 3, 4 and 7 proteins, and a tandem-motif fold adopted by types 5 and 6 proteins. Our comprehensive structural, sequential and phylogenetic analysis provides significant insight into the assembly principles and evolutionary relationship of CISDs. PMID:21949752

  7. The structural evolution of a P2Y-like G-protein-coupled receptor.

    PubMed

    Schulz, Angela; Schöneberg, Torsten

    2003-09-12

    Based on the now available crystallographic data of the G-protein-coupled receptor (GPCR) prototype rhodopsin, many studies have been undertaken to build or verify models of other GPCRs. Here, we mined evolution as an additional source of structural information that may guide GPCR model generation as well as mutagenesis studies. The sequence information of 61 cloned orthologs of a P2Y-like receptor (GPR34) enabled us to identify motifs and residues that are important for maintaining the receptor function. The sequence data were compared with available sequences of 77 rhodopsin orthologs. Under a negative selection mode, only 17% of amino acid residues were preserved during 450 million years of GPR34 evolution. On the contrary, in rhodopsin evolution approximately 43% residues were absolutely conserved between fish and mammals. Despite major differences in their structural conservation, a comparison of structural data suggests that the global arrangement of the transmembrane core of GPR34 orthologs is similar to rhodopsin. The evolutionary approach was further applied to functionally analyze the relevance of common scaffold residues and motifs found in most of the rhodopsin-like GPCRs. Our analysis indicates that, in contrast to other GPCRs, maintaining the unique function of rhodopsin requires a more stringent network of relevant intramolecular constrains. PMID:12835326

  8. Structure and Evolution of Kuiper Belt Objects and Dwarf Planets

    NASA Astrophysics Data System (ADS)

    McKinnon, W. B.; Prialnik, D.; Stern, S. A.; Coradini, A.

    Kuiper belt objects (KBOs) accreted from a mélange of volatile ices, carbonaceous matter, and rock of mixed interstellar and solar nebular provenance. The transneptunian region, where this accretion took place, was likely more radially compact than today. This and the influence of gas drag during the solar nebula epoch argue for more rapid KBO accretion than usually considered. Early evolution of KBOs was largely the result of heating due to radioactive decay, the most important potential source being 26Al, whereas long-term evolution of large bodies is controlled by the decay of U, Th, and 40K. Several studies are reviewed dealing with the evolution of KBO models, calculated by means of one-dimensional numerical codes that solve the heat and mass balance equations. It is shown that, depending on parameters (principally rock content and porous conductivity), KBO interiors may have reached relatively high temperatures. The models suggest that KBOs likely lost ices of very volatile species during early evolution, whereas ices of less-volatile species should be retained in cold, less-altered subsurface layers. Initially amorphous ice may have crystallized in KBO interiors, releasing volatiles trapped in the amorphous ice, and some objects may have lost part of these volatiles as well. Generally, the outer layers are far less affected by internal evolution than the inner part, which in the absence of other effects (such as collisions) predicts a stratified composition and altered porosity distribution. Kuiper belt objects are thus unlikely to be "the most pristine objects in the solar system," but they do contain key information as to how the early solar system accreted and dynamically evolved. For large (dwarf planet) KBOs, long-term radiogenic heating alone may lead to differentiated structures -- rock cores, ice mantles, volatile-ice-rich "crusts," and even oceans. Persistence of oceans and (potential) volcanism to the present day depends strongly on body size and

  9. Regularized Generalized Structured Component Analysis

    ERIC Educational Resources Information Center

    Hwang, Heungsun

    2009-01-01

    Generalized structured component analysis (GSCA) has been proposed as a component-based approach to structural equation modeling. In practice, GSCA may suffer from multi-collinearity, i.e., high correlations among exogenous variables. GSCA has yet no remedy for this problem. Thus, a regularized extension of GSCA is proposed that integrates a ridge…

  10. Towards Controlling the Structural Evolution and Kinetic Properties of Monolayer (Hydr)oxide-Metal Interfaces

    NASA Astrophysics Data System (ADS)

    Zeng, Zhenhua; Kubal, Joseph; Greeley, Jeff

    2015-03-01

    Ultrathin (hydr)oxide films grown on transition metal surfaces have widespread applications in processes related to electrocatalysis, photocatalysis, coating and corrosion inhibition, and heterogeneous catalysis, among others. These hybrid systems with novel properties are often prepared and characterized under very specific conditions, such as ultrahigh vacuum. When subsequently used in various applications, however, significant structural evolution, which depends strongly on the reaction conditions in-situ, is expected and has been widely observed. Nevertheless, the atomic-level details of these structural changes are generally unknown, particularly in the case of electrocatalytic environments. In order to identify structure-property relationships and, ultimately, predict new materials with improved performance, the development of such understanding is essential. In the present study, on the basis of detailed density functional theory calculations, and using Ni (hydr)oxide films on Pt(111) and Au(111) electrodes as model systems, we describe a detailed structural analysis of film growth and electrocatalytic analysis of hydrogen evolution at three-phase boundaries under alkaline electrochemical conditions.

  11. Evolution of Diversity in Spatially Structured Escherichia coli Populations▿

    PubMed Central

    Ponciano, José Miguel; La, Hyun-Joon; Joyce, Paul; Forney, Larry J.

    2009-01-01

    The stochastic Ricker population model was used to investigate the generation and maintenance of genetic diversity in a bacterial population grown in a spatially structured environment. In particular, we showed that Escherichia coli undergoes dramatic genetic diversification when grown as a biofilm. Using a novel biofilm entrapment method, we retrieved 64 clones from each of six different depths of a mature biofilm, and after subculturing for ∼30 generations, we measured their growth kinetics in three different media. We fit a stochastic Ricker population growth model to the recorded growth curves. The growth kinetics of clonal lineages descendant from cells sampled at different biofilm depths varied as a function of both the depth in the biofilm and the growth medium used. We concluded that differences in the growth dynamics of clones were heritable and arose during adaptive evolution under local conditions in a spatially heterogeneous environment. We postulate that under nutrient-limited conditions, selective sweeps would be protracted and would be insufficient to purge less-fit variants, a phenomenon that would allow the coexistence of genetically distinct clones. These findings contribute to the current understanding of biofilm ecology and complement current hypotheses for the maintenance and generation of microbial diversity in spatially structured environments. PMID:19648364

  12. Evolution of myelin ultrastructure and the major structural myelin proteins.

    PubMed

    Inouye, Hideyo; Kirschner, Daniel A

    2016-06-15

    Myelin sheaths, as the specialized tissue wrapping the nerve fibers in the central and peripheral nervous systems (CNS and PNS), are responsible for rapid conduction of electrical signals in these fibers. We compare the nerve myelin sheaths of different phylogenetic origins-including mammal, rodent, bird, reptile, amphibian, lungfish, teleost, and elasmobranch-with respect to periodicities and inter-membrane separations at their cytoplasmic and extracellular appositions, and correlate these structural parameters with biochemical composition. P0 glycoprotein and P0-like proteins are present in PNS of terrestrial species or land vertebrates (Tetrapod) and in CNS and PNS of aquatic species. Proteolipid protein (PLP) is a major component only in the CNS myelin of terrestrial species and is involved in compaction of the extracellular apposition. The myelin structures of aquatic garfish and lungfish, which contain P0-like protein both in CNS and PNS, are similar to those of terrestrial species, indicating that they may be transitional organisms between water and land species. This article is part of a Special Issue entitled SI: Myelin Evolution. PMID:26519753

  13. Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins

    PubMed Central

    Murungi, Edwin K.; Kariithi, Henry M.; Adunga, Vincent; Obonyo, Meshack; Christoffels, Alan

    2014-01-01

    Tetraspanins are important conserved integral membrane proteins expressed in many organisms. Although there is limited knowledge about the full repertoire, evolution and structural characteristics of individual members in various organisms, data obtained so far show that tetraspanins play major roles in membrane biology, visual processing, memory, olfactory signal processing, and mechanosensory antennal inputs. Thus, these proteins are potential targets for control of insect pests. Here, we report that the genome of the tsetse fly, Glossina morsitans (Diptera: Glossinidae) encodes at least seventeen tetraspanins (GmTsps), all containing the signature features found in the tetraspanin superfamily members. Whereas six of the GmTsps have been previously reported, eleven could be classified as novel because their amino acid sequences do not map to characterized tetraspanins in the available protein data bases. We present a model of the GmTsps by using GmTsp42Ed, whose presence and expression has been recently detected by transcriptomics and proteomics analyses of G. morsitans. Phylogenetically, the identified GmTsps segregate into three major clusters. Structurally, the GmTsps are largely similar to vertebrate tetraspanins. In view of the exploitation of tetraspanins by organisms for survival, these proteins could be targeted using specific antibodies, recombinant large extracellular loop (LEL) domains, small-molecule mimetics and siRNAs as potential novel and efficacious putative targets to combat African trypanosomiasis by killing the tsetse fly vector. PMID:26462947

  14. Functional role, structure, and evolution of the melanocortin-4 receptor.

    PubMed

    Schiöth, Helgi B; Lagerström, Malin C; Watanobe, Hajime; Jonsson, Logi; Vergoni, Anna Valeria; Ringholm, Aneta; Skarphedinsson, Jon O; Skuladottir, Gudrun V; Klovins, Janis; Fredriksson, Robert

    2003-06-01

    The melanocortin (MC)-4 receptor participates in regulating body weight homeostasis. We demonstrated early that acute blockage of the MC-4 receptor increases food intake and relieves anorexic conditions in rats. Our recent studies show that 4-week chronic blockage of the MC-4 receptor leads to robust increases in food intake and development of obesity, whereas stimulation of the receptor leads to anorexia. Interestingly, the food conversion ratio was clearly increased by MC-4 receptor blockage, whereas it was decreased in agonist-treated rats in a transient manner. Chronic infusion of an agonist caused a transient increase in oxygen consumption. Our studies also show that the MC-4 receptor plays a role in luteinizing hormone and prolactin surges in female rats. The MC-4 receptor has a role in mediating the effects of leptin on these surges. The phylogenetic relation of the MC-4 receptor to other GPCRs in the human genome was determined. The three-dimensional structure of the protein was studied by construction of a high-affinity zinc binding site between the helices, using two histidine residues facing each other. We also cloned the MC-4 receptor from evolutionary important species and showed by chromosomal mapping a conserved synteny between humans and zebrafish. The MC-4 receptor has been remarkably conserved in structure and pharmacology for more than 400 million years, implying that the receptor participated in vital physiological functions early in vertebrate evolution. PMID:12851300

  15. Orchestrated structure evolution: modeling growth-regulated nanomanufacturing.

    PubMed

    Abbasi, Shaghayegh; Kitayaporn, Sathana; Schwartz, Daniel T; Böhringer, Karl F

    2011-04-22

    Orchestrated structure evolution (OSE) is a scalable manufacturing method that combines the advantages of top-down (tool-directed) and bottom-up (self-propagating) approaches. The method consists of a seed patterning step that defines where material nucleates, followed by a growth step that merges seeded islands into the final patterned thin film. We develop a model to predict the completed pattern based on a computationally efficient approximate Green's function solution of the diffusion equation plus a Voronoi diagram based approach that defines the final grain boundary structure. Experimental results rely on electron beam lithography to pattern the seeds, followed by the mass transfer limited growth of copper via electrodeposition. The seed growth model is compared with experimental results to quantify nearest neighbor seed-to-seed interactions as well as how seeds interact with the pattern boundary to impact the local growth rate. Seed-to-seed and seed-to-pattern interactions are shown to result in overgrowth of seeds on edges and corners of the shape, where seeds have fewer neighbors. We explore how local changes to the seed location can be used to improve the patterning quality without increasing the manufacturing cost. OSE is shown to enable a unique set of trade-offs between the cost, time, and quality of thin film patterning. PMID:21393828

  16. Effect of spatial structure on the evolution of cooperation

    NASA Astrophysics Data System (ADS)

    Roca, Carlos P.; Cuesta, José A.; Sánchez, Angel

    2009-10-01

    Spatial structure is known to have an impact on the evolution of cooperation, and so it has been intensively studied during recent years. Previous work has shown the relevance of some features, such as the synchronicity of the updating, the clustering of the network, or the influence of the update rule. This has been done, however, for concrete settings with particular games, networks, and update rules, with the consequence that some contradictions have arisen and a general understanding of these topics is missing in the broader context of the space of 2×2 games. To address this issue, we have performed a systematic and exhaustive simulation in the different degrees of freedom of the problem. In some cases, we generalize previous knowledge to the broader context of our study and explain the apparent contradictions. In other cases, however, our conclusions refute what seems to be established opinions in the field, as for example the robustness of the effect of spatial structure against changes in the update rule, or offer new insights into the subject, e.g., the relation between the intensity of selection and the asymmetry between the effects on games with mixed equilibria.

  17. Tatooine Nurseries: Structure and Evolution of Circumbinary Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Vartanyan, David; Garmilla, José A.; Rafikov, Roman R.

    2016-01-01

    Recent discoveries of circumbinary planets by the Kepler mission provide motivation for understanding their birthplaces—protoplanetary disks around stellar binaries with separations ≲ 1 {{AU}}. We explore properties and evolution of such circumbinary disks focusing on modification of their structure caused by tidal coupling to the binary. We develop a set of analytical scaling relations describing viscous evolution of the disk properties, which are verified and calibrated using 1D numerical calculations with realistic inputs. Injection of angular momentum by the central binary suppresses mass accretion onto the binary and causes radial distribution of the viscous angular momentum flux {F}J to be different from that in a standard accretion disk around a single star with no torque at the center. Disks with no mass accretion at the center develop an {F}J profile that is flat in radius. Radial profiles of temperature and surface density are also quite different from those in disks around single stars. Damping of the density waves driven by the binary and viscous dissipation dominates heating of the inner disk (within 1-2 AU), pushing the ice line beyond 3-5 AU, depending on disk mass and age. Irradiation by the binary governs disk thermodynamics beyond ˜10 AU. However, self-shadowing by the hot inner disk may render central illumination irrelevant out to ˜20 AU. Spectral energy distribution of a circumbinary disk exhibits a distinctive bump around 10 μm, which may facilitate identification of such disks around unresolved binaries. Efficient tidal coupling to the disk drives orbital inspiral of the binary and may cause low-mass and relatively compact binaries to merge into a single star within the disk lifetime. We generally find that circumbinary disks present favorable sites for planet formation (despite their wider zone of volatile depletion), in agreement with the statistics of Kepler circumbinary planets.

  18. Structural evolution mechanisms of amorphous and liquid As2Se3 at high pressures

    NASA Astrophysics Data System (ADS)

    Properzi, L.; Santoro, M.; Minicucci, M.; Iesari, F.; Ciambezi, M.; Nataf, L.; Le Godec, Y.; Irifune, T.; Baudelet, F.; Di Cicco, A.

    2016-06-01

    The elusive structure of compressed, melt-quenched As2Se3 was studied in both its liquid and amorphous form up to 4.4 and 30 GPa, respectively, by means of x-ray absorption spectroscopy and diffraction. The evolution of the short-range structure is studied by As and Se multiple K -edge extended x-ray absorption fine structure (EXAFS) refinement, while changes in intermediate-range ordering are revealed by x-ray diffraction and near-edge structures. In the liquid, at the nearest-neighbor length scales, a gradual disordering and slight elongation of the As-Se average distances is observed, preserving the local coordination upon increasing pressure, whereas substantial compression and disordering are observed at intermediate distances. Similarly, in the amorphous form we found a progressive slight elongation and disordering of the first-neighbor As-Se average distance R (from ˜2.42 to 2.44 Å) and bond variance σ2 (from ˜0.004 to 0.008 Å2) upon increasing pressures up to 30 GPa. On the other hand, gradual shortening of the second and farther neighbor distances, more evident below 15 GPa, are compatible with data analysis. No sign of crystallization and gradual metallization are observed for amorphous a-As2Se3 up to 30 GPa. The emerging picture for the structure evolution under high pressures is a compaction mechanism involving mainly changes at intermediate distances, weakly affecting the first-neighbor bonding character.

  19. Tectonic structure and evolution of the Atlantic continental margin

    SciTech Connect

    Klitgord, K.D.; Schouten, H.; Hutchinson, D.R.

    1985-01-01

    The Atlantic continental margin developed across the boundary between continental and oceanic crust as rifting and then sea-floor spreading broke apart and separated the North American and African plates, forming the Atlantic Ocean Basin. Continental rifting began in Late Triassic with reactivation of Paleozoic thrust faults as normal faults and with extension across a broad zone of subparallel rift basins. Extension became localized in Early to Middle Jurassic along the zone that now underlies the large marginal basins, and other rift zones, such as the Newark, Hartford, and Fundy basins, were abandoned. Rifting and crustal stretching between the two continents gave way to sea-floor spreading Middle Jurassic and the formation of oceanic crust. This tectonic evolution resulted in formation of distinctive structural features. The marginal basins are underlain by a thinner crust and contain a variety of fault-controlled structures, including half-grabens, seaward- and landward-tilted blocks, faults that die out within the crust, and faults that penetrate the entire crust. This variable structure probably resulted from the late Triassic-Early Jurassic pattern of normal, listric, and antithetic faults that evolved from the Paleozoic thrust fault geometry. The boundary between marginal basins and oceanic crust is marked approximately by the East Coast Magnetic Anomaly (ECMA). A major basement fault is located in the Baltimore Canyon trough at the landward edge of the ECMA and a zone of seaward dipping reflectors is found just seaward of the ECMA off Georges Bank. The fracture zone pattern in Mesozoic oceanic crust can be traced landward to the ECMA.

  20. Diverse structural evolution at z > 1 in cosmologically simulated galaxies

    NASA Astrophysics Data System (ADS)

    Snyder, Gregory F.; Lotz, Jennifer; Moody, Christopher; Peth, Michael; Freeman, Peter; Ceverino, Daniel; Primack, Joel; Dekel, Avishai

    2015-08-01

    From mock Hubble Space Telescope images, we quantify non-parametric statistics of galaxy morphology, thereby predicting the emergence of relationships among stellar mass, star formation, and observed rest-frame optical structure at 1 < z < 3. We measure automated diagnostics of galaxy morphology in cosmological simulations of the formation of 22 central galaxies with 9.3 < log10M*/M⊙ < 10.7. These high-spatial-resolution zoom-in calculations enable accurate modelling of the rest-frame UV and optical morphology. Even with small numbers of galaxies, we find that structural evolution is neither universal nor monotonic: galaxy interactions can trigger either bulge or disc formation, and optically bulge-dominated galaxies at this mass may not remain so forever. Simulated galaxies with M* > 1010M⊙ contain relatively more disc-dominated light profiles than those with lower mass, reflecting significant disc brightening in some haloes at 1 < z < 2. By this epoch, simulated galaxies with specific star formation rates below 10- 9.7 yr- 1 are more likely than normal star-formers to have a broader mix of structural types, especially at M* > 1010 M⊙. We analyse a cosmological major merger at z ˜ 1.5 and find that the newly proposed Multimode-Intensity-Deviation (MID) morphology diagnostics trace later merger stages while Gini-M20 trace earlier ones. MID is sensitive also to clumpy star-forming discs. The observability time of typical MID-enhanced events in our simulation sample is <100 Myr. A larger sample of cosmological assembly histories may be required to calibrate such diagnostics in the face of their sensitivity to viewing angle, segmentation algorithm, and various phenomena such as clumpy star formation and minor mergers.

  1. Coda Wave Interferometry Method Applied in Structural Monitoring to Assess Damage Evolution in Masonry and Concrete Structures

    NASA Astrophysics Data System (ADS)

    Masera, D.; Bocca, P.; Grazzini, A.

    2011-07-01

    In this experimental program the main goal is to monitor the damage evolution in masonry and concrete structures by Acoustic Emission (AE) signal analysis applying a well-know seismic method. For this reason the concept of the coda wave interferometry is applied to AE signal recorded during the tests. Acoustic Emission (AE) are very effective non-destructive techniques applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate the velocity of ultrasound waves propagation and the amount of energy released during fracture propagation to obtain information on the criticality of the ongoing process. By means of AE monitoring, an experimental analysis on a set of reinforced masonry walls under variable amplitude loading and strengthening reinforced concrete (RC) beams under monotonic static load has been carried out. In the reinforced masonry wall, cyclic fatigue stress has been applied to accelerate the static creep and to forecast the corresponding creep behaviour of masonry under static long-time loading. During the tests, the evaluation of fracture growth is monitored by coda wave interferometry which represents a novel approach in structural monitoring based on AE relative change velocity of coda signal. In general, the sensitivity of coda waves has been used to estimate velocity changes in fault zones, in volcanoes, in a mining environment, and in ultrasound experiments. This method uses multiple scattered waves, which travelled through the material along numerous paths, to infer tiny temporal changes in the wave velocity. The applied method has the potential to be used as a "damage-gauge" for monitoring velocity changes as a sign of damage evolution into masonry and concrete structures.

  2. SUBSIDENCE, CRUSTAL STRUCTURE, AND THERMAL EVOLUTION OF GEORGES BANK BASIN.

    USGS Publications Warehouse

    Swift, B. Ann; Sawyer, D.S.; Grow, J.A.; Klitgord, Kim D.

    1987-01-01

    A geographical study of Georges Bank basin defines a deep crustal structure that is interpreted in terms of the basin's tectonic and thermal history. Gravity models along three basin cross sections delineate two zones of crustal thinning at the basement hinge zone and oceanic crustal margins. These two zones bound rift-stage crust (about 25 km thick) which underlies the central portion of the basin. Subsidence analysis of the basin, using data from multichannel seismic reflection lines and two COST wells, suggests a rifting and (uniform) extensional origin. Two-dimensional finite difference modeling of the basin defines a crustal structure that concurs with the gravity and subsidence studies. The resulting isotherms show no major changes in the thermal structure since the Late Jurassic. In some areas of the basin, temperature sufficient for oil generation are determined from maturation studies of Jurassic sediments. Hydrocarbon generation is questionable, however, because of the probable lack of proper and sufficient kerogen in the Jurassic deposits.

  3. Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability.

    PubMed

    Fraser, Nicholas J; Liu, Jian-Wei; Mabbitt, Peter D; Correy, Galen J; Coppin, Chris W; Lethier, Mathilde; Perugini, Matthew A; Murphy, James M; Oakeshott, John G; Weik, Martin; Jackson, Colin J

    2016-06-01

    Oligomerization has been suggested to be an important mechanism for increasing or maintaining the thermostability of proteins. Although it is evident that protein-protein contacts can result in substantial stabilization in many extant proteins, evidence for evolutionary selection for oligomerization is largely indirect and little is understood of the early steps in the evolution of oligomers. A laboratory-directed evolution experiment that selected for increased thermostability in the αE7 carboxylesterase from the Australian sheep blowfly, Lucilia cuprina, resulted in a thermostable variant, LcαE7-4a, that displayed increased levels of dimeric and tetrameric quaternary structure. A trade-off between activity and thermostability was made during the evolution of thermostability, with the higher-order oligomeric species displaying the greatest thermostability and lowest catalytic activity. Analysis of monomeric and dimeric LcαE7-4a crystal structures revealed that only one of the oligomerization-inducing mutations was located at a potential protein-protein interface. This work demonstrates that by imposing a selective pressure demanding greater thermostability, mutations can lead to increased oligomerization and stabilization, providing support for the hypothesis that oligomerization is a viable evolutionary strategy for protein stabilization. PMID:27016206

  4. Structural evolution and petroleum productivity of the Baltic basin

    SciTech Connect

    Ulmishek, G.F. )

    1991-08-01

    The Baltic basin is an oval depression located in the western part of the Russian craton; it occupies the eastern Baltic Sea and adjacent onshore areas. The basin contains more than 5,000 m of sedimentary rocks ranging from latest Proterozoic to Tertiary in age. These rocks consist of four tectonostratigraphic sequences deposited during major tectonic episodes of basin evolution. Principal unconformities separate the sequences. The basin is underlain by a rift probably filled with Upper Proterozoic rocks. Vendian and Lower Cambrian rocks (Baikalian sequence) form two northeast-trending depressions. The principal stage of the basin development was during deposition of a thick Middle Cambrian-Lower Devonian (Caledonian) sequence. This stage was terminated by the most intense deformations in the basin history. The Middle Devonian-Carboniferous (Hercynian) and Permian-Tertiary (Kimmerian-Alpine) tectonic and depositional cycles only slightly modified the basin geometry and left intact the main structural framework of underlying rocks. The petroleum productivity of the basin is related to the Caledonian tectonostratigraphic sequence that contains both source rocks and reservoirs. However, maturation of source rocks, migration of oil, and formation of fields took place mostly during deposition of the Hercynian sequence.

  5. Magnetic field structure evolution in rotating magnetic field plasmas

    SciTech Connect

    Petrov, Yuri; Yang Xiaokang; Huang, T.-S.

    2008-07-15

    A study of magnetic field structure evolution during 40-ms plasma discharge has been performed in a new device with 80 cm long/40 cm diameter cylindrical chamber, in which a plasma current I{sub p}{approx_equal}2 kA was driven and sustained by a rotating magnetic field. The main focus of the experiments is on how the changes in externally applied magnetic field affect the current profile and magnetic field in plasma. During plasma discharge, a pulse current was briefly fed to a magnetic coil located at the midplane (middle coil). The magnetic field in cross section of plasma was scanned with pickup probes. Two regimes were studied: without and with an external toroidal field (TF) produced by axial I{sub z} current. With a relatively small current (I{sub m} {<=} 600 A) in the middle coil, the plasma current is boosted up to 5 kA. The magnetic flux surfaces become extended along the axial Z direction, sometimes with the formation of doublet shape plasma. The regime without TF appears to be less stable, presumably due to the reversal of plasma current in central area of plasma column.

  6. Evolution of grain structures during directional solidification of silicon wafers

    NASA Astrophysics Data System (ADS)

    Lin, H. K.; Wu, M. C.; Chen, C. C.; Lan, C. W.

    2016-04-01

    The evolution of grain structures, especially the types of grain boundaries (GBs), during directional solidification is crucial to the electrical properties of multicrystalline silicon used for solar cells. To study this, the electric molten zone crystallization (EMZC) of silicon wafers at different drift speeds from 2 to 6 mm/min was considered. It was found that <111> orientation was dominant at the lower drift velocity, while <112> orientation at the higher drift velocity. Most of the non-∑GBs tended to align with the thermal gradient, but some tilted toward the unfavorable grains having higher interfacial energies. On the other hand, the tilted ∑3GBs tended to decrease during grain competition, except at the higher speed, where the twin nucleation became frequent. The competition of grains separated by ∑GBs could be viewed as the interactions of GBs that two coherent ∑3n GBs turned into one ∑3nGB following certain relations as reported before. On the other hand, when ∑ GBs met non-∑ GBs, the non-∑ GBs remained which explained the decrease of ∑ GBs at the lower speed.

  7. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    PubMed Central

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; Brown Jr., G.E.

    2015-01-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Yet, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils. PMID:27123494

  8. The structure and evolution of buyer-supplier networks.

    PubMed

    Mizuno, Takayuki; Souma, Wataru; Watanabe, Tsutomu

    2014-01-01

    In this paper, we investigate the structure and evolution of customer-supplier networks in Japan using a unique dataset that contains information on customer and supplier linkages for more than 500,000 incorporated non-financial firms for the five years from 2008 to 2012. We find, first, that the number of customer links is unequal across firms; the customer link distribution has a power-law tail with an exponent of unity (i.e., it follows Zipf's law). We interpret this as implying that competition among firms to acquire new customers yields winners with a large number of customers, as well as losers with fewer customers. We also show that the shortest path length for any pair of firms is, on average, 4.3 links. Second, we find that link switching is relatively rare. Our estimates indicate that the survival rate per year for customer links is 92 percent and for supplier links 93 percent. Third and finally, we find that firm growth rates tend to be more highly correlated the closer two firms are to each other in a customer-supplier network (i.e., the smaller is the shortest path length for the two firms). This suggests that a non-negligible portion of fluctuations in firm growth stems from the propagation of microeconomic shocks - shocks affecting only a particular firm - through customer-supplier chains. PMID:25000368

  9. Mutation rates and the evolution of germline structure

    PubMed Central

    2016-01-01

    Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and changes in cellular mutation processes at different stages of the germline. I suggest a revised model of stem-cell state transitions during spermatogenesis, in which ‘dark’ gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates. This article is part of the themed issue ‘Dating species divergences using rocks and clocks'. PMID:27325834

  10. The Structure and Evolution of Buyer-Supplier Networks

    PubMed Central

    Mizuno, Takayuki; Souma, Wataru; Watanabe, Tsutomu

    2014-01-01

    In this paper, we investigate the structure and evolution of customer-supplier networks in Japan using a unique dataset that contains information on customer and supplier linkages for more than 500,000 incorporated non-financial firms for the five years from 2008 to 2012. We find, first, that the number of customer links is unequal across firms; the customer link distribution has a power-law tail with an exponent of unity (i.e., it follows Zipf's law). We interpret this as implying that competition among firms to acquire new customers yields winners with a large number of customers, as well as losers with fewer customers. We also show that the shortest path length for any pair of firms is, on average, 4.3 links. Second, we find that link switching is relatively rare. Our estimates indicate that the survival rate per year for customer links is 92 percent and for supplier links 93 percent. Third and finally, we find that firm growth rates tend to be more highly correlated the closer two firms are to each other in a customer-supplier network (i.e., the smaller is the shortest path length for the two firms). This suggests that a non-negligible portion of fluctuations in firm growth stems from the propagation of microeconomic shocks – shocks affecting only a particular firm – through customer-supplier chains. PMID:25000368

  11. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    SciTech Connect

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.

  12. Mutation rates and the evolution of germline structure.

    PubMed

    Scally, Aylwyn

    2016-07-19

    Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and changes in cellular mutation processes at different stages of the germline. I suggest a revised model of stem-cell state transitions during spermatogenesis, in which 'dark' gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325834

  13. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    DOE PAGESBeta

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure ofmore » sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.« less

  14. Evolution of sperm structure and energetics in passerine birds.

    PubMed

    Rowe, Melissah; Laskemoen, Terje; Johnsen, Arild; Lifjeld, Jan T

    2013-02-22

    Spermatozoa exhibit considerable interspecific variability in size and shape. Our understanding of the adaptive significance of this diversity, however, remains limited. Determining how variation in sperm structure translates into variation in sperm performance will contribute to our understanding of the evolutionary diversification of sperm form. Here, using data from passerine birds, we test the hypothesis that longer sperm swim faster because they have more available energy. We found that sperm with longer midpieces have higher levels of intracellular adenosine triphosphate (ATP), but that greater energy reserves do not translate into faster-swimming sperm. Additionally, we found that interspecific variation in sperm ATP concentration is not associated with the level of sperm competition faced by males. Finally, using Bayesian methods, we compared the evolutionary trajectories of sperm morphology and ATP content, and show that both traits have undergone directional evolutionary change. However, in contrast to recent suggestions in other taxa, we show that changes in ATP are unlikely to have preceded changes in morphology in passerine sperm. These results suggest that variable selective pressures are likely to have driven the evolution of sperm traits in different taxa, and highlight fundamental biological differences between taxa with internal and external fertilization, as well as those with and without sperm storage. PMID:23282997

  15. Structure and evolution of the global seafood trade network

    NASA Astrophysics Data System (ADS)

    Gephart, Jessica A.; Pace, Michael L.

    2015-12-01

    The food production system is increasingly global and seafood is among the most highly traded commodities. Global trade can improve food security by providing access to a greater variety of foods, increasing wealth, buffering against local supply shocks, and benefit the environment by increasing overall use efficiency for some resources. However, global trade can also expose countries to external supply shocks and degrade the environment by increasing resource demand and loosening feedbacks between consumers and the impacts of food production. As a result, changes in global food trade can have important implications for both food security and the environmental impacts of production. Measurements of globalization and the environmental impacts of food production require data on both total trade and the origin and destination of traded goods (the network structure). While the global trade network of agricultural and livestock products has previously been studied, seafood products have been excluded. This study describes the structure and evolution of the global seafood trade network, including metrics quantifying the globalization of seafood, shifts in bilateral trade flows, changes in centrality and comparisons of seafood to agricultural and industrial trade networks. From 1994 to 2012 the number of countries trading in the network remained relatively constant, while the number of trade partnerships increased by over 65%. Over this same period, the total quantity of seafood traded increased by 58% and the value increased 85% in real terms. These changes signify the increasing globalization of seafood products. Additionally, the trade patterns in the network indicate: increased influence of Thailand and China, strengthened intraregional trade, and increased exports from South America and Asia. In addition to characterizing these network changes, this study identifies data needs in order to connect seafood trade with environmental impacts and food security outcomes.

  16. Structures of two molluscan hemocyanin genes: Significance for gene evolution

    PubMed Central

    Lieb, Bernhard; Altenhein, Benjamin; Markl, Jürgen; Vincent, Alexandra; van Olden, Erin; van Holde, Kensal E.; Miller, Karen I.

    2001-01-01

    We present here the description of genes coding for molluscan hemocyanins. Two distantly related mollusks, Haliotis tuberculata and Octopus dofleini, were studied. The typical architecture of a molluscan hemocyanin subunit, which is a string of seven or eight globular functional units (FUs, designated a to h, about 50 kDa each), is reflected by the gene organization: a series of eight structurally related coding regions in Haliotis, corresponding to FU-a to FU-h, with seven highly variable linker introns of 174 to 3,198 bp length (all in phase 1). In Octopus seven coding regions (FU-a to FU-g) are found, separated by phase 1 introns varying in length from 100 bp to 910 bp. Both genes exhibit typical signal (export) sequences, and in both cases these are interrupted by an additional intron. Each gene also contains an intron between signal peptide and FU-a and in the 3′ untranslated region. Of special relevance for evolutionary considerations are introns interrupting those regions that encode a discrete functional unit. We found that five of the eight FUs in Haliotis each are encoded by a single exon, whereas FU-f, FU-g, and FU-a are encoded by two, three and four exons, respectively. Similarly, in Octopus four of the FUs each correspond to an uninterrupted exon, whereas FU-b, FU-e, and FU-f each contain a single intron. Although the positioning of the introns between FUs is highly conserved in the two mollusks, the introns within FUs show no relationship either in location nor phase. It is proposed that the introns between FUs were generated as the eight-unit polypeptide evolved from a monomeric precursor, and that the internal introns have been added later. A hypothesis for evolution of the ring-like quaternary structure of molluscan hemocyanins is presented. PMID:11287637

  17. Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus)

    PubMed Central

    Matsunami, Masatoshi; Igawa, Takeshi; Michimae, Hirofumi; Miura, Toru; Nishimura, Kinya

    2016-01-01

    The Hokkaido salamander (Hynobius retardatus) is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies. PMID:27257807

  18. Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus).

    PubMed

    Matsunami, Masatoshi; Igawa, Takeshi; Michimae, Hirofumi; Miura, Toru; Nishimura, Kinya

    2016-01-01

    The Hokkaido salamander (Hynobius retardatus) is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies. PMID:27257807

  19. CODSTRAN: Composite durability structural analysis

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Smith, G. T.

    1978-01-01

    CODSTRAN (COmposite Durability STRuctural ANalysis) is an integrated computer program being developed for the prediction of defect growth and fracture of composite structures subjected to service loads and environments. CODSTRAN is briefly described with respect to organization, capabilities and present status. Application of CODSTRAN current capability to a flat composite laminate with a center slit which was subjected to axial tension loading predicted defect growth which is in good agreement with C-scan ultrasonic test records.

  20. THE STRUCTURAL EVOLUTION OF FORMING AND EARLY STAGE STAR CLUSTERS

    SciTech Connect

    Jaehnig, Karl O.; Da Rio, Nicola; Tan, Jonathan C. E-mail: ndario@ufl.edu

    2015-01-10

    We study the degree of angular substructure in the stellar position distribution of young members of Galactic star-forming regions, looking for correlations with distance from cluster center, surface number density of stars, and local dynamical age. To this end we adopt the catalog of members in 18 young (∼1-3 Myr) clusters from the Massive Young Star-Forming Complex Study in Infrared and X-ray Survey and the statistical analysis of the angular dispersion parameter, δ{sub ADP,} {sub N}. We find statistically significant correlation between δ{sub ADP,} {sub N} and physical projected distance from the center of the clusters, with the centers appearing smoother than the outskirts, consistent with more rapid dynamical processing on local dynamical, free-fall or orbital timescales. Similarly, smoother distributions are seen in regions of higher surface density, or older dynamical ages. These results indicate that dynamical processing that erases substructure is already well-advanced in young, sometimes still-forming, clusters. Such observations of the dissipation of substructure have the potential to constrain theoretical models of the dynamical evolution of young and forming clusters.

  1. The Structural Evolution of Forming and Early Stage Star Clusters

    NASA Astrophysics Data System (ADS)

    Jaehnig, Karl; Da Rio, Nicola; Tan, Jonathan C.

    2016-05-01

    We study the degree of angular substructure in the stellar position distribution of young members of Galactic star-forming regions, looking for correlations with distance from cluster center, surface number density of stars, and local dynamical age. To this end we adopt the catalog of members in 18 young (∼1-3 Myr) clusters from the Massive Young Star-Forming Complex Study in Infrared and X-ray (MYStIX) Survey and the statistical analysis of the Angular Dispersion Parameter, δADP. We find statistically significant correlation between δADP and physical projected distance from the center of the clusters, with the centers appearing smoother than the outskirts, consistent with more rapid dynamical processing on local dynamical, free-fall or orbital timescales. Similarly, smoother distributions are seen in regions of higher surface density, or older dynamical ages. These results indicate that dynamical processing that erases substructure is already well-advanced in young, sometimes still-forming, clusters. Such observations of the dissipation of substructure have the potential to constrain theoretical models of the dynamical evolution of young and forming clusters.

  2. Spectral properties of the temporal evolution of brain network structure

    NASA Astrophysics Data System (ADS)

    Wang, Rong; Zhang, Zhen-Zhen; Ma, Jun; Yang, Yong; Lin, Pan; Wu, Ying

    2015-12-01

    The temporal evolution properties of the brain network are crucial for complex brain processes. In this paper, we investigate the differences in the dynamic brain network during resting and visual stimulation states in a task-positive subnetwork, task-negative subnetwork, and whole-brain network. The dynamic brain network is first constructed from human functional magnetic resonance imaging data based on the sliding window method, and then the eigenvalues corresponding to the network are calculated. We use eigenvalue analysis to analyze the global properties of eigenvalues and the random matrix theory (RMT) method to measure the local properties. For global properties, the shifting of the eigenvalue distribution and the decrease in the largest eigenvalue are linked to visual stimulation in all networks. For local properties, the short-range correlation in eigenvalues as measured by the nearest neighbor spacing distribution is not always sensitive to visual stimulation. However, the long-range correlation in eigenvalues as evaluated by spectral rigidity and number variance not only predicts the universal behavior of the dynamic brain network but also suggests non-consistent changes in different networks. These results demonstrate that the dynamic brain network is more random for the task-positive subnetwork and whole-brain network under visual stimulation but is more regular for the task-negative subnetwork. Our findings provide deeper insight into the importance of spectral properties in the functional brain network, especially the incomparable role of RMT in revealing the intrinsic properties of complex systems.

  3. Spectral properties of the temporal evolution of brain network structure.

    PubMed

    Wang, Rong; Zhang, Zhen-Zhen; Ma, Jun; Yang, Yong; Lin, Pan; Wu, Ying

    2015-12-01

    The temporal evolution properties of the brain network are crucial for complex brain processes. In this paper, we investigate the differences in the dynamic brain network during resting and visual stimulation states in a task-positive subnetwork, task-negative subnetwork, and whole-brain network. The dynamic brain network is first constructed from human functional magnetic resonance imaging data based on the sliding window method, and then the eigenvalues corresponding to the network are calculated. We use eigenvalue analysis to analyze the global properties of eigenvalues and the random matrix theory (RMT) method to measure the local properties. For global properties, the shifting of the eigenvalue distribution and the decrease in the largest eigenvalue are linked to visual stimulation in all networks. For local properties, the short-range correlation in eigenvalues as measured by the nearest neighbor spacing distribution is not always sensitive to visual stimulation. However, the long-range correlation in eigenvalues as evaluated by spectral rigidity and number variance not only predicts the universal behavior of the dynamic brain network but also suggests non-consistent changes in different networks. These results demonstrate that the dynamic brain network is more random for the task-positive subnetwork and whole-brain network under visual stimulation but is more regular for the task-negative subnetwork. Our findings provide deeper insight into the importance of spectral properties in the functional brain network, especially the incomparable role of RMT in revealing the intrinsic properties of complex systems. PMID:26723151

  4. Evolution of cosmic structures in different environments in the quasispherical Szekeres model

    SciTech Connect

    Bolejko, Krzysztof

    2007-02-15

    This paper investigates evolution of cosmic structures in different environments. For this purpose the quasispherical Szekeres model is employed. The Szekeres model is an exact solution of the Einstein field equations within which it is possible to describe more than one structure. In this way investigations of the evolution of the cosmic structures presented here can be freed from such assumptions as a small value of the density contrast. Also, studying the evolution of two or three structures within one framework enables us to follow the interaction between these structures and their impact on the evolution. Main findings include a conclusion that small voids surrounded by large overdensities evolve slower than large, isolated voids do. On the other hand, large voids enhance the evolution of adjacent galaxy superclusters which evolve much faster than isolated superclusters.

  5. Structure and Evolution of Convection Band Occurred over the Korean Peninsula

    NASA Astrophysics Data System (ADS)

    Kim, W.; Lee, T.

    2011-12-01

    A significant portion of the annual precipitation on the Korean peninsula is produced by heavy precipitation systems (HPSs) during summer. HPSs over the Korean peninsula could be classified into four major types (convection bands, cloud clusters, isolated thunderstorms, and squall lines) by phenomenological analysis. Among four major types of HPSs, convection bands (CBs) tend to concentrate a large amount of rainfall over limited area due to their quasi-stationary behavior for several hours. Convective cells embedded in CB move along the band and new cells are continuously formed in the upstream of the band. In this study, the structure and evolution of CB have been investigated using NCEP Climate Forecast System Reanalysis (CFSR) data and Weather Research and Forecasting (WRF) model. Thirty CB cases occurred during 2000-2010 were selected to conduct composite analysis. We obtained several profiles which represent northern area (NA), southern area (SA), and upstream area (UA) of CB by composite analysis. Modest band-perpendicular wind component (5 m s-1) is found in the level of 925-1000 hPa in SA, while band-perpendicular wind component of NA is nearly zero. Additionally, equivalent potential temperature in the lower-troposphere of SA is about 10 K larger than that of NA. Low-level band-perpendicular wind component of SA seems to play an important role in the development of CB by providing the environment for large-scale convergence and transporting warm and moist air from southern area of CB. Band-parallel wind component is predominant in the middle- and lower-troposphere. On the basis of the results of composite analysis, ideal simulation for the evolution of CB was set up. The analysis for the evolution of CB is in progress.

  6. Mathematical Methods for the Analysis of Polycrystal Phase Evolutions

    NASA Astrophysics Data System (ADS)

    Zlokazov, V. B.; Bobrikov, I. A.; Balagurov, A. M.

    2016-02-01

    Two methods for an automatic analysis of the temporal evolution of a multiphase polycrystalline sample are described: The Upeak method, analyzing the spectra formally, i.e., carrying the peak search in them, and so describing the evolution in terms of spectral peaks, or having made additionally the autoindexing of the found peaks, preparing the crystallographic information for the Rietveld analysis. The Rietveld method, using an already available crystallographic information about the phase reflections, and describing the unit cell and atomic characteristics of each phase, and the mutual phase contributions to the total intensity for each item of the analyzed sequence of neutron scattering spectra. The paper describes difficulties of an automatic analysis securing the convergence of a non-linear and at the same time non-stationary fitting. The evolution of the polycrystalline compound CuFe2O4 with the temperature T in the range from 300 to 500 degrees Celsius illustrates the performance of the methods.

  7. Structural evolution of tetragonal MnO2 and its electrochemical behavior

    NASA Astrophysics Data System (ADS)

    Shafi, P. Muhammed; Bose, A. Chandra

    2016-05-01

    MnO2 nanoparticles were synthesized by simple chemical precipitation method and were subjected to different heat treatment process. The structural evolution of as-prepared MnO2 nanoparticles at different annealing temperature was confirmed by XRD analysis. The weight loss as well as the heat flow associated with the thermal decomposition was studied by thermogravimetric analysis (TGA) along with differential thermal analysis (DTA). The functional group and phase formation were confirmed by Fourier transform infrared spectroscopy (FTIR). Finally electrochemical properties were evaluated using cyclic voltammetry (CV) and galvanostatic charge-discharge techniques. The cyclic voltammogram and charge-discharge curve of 450 ˚C annealed MnO2 nanoparticles exhibited relatively good capacitive behavior.

  8. Evolution of Dust Structures from Room to Cryogenic Temperatures

    SciTech Connect

    Antipov, S. N.; Asinovskii, E. I.; Kirillin, A. V.; Markovets, V. V.; Petrov, O. F.; Fortov, V. E.

    2008-09-07

    In this work dusty plasma of dc glow discharge at the temperatures in the range of 4.2-300 K was experimentally and numerically investigated. As it was shown in the experiments, the deep cooling of discharge tube walls leads to dramatic change of dusty plasma properties. In particular, sufficient increase of dust particle kinetic temperature (by about an order) and dust density (by several orders) was observed at low (cryogenic) temperatures. At 4.2 K, this can lead to the forming of a super dense dust structures with novel properties. Numerical simulations of charging process, dust charge fluctuation and screening of dust particle charge in plasma were made in dependence with the neutral gas temperature and dust density. The main attention was given to proper ion-atom collision analysis that allows us to investigate mechanisms of dust structure transformation observed in the cryogenic experiments.

  9. Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

    PubMed

    Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

    2016-05-24

    Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution. PMID:27166421

  10. Population genomics of dengue virus serotype 4: insights into genetic structure and evolution.

    PubMed

    Waman, Vaishali P; Kasibhatla, Sunitha Manjari; Kale, Mohan M; Kulkarni-Kale, Urmila

    2016-08-01

    The spread of dengue disease has become a global public health concern. Dengue is caused by dengue virus, which is a mosquito-borne arbovirus of the genus Flavivirus, family Flaviviridae. There are four dengue virus serotypes (1-4), each of which is known to trigger mild to severe disease. Dengue virus serotype 4 (DENV-4) has four genotypes and is increasingly being reported to be re-emerging in various parts of the world. Therefore, the population structure and factors shaping the evolution of DENV-4 strains across the world were studied using genome-based population genetic, phylogenetic and selection pressure analysis methods. The population genomics study helped to reveal the spatiotemporal structure of the DENV-4 population and its primary division into two spatially distinct clusters: American and Asian. These spatial clusters show further time-dependent subdivisions within genotypes I and II. Thus, the DENV-4 population is observed to be stratified into eight genetically distinct lineages, two of which are formed by American strains and six of which are formed by Asian strains. Episodic positive selection was observed in the structural (E) and non-structural (NS2A and NS3) genes, which appears to be responsible for diversification of Asian lineages in general and that of modern lineages of genotype I and II in particular. In summary, the global DENV-4 population is stratified into eight genetically distinct lineages, in a spatiotemporal manner with limited recombination. The significant role of adaptive evolution in causing diversification of DENV-4 lineages is discussed. The evolution of DENV-4 appears to be governed by interplay between spatiotemporal distribution, episodic positive selection and intra/inter-genotype recombination. PMID:27169727

  11. Protein Structure and Evolution: Are They Constrained Globally by a Principle Derived from Information Theory?

    PubMed Central

    Hatton, Leslie; Warr, Gregory

    2015-01-01

    That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein. PMID:25970335

  12. The evolution of the Piedemonte Llanero petroleum system, Cordillera Oriental, Colombia: (1) Structural evolution and play definition

    SciTech Connect

    Graham, R.; Howe, S.; O`Leary, J.

    1996-08-01

    The Piedemonte Llanero petroleum trend of the Cordillera Oriental in Colombia has proven to be one of the most prolific hydrocarbon provinces discovered in recent years. The Piedemonte Llanero is a fold and thrust belt of complex, multi-phase structuration and hydrocarbon generation. Following the discovery of the Cusiana and Cupiagua fields in the southern part of the trend, BP and its partners began exploration further to the northeast. Early seismic data showed the existence of two structural trends: the frontal (or basal) thrust trend, with structures similar to Cusiana; and the overthrust (or duplex) trend, with multiple imbricated structures. Improved quality seismic data defined the gross structures and allowed them to be successfully drilled, but did not give a constrained model for the kinematic evolution of the fold and thrust belt nor the petroleum play. This resulted in no clear predictive models for reservoir quality and hydrocarbon phase distribution in the undrilled parts of the trend. A wide variety of geological and geochemical analytical techniques including biostratigraphy, reservoir petrology, petroleum geochemistry, thermal maturity data, basin modelling and fluid inclusion studies were undertaken. These were iteratively integrated into the seismo-structural model to develop a constrained interpretation for the evolution of the Piedemonte Llanero petroleum system. This paper summarizes the current understanding of the structural evolution of the trend and the development of a major petroleum system. A companion paper details the reservoir petrography and petroleum geochemistry studies.

  13. Structure and evolution of high-mass stellar mergers

    NASA Astrophysics Data System (ADS)

    Glebbeek, Evert; Gaburov, Evghenii; Portegies Zwart, Simon; Pols, Onno R.

    2013-10-01

    In young dense clusters repeated collisions between massive stars may lead to the formation of a very massive star (above 100 M⊙). In the past, the study of the long-term evolution of merger remnants has mostly focused on collisions between low-mass stars (up to about 2 M⊙) in the context of blue-straggler formation. The evolution of collision products of more massive stars has not been as thoroughly investigated. In this paper, we study the long-term evolution of a number of stellar mergers formed by the head-on collision of a primary star with a mass of 5-40 M⊙ with a lower mass star at three points in its evolution in order to better understand their evolution. We use smooth particle hydrodynamics calculations to model the collision between the stars. The outcome of this calculation is reduced to one dimension and imported into a stellar evolution code. We follow the subsequent evolution of the collision product through the main sequence at least until the onset of helium burning. We find that little hydrogen is mixed into the core of the collision products, in agreement with previous studies of collisions between low-mass stars. For collisions involving evolved stars, we find that during the merger the surface nitrogen abundance can be strongly enhanced. The evolution of most of the collision products proceeds analogously to that of normal stars with the same mass, but with a larger radius and luminosity. However, the evolution of collision products that form with a hydrogen-depleted core is markedly different from that of normal stars with the same mass. They undergo a long-lived period of hydrogen-shell burning close to the main-sequence band in the Hertzsprung-Russell diagram and spend the initial part of core-helium burning as compact blue supergiants.

  14. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  15. Structural Analysis of Communication Development.

    ERIC Educational Resources Information Center

    Conville, Richard L.

    This paper discusses the question of the legitimacy of applying structural analysis to actual human behavior and illustrates its legitimacy by using the reasoning in an essay by Paul Ricoeur. It then asks if the principles of communication development (obliqueness, exchange, and dying) derived from Helen Keller's experience of communication…

  16. Structural Analysis in the Classroom

    ERIC Educational Resources Information Center

    Gage, Nicholas A.; Lewis, Timothy J.

    2010-01-01

    The purpose of this article is to describe an applied method of assessing and manipulating environmental factors influencing student behavior. The assessment procedure is called structural analysis (SA) and can be a part of a functional behavioral assessment (FBA) process or a stand-alone set of procedures for teachers to use in their classrooms.…

  17. Structure and evolution of the magnetochrome domains: no longer alone

    PubMed Central

    Arnoux, Pascal; Siponen, Marina I.; Lefèvre, Christopher T.; Ginet, Nicolas; Pignol, David

    2014-01-01

    Magnetotactic bacteria (MTB) can swim along Earth's magnetic field lines, thanks to the alignment of dedicated cytoplasmic organelles. These organelles, termed magnetosomes, are proteolipidic vesicles filled by a 35–120 nm crystal of either magnetite or greigite. The formation and alignment of magnetosomes are mediated by a group of specific genes, the mam genes, encoding the magnetosome-associated proteins. The whole process of magnetosome biogenesis can be divided into four sequential steps; (i) cytoplasmic membrane invagination, (ii) magnetosomes alignment, (iii) iron crystal nucleation and (iv) species-dependent mineral size and shape control. Since both magnetite and greigite are a mix of iron (III) and iron (II), iron redox state management within the magnetosome vesicle is a key issue. Recently, studies have started pointing out the importance of a MTB-specific c-type cytochrome domain found in several magnetosome-associated proteins (MamE, P, T, and X). This magnetochrome (MCR) domain is almost always found in tandem, and this tandem is either found alone (MamT), in combination with a PDZ domain (MamP), a domain of unknown function (MamX) or with a trypsin combined to one or two PDZ domains (MamE). By taking advantage of new genomic data available on MTB and a recent structural study of MamP, which helped define the MCR domain boundaries, we attempt to retrace the evolutionary history within and between the different MCR-containing proteins. We propose that the observed tandem repeat of MCR is the result of a convergent evolution and attempt to explain why this domain is rarely found alone. PMID:24723915

  18. Understanding the Structure and Evolution of Nearby Disk Galaxies

    NASA Astrophysics Data System (ADS)

    Zheng, Zheng

    2014-01-01

    In order to understand the structure and evolution of disk galaxies, we studied the stellar and gaseous components as well as the star formation rate in nearby disk galaxies. We used PS1 medium deep survey images to derive five-band (grizy) surface brightness profiles down to 30 ABmag/arcsec^2 for about 700 galaxies. From these stellar mass and mass-to-light ratio radial profiles are derived. The stellar mass radial profiles tend to bend-up at large radii, this often traces an extended old stellar population. The mass-to-light ratio profiles tend to rise outside the r25 radii. We also find a larger fraction of up-bending surface brightness profiles than Polen & Trujillo (2006). This may be because their sample is biased towards low surface brightness galaxies. We used HIPASS data as well as VLA HI 21cm data to study the gas component and dynamics of disk galaxies. We used the GALEX UV images to study the star formation of a HI-selected star-forming sample of about 400 galaxies, compiling a database of FUV and NUV radial profiles and related parameters. We used this to study the star forming efficiency (SFE, star formation rate per unit area divided by gas surface mass density) of the sample galaxies. We found that the UV based SFE has a tighter relationship with HI mass than an H_alpha based SFE as typically used in previous studies and the UV SFE is flat across wide range of stellar mass. We constructed a simple model to predict the distribution of interstellar medium and star formation rate in an equilibrium disk with constant two-fluid Toomre Q. This model can reproduces the SFE relations we derived.

  19. Structure and evolution of the magnetochrome domains: no longer alone.

    PubMed

    Arnoux, Pascal; Siponen, Marina I; Lefèvre, Christopher T; Ginet, Nicolas; Pignol, David

    2014-01-01

    Magnetotactic bacteria (MTB) can swim along Earth's magnetic field lines, thanks to the alignment of dedicated cytoplasmic organelles. These organelles, termed magnetosomes, are proteolipidic vesicles filled by a 35-120 nm crystal of either magnetite or greigite. The formation and alignment of magnetosomes are mediated by a group of specific genes, the mam genes, encoding the magnetosome-associated proteins. The whole process of magnetosome biogenesis can be divided into four sequential steps; (i) cytoplasmic membrane invagination, (ii) magnetosomes alignment, (iii) iron crystal nucleation and (iv) species-dependent mineral size and shape control. Since both magnetite and greigite are a mix of iron (III) and iron (II), iron redox state management within the magnetosome vesicle is a key issue. Recently, studies have started pointing out the importance of a MTB-specific c-type cytochrome domain found in several magnetosome-associated proteins (MamE, P, T, and X). This magnetochrome (MCR) domain is almost always found in tandem, and this tandem is either found alone (MamT), in combination with a PDZ domain (MamP), a domain of unknown function (MamX) or with a trypsin combined to one or two PDZ domains (MamE). By taking advantage of new genomic data available on MTB and a recent structural study of MamP, which helped define the MCR domain boundaries, we attempt to retrace the evolutionary history within and between the different MCR-containing proteins. We propose that the observed tandem repeat of MCR is the result of a convergent evolution and attempt to explain why this domain is rarely found alone. PMID:24723915

  20. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    PubMed

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)<100nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  1. Structural Analysis and Design Software

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Collier Research and Development Corporation received a one-of-a-kind computer code for designing exotic hypersonic aircraft called ST-SIZE in the first ever Langley Research Center software copyright license agreement. Collier transformed the NASA computer code into a commercial software package called HyperSizer, which integrates with other Finite Element Modeling and Finite Analysis private-sector structural analysis program. ST-SIZE was chiefly conceived as a means to improve and speed the structural design of a future aerospace plane for Langley Hypersonic Vehicles Office. Including the NASA computer code into HyperSizer has enabled the company to also apply the software to applications other than aerospace, including improved design and construction for offices, marine structures, cargo containers, commercial and military aircraft, rail cars, and a host of everyday consumer products.

  2. Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

    PubMed Central

    Furnham, Nicholas; Dawson, Natalie L.; Rahman, Syed A.; Thornton, Janet M.; Orengo, Christine A.

    2016-01-01

    Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. PMID:26585402

  3. Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

    PubMed

    Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A

    2016-01-29

    Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. PMID:26585402

  4. Structural and stratigraphic evolution of the Anza rift, Kenya

    NASA Astrophysics Data System (ADS)

    Bosworth, William; Morley, Chris K.

    1994-09-01

    The Anza rift is a large, multi-phase continental rift basin that links the Lamu embayment of southern Kenya with the South Sudan rifts. Extension and deposition of syn-rift sediments are known to have commenced by the Neocomian. Aptian-Albian strata have, thus far, not been encountered during limited drilling campaigns and, in at least one well, are replaced by a significant unconformity. Widespread rifting occurred during the Cenomanian to Maastrichtian, and continued into the Early Tertiary. Marine waters appear to have reached the central Anza rift in the Cenomanian, and a second marine incursion may have occurred during the Campanian. As no wells have yet reached basement in the basinal deeps, the possibility exists that the Anza rift may have initiated in the Late Jurassic, in conjunction with extension to the south in the Lamu embayment and to the north in the Blue Nile rift of Sudan. Structural and stratigraphic evolution in the Anza rift followed a pattern that has now been inferred in several rift settings. Early phases of extension were accommodated by moderately dipping faults that produced large stratal rotations. Sedimentary environments were dominantly fluvial, with associated small lakes and dune fields. Volcanic activity is documented for the early Neocomian, but its extent is unknown. This initial style of deformation and sedimentation may have continued through several of the earliest pulses of rifting. By the Late Cretaceous, a new system of steeply dipping faults was established, that produced a deep basin without significant rotation of strata in the north, and only minor rotation in the south. This basin geometry favored the establishment of large, deep lakes, which occasionally were connected to the sea. The older basins were partly cannibalized during the sedimentary in-filling of these successor basins. Early Senonian volcanism was encountered in one well, and reflection seismic evidence suggests that one or more thick, regionally

  5. Real Time Pore Structure Evolution during Olivine Mineral Carbonation

    NASA Astrophysics Data System (ADS)

    Zhu, W.; Fusseis, F.; Lisabeth, H. P.; Xiao, X.

    2014-12-01

    Aqueous carbonation of ultramafic rocks has been proposed as a promising method for long-term, secure sequestration of carbon dioxide. While chemical kinetics data indicate that carbonation reaction in olivine is one of the fastest among the mg-bearing minerals, in practice, the factors that limit the extent and rate of carbonation in ultramafic rocks are fluid supply and flux. On the one hand, reaction products could produce passivating layer that prohibits further reactions. On the other hand, the increases in solid volume during carbonation could lead to cracking and create new fluid paths. Whether carbonation in ultramafic rocks is self-limiting or self-sustaining has been hotly debated. Experimental evidence of precipitation of reaction products during olivine carbonation was reported. To date, reaction-driven cracking has not been observed. In this paper, we present the first real-time pore structure evolution data using the x-ray synchrotron microtomography. Sodium bicarbonate (NaHCO3) solution was injected into porous olivine aggregates and in-situ pore structure change during olivine carbonation at a constant confining pressure (12 MPa) and a temperature of 200oC was captured at 30 min. interval for ~160 hours. Shortly after the experiment started, filling-in of the existing pores by precipitation of reaction products was visible. The size of the in-fills kept increasing as reactions continued. After ~48 hours, cracking around the in-fill materials became visible. After ~60 hours, these cracks started to show a clear polygonal pattern, similar to the crack patterns usually seen on the surface of drying mud. After ~72 hours, some of the cracks coalesced into large fractures that cut-through the olivine aggregates. New fractures continued to develop and at the end of the experiment, the sample was completely disintegrated by these fractures. We also conducted nanotomography experiments on a sub-volume of the reacted olivine aggregate. Orthogonal sets of

  6. INTERNAL STRUCTURE OF PROTOCLUSTER GALAXIES: ACCELERATED STRUCTURAL EVOLUTION IN OVERDENSE ENVIRONMENTS?

    SciTech Connect

    Zirm, Andrew W.; Toft, Sune; Tanaka, Masayuki E-mail: sune@dark-cosmology.dk

    2012-01-10

    We present a high spatial resolution Hubble Space Telescope/NICMOS imaging survey in the field of a known protocluster surrounding the powerful radio galaxy MRC1138-262 at z = 2.16. Previously, we have shown that this field exhibits a substantial surface overdensity of red J-H galaxies. Here we focus on the stellar masses and galaxy effective radii in an effort to compare and contrast the properties of likely protocluster galaxies with their field counterparts and to look for correlations between galaxy structure and (projected) distance relative to the radio galaxy. We find a hint that quiescent, cluster galaxies are on average less dense than quiescent field galaxies of similar stellar mass and redshift. In fact, we find that only two (of eight) quiescent protocluster galaxies are of similar density to the majority of the massive, quiescent compact galaxies (Semi-Evolved Elephantine Dense galaxies; SEEDs) found in several field surveys. Furthermore, there is some indication that the structural Sersic n parameter is higher (n {approx} 3-4) on average for cluster galaxies compared to the field SEEDs (n {approx} 1-2). This result may imply that the accelerated galaxy evolution expected (and observed) in overdense regions also extends to structural evolution presuming that massive galaxies began as dense (low n) SEEDs and have already evolved to be more in line with local galaxies of the same stellar mass.

  7. Application of Quasi-Separatrix Layer Maps to Understanding the Structure and Evolution of Sigmoids

    NASA Astrophysics Data System (ADS)

    Savcheva, Antonia; DeLuca, E.; Van Ballegooijen, A.

    2010-05-01

    We present some preliminary work in attempt to utilize Quasi-Separatrix Layer (QSL) maps for understanding the structure and evolution of sigmoids. We show sample QSL maps calculated at different heights above the photosphere and different times over the evolution of the quiescent sigmoid from February, 2007, observed with Hinode/XRT. The QSL maps use already existing static MHD models of the sigmoid, based on the flux rope insertion method. We give a short overview of the method used to set-up these maps. By comparing current distributions and the squashing factors at different height and cross sections over the sigmoid location we suggest the use of QSLs as tracers of surface and/or volumetric currents. We look at the distribution, structure, and concentration of QSLs in combination with the size and location of bald patches at different stages of the sigmoid development. We attempt to use this analysis to help us discriminate between the main scenarios for the formation and X-ray appearance of the S-like structure - flux emergence (or cancellation) and twisting foot point motions. This method may possibly shed some light on the pre-eruption configuration and eruption mechanism in sigmoids as well.

  8. Structural design and molecular evolution of a cytokine receptor superfamily.

    PubMed Central

    Bazan, J F

    1990-01-01

    A family of cytokine receptors comprising molecules specific for a diverse group of hematopoietic factors and growth hormones has been principally defined by a striking homology of binding domains. This work proposes that the approximately 200-residue binding segment of the canonical cytokine receptor is composed of two discrete folding domains that share a significant sequence and structural resemblance. Analogous motifs are found in tandem approximately 100-amino acid domains in the extracellular segments of a receptor family formed by the interferon-alpha/beta and -gamma receptors and tissue factor, a membrane tether for a coagulation protease. Domains from the receptor supergroup reveal clear evolutionary links to fibronectin type III structures, approximately 90-amino acid modules that are typically found in cell surface molecules with adhesive functions. Predictive structural analysis of the shared receptor and fibronectin domains locates seven beta-strands in conserved regions of the chain; these strands are modeled to fold into antiparallel beta-sandwiches with a topology that is similar to immunoglobulin constant domains. These findings have strong implications for understanding the evolutionary emergence of an important class of regulatory molecules from primitive adhesive modules. In addition, the resulting double-barrel design of the receptors and the spatial clustering of conserved residues suggest a likely binding site for cytokine ligands. Images PMID:2169613

  9. Analysis of the Science and Technology Preservice Teachers' Opinions on Teaching Evolution and Theory of Evolution

    ERIC Educational Resources Information Center

    Töman, Ufuk; Karatas, Faik Özgür; Çimer, Sabiha Odabasi

    2014-01-01

    In this study, we investigate of science and technology teachers' opinions about the theory of evolution and the evolution teaching. The aim of this study, we investigate of science and technology teachers' opinions about the theory of evolution and the evolution teaching. This study is a descriptive study. Open-ended questions were used to…

  10. Concurrent Evolution of Structural Deformation and Carbonate Diagenesis within the Moab Fault, UT

    NASA Astrophysics Data System (ADS)

    Hodson, K. R.; Crider, J. G.; Huntington, K. W.; Luetkemeyer, P. B.

    2015-12-01

    Fluid-driven diagenetic processes within the fault damage zone drive direct feedbacks to mechanical and fluid-permeability properties of the host rock. Because these factors can be of great importance to fault seismicity and reservoir integrity, it is important to constrain their evolution over the lifespan of a fault zone. The Moab Fault, SE Utah, is a prime location to address these questions, representing an exhumed fault system offsetting a package of paleo-reservoir rocks. We return to a well-studied segment linkage zone, Courthouse Junction, building upon detailed earlier work. Here, the fault zone contains multiple phases of structural deformation, expressed as distinct structural elements. Associated carbonate mineralization provides a record of past fluid flow through the fault zone. Earlier bulk and clumped isotope measurements of the carbonate have demonstrated a range of isotopic compositions and precipitation temperatures. In this work, we apply new carbonate isotope and trace element geochemistry, cathodoluminescence microscopy, and fluid inclusion analysis to synthesize the structural and diagenetic histories of the Moab Fault. Carbonate trace element signatures and clumped isotope-based precipitation temperatures allow us to identify variability in parent fluid composition and characterize fluid sources, constraining migration pathways through the fault zone. Distinct phases of carbonate deposition display different cathodoluminescence, allowing us to observe their textural relationships to the host rock and each other, as well as constrain the relative timing of episodes of carbonate deposition and structural deformation. Taken together, these data provide new perspective into the co-evolution of permeability and structural deformation in the Moab Fault by connecting variability in fluid transmission and source to changes in the style of structural deformation.

  11. Application of integrated fluid-thermal-structural analysis methods

    NASA Technical Reports Server (NTRS)

    Wieting, Allan R.; Dechaumphai, Pramote; Bey, Kim S.; Thornton, Earl A.; Morgan, Ken

    1988-01-01

    Hypersonic vehicles operate in a hostile aerothermal environment which has a significant impact on their aerothermostructural performance. Significant coupling occurs between the aerodynamic flow field, structural heat transfer, and structural response creating a multidisciplinary interaction. Interfacing state-of-the-art disciplinary analysis methods is not efficient, hence interdisciplinary analysis methods integrated into a single aerothermostructural analyzer are needed. The NASA Langley Research Center is developing such methods in an analyzer called LIFTS (Langley Integrated Fluid-Thermal-Structural) analyzer. The evolution and status of LIFTS is reviewed and illustrated through applications.

  12. Reverse microemulsion-mediated synthesis and structural evolution of barium hexaaluminate nanoparticles

    SciTech Connect

    Zarur, A.J.; Hwu, H.H.; Ying, J.Y.

    2000-04-04

    Nanocrystalline barium hexaaluminate has been successfully synthesized through the use of a reverse microemulsion as a medium for controlled hydrolysis and polycondensation of barium and aluminum alkoxides. The nanoparticles derived were characterized with electron microscopy, X-ray diffraction, and nitrogen adsorption analysis. This novel material possessed a well-defined particle morphology and an ultrahigh surface area, and exhibited excellent catalytic performance in methane combustion. Its structural evolution was found to be strongly dependent on synthesis parameters, such as water/alkoxide ratio and aging period. Powder recovery and drying techniques also had an important impact on particle agglomeration and structural development. Through the unique synthesis approach described, barium hexaaluminate with superb thermal stability was achieved, with surface areas in excess of 100 m{sup 2}/g retained even after calcination at 1,300 C.

  13. Evolution of microwave ferromagnetic resonance with magnetic domain structure in FeCoBSi antidot arrays

    NASA Astrophysics Data System (ADS)

    Zhou, Peiheng; Zhang, Nan; Liu, Tao; Xie, Jianliang; Deng, Longjiang

    2014-08-01

    Magnetic domain structure of FeCoBSi antidot array thin films of varying thickness were characterized using surface magneto-optic Kerr effect. Vibrating sample magnetometry and microstrip transmission line measurements helped to associate the microwave magnetic analysis of the antidot arrays with hysteresis studies. The domain structure evolution from quasi-continuous domains to strip domains induced by the competing exchange and dipolar interaction resulted in the change of ferromagnetic resonance from multi-band to single-band. Hence, the mechanisms of multi-resonance are proposed to be related to domain wall motion, natural resonance and spin wave modes. This phenomenon can be used to control the magnetization dynamics in spin wave devices.

  14. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

    SciTech Connect

    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.

    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.

  15. Efficient Analysis of Complex Structures

    NASA Technical Reports Server (NTRS)

    Kapania, Rakesh K.

    2000-01-01

    Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

  16. Structural analysis of vibroacoustical processes

    NASA Technical Reports Server (NTRS)

    Gromov, A. P.; Myasnikov, L. L.; Myasnikova, Y. N.; Finagin, B. A.

    1973-01-01

    The method of automatic identification of acoustical signals, by means of the segmentation was used to investigate noises and vibrations in machines and mechanisms, for cybernetic diagnostics. The structural analysis consists of presentation of a noise or vibroacoustical signal as a sequence of segments, determined by the time quantization, in which each segment is characterized by specific spectral characteristics. The structural spectrum is plotted as a histogram of the segments, also as a relation of the probability density of appearance of a segment to the segment type. It is assumed that the conditions of ergodic processes are maintained.

  17. Structured Functional Principal Component Analysis

    PubMed Central

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  18. Structured functional principal component analysis.

    PubMed

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M; Greven, Sonja

    2015-03-01

    Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  19. Models of the Protocellular Structures, Functions and Evolution

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; New, Michael; Keefe, Anthony; Szostak, Jack W.; Lanyi, Janos F.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    In the absence of extinct or extant record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids: First, a very large population of candidate molecules is generated using a random synthetic approach. Next, the small numbers of molecules that can accomplish the desired task are selected. These molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. To date, we have obtained "a proof of concept" by evolving simple, novel proteins capable of selectively binding adenosine tri-phosphate (ATP). Our next goal is to create an enzyme that can phosphorylate amino acids and another to catalyze the formation of peptide bonds in the absence of nucleic acid templates. This latter reaction does not take place in contemporary cells. once developed, these enzymes will be encapsulated in liposomes so that they will function in a simulated cellular

  20. Structural Evolution of a Granular Pack under Manual Tapping

    NASA Astrophysics Data System (ADS)

    Iikawa, Naoki; Bandi, Mahesh M.; Katsuragi, Hiroaki

    2015-09-01

    We experimentally study a two-dimensional (2D) granular pack of photoelastic disks subject to vertical manual tapping. Using bright- and dark-field images, we employ gradient-based image analysis methods to analyze various structural quantities. These include the packing fraction (ϕ), force per disk (Fd), and force chain segment length (l) as functions of the tapping number (τ). The increase in the packing fraction with the tapping number is found to exponentially approach an asymptotic value. An exponential distribution is observed for the cumulative numbers of both the force per disk Fd:Ncum(Fd) = AFexp ( - Fd/F0), and the force chain segment length l:Ncum(l) = Alexp ( - l/l0). Whereas the coefficient AF varies with τ for Fd, l shows no dependence on τ. The τ dependences of Fd and ϕ allow us to posit a linear relationship between the total force of the granular pack Ftot*(τ ) and ϕ(τ).

  1. Uncertainty Analysis of Composite Structures

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Starnes, James H., Jr.; Peters, Jeanne M.

    2000-01-01

    A two-phase approach and a computational procedure are presented for predicting the variability in the nonlinear response of composite structures associated with variations in the geometric and material parameters of the structure. In the first phase, hierarchical sensitivity analysis is used to identify the major parameters, which have the most effect on the response quantities of interest. In the second phase, the major parameters are taken to be fuzzy parameters, and a fuzzy set analysis is used to determine the range of variation of the response, associated with preselected variations in the major parameters. The effectiveness of the procedure is demonstrated by means of a numerical example of a cylindrical panel with four T-shaped stiffeners and a circular cutout.

  2. Structure and evolution of the human IKBA gene

    SciTech Connect

    Ito, C.Y.; Bautch, V.L.; Baldwin, A.S. Jr.

    1995-09-20

    I{kappa}B{alpha} belongs to a gene family whose members are characterized by their 6-7 Ankyrin repeats, which allow them to interact with members of the Rel family of transcription factors. We have sequenced a human I{kappa}B{alpha} genomic clone to determine its gene structure. The human I{kappa}B{alpha} gene (IKBA) has six exons and five introns that span approximately 3.5 kb. This genomic organization is similiar to that of other members of the Ankyrin gene family. The human IKBA gene shares similiar intron/exon boundaries with the human BCL3 and NFKB2 genes, which is consistent with their conserved Ankyrin repeats. To examine further the evolutionary relationship between human I{kappa}B{alpha} and other members of its gene family, we performed a phylogenetic analysis. Although the resulting phylogenetic tree does not identify a common ancestor of the I{kappa}B{alpha} gene family, it indicates that this family diverges into two groups based on structure and function. 41 refs., 4 figs., 1 tab.

  3. The venus kinase receptor (VKR) family: structure and evolution

    PubMed Central

    2013-01-01

    Background Receptor tyrosine kinases (RTK) form a family of transmembrane proteins widely conserved in Metazoa, with key functions in cell-to-cell communication and control of multiple cellular processes. A new family of RTK named Venus Kinase Receptor (VKR) has been described in invertebrates. The VKR receptor possesses a Venus Fly Trap (VFT) extracellular module, a bilobate structure that binds small ligands to induce receptor kinase activity. VKR was shown to be highly expressed in the larval stages and gonads of several invertebrates, suggesting that it could have functions in development and/or reproduction. Results Analysis of recent genomic data has allowed us to extend the presence of VKR to five bilaterian phyla (Platyhelminthes, Arthropoda, Annelida, Mollusca, Echinodermata) as well as to the Cnidaria phylum. The presence of NveVKR in the early-branching metazoan Nematostella vectensis suggested that VKR arose before the bilaterian radiation. Phylogenetic and gene structure analyses showed that the 40 receptors identified in 36 animal species grouped monophyletically, and likely evolved from a common ancestor. Multiple alignments of tyrosine kinase (TK) and VFT domains indicated their important level of conservation in all VKRs identified up to date. We showed that VKRs had inducible activity upon binding of extracellular amino-acids and molecular modeling of the VFT domain confirmed the structure of the conserved amino-acid binding site. Conclusions This study highlights the presence of VKR in a large number of invertebrates, including primitive metazoans like cnidarians, but also its absence from nematodes and chordates. This little-known RTK family deserves to be further explored in order to determine its evolutionary origin, its possible interest for the emergence and specialization of Metazoa, and to understand its function in invertebrate development and/or reproductive biology. PMID:23721482

  4. HOST structural analysis program overview

    NASA Technical Reports Server (NTRS)

    Thompson, Robert L.

    1986-01-01

    Hot-section components of aircraft gas turbine engines are subjected to severe thermal structural loading conditions, especially during the startup and takeoff portions of the engine cycle. The most severe and damaging stresses and strains are those induced by the steep thermal gradients induced during the startup transient. These transient stresses and strains are also the most difficult to predict, in part because the temperature gradients and distributions are not well known or readily predictable and, in part, because the cyclic elastic-viscoplastic behavior of the materials at these extremes of temperature and strain are not well known or readily predictable. A broad spectrum of structures related technology programs is underway to address these deficiencies at the basic as well as the applied level. The three key program elements in the HOST structural analysis program are computations, constitutive modeling, and experiments for each research activity. Also shown are tables summarizing each of the activities.

  5. Grid Stiffened Structure Analysis Tool

    NASA Technical Reports Server (NTRS)

    1999-01-01

    The Grid Stiffened Analysis Tool contract is contract performed by Boeing under NASA purchase order H30249D. The contract calls for a "best effort" study comprised of two tasks: (1) Create documentation for a composite grid-stiffened structure analysis tool, in the form of a Microsoft EXCEL spread sheet, that was developed by originally at Stanford University and later further developed by the Air Force, and (2) Write a program that functions as a NASTRAN pre-processor to generate an FEM code for grid-stiffened structure. In performing this contract, Task 1 was given higher priority because it enables NASA to make efficient use of a unique tool they already have; Task 2 was proposed by Boeing because it also would be beneficial to the analysis of composite grid-stiffened structures, specifically in generating models for preliminary design studies. The contract is now complete, this package includes copies of the user's documentation for Task 1 and a CD ROM & diskette with an electronic copy of the user's documentation and an updated version of the "GRID 99" spreadsheet.

  6. Space–time isogeometric analysis of parabolic evolution problems

    NASA Astrophysics Data System (ADS)

    Langer, Ulrich; Moore, Stephen E.; Neumüller, Martin

    2016-07-01

    We present and analyze a new stable space-time Isogeometric Analysis (IgA) method for the numerical solution of parabolic evolution equations in fixed and moving spatial computational domains. The discrete bilinear form is elliptic on the IgA space with respect to a discrete energy norm. This property together with a corresponding boundedness property, consistency and approximation results for the IgA spaces yields an a priori discretization error estimate with respect to the discrete norm. The theoretical results are confirmed by several numerical experiments with low- and high-order IgA spaces.

  7. Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

    PubMed

    Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

    2015-02-01

    Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities. PMID:25424655

  8. RED NUGGETS AT HIGH REDSHIFT: STRUCTURAL EVOLUTION OF QUIESCENT GALAXIES OVER 10 Gyr OF COSMIC HISTORY

    SciTech Connect

    Damjanov, Ivana; Abraham, Roberto G.; Carlberg, Raymond G.; Mentuch, Erin; Glazebrook, Karl; Caris, Evelyn; Green, Andrew W.; McCarthy, Patrick J.; Chen, Hsiao-Wen; Crampton, David; Murowinski, Richard; Joergensen, Inger; Roth, Kathy; Juneau, Stephanie; Marzke, Ronald O.; Savaglio, Sandra; Yan Haojing

    2011-10-01

    We present an analysis of the size growth seen in early-type galaxies over 10 Gyr of cosmic time. Our analysis is based on a homogeneous synthesis of published data from 16 spectroscopic surveys observed at similar spatial resolution, augmented by new measurements for galaxies in the Gemini Deep Deep Survey. In total, our sample contains structural data for 465 galaxies (mainly early-type) in the redshift range 0.2 < z < 2.7. The size evolution of passively evolving galaxies over this redshift range is gradual and continuous, with no evidence for an end or change to the process around z {approx} 1, as has been hinted at by some surveys which analyze subsets of the data in isolation. The size growth appears to be independent of stellar mass, with the mass-normalized half-light radius scaling with redshift as R{sub e} {proportional_to}(1 + z){sup -1.62{+-}0.34}. Surprisingly, this power law seems to be in good agreement with the recently reported continuous size evolution of UV-bright galaxies in the redshift range z {approx} 0.5-3.5. It is also in accordance with the predictions from recent theoretical models.

  9. Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

    NASA Technical Reports Server (NTRS)

    Donohue, D. J.; Zank, G. P.; Webb, G. M.

    1994-01-01

    Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

  10. Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

    NASA Astrophysics Data System (ADS)

    Donohue, D. J.; Zank, G. P.; Webb, G. M.

    1994-03-01

    Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

  11. Statistical analysis on the evolution of OpenStreetMap road networks in Beijing

    NASA Astrophysics Data System (ADS)

    Zhao, Pengxiang; Jia, Tao; Qin, Kun; Shan, Jie; Jiao, Chenjing

    2015-02-01

    In recent years, extensive efforts have been paid on the investigation of OpenStreetMap (OSM) in developed countries, but little attention has been given to the cities in developing countries. This paper presents the results regarding the evolution of OSM road networks in Beijing, China, from four aspects. First, findings from general analysis indicate that (1) the overall growth pattern could be mainly explained by the increasing number of volunteers and their mapping contributions. Second, findings from geometric analysis suggest: (2) mapping intensity exhibits heavy-tailed pattern both for a certain time period and across time; (3) mapping direction moves from outskirts to downtown distinguished from other regions; and (4) mapping behaviors are mainly constrained by the underlying structure of road networks. Third, results of topological analysis indicate that (5) OSM road networks resemble the growth of real road networks and are undergoing an evolution process depicted by exploration and densification. Last, from the perspective of centrality analysis, (6) two kinds of nodes are identified with the ones accounting for the exploration and the other ones for the densification, which further hints the evolution process of continuous strong exploration accompanied by weak densification.

  12. Probabilistic methods for structural response analysis

    NASA Technical Reports Server (NTRS)

    Wu, Y.-T.; Burnside, O. H.; Cruse, T. A.

    1988-01-01

    This paper addresses current work to develop probabilistic structural analysis methods for integration with a specially developed probabilistic finite element code. The goal is to establish distribution functions for the structural responses of stochastic structures under uncertain loadings. Several probabilistic analysis methods are proposed covering efficient structural probabilistic analysis methods, correlated random variables, and response of linear system under stationary random loading.

  13. Bifurcation analysis of a model for atherosclerotic plaque evolution

    NASA Astrophysics Data System (ADS)

    Bulelzai, M. A. K.; Dubbeldam, J. L. A.; Meijer, H. G. E.

    2014-06-01

    We analyze two ordinary differential equation (ODE) models for atherosclerosis. The ODE models describe long time evolution of plaques in arteries. We show how the dynamics of the first atherosclerosis model (model A) can be understood using codimension-two bifurcation analysis. The Low-Density Lipoprotein (LDL) intake parameter (d) is the first control parameter and the second control parameter is either taken to be the conversion rate of macrophages (b) or the wall shear stress (σ). Our analysis reveals that in both cases a Bogdanov-Takens (BT) point acts as an organizing center. The bifurcation diagrams are calculated partly analytically and to a large extent numerically using AUTO07 and MATCONT. The bifurcation curves show that the concentration of LDL in the plaque as well as the monocyte and the macrophage concentrations exhibit oscillations for a certain range of values of the control parameters. Moreover, we find that there are threshold values for both the cholesterol intake rate dcrit and the conversion rate of the macrophages bcrit, which depend on the values of other parameters, above which the plaque volume increases with time. It is found that larger conversion rates of macrophages lower the threshold value of cholesterol intake and vice versa. We further argue that the dynamics for model A can still be discerned in the second model (model B) in which the slow evolution of the radius of the artery is coupled self-consistently to changes in the plaque volume. The very slow evolution of the radius of the artery compared to the other processes makes it possible to use a slow manifold approximation to study the dynamics in this case. We find that in this case the model predicts that the concentrations of the plaque constituents may go through a period of oscillations before the radius of the artery will start to decrease. These oscillations hence act as a precursor for the reduction of the artery radius by plaque growth.

  14. Kinematic and Structural Evolution of Field and Cluster Spiral Galaxies

    NASA Astrophysics Data System (ADS)

    Ziegler, B. L.; Kutdemir, E.; Da Rocha, C.; Böhm, A.; Peletier, R. F.; Verdugo, M.

    2010-10-01

    To understand the processes that build up galaxies we investigate the stellar structure and gas kinematics of spiral and irregular galaxies out to redshift 1. We target 92 galaxies in four cluster ( z = 0.3 & 0.5 ) fields to study the environmental influence. Their stellar masses derived from multiband VLT/FORS photometry are distributed around but mostly below the characteristic Schechter-fit mass. From HST/ACS images we determine morphologies and structural parameters like disk length, position angle and ellipticity. Combining the spectra of three slit positions per galaxy using the MXU mode of VLT/FORS2 we construct the two-dimensional velocity field from gas emission lines for 16 cluster members and 33 field galaxies. The kinematic position angle and flatness are derived by a Fourier expansion of elliptical velocity profiles. To trace possible interaction processes, we define three irregularity indicators based on an identical analysis of local galaxies from the SINGS project. Our distant sample displays a higher fraction of disturbed velocity fields with varying percentages (10%, 30% and 70%) because they trace different features. While we find far fewer candidates for major mergers than the SINS sample at z ˜ 2, our data are sensitive enough to trace less violent processes. Most irregular signatures are related to star formation events and less massive disks are affected more than Milky-Way type objects. We detect similarly high fractions of irregular objects both for the distant field and cluster galaxies with similar distributions. We conclude that we may witness the building-up of disk galaxies still at redshifts z ˜ 0.5 via minor mergers and gas accretion, while some cluster members may additionally experience stripping, evaporation or harassment interactions.

  15. Distribution functions for internal interface energy as a characteristic of submicrocrystalline copper structure evolution under low-temperature annealing

    NASA Astrophysics Data System (ADS)

    Kuznetsov, P.; Rakhmatulina, T.; Koznikov, A.; Belyaeva, I.

    2015-10-01

    Submicrocrystalline structure of 99.99% pure copper produced by equal channel angular pressing was under investigation. After deformation the samples were subjected to low-temperature annealing. Grain and subgrain structure was studied by scanning tunnel microscopy. Internal interface energy was estimated using the method based on measurement of dihedral angles (ψ) of the boundary grooves formed by electrochemical etching. Analysis of the differential and cumulative distribution functions for relative grain boundary energy enabled to qualitatively evaluate energy redistribution between the boundaries of different types and internal bulk crystallites and to study evolution of submicrocrystalline structure under low-temperature annealing.

  16. Microeconomic co-evolution model for financial technical analysis signals

    NASA Astrophysics Data System (ADS)

    Rotundo, G.; Ausloos, M.

    2007-01-01

    Technical analysis (TA) has been used for a long time before the availability of more sophisticated instruments for financial forecasting in order to suggest decisions on the basis of the occurrence of data patterns. Many mathematical and statistical tools for quantitative analysis of financial markets have experienced a fast and wide growth and have the power for overcoming classical TA methods. This paper aims to give a measure of the reliability of some information used in TA by exploring the probability of their occurrence within a particular microeconomic agent-based model of markets, i.e., the co-evolution Bak-Sneppen model originally invented for describing species population evolutions. After having proved the practical interest of such a model in describing financial index so-called avalanches, in the prebursting bubble time rise, the attention focuses on the occurrence of trend line detection crossing of meaningful barriers, those that give rise to some usual TA strategies. The case of the NASDAQ crash of April 2000 serves as an illustration.

  17. Evolution of human brain functions: the functional structure of human consciousness.

    PubMed

    Cloninger, C Robert

    2009-11-01

    The functional structure of self-aware consciousness in human beings is described based on the evolution of human brain functions. Prior work on heritable temperament and character traits is extended to account for the quantum-like and holographic properties (i.e. parts elicit wholes) of self-aware consciousness. Cladistic analysis is used to identify the succession of ancestors leading to human beings. The functional capacities that emerge along this lineage of ancestors are described. The ecological context in which each cladogenesis occurred is described to illustrate the shifting balance of evolution as a complex adaptive system. Comparative neuroanatomy is reviewed to identify the brain structures and networks that emerged coincident with the emergent brain functions. Individual differences in human temperament traits were well developed in the common ancestor shared by reptiles and humans. Neocortical development in mammals proceeded in five major transitions: from early reptiles to early mammals, early primates, simians, early Homo, and modern Homo sapiens. These transitions provide the foundation for human self-awareness related to sexuality, materiality, emotionality, intellectuality, and spirituality, respectively. The functional structure of human self-aware consciousness is concerned with the regulation of five planes of being: sexuality, materiality, emotionality, intellectuality, and spirituality. Each plane elaborates neocortical functions organized around one of the five special senses. The interactions among these five planes gives rise to a 5 x 5 matrix of subplanes, which are functions that coarsely describe the focus of neocortical regulation. Each of these 25 neocortical functions regulates each of five basic motives or drives that can be measured as temperaments or basic emotions related to fear, anger, disgust, surprise, and happiness/sadness. The resulting 5 x 5 x 5 matrix of human characteristics provides a general and testable model of the

  18. The structure and evolution of seasonal wind anomalies over the near-equatorial eastern Indian and western Pacific Oceans

    NASA Technical Reports Server (NTRS)

    Gutzler, David S.; Harrison, D. E.

    1987-01-01

    The longitude-height-time structure and evolution of near-equatorial wind variability over the eastern Indian and western Pacific Oceans are studied using data obtained from a network of eight radiosonde stations extending from southern India to the central Pacific Ocean. The seasonal zonal wind anomalies observed at the cross section beween Trivandrum and Majuro stations are analyzed using an empirical orthogonal function. The Walker Circulation fluctuations are described in terms of standing oscillations in the longitude-height plane, and it is determined that Southern Oscillation propagation anomaly best represents the wind fluctuations. A complex empirical orthogonal function (CEOF) analysis and an El Nino compositing methodology are applied to the seasonal zonal wind anomalies. It is determined that the composite El Nino anomalies correspond to the spatial structure and temporal evolution of anomalies implied by the CEOF analysis.

  19. The structural evolution process and the electronic properties of armchair silicon nanotubes

    NASA Astrophysics Data System (ADS)

    Liu, Deng-Hui; Tang, Yu-Chao; Yao, Cheng-Peng; Zhu, Heng-Jiang

    2016-04-01

    The structural evolution process of the capped armchair single- and double-walled SiNTs grown from silicon clusters was investigated using the DFT method. The evolution process was described quantitatively by monitoring change of the geometry structures. The initial structural configuration of the single- and double-walled SiNTs was determined by optimizing structure of the small silicon clusters. The evolution process of the SWSiNTs is through forming tubular clusters with a global reconstruction from structure of the double-rings. Then, it elongates through the layer-by-layer growth process with local reconstructions. Eventually, the infinite SiNTs can be constructed with corresponding repeat unit, designed by the periodic characteristics on the basis of tubular clusters. Eventually, All of the SiNTs have a narrow band gap. From calculation of band structure, the band gap which occurs oscillations and gradually decreases with increase of the diameter, length, and the number of walls.

  20. HOST structural analysis program overview

    NASA Technical Reports Server (NTRS)

    Johns, R. H.

    1983-01-01

    Hot section components of aircraft gas turbine engines are subjected to severe thermal structural loading conditions, especially during the start up and take off portions of the engine cycle. The most severe and damaging stresses and strains are those induced by the steep thermal gradients induced during the start up transient. These transient stresses and strains are also the most difficult to predict, in part because of the temperature gradients and distributions are not well known or readily predictable, and also because the cyclic elastic viscoplastic behavior of the materials at these extremes of temperature and strain are not well known or readily predictable. A broad spectrum of structures related technology programs is underway to address these deficiencies. One element of the structures program is developing improved time varying thermal mechanical load models for the entire engine mission cycle from start up to shutdown. Another major part of the program is the development of new and improved nonlinear 3-D finite elements and associated structural analysis programs, including the development of temporal elements with time dependent properties to account for creep effects in the materials and components.

  1. Structural limits for evolutive capacities in complex molecular systems.

    PubMed

    Bergareche, A M; Ostolaza, J F

    1990-01-01

    The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit. PMID:1707552

  2. The structure and evolution of interacting binary galaxies

    NASA Astrophysics Data System (ADS)

    Borne, K. D.

    1983-08-01

    A numerical code was constructed for the study of the evolution of interacting binary galaxies. This "multiple three-body" algorithm (MTBA) essentially involves N concurrent three-body integrations. MTBA incorporates a violent relaxation phase that allows the particles to redistribute themselves in the gravitational field of the perturber prior to the full binary orbital evolution calculation. This redistribution is important for systems with an initially strong tidal potential; their predicted merger times are 50-100% larger than previously estimated. Merger times are tabulated both for circular and for elliptical orbits. Typical close binary galaxies will merge in about twice their initial binary oribtal periods. A specific interacting binary simulation is described in detail in the first paper. Many of the results reported here are consistent with those obtained from the larger, more expensive N-body simulations. MTBA is altered so that each "galaxy" is represented by a configuration of test particles.

  3. Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions.

    PubMed

    Hayden, Eric J

    2016-08-15

    RNA molecules provide a realistic but tractable model of a genotype to phenotype relationship. This relationship has been extensively investigated computationally using secondary structure prediction algorithms. Enzymatic RNA molecules, or ribozymes, offer access to genotypic and phenotypic information in the laboratory. Advancements in high-throughput sequencing technologies have enabled the analysis of sequences in the lab that now rivals what can be accomplished computationally. This has motivated a resurgence of in vitro selection experiments and opened new doors for the analysis of the distribution of RNA functions in genotype space. A body of computational experiments has investigated the persistence of specific RNA structures despite changes in the primary sequence, and how this mutational robustness can promote adaptations. This article summarizes recent approaches that were designed to investigate the role of mutational robustness during the evolution of RNA molecules in the laboratory, and presents theoretical motivations, experimental methods and approaches to data analysis. PMID:27215494

  4. Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

    NASA Astrophysics Data System (ADS)

    Manojkumar, P. A.; Chirayath, V. A.; Balamurugan, A. K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A. K.; Raj, Baldev

    2016-09-01

    Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  5. Gravitational Lenses and the Structure and Evolution of Galaxies

    NASA Technical Reports Server (NTRS)

    Oliversen, Ronald J. (Technical Monitor); Kochanek, Christopher

    2004-01-01

    During the first year of the project we completed five papers, each of which represents a new direction in the theory and interpretation of gravitational lenses. In the first paper, The Importance of Einstein Rings, we developed the first theory for the formation and structure of the Einstein rings formed by lensing extended sources like the host galaxies of quasar and radio sources. In the second paper, Cusped Mass Models Of Gravitational Lenses, we introduced a new class of lens models. In the third paper, Global Probes of the Impact of Baryons on Dark Matter Halos, we made the first globally consistent models for the separation distribution of gravitational lenses including both galaxy and cluster lenses. The last two papers explore the properties of two lenses in detail. During the second year we have focused more closely on the relationship of baryons and dark matter. In the third year we have been further examining the relationship between baryons and dark matter. In the present year we extended our statistical analysis of lens mass distributions using a self-similar model for the halo mass distribution as compared to the luminous galaxy.

  6. Onset and Evolution of Digitated Structures in Spreading Surfactant Films

    NASA Astrophysics Data System (ADS)

    Matar, Omar K.; Troian, Sandra M.

    1998-11-01

    A linearized transient analysis describing the spreading of an insoluble surfactant monolayer on a thin viscous film has revealed significant amplification in the disturbance film thickness on a time scale comparable to a Marangoni shear time (Matar and Troian, Phys. Fluids, 10 (5)), 1234 (1998). The onset, location and shape of typical excitations resemble digitated structures observed experimentally. Our numerical studies reveal which parameters control the amplification ratio, why disturbances localize behind the leading edge, and why van der Waals forces enhance the disturbance amplitude and lifetime. For the parameter set chosen, we also find that the solutions to the fully nonlinear equations mimic the behavior captured by the linearized description. For example, the equations favor disturbances of increasing wavelength as time advances. Interestingly, initial disturbances consisting of several harmonics of a preferred wavenumber do not couple through the nonlinear terms to any significant degree. We conclude from our work that the digitation observed experimentally is a transient response which nonetheless strongly influences the spreading process by channeling the liquid and surfactant flux to produce nonuniform surface coverage.

  7. Dissipative structures in a plasma with volume heat evolution

    SciTech Connect

    Pavlov, G.A.; Shiryaev, A.A.

    1983-11-01

    We analyzed the system of parabolic equations with a nonlinear and nondiagonal transport-coefficient matrix and with a linear vector-function source. This system of equations corresponds, for example, to an interaction of multicomponent diffusion processes with the volume heat evolution in the cavity of a gas-phase nuclear reactor, a topic which has not been studied previously. This reactor holds promise for the development of power plants. (AIP)

  8. Evolution of plant δ1-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives

    PubMed Central

    Forlani, Giuseppe; Makarova, Kira S.; Ruszkowski, Milosz; Bertazzini, Michele; Nocek, Boguslaw

    2015-01-01

    Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughout evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We also attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family. PMID:26284089

  9. Evolution of plant δ1-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives

    DOE PAGESBeta

    Forlani, Giuseppe; Makarova, Kira S.; Ruszkowski, Milosz; Bertazzini, Michele; Nocek, Boguslaw

    2015-08-03

    Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughout evolution.more » However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.« less

  10. Detection of structural damage in multiwire cables by monitoring the entropy evolution of wavelet coefficients

    NASA Astrophysics Data System (ADS)

    Ibáñez, Flor; Baltazar, Arturo; Mijarez, Rito; Aranda, Jorge

    2015-03-01

    Multiwire cables are widely used in important civil structures. Since they are exposed to several dynamic and static loads, their structural health can be compromised. The cables can also be submitted to mechanical contact, tension and energy propagation in addition to changes in size and material within their wires. Due to the critical role played by multiwire cables, it is necessary to develop a non-destructive health monitoring method to maintain their structure and proper performance. Ultrasonic inspection using guided waves is a promising non-destructive damage monitoring technique for rods, single wires and multiwire cables. The propagated guided waves are composed by an infinite number of vibrational modes making their analysis difficult. In this work, an entropy-based method to identify small changes in non-stationary signals is proposed. A system to capture and post-process acoustic signals is implemented. The Discrete Wavelet Transform (DWT) is computed in order to obtain the reconstructed wavelet coefficients of the signals and to analyze the energy at different scales. The feasibility of using the concept of entropy evolution of non-stationary signals to detect damage in multiwire cables is evaluated. The results show that there is a high correlation between the entropy value and damage level of the cable. The proposed method has low sensitivity to noise and reduces the computational complexity found in a typical time-frequency analysis.

  11. Deep Structure and Evolution of the Cyprus Arc, With Implications for the Tectonic Evolution of Anatolia

    NASA Astrophysics Data System (ADS)

    Wortel, M. J.; Spakman, W.; Govers, R.; Ben-Avraham, Z.

    2006-12-01

    This study addresses the easternmost segment of the convergent plate boundary in the Mediterranean, encompassing the Cyprus arc and its connection to the Arabia-Eurasia collision zone and the Dead Sea fault. Seismic activity along the arc is limited (certainly relative to the adjacent Hellenic arc). Although marine geophysical surveys have elucidated many pertinent features of the region, the plate boundary configuration is not well understood. Therefore, we use seismic tomography results to study the deep structure of this plate boundary segment. We find that the deep structure of the eastern part of the Cyprus arc, exhibiting a broad zone of sinistral deformation at the surface, is very similar to the eastern segment of the Hellenic subduction zone. A slab related anomaly is missing here in the upper mantle, and this part can be identified as a STEP fault zone (Subduction-Transform Edge Propagator; see Govers and Wortel, EPSL, v. 236, p. 505-523, 2005), allowing S-SW directed slab retreat. We propose that the inception of the STEP fault and the associated back-arc extension is triggered by the continental collision and subsequent slab detachment in the Bitlis suture to the east. From a quantitative analysis of tomographic anomalies in the mantle below the Bitlis suture zone (Hafkenscheid et al., JGR, v. 111, 2006) slab detachment is inferred to have taken place at 8-12 Ma, the younger end of this age range being more pertinent for the westernmost Bitlis segment. Slab detachment creates an edge to the subducting slab, which is a favourable condition for the inception of a STEP fault. The slab in the central part of the Cypus arc has become detached possibly resulting from the collision with the Eratosthenes Seamount in the (Late) Pliocene. Only in the northwestern segment of the arc below the Antalya Basin and the Isparta Angle the slab appears to be continuous. The short duration of the time window between inception of STEP faulting and collision with the

  12. Tectonic and volcanic evolution of dark terrain and its implications for the internal structure and evolution of Ganymede

    NASA Technical Reports Server (NTRS)

    Murchie, Scott L.; Head, James W.; Plescia, Jeffrey B.

    1990-01-01

    The origins of the ancient dark terrain on Ganymede and its three furrow systems are investigated using detailed geologic mapping of the furrows and dark-terrain units, observations and crater density measurements, and calculations of relative crater ages of material units. The results of the analysis are used to develop a hypothesis of the early evolution of Ganymede. Multiple testable models of furrow origin are presented.

  13. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians

    PubMed Central

    Bonetti, Maria Fernanda; Wiens, John J.

    2014-01-01

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change. PMID:25274369

  14. Observations of the structure and evolution of solar flares with a soft X-ray telescope

    NASA Technical Reports Server (NTRS)

    Vorpahl, J. A.; Gibson, E. G.; Landecker, P. B.; Mckenzie, D. L.; Underwood, J. M.

    1975-01-01

    Soft X ray flare events were observed with the S-056 X-ray telescope that was part of the ATM complement of instruments aboard SKYLAB. Analyses of these data are reported. The observations are summarized and a detailed discussion of the X-ray flare structures is presented. The data indicated that soft X-ray emitted by a flare come primarily from an intense well-defined core surrounded by a region of fainter, more diffuse emission. An analysis of flare evolution indicates evidence for preliminary heating and energy release prior to the main phase of the flare. Core features are found to be remarkably stable and retain their shape throughout a flare. Most changes in the overall configuration seem to be result of the appearance, disappearance or change in brightness of individual features, rather than the restructuring or reorientation of these features. Brief comparisons with several theories are presented.

  15. The evolution of interface phonon polariton modes in a finite superlattice with a structural defect

    NASA Astrophysics Data System (ADS)

    He, Meng-Dong; Wang, Ling-Ling; Huang, Wei-Qing; Wang, Xin-Jun; Zou, Bing-Suo

    2006-12-01

    Using a transfer matrix method, we derive the dispersion equation for interface phonon-polariton modes (IPPMs) in a finite superlattice (SL) with a structural defect. The numerical results show that, in the nonradiative regime, there exist localized IPPMs (including retardation) inside or outside the Reststrahlen regions defined by the interval [ωTO, ωLO]. The localized IPPMs lie either in the minigaps or below and above the bulk bands, and their transversal electric field amplitudes are located in the vicinity of the defect layer or surface layers. The evolution of the IPPMs localized in the vicinity of a different interface can clearly be tracked. In addition, a brief analysis that radiative IPPMs evolve into nonradiative IPPMs is given.

  16. Structure and property evolutions of ECAPed 7075 Al alloy during annealing.

    SciTech Connect

    Zhao, Y.; Liao, Xiaozhou; Zhu, Y. T.; Valiev, R. Z.

    2004-01-01

    Structure and microhardness evolutions of equal-channel angular pressing (ECAP) processed and coarse-grained (CG) 7075 A1 alloys during differential scanning calorimeter (DSC) were investigated by x-ray diffraction (XRD), transmission electron microscopy (TEM) and microhardness measurements. After one-month aging at room temperature, the microhardness of the ECAP processed sample is about 50% larger than that of the CG sample. During DSC annealing, the microhardness of the ECAP processed sample decreased gradually, while a hardening peak appeared for the CG sample. XRD and TEM show that the hardening peak of the CG sample was mainly caused by the precipitation hardening of the Guinier-Preston (GP) zone. For the ECAP processed sample, upon annealing the microstrain (dislocation density) decreased and the crystallites grew, which decreased the hardness and overcompensated the GP zone precipitation hardening. DSC analysis indicates ECAP process only promoted the phase precipitation, but did not change the sequence of phase precipitation.

  17. Planform evolution of two anabranching structures in the Upper Peruvian Amazon River

    NASA Astrophysics Data System (ADS)

    Frias, C. E.; Abad, J. D.; Mendoza, A.; Paredes, J.; Ortals, C.; Montoro, H.

    2015-04-01

    We present a study to relate the sinuosity of the main channel and its effect on the dynamics of the secondary channels of anabranching structures. For this purpose, two locations of the Peruvian Amazon River were selected: (1) a site with a medium to high-sinuosity main channel (MS site: Muyuy, Peru) and (2) a site with a low-sinuosity main channel (LS site: at the triple boundary between Brazil, Colombia, and Peru). The main channels for both the MS and LS anabranching structures have freedom to migrate in the lateral direction, while at least one of their secondary channels is adjacent to the geological valley. For MS and LS sites, temporal analysis of planform evolution was carried out using 30 years of satellite imagery from which metrics such as width, sinuosity, and annual maximum migration rates of main and secondary channels were calculated. Additionally, detailed hydrodynamic and bed morphology field measurements were carried out, and a two-dimensional shallow water numerical model was developed. For a medium to high-sinuosity main channel anabranching structure, the secondary channels present a dominant mechanism for reworking the floodplain, while for the low-sinuosity anabranching structure, the main channel planform dynamics is dominant. Flow velocities along the main and secondary channels for low, transition, and high-flow discharges describe that for MS (LS) site, the velocities are much higher along the secondary (main) channels.

  18. Evolution

    NASA Astrophysics Data System (ADS)

    Peter, Ulmschneider

    When we are looking for intelligent life outside the Earth, there is a fundamental question: Assuming that life has formed on an extraterrestrial planet, will it also develop toward intelligence? As this is hotly debated, we will now describe the development of life on Earth in more detail in order to show that there are good reasons why evolution should culminate in intelligent beings.

  19. Inception and evolution of coherent structures in under-expanded supersonic jets

    NASA Astrophysics Data System (ADS)

    Stegeman, P. C.; Pérez, J. M.; Soria, J.; Theofilis, V.

    2016-04-01

    The purpose of this paper is to examine the generation and nature of the large coherent structures observed experimentally in an under-expanded supersonic impinging jet. More specifically, the questions to answer are: What mechanisms govern the receptivity process at the nozzle lip?, how does the underlying flow field affect the evolution of the large-scale coherent structure generated from the initial instability? and what are the interactions between the large-scale (forced) coherent structures and the developing turbulence in the jet shear layer? In order to answer some of these questions both alternatives, that these structures come from global modal flow instabilities or from convective instabilities, the latter, are considered in this work. The stability analysis considered in the former case is performed in this work near the nozzle around the temporal average of the flow obtained by using an in-house LES (Large Eddy Simulation) code. The flow in this region is considered laminar, steady and without non-linear effects. The well known feedback loop in the impinging jet, according to which acoustic waves propagate upstream and excite the jet shear-layer (see Figure 2), advises against some of the hypothesis considered previously in the global stability analysis (ie. non-linear approximation). However the acoustic waves are orders of magnitude smaller than the hydrodynamic waves and should be smoothed out in the temporal average used in the calculation of the mean flow. The results show that both, axisymmetrical (m = 0) and azimuthal modes (m ≥ 1) are stable to global modal analysis and only convective instability could justify the instabilities observed in experiments in the shear layer. A study on the receptivity problem confirms that external disturbances may enter and excite the shear layer, being responsible of the instabilities observed in both experiments and direct numerical simulations.

  20. Progress in thermostructural analysis of space structures

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.; Dechaumphai, P.; Mahaney, J.; Pandey, A. K.

    1982-01-01

    A finite element space structures research focused on the interdisciplinary problems of heating, thermal, and structural analysis is discussed. Slender member shadowing effects, and cable stiffened structures are described.

  1. Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

    PubMed

    Sanseverino, Walter; Hénaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastián E; Garcia-Mas, Jordi; Casacuberta, Josep Maria

    2015-10-01

    The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution. PMID:26174143

  2. Structural evolution history of the Red Sea Rift

    NASA Astrophysics Data System (ADS)

    D'Almeida, G. A. F.

    2010-05-01

    The Red Sea Rift has been an object of comprehensive studies by several generations of geologists and geophysicists. Many publications and open-file reports provide insights into the geological history of this rift. Paleogene and Cretaceous rocks, which are considered to be prerift, are locally exposed at the margins of the Red Sea Rift. At the same time, some evidence indicates that at least some of these rocks are related to the early stage of the evolution of the Red Sea Rift. The available geological data suggest that the Red Sea region started its active evolution in the Cretaceous. As follows from lithostratigraphic data, the Cretaceous-Paleogene trough that predated the Oligocene-Quaternary rift covered this region completely or partially. The pre-Oligocene magmatism and geological evidence show that the Cretaceous-Paleogene trough was of the rift type. The Cretaceous-Eocene and Oligocene-Quaternary phases of rifting were separated by an epoch of uplifting and denudation documented by the erosion surface and unconformity.

  3. Visualization and Evolution of the Scientific Structure of Fuzzy Sets Research in Spain

    ERIC Educational Resources Information Center

    Lopez-Herrera, A. G.; Cobo, M. J.; Herrera-Viedma, E.; Herrera, F.; Bailon-Moreno, R.; Jimenez-Contreras, E.

    2009-01-01

    Introduction: Presents the first bibliometric study on the evolution of the fuzzy sets theory field. It is specially focused on the research carried out by the Spanish community. Method. The CoPalRed software, for network analysis, and the co-word analysis technique are used. Analysis: Bibliometric maps showing the main associations among the…

  4. Effects of Melt Processing on Evolution of Structure in PEEK

    NASA Technical Reports Server (NTRS)

    Georgiev, Georgi; Dai, Patrick Shuanghua; Oyebode, Elizabeth; Cebe, Peggy; Capel, Malcolm

    1999-01-01

    We report on the effects of melt processing temperature on structure formation in Poly(ether-ether-ketone), PEEK. Real time Small Angle X-ray Scattering, SAXS, and thermal analysis are used to follow the melting behavior after various stages of processing. Assignment of peaks to structural entities within the material, the relative perfection of the crystals, and the possibility of their reorganization, are all influenced by the melt processing history. With the advent of high intensity synchrotron sources of X-radiation, polymer scientists gain a research tool which, when used along with thermal analysis, provides additional structural information about the crystals during growth and subsequent melting. PEEK is an engineering thermoplastic polymer with a very high glass transition temperature (145 C) and crystal melting point (337 C). PEEK has been the subject of recent studies by X-ray scattering in which melt and cold crystallization were followed in real-time. X-ray scattering and thermal studies have been used to address the formation of dual endothermic response which has been variously ascribed to lamellar insertion, dual crystal populations, or melting followed by re-crystallization. Another important issue is whether all of the amorphous phase is located in interlamellar regions, or alternatively whether some is located in "pockets" away from the crystalline lamellar stacks. The interpretation of scattering from lamellar stacks varies depending upon whether such amorphous pockets are formed. Some groups believe all of the amorphous phase is interlamellar. This leads to selection of a smaller thickness for the crystals. Other groups suggest that most amorphous phase is not interlamellar, and this leads to the suggestion that the crystal thickness is larger than the amorphous layer within the stacks. To investigate these ideas, we used SAXS and Differential Scanning Calorimetry to compare results of single and dual stage melt crystallization of PEEK using a

  5. Effects of Melt Processing on Evolution of Structure in PEEK

    NASA Technical Reports Server (NTRS)

    Georgiev, Georgi; Dai, Patrick Shuanghua; Oyebode, Elizabeth; Cebe, Peggy; Capel, Malcolm

    1999-01-01

    We report on the effects of melt processing temperature on structure formation in Poly(ether-ether-ketone), PEEK. Real time Small Angle X-ray Scattering, SAXS, and thermal analysis are used to follow the melting behavior after various stages of processing. Assignment of peaks to structural entities within the material, the relative perfection of the crystals, and the possibility of their reorganization, are all influenced by the melt processing history. With the advent of high intensity synchrotron sources of X-radiation, polymer scientists gain a research tool which, when used along with thermal analysis, provides additional structural information about the crystals during growth and subsequent melting. PEEK is an engineering thermoplastic polymer with a very high glass transition temperature (145 C) and crystal melting point (337 C). PEEK has been the subject of recent studies by X-ray scattering in which melt and cold crystallization were followed in real-time. X-ray scattering and thermal studies have been used to address the formation of dual endothermic response which has been variously ascribed to lamellar insertion, dual crystal populations, or melting followed by re-crystallization. Another important issue is whether all of the amorphous phase is located in interlamellar regions, or alternatively whether some is located in "pockets" away from the crystalline lamellar stacks. The interpretation of scattering from lamellar stacks varies depending upon whether such amorphous pockets are formed. Some groups believe all of the amorphous phase is interlamellar. This leads to selection of a smaller thickness for the crystals. Other groups suggest that most amorphous phase is not interlamellar, and this leads to the suggestion that the crystal thickness is larger than the amorphous layer within the stacks. To investigate these ideas, we used SAXS and Differential Scanning Calorimetry to compare results of single and dual stage melt crystallization of PEEK using a

  6. BASE-9: Bayesian Analysis for Stellar Evolution with nine variables

    NASA Astrophysics Data System (ADS)

    Robinson, Elliot; von Hippel, Ted; Stein, Nathan; Stenning, David; Wagner-Kaiser, Rachel; Si, Shijing; van Dyk, David

    2016-08-01

    The BASE-9 (Bayesian Analysis for Stellar Evolution with nine variables) software suite recovers star cluster and stellar parameters from photometry and is useful for analyzing single-age, single-metallicity star clusters, binaries, or single stars, and for simulating such systems. BASE-9 uses a Markov chain Monte Carlo (MCMC) technique along with brute force numerical integration to estimate the posterior probability distribution for the age, metallicity, helium abundance, distance modulus, line-of-sight absorption, and parameters of the initial-final mass relation (IFMR) for a cluster, and for the primary mass, secondary mass (if a binary), and cluster probability for every potential cluster member. The MCMC technique is used for the cluster quantities (the first six items listed above) and numerical integration is used for the stellar quantities (the last three items in the above list).

  7. Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications.

    PubMed

    Barthlott, W; Mail, M; Neinhuis, C

    2016-08-01

    A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'. PMID:27354736

  8. Structural characteristics of Pavonis Mons, Mars, and implications for its volcano-tectonic evolution

    NASA Astrophysics Data System (ADS)

    Gwinner, Klaus; Head, James W.; Wilson, Lionel

    2010-05-01

    Pavonis Mons is the smallest of the three large Tharsis Montes volcanic edifices on Mars. While Viking-based studies have already revealed main structural features of these shields and have provided a framework on their evolution, detailed information on major aspects of their volcano-tectonic structure and evolution is still incomplete. In particular this is the case for the nature of asymmetries that develop along a NE direction, roughly coincident with the crest line of the Tharsis rise, as well as the evolution of the magma reservoir as the shields were built above the ground, and the related consequences for caldera formation and edifice stability. In addition, different morpho-structural features of the Martian shields have been discussed controversially, such as flank "terraces", rillelike channels, and evidence of flank instabilities. We have analyzed recently available high-resolution data, in particular DTMs with up to 50 m grid spacing derived from HRSC data, as well as high-resolution imagery (HRSC, CTX, HIRISE) and regional-scale MOLA DTMs for obtaining new constraints on the volcano-tectonic structure and evolution of Pavonis. We mapped tectonic elements (faults and fractures, wrinkle ridges, collapse pits), main volcanic elements (vent locations, limits of shield, apron and caldera floor units), and elements of flank morphology. Analysis of edifice morphometry is based on slope maps and slope statistics. We were able to identify several major fault systems affecting flanks and base of the edifice. Widespread occurrence of normal faulting from 2-3 km below the summit plateau to the base shows that the middle and lower flanks are characterized by extension. While the summit plateau and uppermost flanks show evidence for compressional deformation, including wrinkle ridges and downslope-convex flank facets interpreted as surface expression of flank thrusts, the system of intersecting flank facets that have been denoted as compressional "terraces" instead

  9. Cenozoic structural evolution and tectono-stratigraphic framework of the northern Gulf Coast continental margin

    SciTech Connect

    Diegel, F.A.; Karlo, J.F.; Shoup, R.C.; Schuster, D.C.

    1996-12-31

    The Cenozoic structural evolution of the northern Gulf of Mexico Basin is controlled by progradation over deforming, largely allochthonous salt structures derived from an underlying autochthonous Jurassic salt. The wide variety of structural styles is due to a combination of (1) original distribution of Jurassic and Mesozoic salt structures, (2) different slope depositional environments during the Cenozoic, and (3) varying degrees of salt withdrawal from allochthonous salt sheets. Tectono-stratigraphic provinces describe regions of contrasting structural styles and ages. Provinces include (1) a contractional foldbelt province, (2) a tabular salt-minibasin-province, (3) a Pliocene-Pleistocene detachment province, (4) a salt dome-minibasin province, (5) an Oligocene-Miocene detachment province, (6) a lower Oligocene Vicksburg detachment province, (7) an upper Eocene detachment province, and (8) the Wilcox growth fault province of Paleocene-Eocene age. Within several tectono-stratigraphic provinces, shale-based detachment systems, dominated by lateral extension, and allochthonous salt-based detachment systems, dominated by subsidence, can be distinguished by geometry, palinspastic reconstructions, and subsidence analysis. Many shale-based detachments are linked downdip to deeper salt-based detachments. Large extensions above detachments are typically balanced by salt withdrawal. Salt-withdrawal minibasins with flanking salt bodies occur as both isolated structural systems and components of salt-based detachment systems. During progradation, progressive salt withdrawal from tabular salt bodies on the slope formed salt-bounded minibasins which, on the shelf, evolved into minibasins bounded by arcuate growth faults and remnant salt bodies. Associated secondary salt bodies above allochthonous salt evolved from pillows, ridges, and massifs to leaning domes and steep-sided stocks.

  10. Building intuition of iron evolution during solar cell processing through analysis of different process models

    NASA Astrophysics Data System (ADS)

    Morishige, Ashley E.; Laine, Hannu S.; Schön, Jonas; Haarahiltunen, Antti; Hofstetter, Jasmin; del Cañizo, Carlos; Schubert, Martin C.; Savin, Hele; Buonassisi, Tonio

    2015-09-01

    An important aspect of Process Simulators for photovoltaics is prediction of defect evolution during device fabrication. Over the last twenty years, these tools have accelerated process optimization, and several Process Simulators for iron, a ubiquitous and deleterious impurity in silicon, have been developed. The diversity of these tools can make it difficult to build intuition about the physics governing iron behavior during processing. Thus, in one unified software environment and using self-consistent terminology, we combine and describe three of these Simulators. We vary structural defect distribution and iron precipitation equations to create eight distinct Models, which we then use to simulate different stages of processing. We find that the structural defect distribution influences the final interstitial iron concentration ([]) more strongly than the iron precipitation equations. We identify two regimes of iron behavior: (1) diffusivity-limited, in which iron evolution is kinetically limited and bulk [] predictions can vary by an order of magnitude or more, and (2) solubility-limited, in which iron evolution is near thermodynamic equilibrium and the Models yield similar results. This rigorous analysis provides new intuition that can inform Process Simulation, material, and process development, and it enables scientists and engineers to choose an appropriate level of Model complexity based on wafer type and quality, processing conditions, and available computation time.

  11. Finite element analysis of helicopter structures

    NASA Technical Reports Server (NTRS)

    Rich, M. J.

    1978-01-01

    Application of the finite element analysis is now being expanded to three dimensional analysis of mechanical components. Examples are presented for airframe, mechanical components, and composite structure calculations. Data are detailed on the increase of model size, computer usage, and the effect on reducing stress analysis costs. Future applications for use of finite element analysis for helicopter structures are projected.

  12. The evolution of the plasmoidal structure in the pinched column in plasma focus discharge

    NASA Astrophysics Data System (ADS)

    Kubes, P.; Paduch, M.; Cikhardt, J.; Klir, D.; Kravarik, J.; Rezac, K.; Cikhardtova, B.; Kortanek, J.; Zielinska, E.

    2016-04-01

    In this paper, a description is provided of the evolution of the dense spherical-like structures—plasmoids—formed in the pinched column of the dense plasma focus at the current of 1 MA at the final phase of implosion of the deuterium plasma sheath and at the phase of evolution of instabilities both at the time of HXR and neutron production. At the stratification of the plasma column, the plasma injected to the dense structures from the axially neighboring regions forms small turbulences which increase first the toroidal structures, and finally generates a non-chaotic current plasmoidal structure with central maximal density. This spontaneous evolution supports the hypothesis of the spheromak-like model of the plasmoid and its sub-millimeter analogy, high-energy spot. These spots, also called nodules formed in the filamentary structure of the current can be a source of the energy capable of accelerating the fast charged particles.

  13. Evolution of the magnetic field structure of the Crab pulsar.

    PubMed

    Lyne, Andrew; Graham-Smith, Francis; Weltevrede, Patrick; Jordan, Christine; Stappers, Ben; Bassa, Cees; Kramer, Michael

    2013-11-01

    Pulsars are highly magnetized rotating neutron stars and are well known for the stability of their signature pulse shapes, allowing high-precision studies of their rotation. However, during the past 22 years, the radio pulse profile of the Crab pulsar has shown a steady increase in the separation of the main pulse and interpulse components at 0.62° ± 0.03° per century. There are also secular changes in the relative strengths of several components of the profile. The changing component separation indicates that the axis of the dipolar magnetic field, embedded in the neutron star, is moving toward the stellar equator. This evolution of the magnetic field could explain why the pulsar does not spin down as expected from simple braking by a rotating dipolar magnetic field. PMID:24179221

  14. Probing the Evolution of the Shell Structures in Exotic Nuclei

    SciTech Connect

    De Angelis, Giacomo

    2008-11-11

    Magic numbers are a key feature in finite Fermion systems since they are strongly related to the underlying mean field. The size of the shell gaps and their evolution far from stability can be linked to the shape and symmetry of the nuclear mean field. Moreover the study of nuclei with large neutron/proton ratio allow to probe the density dependence of the effective interaction. Changes of the nuclear density and size in nuclei with increasing N/Z ratios are expected to lead to different nuclear symmetries and excitations. In this contribution I will discuss some selected examples which show the big potential of stable beams and of binary reactions for the study of the properties of the neutron-rich nuclear many body systems.

  15. Structural evolution of polyelectrolyte-complex-core micelles and ordered-phase bulk materials

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew; Krogstad, Daniel; Kramer, Edward

    2015-03-01

    The kinetics of formation and structural evolution of novel polyelectrolyte complex materials formed by the assembly of water-soluble di- and tri-block copolymers, with one neutral block and one block either cationic or anionic, have been investigated. The mechanism and speed of the assembly process, and the organization of these domains, were probed using dynamic mechanical spectroscopy and small angle X-ray scattering (SAXS). SAXS revealed that the equilibrium morphologies of both the di-block copolymer and the tri-block copolymer materials were generally qualitatively the same with some apparent quantitative differences in phase boundaries, possibly attributable to lack of full equilibration. Slow kinetics and difficulties in reaching equilibrium phase structures, especially in tri-block materials, is a principal message of this article. Detailed analysis of the SAXS data revealed that the tri-block copolymer materials formed ordered phases via a nucleation and growth pathway and that the addition of small amounts (~20%) of corresponding di-block copolymers increased the rate of structure formation and enhanced several key physical properties. This work was supported by the U.S. Department of Energy Office of Science Program in Basic Energy Sciences, Materials Sciences and Engineering Division.

  16. Structure, function and evolution of topologically associating domains (TADs) at HOX loci.

    PubMed

    Lonfat, Nicolas; Duboule, Denis

    2015-10-01

    Hox genes encode transcription factors necessary for patterning the major developing anterior to posterior embryonic axis. In addition, during vertebrate evolution, various subsets of this gene family were co-opted along with the emergence of novel body structures, such as the limbs or the external genitalia. The morphogenesis of these axial structures thus relies in part upon the precisely controlled transcription of specific Hox genes, a mechanism involving multiple long-range enhancers. Recently, it was reported that such regulatory mechanisms were largely shared between different developing tissues, though with some specificities, suggesting the recruitment of ancestral regulatory modalities from one tissue to another. The analysis of chromatin architectures at HoxD and HoxA loci revealed the existence of two flanking topologically associating domains (TADs), precisely encompassing the adjacent regulatory landscapes. Here, we discuss the function of these TADs in the control of Hox gene regulation and we speculate about their capacity to serve as structural frameworks for the emergence of novel enhancers. In this view, TADs may have been used as genomic niches to evolve pleiotropic regulations found at many developmental loci. PMID:25913784

  17. Detection of early landscape evolution through controlled experimentation, data analysis, and numerical modeling at the Landscape Evolution Observatory

    NASA Astrophysics Data System (ADS)

    Troch, Peter A.; Pangle, Luke; Niu, Guo-Yue; Dontsova, Katerina; Barron-Gafford, Greg; van Haren, Joost; Pavao-Zuckerman, Mitch

    2014-05-01

    The Landscape Evolution Observatory (LEO) at Biosphere 2-The University of Arizona consists of three identical, sloping, 333 m2 convergent landscapes inside a 5,000 m2 environmentally controlled facility. These engineered landscapes contain 1-meter depth of basaltic tephra, ground to homogenous loamy sand that will undergo physical, chemical, and mineralogical changes over many years. Each landscape contains a spatially dense sensor and sampler network capable of resolving meter-scale lateral heterogeneity and sub-meter scale vertical heterogeneity in moisture, energy and carbon states and fluxes. The density of sensors and frequency at which they can be polled allows for data collection at spatial and temporal scales that are impossible in natural field settings. Embedded solution and gas samplers allow for quantification of biogeochemical processes, and facilitate the use of chemical tracers to study water movement at very high spatial resolutions. Each ~600 metric ton landscape has load cells embedded into the structure to measure changes in total system mass with 0.05% full-scale repeatability (equivalent to less than 1 cm of precipitation). This facilitates the real time accounting of hydrological partitioning at the hillslope scale. Each hillslope is equipped with an engineered rain system capable of raining at rates between 3 and 45 mm/hr in a range of spatial patterns. The rain systems are capable of creating long-term steady state conditions or running complex simulations. The precipitation water supply storage system is flexibly designed to facilitate addition of tracers at constant or time-varying rates for any of the three hillslopes. This presentation will discuss detection of early landscape evolution in terms of hydrological, geochemical and microbial processes through controlled experimentation, data analysis, and numerical modeling during the commissioning phase of the first hillslope at LEO.

  18. Stable Isotope Analysis of Precipitation Samples Obtained via Crowdsourcing Reveals the Spatiotemporal Evolution of Superstorm Sandy

    PubMed Central

    Good, Stephen P.; Mallia, Derek V.; Lin, John C.; Bowen, Gabriel J.

    2014-01-01

    Extra-tropical cyclones, such as 2012 Superstorm Sandy, pose a significant climatic threat to the northeastern United Sates, yet prediction of hydrologic and thermodynamic processes within such systems is complicated by their interaction with mid-latitude water patterns as they move poleward. Fortunately, the evolution of these systems is also recorded in the stable isotope ratios of storm-associated precipitation and water vapor, and isotopic analysis provides constraints on difficult-to-observe cyclone dynamics. During Superstorm Sandy, a unique crowdsourced approach enabled 685 precipitation samples to be obtained for oxygen and hydrogen isotopic analysis, constituting the largest isotopic sampling of a synoptic-scale system to date. Isotopically, these waters span an enormous range of values (21‰ for O, 160‰ for H) and exhibit strong spatiotemporal structure. Low isotope ratios occurred predominantly in the west and south quadrants of the storm, indicating robust isotopic distillation that tracked the intensity of the storm's warm core. Elevated values of deuterium-excess (25‰) were found primarily in the New England region after Sandy made landfall. Isotope mass balance calculations and Lagrangian back-trajectory analysis suggest that these samples reflect the moistening of dry continental air entrained from a mid-latitude trough. These results demonstrate the power of rapid-response isotope monitoring to elucidate the structure and dynamics of water cycling within synoptic-scale systems and improve our understanding of storm evolution, hydroclimatological impacts, and paleo-storm proxies. PMID:24618882

  19. The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

    NASA Astrophysics Data System (ADS)

    Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

    2016-08-01

    Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

  20. The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

    NASA Astrophysics Data System (ADS)

    Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

    2016-04-01

    Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

  1. Probabilistic structural analysis methods of hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1989-01-01

    Development of probabilistic structural analysis methods for hot engine structures is a major activity at Lewis Research Center. Recent activities have focused on extending the methods to include the combined uncertainties in several factors on structural response. This paper briefly describes recent progress on composite load spectra models, probabilistic finite element structural analysis, and probabilistic strength degradation modeling. Progress is described in terms of fundamental concepts, computer code development, and representative numerical results.

  2. The importance of inherited structures in slope evolution: the Ridnaun Valley case, Italy

    NASA Astrophysics Data System (ADS)

    Zorzi, L.; Flaim, L.; Massironi, M.; Genevois, R.; Stead, D.

    2013-12-01

    The south facing slope of the Ridnaun Valley (South Tyrol, Italy) comprises the crystalline units belonging to the Austoalpine Nappe of the Alpine orogenic wedge and shows evidence of quaternary gravitational evolution which is highly dependent on the interaction between the slope trend and the brittle/ductile structural setting. The slope valley is incised within the paragneiss rocks of the Oetztal - Stubei Unit and the micaschists of the Schneeberg Unit. These two units are separated by a NNW gentle dipping tectonic contact, which obliquely intersects the E-W slope, and is characterized by multiple ultracataclasitic layers that follow the regional low angle north-dipping schistosity. Folds with sub-horizontal E-trending axes induce a change in the dip direction of the regional schistosity from N dipping (unfavorable to the slip) to SE dipping (favorable to the slip). NNE-SSW and N-S trending faults, having a mean thickness of incoherent fault breccias of 1 m, affect the entire slope. These along with the folds and the ultracataclastic layers, have significant influence on rock mass mechanical properties and on mechanisms and timing of the observed gravitational phenomena. Field work and ALS-HRDEM analysis has revealed different gravitational movements along the slope. A fully evolved gravitational collapse, having the features of a Rock Avalanche (RA), characterizes the central part covering an area of about 2.4 km2; whereas to the east and west of the RA, deep seated gravitational slope deformations (DSGSDs) still affect the slope. An ongoing gravitational deformation is apparent in the uphill sections of the slope, next to the crown area of the RA. PS and DS - SAR interferometry data (provided by the Geological Survey of the Autonomous Province of Bolzano, Italy), testify an ongoing movement on both the DSGSDs bordering the RA, highlighting a most unstable area at the western sector. The heterogeneous behavior of the slope is most likely controlled by the

  3. Evolution of dendrimer conformational structure with generation number

    NASA Astrophysics Data System (ADS)

    Betancourt, Beatriz A. Pazmiño; Douglas, Jack F.

    2016-05-01

    We simulate the conformational structure of a coarse-grained model of dendrimer molecules in a good solvent as a function of generation number G and find that they evolve through substantially more complex structures than regular star polymers with increasing arms because of their hierarchical topological structure. As G increases, they evolve from 3-arm stars to branched polymers that geometrically resemble lattice animals, and then percolation clusters for G = 4 - 6 range. For larger G, the dendrimers become similar to porous particles, but the molecule segregates segregates into subdomains at G = 9, reflecting the branching complexity of the first dendrimer generation.

  4. Probabilistic structural analysis methods development for SSME

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1988-01-01

    The development of probabilistic structural analysis methods is a major part of the SSME Structural Durability Program and consists of three program elements: composite load spectra, probabilistic finite element structural analysis, and probabilistic structural analysis applications. Recent progress includes: (1) the effects of the uncertainties of several factors on the HPFP blade temperature pressure and torque, (2) the evaluation of the cumulative distribution function of structural response variables based on assumed uncertainties on primitive structural variables, and (3) evaluation of the failure probability. Collectively, the results obtained demonstrate that the structural durability of critical SSME components can be probabilistically evaluated.

  5. Design of structurally distinct proteins using strategies inspired by evolution.

    PubMed

    Jacobs, T M; Williams, B; Williams, T; Xu, X; Eletsky, A; Federizon, J F; Szyperski, T; Kuhlman, B

    2016-05-01

    Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. We describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. This method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds. PMID:27151863

  6. Clear air convection - A close look at its evolution and structure

    NASA Technical Reports Server (NTRS)

    Richter, J. H.; Jensen, D. R.; Noonkester, V. R.; Konrad, T. G.; Arnold, A.; Rowland, J. R.

    1974-01-01

    A unique experiment using advanced remote and direct sensing techniques was designed to investigate the detailed evolution and structure of clear-air convection. The measurements involved a high-power, narrow-beam pulse radar, a frequency modulated, continuous wave radar, an acoustic echo sounder, and instrumented aircraft. The various probing methods when used together complement each other and give a compatible and comprehensive description of the spatial and temporal evolution of clear-air convection.

  7. On the formation and evolution of gaseous structures in Comet P/Halley

    NASA Astrophysics Data System (ADS)

    Schulz, R.; A'Hearn, M. F.; Samarasinha, N. H.

    1993-06-01

    The possibility of a dynamic connection between the CN jets and CN shells in the coma of Comet P/Halley is here investigated through numerical simulations on the spatial and temporal evolution of gaseous jets. The evolution of such a jet into a shell is found to be straightforward for several geometries. It is noted that a closed shell structure may be due to a near-equatorial observational view of material derived from the active region near the nucleus equator.

  8. Structural and Stratigraphic Evolution of the Iberia and Newfoundland Rifted Margins: A Quantitative Modeling Approach

    NASA Astrophysics Data System (ADS)

    Mohn, G.; Karner, G. D.; Manatschal, G.; Johnson, C. A.

    2014-12-01

    Rifted margins develop generally through polyphased extensional events leading eventually to break-up. We investigate the spatial and temporal evolution of the Iberia-Newfoundland rifted margin from its Permian post-orogenic stage to early Cretaceous break-up. We have applied Quantitative Basin Analysis to integrate seismic stratigraphic interpretations and drill hole data of representative sections across the Iberia-Newfoundland margins with kinematic models for the thinning of the lithosphere and subsequent isostatic readjustment. Our goal is to predict the distribution of extension and thinning, environments of deposition, crustal structure and subsidence history as functions of space and time. The first sediments deposited on the Iberian continental crust were in response to Permian lithospheric thinning, associated with magmatic underplating and subsequent thermal re-equilibration of the lithosphere. During late Triassic-early Jurassic rifting, a broadly distributed depth-independent lithospheric extension occurred, followed by late Jurassic rifting that increasingly focused with time and became depth-dependent during the early Cretaceous. However, there exists a temporality in the along-strike deformation of the Iberia-Newfoundland margin: significant Valanginian-Hauterivian deformation characterizes the northern Galicia Bank-Flemish Cap while the southern Iberian-Newfoundland region is characterized by Tithonian-early Berriasian extension. Deformation localized with time on both margins leading to late Aptian break-up. To match the distribution and magnitude of subsidence across the profiles requires significant thinning of middle/lower crustal level and subcontinental lithospheric mantle, leading to the formation of the hyper-extended domains. The late-stage deformation of both margins was characterized by a predominantly brittle deformation of the residual continental crust, leading to exhumation of subcontinental mantle and ultimately to seafloor

  9. Structural evolution in crystalline MoO{sub 3} nanoparticles with tunable size

    SciTech Connect

    Barros Santos, Elias de; Aparecido Sigoli, Fernando; Odone Mazali, Italo

    2012-06-15

    In this study MoO{sub 3} nanoparticles were prepared in porous Vycor glass by impregnation-decomposition cycles (IDC) with molybdenum(VI) 2-ethylhexanoate. X-ray diffraction data show that the nanoparticles are crystalline and are in the orthorhombic {alpha}-MoO{sub 3} phase. Raman spectroscopy data also indicate the formation of this phase. The profiles in the Raman spectra changed with the number of IDC, indicating a structural evolution of the MoO{sub 3} nanoparticles. The IDC methodology promoted a linear mass increase and allowed tuning the nanoparticle size. Analysis of HRTEM images revealed that for 3, 5 and 7 IDC, the MoO{sub 3} nanoparticle average diameters are 3.2, 3.6 and 4.2 nm. Diffuse reflectance spectroscopy indicates a consistent red shift in the band gap from 3.35 to 3.29 eV as the size increases from 3.2 to 4.2 nm. This observed red shift in the band gap of the MoO{sub 3} nanoparticles is presumably due to quantum confinement effects. - Graphical abstract: Modification of profile Raman spectra for crystalline MoO{sub 3} nanoparticles in function of the particle size. Highlights: Black-Right-Pointing-Pointer Structural evolution of the MoO{sub 3} nanoparticles as a function of the crystallite size. Black-Right-Pointing-Pointer Tunable optical properties by controlling the MoO{sub 3} nanoparticle size. Black-Right-Pointing-Pointer The impregnation-decomposition methodology allowed tuning the nanoparticle size. Black-Right-Pointing-Pointer The red shift in the band gap of the MoO{sub 3} nanoparticles is due to quantum size effect. Black-Right-Pointing-Pointer The short-distance order in MoO{sub 3} nanoparticle is function to area/volume ratio.

  10. A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?

    PubMed

    Meier, Sebastian; Ozbek, Suat

    2007-11-01

    While Darwin pictured organismal evolution as "descent with modification" more than 150 years ago, a detailed reconstruction of the basic evolutionary transitions at the molecular level is only emerging now. In particular, the evolution of today's protein structures and their concurrent functions has remained largely mysterious, as the destruction of these structures by mutation seems far easier than their construction. While the accumulation of genomic and structural data has indicated that proteins are related via common ancestors, naturally occurring protein structures are often considered to be evolutionarily robust, thus leaving open the question of how protein structures can be remodelled while selective pressure forces them to function. New information on the proteome, however, increasingly explains the nature of local and global conformational diversity in protein evolution, which allows the acquisition of novel functions via molecular transition forms containing ancestral and novel structures in dynamic equilibrium. Such structural plasticity may permit the evolution of new protein folds and help account for both the origins of new biological functions and the nature of molecular defects. PMID:17935152

  11. The tRNA Elbow in Structure, Recognition and Evolution

    PubMed Central

    Zhang, Jinwei; Ferré-D’Amaré, Adrian R.

    2016-01-01

    Prominent in the L-shaped three-dimensional structure of tRNAs is the “elbow” where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow. PMID:26771646

  12. Three-dimensional evolution of flow structures in transitional circular and chevron jets

    NASA Astrophysics Data System (ADS)

    Violato, Daniele; Scarano, Fulvio

    2011-12-01

    The three-dimensional behavior of flow transition in circular and 6-chevron jets at Re = 5000 is investigated with experiments conducted on a free water jet by time-resolved tomographic particle image velocimetry. The emphasis is on the unsteady organization of coherent flow structures, which play a role in the generation of acoustic noise. Shedding and pairing of vortices are the most pronounced phenomena observed in the near field of the circular jet. The first and second pairing amplify the axial pulsatile motion in the jet column and lead to the growth of azimuthal waves culminating in the breakup of the vortex ring. Streamwise vortices of axial and radial vorticity are observed in the outer region and move inward and outward under the effect of the vortex rings. In the jet with chevrons, the axisymmetric ring-like coherence of the circular jet is not encountered. Instead, streamwise flow structures of azimuthal vorticity emanate from the chevron apices, and counter-rotating streamwise vortices of axial and radial vorticity develop from the chevron notches. The decay of streamwise vortices is accompanied by the formation of C-shaped structures. The three-dimensional analysis allows quantifying the vortex stretching and tilting activity, which, for the circular jet exit, is related to the azimuthal instabilities and the streamwise vortices connecting the vortex rings. In the chevron jet, stretching and tilting peak during the formation of C-structures. Following Powell's aeroacoustic analogy, the spatial distribution of the source term is mapped, evaluating the temporal derivative of the Lamb vector. The spatio-temporal evolution of such source term is visualized revealing that the events of highest activity are associated with the processes of vortex-ring pairing and vortex-ring disruption for the circular jet, and with the decay of streamwise instabilities and the formation of C-shaped structures for the chevron case.

  13. Graph spectral analysis of protein interaction network evolution.

    PubMed

    Thorne, Thomas; Stumpf, Michael P H

    2012-10-01

    We present an analysis of protein interaction network data via the comparison of models of network evolution to the observed data. We take a bayesian approach and perform posterior density estimation using an approximate bayesian computation with sequential Monte Carlo method. Our approach allows us to perform model selection over a selection of potential network growth models. The methodology we apply uses a distance defined in terms of graph spectra which captures the network data more naturally than previously used summary statistics such as the degree distribution. Furthermore, we include the effects of sampling into the analysis, to properly correct for the incompleteness of existing datasets, and have analysed the performance of our method under various degrees of sampling. We consider a number of models focusing not only on the biologically relevant class of duplication models, but also including models of scale-free network growth that have previously been claimed to describe such data. We find a preference for a duplication-divergence with linear preferential attachment model in the majority of the interaction datasets considered. We also illustrate how our method can be used to perform multi-model inference of network parameters to estimate properties of the full network from sampled data. PMID:22552917

  14. Analysis on the long term orbital evolution of Molniya satellites

    NASA Astrophysics Data System (ADS)

    Zhu, Ting-Lei; Zhao, Chang-Yin; Wang, Hong-Bo; Zhang, Ming-Jiang

    2015-06-01

    Long term evolution of the Molniya satellites are investigated by means of historical data analysis, theoretical analysis and numerical integration. Both the mean motion resonance problem and the critical inclination problem are studied. The period and the amplitude of the semi-major axis for each satellite are obtained analytically and compared with the observational data. In addition, the reason of the observed sudden changes in the center and the amplitude of the oscillating semi-major axes is determined as the effect of the atmosphere drag. For the long period perigee motion, the dominant perturbations come from the luni-solar gravity. A two-degree-of freedom system is established by adding the two periodic terms of the neighbor resonances to the Hamiltonian of the classical single resonance model. In theory, the resulting resonance overlap model is responsible for the chaotic layer between the libration region and the circulation region. In practice, it is applied to explain the quick decay of the earliest Molniya satellites and to study the satellites that still orbiting the Earth at present.

  15. Probabilistic structural analysis methods of hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Hopkins, D. A.

    1989-01-01

    Development of probabilistic structural analysis methods for hot engine structures at Lewis Research Center is presented. Three elements of the research program are: (1) composite load spectra methodology; (2) probabilistic structural analysis methodology; and (3) probabilistic structural analysis application. Recent progress includes: (1) quantification of the effects of uncertainties for several variables on high pressure fuel turbopump (HPFT) turbine blade temperature, pressure, and torque of the space shuttle main engine (SSME); (2) the evaluation of the cumulative distribution function for various structural response variables based on assumed uncertainties in primitive structural variables; and (3) evaluation of the failure probability. Collectively, the results demonstrate that the structural durability of hot engine structural components can be effectively evaluated in a formal probabilistic/reliability framework.

  16. The pig X and Y Chromosomes: structure, sequence, and evolution

    PubMed Central

    Skinner, Benjamin M.; Sargent, Carole A.; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane E.; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Jo; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J.I.; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan M.D.; Yang, Fengtang; Harrow, Jen; Affara, Nabeel A.; Tyler-Smith, Chris

    2016-01-01

    We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution. PMID:26560630

  17. Evolution, structure, and expression of GNPI/Oscillin orthologous genes.

    PubMed

    Nakamura, Y; Miura, K; Fujino, Y; Iwao, H; Ogita, S; Yamanaka, S

    2000-09-01

    Oscillin was identified from hamster sperm as a factor responsible for oocyte calcium oscillations. However, its high level of homology with the bacterial glucosamine-6-phosphate isomerase suggests that it may play more fundamental roles. In the current study, we identified Oscillin orthologs from Caenorhabditis elegans, Drosophila melanogaster, mouse, and human. Their amino acid identities with hamster oscillin were 67.0, 72.3, 97.6, and 95.5%, respectively. No Oscillin orthologs were found in Saccharomyces cerevisiae. The human Oscillin gene (HGMW-approved symbol GNPI) spans 12.4 kb and consists of eight exons. The position of the fourth intron was conserved in other species. The human Oscillin promoter has features characteristic of housekeeping genes, including a GC-rich content, multiple SP1 binding sites, and the absence of a TATA motif. Human and mouse Oscillin genes were ubiquitously expressed in all tissues examined. These data showed that Oscillin is a housekeeping gene conserved throughout evolution and do not support the notion that Oscillin is the sperm-specific factor responsible for calcium oscillations. PMID:10964516

  18. Structural evolution and stability of sol gel biocatalysts

    NASA Astrophysics Data System (ADS)

    Rodgers, L. E.; Knott, R. B.; Holden, P. J.; Pike, K. J.; Hanna, J. V.; Foster, L. J. R.; Bartlett, J. R.

    2006-11-01

    Immobilisation strategies for catalytic enzymes are important as they allow recovery and reuse of the biocatalysts. In this work, sol-gel matrices have been used to immobilise Candida antarctica lipase B (CALB), a commonly used industrial enzyme. The sol-gel bioencapsulate is produced through fluoride-catalysed hydrolysis of mixtures of tetramethylorthosilicate (TMOS) and methyltrimethoxysilane (MTMS) in the presence of CALB, yielding materials with controlled pore sizes and surface chemistries. Sol-gel matrices prolong the catalytic life and enhance the activity of CALB, although the molecular basis for this effect has yet to be elucidated due to the limitations of analytical techniques applied to date. Small angle neutron scattering (SANS) allows such multi-component systems to be characterised through contrast matching. In the sol-gel bioencapsulate system at the contrast match point for silica, residual scattering intensity is due to the CALB and density fluctuations in the matrix. A SANS contrast variation series found the match point for the silica matrix, both with and without enzyme present, to be around 35%. The model presented here proposes a mechanism for the interaction between CALB and the surrounding sol-gel matrix, and the observed improvement in enzyme activity and matrix strength. Essentially, the inclusion of CALB modulates silicate speciation during evolution of the inorganic network, leading to associated variations in SANS contrast. The SANS protocol developed here may be applied more generally to other encapsulated enzyme systems.

  19. Evolution of the Alboran Sea hydrographic structures during July 1993

    NASA Astrophysics Data System (ADS)

    Lafuente, Jesús García.; Cano, Natalio; Vargas, Manuel; Rubín, Juan P.; Hernández-Guerra, Alonso

    1998-01-01

    During the ICTIOALBORAN-0793 multidisciplinary oceanographic survey carried out in July 1993 by the Instituto Español de Oceanografı´a (IEO) in the Alboran Sea, some anomalous features were detected. One was the presence of a small cyclonic eddy in the western Alboran Basin, close to the African coast. The upper layer of the eddy consisted of Mediterranean Surface Water and was separated from its supposed source (the northern Alboran Sea) by the Atlantic Jet. Another feature was the probable temporary interruption of the flow of fresh Atlantic Water (S≈36.5) into the eastern Alboran Basin and its replacement by a modified (saltier) Atlantic Water. These features can be explained assuming a time evolution of the surface circulation in the Alboran Sea forced by speed variations in the inflowing Atlantic Water through the Strait of Gibraltar. A collection of satellite images covering the survey period and across-strait sea level difference data, indicative of the geostrophic velocity of the inflow through the Strait, were used to check this assumption. Both sets of data supplied independent but compatible information in the sense that they complemented each other and gave support to the proposed evolving model. Finally, some speculative ideas attempting to correlate the inferred variability in the Alboran Sea with the state of the baroclinic water exchange through the Strait of Gibraltar (maximal or submaximal) are discussed.

  20. The pig X and Y Chromosomes: structure, sequence, and evolution.

    PubMed

    Skinner, Benjamin M; Sargent, Carole A; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane E; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Jo; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J I; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan M D; Yang, Fengtang; Harrow, Jen; Affara, Nabeel A; Tyler-Smith, Chris

    2016-01-01

    We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution. PMID:26560630

  1. The structural evolution of superalloy ingots during hot working

    NASA Astrophysics Data System (ADS)

    Forbes Jones, Robin M.; Jackman, Laurence A.

    1999-01-01

    This article provides an overview of structural changes that occur during the hot working of superalloys and provides insight into the use of precipitated particles and other thermomechanical factors to achieve desired structures. Examples will focus primarily on alloys 718 and 720, which are iron-nickel and nickel-based alloys, respectively. The availability of a second phase to control grain size is a characteristic of some iron-nickel-and nickel-based superalloys that is not usually available to cobalt-based superalloys; processing with and without the use of a precipitated phase that influences microstructures will be illustrated by the use of these examples.

  2. The endoskeletal structures in arthropods: cytology, morphology and evolution.

    PubMed

    Bitsch, Colette; Bitsch, Jacques

    2002-02-01

    The paper proposes an overview of the endoskeletal structures of the head and trunk in the different arthropod groups: Chelicerata, Crustacea, Myriapoda and Hexapoda (=Insecta s.l.). Two major endoskeletal systems are reported with their cytological characteristics: those made up of connective tissue derived from muscular tendons, and those consisting of cuticular rods or plates arising from integumentary ingrowths. The morphological value of the various endoskeletal structures, their possible homologies in different groups, and their presumed evolutionary changes are discussed. This survey may be considered as a first step to use morphological characteristics of the endoskeleton in future cladistic analyses to assess the phylogeny of arthropods. PMID:18088953

  3. The evolution of cerebellum structure correlates with nest complexity.

    PubMed

    Hall, Zachary J; Street, Sally E; Healy, Susan D

    2013-01-01

    Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird's ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level. PMID:24307527

  4. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water

    PubMed Central

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P.; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  5. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    PubMed

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-01-01

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry. PMID:26286479

  6. Structural evolution during protein denaturation as induced by different methods.

    PubMed

    Chodankar, S; Aswal, V K; Kohlbrecher, J; Vavrin, R; Wagh, A G

    2008-03-01

    Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been used to study conformational changes in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by varying temperature and pressure, and in presence of protein denaturating agents urea and surfactant. BSA has prolate ellipsoidal shape at ambient temperature and we observe no effect of temperature on its structure up to a temperature of about 60 degrees C . At temperatures beyond 60 degrees C , protein denaturation leads to aggregation. The protein solution exhibits a fractal structure at temperatures above 64 degrees C , and its fractal dimension increases with temperature. This is an indication of aggregation followed by gelation that evolves with increasing temperature. It is known for some of the proteins (e.g., Staphylococcal Nuclease) that pressure of 200 MPa can unfold the protein, whereas BSA does not show any protein unfolding even up to the pressure of 450 MPa . In presence of urea, the BSA protein unfolds for urea concentrations greater than 4M and acquires a random coil configuration. We make use of the dilution method to show the reversibility of protein unfolding with urea. The addition of surfactant denaturates the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein. We show such structure of the protein-surfactant complex can be stabilized at higher temperatures, which is not the case for pure protein. PMID:18517416

  7. Structural evolution during protein denaturation as induced by different methods

    NASA Astrophysics Data System (ADS)

    Chodankar, S.; Aswal, V. K.; Kohlbrecher, J.; Vavrin, R.; Wagh, A. G.

    2008-03-01

    Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been used to study conformational changes in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by varying temperature and pressure, and in presence of protein denaturating agents urea and surfactant. BSA has prolate ellipsoidal shape at ambient temperature and we observe no effect of temperature on its structure up to a temperature of about 60°C . At temperatures beyond 60°C , protein denaturation leads to aggregation. The protein solution exhibits a fractal structure at temperatures above 64°C , and its fractal dimension increases with temperature. This is an indication of aggregation followed by gelation that evolves with increasing temperature. It is known for some of the proteins (e.g., Staphylococcal Nuclease) that pressure of 200MPa can unfold the protein, whereas BSA does not show any protein unfolding even up to the pressure of 450MPa . In presence of urea, the BSA protein unfolds for urea concentrations greater than 4M and acquires a random coil configuration. We make use of the dilution method to show the reversibility of protein unfolding with urea. The addition of surfactant denaturates the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein. We show such structure of the protein-surfactant complex can be stabilized at higher temperatures, which is not the case for pure protein.

  8. Correlation between atomic structure evolution and strength in a bulk metallic glass at cryogenic temperature

    PubMed Central

    Tan, J.; Wang, G.; Liu, Z. Y.; Bednarčík, J.; Gao, Y. L.; Zhai, Q. J.; Mattern, N.; Eckert, J.

    2014-01-01

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

  9. Structural constraints on the evolution of the collagen fibril: convergence on a 1014-residue COL domain

    PubMed Central

    Slatter, David Anthony; Farndale, Richard William

    2015-01-01

    Type I collagen is the fundamental component of the extracellular matrix. Its α1 gene is the direct descendant of ancestral fibrillar collagen and contains 57 exons encoding the rod-like triple-helical COL domain. We trace the evolution of the COL domain from a primordial collagen 18 residues in length to its present 1014 residues, the limit of its possible length. In order to maintain and improve the essential structural features of collagen during evolution, exons can be added or extended only in permitted, non-random increments that preserve the position of spatially sensitive cross-linkage sites. Such sites cannot be maintained unless the twist of the triple helix is close to 30 amino acids per turn. Inspection of the gene structure of other long structural proteins, fibronectin and titin, suggests that their evolution might have been subject to similar constraints. PMID:25994354

  10. Correlation between atomic structure evolution and strength in a bulk metallic glass at cryogenic temperature.

    PubMed

    Tan, J; Wang, G; Liu, Z Y; Bednarčík, J; Gao, Y L; Zhai, Q J; Mattern, N; Eckert, J

    2014-01-01

    A model Zr41.25Ti13.75Ni10Cu12.5Be22.5 (at.%) bulk metallic glass (BMG) is selected to explore the structural evolution on the atomic scale with decreasing temperature down to cryogenic level using high energy X-ray synchrotron radiation. We discover a close correlation between the atomic structure evolution and the strength of the BMG and find out that the activation energy increment of the concordantly atomic shifting at lower temperature is the main factor influencing the strength. Our results might provide a fundamental understanding of the atomic-scale structure evolution and may bridge the gap between the atomic-scale physics and the macro-scale fracture strength for BMGs. PMID:24469299

  11. Fluorous 'ponytails' lead to strong gelators showing thermally induced structure evolution.

    PubMed

    Kumari, Harshita; Armitage, Sarah E; Kline, Steven R; Damodaran, Krishna K; Kennedy, Stuart R; Atwood, Jerry L; Steed, Jonathan W

    2015-11-21

    Appending perfluoroalkyl substituents to bis(urea) gelators results in significantly decreased inter-chain interactions with markedly thinner fibres and hence more cross-linked and more transparent gels with potential applications in the crystallisation of fluorinated pharmaceuticals. Gel structure has been probed by detailed SANS measurements which indicate a surprising structure evolution on thermal cycling, not seen for hydrocarbon analogues. The SANS data are complemented by the single crystal X-ray structure of one fluorinated gelator. PMID:26364926

  12. Subsurface defects structural evolution in nano-cutting of single crystal copper

    NASA Astrophysics Data System (ADS)

    Wang, Quanlong; Bai, Qingshun; Chen, Jiaxuan; Sun, Yazhou; Guo, Yongbo; Liang, Yingchun

    2015-07-01

    In this work, molecular dynamics simulation is performed to study the subsurface defects structural distribution and its evolution during nano-cutting process of single crystal copper. The formation mechanism of chip and machined surface is interviewed by analyzing the dislocation evolution and atomic migration. The centro-symmetry parameter and spherical harmonics method are adopted to characterize the distribution and evolution of the subsurface defect structures and local atomic structures. The results show that stacking faults, dislocation loops, "V-shaped" dislocation loops, and plenty of point defects are formed during the machined surface being formed in shear-slip zone. In subsurface damage layers, stair-rod dislocation, stacking fault tetrahedra, atomic cluster defect, and vacancy defect are formed. And the formation mechanism of stair-rod dislocation is investigated by atomic-scale structure evolution. The local atomic structures of subsurface defects are icosahedrons, hexagonal close packed, body-centered cubic, and defect face center cubic, and the variations of local atomic structures are investigated.

  13. Circumferential graben and the structural evolution of Alba Mons, Mars

    NASA Astrophysics Data System (ADS)

    Öhman, Teemu; McGovern, Patrick J.

    2014-05-01

    Alba Mons is a unique, very extensive but shallow volcanotectonic construct in northern Tharsis, Mars. Numerous models have been presented to explain the formation of Alba Mons and its most characteristic feature, a wristwatch-like pattern of radial and circumferential graben. We used a wide selection of topographic datasets to characterize the fault throw variation on nine topographic transects across the circumferential graben in order to provide observational constraints for the different formation models, and to gain further insight into the evolution of Alba Mons. In most of the transects, summed throws from outwards-facing (away from the center of the volcano) faults are larger than from the inwards-facing (towards the center) ones. Only the very gently sloping western transects show the opposite, emphasizing the east-west-asymmetry of Alba Mons. 10-40% of the observed topographic relief of Alba Mons along the nine transects can be accounted for by this throw difference between the inwards- and outwards-facing faults. These results are consistent with predictions of models suggesting an uplift mechanism to explain the formation of the circumferential graben, but not with models invoking central subsidence. Horizontal extensional strain along the transects varies between 0.5% and 2%, consistent with strain predictions of the late-stage sill complex inflation model of McGovern et al. (McGovern, P.J., Solomon, S.C., Head J.W. III, Smith, D.E., Zuber M.T., Neumann, G.A. [2001]. J. Geophys. Res. 106(E10), 23769-23809).

  14. Urban slum structure: integrating socioeconomic and land cover data to model slum evolution in Salvador, Brazil

    PubMed Central

    2013-01-01

    Background The expansion of urban slums is a key challenge for public and social policy in the 21st century. The heterogeneous and dynamic nature of slum communities limits the use of rigid slum definitions. A systematic and flexible approach to characterize, delineate and model urban slum structure at an operational resolution is essential to plan, deploy, and monitor interventions at the local and national level. Methods We modeled the multi-dimensional structure of urban slums in the city of Salvador, a city of 3 million inhabitants in Brazil, by integrating census-derived socioeconomic variables and remotely-sensed land cover variables. We assessed the correlation between the two sets of variables using canonical correlation analysis, identified land cover proxies for the socioeconomic variables, and produced an integrated map of deprivation in Salvador at 30 m × 30 m resolution. Results The canonical analysis identified three significant ordination axes that described the structure of Salvador census tracts according to land cover and socioeconomic features. The first canonical axis captured a gradient from crowded, low-income communities with corrugated roof housing to higher-income communities. The second canonical axis discriminated among socioeconomic variables characterizing the most marginalized census tracts, those without access to sanitation or piped water. The third canonical axis accounted for the least amount of variation, but discriminated between high-income areas with white-painted or tiled roofs from lower-income areas. Conclusions Our approach captures the socioeconomic and land cover heterogeneity within and between slum settlements and identifies the most marginalized communities in a large, complex urban setting. These findings indicate that changes in the canonical scores for slum areas can be used to track their evolution and to monitor the impact of development programs such as slum upgrading. PMID:24138776

  15. THE GALACTIC STRUCTURE AND CHEMICAL EVOLUTION TRACED BY THE POPULATION OF PLANETARY NEBULAE

    SciTech Connect

    Stanghellini, Letizia; Haywood, Misha E-mail: Misha.Haywood@obspm.f

    2010-05-10

    Planetary nebulae (PNe) derive from the evolution of {approx}1-8 M{sub sun} mass stars, corresponding to a wide range of progenitor ages, and thus are essential probes of the chemical evolution of galaxies, and indispensable to constrain the results from chemical models. We use an extended and homogeneous data set of Galactic PNe to study the metallicity gradients and the Galactic structure and evolution. The most up-to-date abundances, distances (calibrated with Magellanic Cloud PNe), and other parameters have been employed, together with a novel homogeneous morphological classification, to characterize the different PN populations. We confirm that morphological classes have a strong correlation with Peimbert's type PN, and also with their distribution on the Galactic landscape. We studied the {alpha}-element distribution within the Galactic disk, and found that the best selected disk population (i.e., excluding bulge and halo component), together with the most reliable PN distance scale yields to a radial oxygen gradient of {Delta}log(O/H)/{Delta}R{sub G} = -0.023 {+-} 0.006 dex kpc{sup -1} for the whole disk sample, and of {Delta}log(O/H)/{Delta}R{sub G} = -0.035 {+-} 0.024, -0.023 {+-} 0.005, and -0.011 {+-} 0.013 dex kpc{sup -1}, respectively for Type I, II, and III PNe, i.e., for high-, intermediate-, and low-mass progenitors. Neon gradients for the same PN types confirm the trend. Accurate statistical analysis shows moderately high uncertainties in the slopes, but also confirms the trend of steeper gradient for PNe with more massive progenitors, indicating a possible steepening with time of the Galactic disk metallicity gradient for what the {alpha}-elements are concerned. We found that the metallicity gradients are almost independent on the distance scale model used, as long as these scales are equally well calibrated with the Magellanic Clouds. The PN metallicity gradients presented here are consistent with the local metallicity distribution; furthermore

  16. Topological structure dynamics revealing collective evolution in active nematics

    PubMed Central

    Shi, Xia-qing; Ma, Yu-qiang

    2013-01-01

    Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

  17. Structure evolution of nanoparticulate Fe2O3

    NASA Astrophysics Data System (ADS)

    Erlebach, Andreas; Kurland, Heinz-Dieter; Grabow, Janet; Müller, Frank A.; Sierka, Marek

    2015-02-01

    The atomic structure and properties of nanoparticulate Fe2O3 are characterized starting from its smallest Fe2O3 building unit through (Fe2O3)n clusters to nanometer-sized Fe2O3 particles. This is achieved by combining global structure optimizations at the density functional theory level, molecular dynamics simulations by employing tailored, ab initio parameterized interatomic potential functions and experiments. With the exception of nearly tetrahedral, adamantane-like (Fe2O3)2 small (Fe2O3)n clusters assume compact, virtually amorphous structures with little or no symmetry. For n = 2-5 (Fe2O3)n clusters consist mainly of two- and three-membered Fe-O rings. Starting from n = 5 they increasingly assume tetrahedral shape with the adamantane-like (Fe2O3)2 unit as the main building block. However, the small energy differences between different isomers of the same cluster-size make precise structural assignment for larger (Fe2O3)n clusters difficult. The tetrahedral morphology persists for Fe2O3 nanoparticles with up to 3 nm in diameter. Simulated crystallization of larger nanoparticles with diameters of about 5 nm demonstrates pronounced melting point depression and leads to formation of ε-Fe2O3 single crystals with hexagonal morphology. This finding is in excellent agreement with the results obtained for Fe2O3 nanopowders generated by laser vaporization and provides the first direct indication that ε-Fe2O3 may be thermodynamically the most stable phase in this size regime.The atomic structure and properties of nanoparticulate Fe2O3 are characterized starting from its smallest Fe2O3 building unit through (Fe2O3)n clusters to nanometer-sized Fe2O3 particles. This is achieved by combining global structure optimizations at the density functional theory level, molecular dynamics simulations by employing tailored, ab initio parameterized interatomic potential functions and experiments. With the exception of nearly tetrahedral, adamantane-like (Fe2O3)2 small (Fe2O3)n

  18. Structural evolution of an alkali sulfate activated slag cement

    NASA Astrophysics Data System (ADS)

    Mobasher, Neda; Bernal, Susan A.; Provis, John L.

    2016-01-01

    In this study, the effect of sodium sulfate content and curing duration (from fresh paste up to 18 months) on the binder structure of sodium sulfate activated slag cements was evaluated. Isothermal calorimetry results showed an induction period spanning the first three days after mixing, followed by an acceleration-deceleration peak corresponding to the formation of bulk reaction products. Ettringite, a calcium aluminium silicate hydrate (C-A-S-H) phase, and a hydrotalcite-like Mg-Al layered double hydroxide have been identified as the main reaction products, independent of the Na2SO4 dose. No changes in the phase assemblage were detected in the samples with curing from 1 month up to 18 months, indicating a stable binder structure. The most significant changes upon curing at advanced ages observed were growth of the AFt phase and an increase in silicate chain length in the C-A-S-H, resulting in higher strength.

  19. Structural evolution and hydrocarbon accumulation of Luxi Depression

    SciTech Connect

    Li Hongliang; Qian Hua Xiao; Angui Lei )

    1996-01-01

    Located in the eastern Inner Mongolia Autonomous Region, China, Luxi Depression covers an area of 760 km[sup 2] and is one of the more than 250 small rifts of Northeast Rift System, the basement of which is Hercynian told belt. The Depression has undergone two Late Jurassic events: rifting and depression. The rifting sedimentation (the main period) may be divided into four stages: in the initial tensional faulting stage (Yixian Age) are accumulated a set of mantle-sourced volcanic rocks; in the fast subsiding stage (Jiufotang Age) the sedimentary system is distributed in belts under the control of boundary faults; in the steep area alluvial fans and near-shore sublacustrine fans are developed; in the gentle area braided deltas are developed; in the central deep area dark mudstones and sublacustrine gravity flows are developed. Meanwhile the rollover structures began to form on the down-thrown walls of the faults and the drape structures are formed on the convex side of the volcanic rocks. The stable subsiding stage (Shahai Age) is mainly a shallow-semi-deep lacustrine system; the rollover structures are generally finished (Fuxin Age). Most of the fill of the re-rising shrinking stage are near-shallow-lake and marsh facies sedimentation. There are five kinds of oil reservoirs distributed around the oil-generating depressions: rollover anticline, structure-lithology reservoir, updip pinch out, lenticular sandstone, and impermeable sandstone seals. Such reservoir formation models are relatively representative in rift system and can be a model for oil and gas exploration in similar depressions.

  20. Structural evolution and hydrocarbon accumulation of Luxi Depression

    SciTech Connect

    Li Hongliang; Qian Hua Xiao; Angui Lei

    1996-12-31

    Located in the eastern Inner Mongolia Autonomous Region, China, Luxi Depression covers an area of 760 km{sup 2} and is one of the more than 250 small rifts of Northeast Rift System, the basement of which is Hercynian told belt. The Depression has undergone two Late Jurassic events: rifting and depression. The rifting sedimentation (the main period) may be divided into four stages: in the initial tensional faulting stage (Yixian Age) are accumulated a set of mantle-sourced volcanic rocks; in the fast subsiding stage (Jiufotang Age) the sedimentary system is distributed in belts under the control of boundary faults; in the steep area alluvial fans and near-shore sublacustrine fans are developed; in the gentle area braided deltas are developed; in the central deep area dark mudstones and sublacustrine gravity flows are developed. Meanwhile the rollover structures began to form on the down-thrown walls of the faults and the drape structures are formed on the convex side of the volcanic rocks. The stable subsiding stage (Shahai Age) is mainly a shallow-semi-deep lacustrine system; the rollover structures are generally finished (Fuxin Age). Most of the fill of the re-rising shrinking stage are near-shallow-lake and marsh facies sedimentation. There are five kinds of oil reservoirs distributed around the oil-generating depressions: rollover anticline, structure-lithology reservoir, updip pinch out, lenticular sandstone, and impermeable sandstone seals. Such reservoir formation models are relatively representative in rift system and can be a model for oil and gas exploration in similar depressions.

  1. STRUCTURE AND EVOLUTION OF COMPETITION-ORGANIZED ECOLOGICAL COMMUNITIES

    EPA Science Inventory

    It is frequently asserted that conservation biology can advance only by transcending the current species-by-species approach, and refocusing on whole-ecosystem preservation. trong scientific basis does not presently exist for carrying out ecosystem viability analysis, and in part...

  2. Gravitational Lenses and the Structure and Evolution of Galaxies

    NASA Technical Reports Server (NTRS)

    Kochanek, Christopher

    2003-01-01

    The grant has supported the completion of 16 papers and 4 conference proceedings to date. During the first year of the project we completed five papers, each of which represents a new direction in the theory and interpretation of gravitational lenses. In the first paper, "The Importance of Einstein Rings", we developed the first theory for the formation and structure of the Einstein rings formed by lensing extended sources like the host galaxies of quasar and radio sources. We applied the theory to three lenses with lensed host galaxies. For the time delay lens PG 1115+080 we found that the structure of the Einstein ring ruled out models of the gravitational potential which permitted a large Hubble constant (70 km/s Mpc). In the second paper, :Cusped Mass Models Of Gravitational Lenses", we introduced a new class of lens models where the central density is characterized by a cusp ( rho proportional to tau(sup -gamma), 1 less than gamma less than 2) as in most modern models and theories of galaxies rather than a finite core radius. In the third paper, "Global Probes of the Impact of Baryons on Dark Matter Halos", we made the first globally consistent models for the separation distribution of gravitational lenses including both galaxy and cluster lenses. We show that the key physics for the origin of the sharp separation cutoff in the separation distribution near 3 arc sec is the effect of the cooling baryons in galaxies on the density structure of the system.

  3. Structural evolution and petroleum potential of the Norwegian Barents Sea

    SciTech Connect

    Nilsen, K.T.

    1995-08-01

    The tectonic history of the Norwegian Barents Sea has provided potential hydrocarbon traps in clastic reservoirs associated with rotated fault blocks, compressional anticlines and salt domes. Significant stratigraphic potential also resides in Paleozoic carbonates. Drilling in the Hammerfest Basin has yielded large gas discoveries in rotated fault blocks, but other trapping concepts remain relatively untested. The undrilled arm north of 74{degrees} 30 minutes N, currently being mapped by the Norwegian Petroleum Directorate using exclusive seismic and geological data from shallow boreholes, represents a significant area for future exploration. Prospectivity is critically dependent on the scaling of traps following Neogene uplift of large areas of the Barents platform. The area is dominated by structural trends inherited from the Caledonian and older orogens. Carboniferous rifting established a system of half grabens and intervening highs, followed by late Permian faulting in the west which initiated regional subsidence continuing into the early Jurassic. Fault reactivation in early Triassic times triggered salt diapirism and provided structural control for the formation of Triassic shelf margins. During the late Jurassic-early Cretaceous western basins underwent tectonic subsidence, while the northeastern platform arm was subject to gentle compression. In the late Cretaceous salt was reactivated in the Nordkapp Basin and compressional structures developed west of the Loppa High. Further subsidence of the western basins was promoted by late Mesozoic and early Tertiary transtensional movements along the North Atlantic rift system. Subsequent regional compression in these basins, and basin inversion east of the Loppa High, are of post-Eocene age.

  4. Phase-Field Methods for Structure Evolution in Sheared Multiphase Systems

    NASA Technical Reports Server (NTRS)

    Badalassi, Vittorio; Ceniceros, Hector; Banerjee, Sanjoy

    2002-01-01

    A homogeneous disordered phase separates into ordered structures when quenched into a broken-symmetry phase. The competition of broken-symmetry phases to select an equilibrium state may be studied in terms of coarse-grained order parameters described by a suitable Landau free-energy function. A network of equilibrium-phase domains develops on quenching and coarsens with time with a topology that may be controlled by shear. We use three-dimensional simulations, in which time-dependent models for conserved-order parameters coupled to Navier-Stokes fluid models are solved, to investigate the evolution of such domains, e.g. spinodal decompositions of polymeric materials under shear. The numerical problems are formidable because of the strong nonlinearities inherent in the coupled model, and these are amongst the first 3D calculations undertaken. In linear shear fields we find stable nanostrings, also recently seen in experiments. The affinity of the ordered phases to boundaries plays a role in the form of the structures that develop, with stacked plate-like phase distributions emerging under certain conditions. Such methods appear quite promising for design and analysis of multiphase and complex fluid formulations. The behavior of foams in such conditions is of particular interest in microgravity environments. Additional information can be found in the original extended abstract.

  5. Evolution of open magnetic structures on the sun - The Skylab period

    NASA Technical Reports Server (NTRS)

    Levine, R. H.

    1977-01-01

    High-resolution harmonic analysis of the measured photospheric magnetic field of the sun is used to construct models of open magnetic structures over a period of 11 solar rotations. The models successfully reproduce the surface location and topology of all coronal holes during the Skylab period. In addition, there is persistent evidence in the models that open field lines are associated with active regions in a systematic way. These associations are listed for the period studied; they suggest that open field lines are a basic feature of solar magnetism. Specific examples of the evolution of coronal holes and of calculated open structures are presented. Quantitative study of the measured field strength within and neighboring a hole confirms the fact that coronal hole regions are indistinguishable by local magnetic properties. However, the calculated field strengths at the footpoints of open field lines within coronal holes show distinct evolutionary patterns and may indicate that, at least in young coronal holes, a significant amount of magnetic flux is closed. Problems of studying magnetic field divergence by using these models are discussed.

  6. The relativistic equations of stellar structure and evolution. Stars with degenerate neutron cores. 1: Structure of equilibrium models

    NASA Technical Reports Server (NTRS)

    Thorne, K. S.; Zytkow, A. N.

    1976-01-01

    The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. Also, a general relativistic version of the mixing-length formalism for convection is presented. Finally, it is argued that in previous work on spherical systems general relativity theorists have identified the wrong quantity as "total mass-energy inside radius r."

  7. Thermal and Structural Evolution of Asteroid (4) Vesta

    NASA Astrophysics Data System (ADS)

    Davidsson, Bjorn

    2013-10-01

    Placing the formation and evolution of a large differentiated planetesimal like asteroid (4) Vesta into a broader context of Solar System chronology has important implications for our understanding of planetary formation. Vesta is here assumed to form instantaneously at t=1.0 Myr after CAI by low-velocity contraction of a boulder swarm created by streaming instabilities. A novel computer code tracks the last phase of formation, from a radius R=564 km swarm with 90% porosity, via cold-pressing, to hydrostatic equilibrium at R=314 km, porosity above 42% and bulk density d=2.00 g/cc. The code then calculates temperature versus depth and time for an initially homogeneous mixture of metal and rock which contains radioactive Al-26 and Fe-60. Heat conductivities and specific heat capacities are functions of temperature and porosity. The porosity profile is updated continuously as a result of hot-pressing. When the first sign of metal melting occurs at t=1.68 Myr, the core porosity is 35%, R=310 km and d= 2.20 g/cc. The gradual melting of metal and its flow towards the center is modeled. Initially only void spaces are filled out, but as the liquid fraction reaches a threshold, silicate grains migrate upward, thus finalizing the differentiation. Around this time, efficient hot-pressing of weakened warm rock leads to substantial shrinking. By t=1.9 Myr, R=270 km, d=3.14 g/cc, and a compact solid rock mantle separates a ~110 km liquid metal core from a ~10km porous metal/rock crust. At t=2.1 Myr rock melting is initiated, and is completed 0.8 Myr later. The densities of metal and rock are considered temperature dependent, resulting in swelling or shrinking of the body, as well as density gradients within core and mantle. Efforts are ongoing to allow the resulting buoyancy to drive convection, with the corresponding energy transport accounted for. This will allow for studies of the duration of the magnetic dynamo, and more realistic changes of temperature, radius, and density

  8. Identification, characterization and evolution of non-local quasi-Lagrangian structures in turbulence

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-02-01

    The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in viscous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian structures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence.

  9. Thermally Induced Structural Evolution and Performance of Mesoporous Block Copolymer-Directed Alumina Perovskite Solar Cells

    PubMed Central

    2015-01-01

    Structure control in solution-processed hybrid perovskites is crucial to design and fabricate highly efficient solar cells. Here, we utilize in situ grazing incidence wide-angle X-ray scattering and scanning electron microscopy to investigate the structural evolution and film morphologies of methylammonium lead tri-iodide/chloride (CH3NH3PbI3–xClx) in mesoporous block copolymer derived alumina superstructures during thermal annealing. We show the CH3NH3PbI3–xClx material evolution to be characterized by three distinct structures: a crystalline precursor structure not described previously, a 3D perovskite structure, and a mixture of compounds resulting from degradation. Finally, we demonstrate how understanding the processing parameters provides the foundation needed for optimal perovskite film morphology and coverage, leading to enhanced block copolymer-directed perovskite solar cell performance. PMID:24684494

  10. Structure in Teaching Theory and Analysis.

    ERIC Educational Resources Information Center

    Anderson, O. Roger

    A theory of structure in teaching is presented and a system of analysis introduced which allows empirical investigation of verbal behavior in the classroom. Two kinds of structure are distinguished: "static" structure, defined as stable organized clusters of knowledge, and "kinetic" structure, defined as the sequential process of building up…

  11. Evolutions of lamellar structure during melting and solidification of Fe9577 nanoparticle from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wu, Yongquan; Shen, Tong; Lu, Xionggang

    2013-03-01

    A structural evolution during solidification and melting processes of nanoparticle Fe9577 was investigated from MD simulations. A perfect lamellar structure, consisting alternately of fcc and hcp layers, was obtained from solidification process. A structural heredity of early embryo is proposed to explain the structural preference of solidification. Defects were found inside the solid core and play the same role as surface premelting on melting. hcp was found more stable than fcc in high temperature. The difference between melting and solidification points can be deduced coming fully from the overcoming of thermodynamic energy barrier, instead of kinetic delay of structural relaxation.

  12. Insights into the evolution and domain structure of ataxin-2 proteins across eukaryotes

    PubMed Central

    2014-01-01

    Background Ataxin-2 is an evolutionarily conserved protein first identified in humans as responsible for spinocerebellar ataxia type 2 (SCA2). The molecular basis of SCA2 is the expansion of a polyglutamine tract in Ataxin-2, encoding a Lsm domain that may bind RNA and a PAM2 motif that enables interaction with the poly (A) binding protein. Although the association with SCA2 has been verified, a detailed molecular function for Ataxin-2 has not been established. Results We have undertaken a survey of Ataxin-2 proteins across all eukaryotic domains. In eukaryotes, except for vertebrates and land plants, a single ortholog was identified. Notably, with the exception of birds, two Ataxin-2 genes exist in vertebrates. Expansion was observed in land plants and a novel class lacking the LsmAD domain was identified. Large polyQ tracts appear limited to primates and insects of the orders Hymenoptera and Diptera. A common feature across Ataxin-2 orthologs is the presence of proline-rich motifs, formerly described in the human protein. Conclusion Our analysis provides valuable information on the evolution and domain structure of Ataxin-2 proteins. Proline-rich motifs that may mediate protein interactions are widespread in Ataxin-2 proteins, but expansion of polyglutamine tracts associated with spinocerebellar ataxia type 2, is present only in primates, as well as some insects. Our analysis of Ataxin-2 proteins provides also a source to examine orthologs in a number of different species. PMID:25027299

  13. Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach.

    PubMed Central

    Ma, Y; Mathews, M B

    1996-01-01

    To explore the structure and function of a small regulatory RNA, we examined the virus-associated (VA) RNA species of all 47 known human adenovirus serotypes and of one simian virus, SA7. The VA RNA gene regions of 43 human adenoviruses were amplified and sequenced, and the structures of 10 representative VA RNAs were probed by nuclease sensitivity analysis. Most human viruses have two VA RNA species, VA RNA, and VA RNAII, but nine viruses (19%) have a single VA RNA gene. Sequence alignments classified the RNAs into eight families, corresponding broadly to the known virus groups, and three superfamilies. One superfamily contains the single VA RNAs of groups A and F and the VA RNAI species of group C; the second contains the VA RNAI species of groups B1, D, and E and the unclassified viruses (adenovirus types 42 to 47), as well as the single VA RNAs of group B2; and the third contains all VA RNAII species. Fourteen regions of homology occur throughout the molecule. The longest of these correspond to transcription signals; most of the others participate in RNA secondary structure. The previously identified tetranucleotide pair, GGGU:ACCC, is nearly invariant, diverging slightly (to GGGU:ACCU) only in the two group F viruses and forming a stem in the central domain that is critical for VA RNA structure and function. Secondary structure models which accommodate the nuclease sensitivity data and sequence variations within each family were generated. The major structural features-the terminal stem, apical stem-loop, and central domain-are conserved in all VA RNAs, but differences exist in the apical stem and central domains, especially of the VA RNAII species. Sequence analysis suggests that an ancestral VA RNA gene underwent duplication during the evolution of viruses containing two VA RNA genes. Although the VA RNAII gene seems to have been lost or inactivated by secondary deletion events in some viruses, the high degree of homology among the VA RNAII species implies

  14. Tectonic evolution and mantle structure of the Caribbean

    NASA Astrophysics Data System (ADS)

    van Benthem, Steven; Govers, Rob; Spakman, Wim; Wortel, Rinus

    2013-04-01

    In the broad context of investigating the relationship between deep structure & processes and surface expressions, we study the Caribbean plate and underlying mantle. We investigate whether predictions of mantle structure from tectonic reconstructions are in agreement with a detailed tomographic image of seismic P-wave velocity structure under the Caribbean region. In the upper mantle, positive seismic anomalies are imaged under the Lesser Antilles and Puerto Rico. These anomalies are interpreted as remnants of Atlantic lithosphere subduction and confirm tectonic reconstructions that suggest at least 1100 km of convergence at the Lesser Antilles island arc during the past ~45 Myr. The imaged Lesser-Antilles slab consists of a northern and southern anomaly, separated by a low velocity anomaly across most of the upper mantle, which we interpret as the subducted North-South America plate boundary. The southern edge of the imaged Lesser Antilles slab agrees with vertical tearing of South America lithosphere. The northern Lesser Antilles slab is continuous with the Puerto Rico slab along the northeastern plate boundary. This results in an amphitheater-shaped slab and it is interpreted as westward subducting North America lithosphere that remained attached to the surface along the northern boundary. At the Muertos Trough, however, material is imaged until a depth of only 100 km, suggesting a small amount of subduction. The location and length of the imaged South Caribbean slab agrees with proposed subduction of Caribbean lithosphere under the northern South America plate. An anomaly related to proposed Oligocene subduction at the Nicaragua rise is absent in the tomographic model. Beneath Panama, a subduction window exists across the upper mantle, which is related to the cessation of subduction of the Nazca plate under Panama since 9.5 Ma and possibly the preceding subduction of the extinct Cocos-Nazca spreading center. In the lower mantle two large anomaly patterns are

  15. An Analysis on a Negotiation Model Based on Multiagent Systems with Symbiotic Learning and Evolution

    NASA Astrophysics Data System (ADS)

    Hossain, Md. Tofazzal

    This study explores an evolutionary analysis on a negotiation model based on Masbiole (Multiagent Systems with Symbiotic Learning and Evolution) which has been proposed as a new methodology of Multiagent Systems (MAS) based on symbiosis in the ecosystem. In Masbiole, agents evolve in consideration of not only their own benefits and losses, but also the benefits and losses of opponent agents. To aid effective application of Masbiole, we develop a competitive negotiation model where rigorous and advanced intelligent decision-making mechanisms are required for agents to achieve solutions. A Negotiation Protocol is devised aiming at developing a set of rules for agents' behavior during evolution. Simulations use a newly developed evolutionary computing technique, called Genetic Network Programming (GNP) which has the directed graph-type gene structure that can develop and design the required intelligent mechanisms for agents. In a typical scenario, competitive negotiation solutions are reached by concessions that are usually predetermined in the conventional MAS. In this model, however, not only concession is determined automatically by symbiotic evolution (making the system intelligent, automated, and efficient) but the solution also achieves Pareto optimal automatically.

  16. Modeling, Analysis, and Optimization Issues for Large Space Structures

    NASA Technical Reports Server (NTRS)

    Pinson, L. D. (Compiler); Amos, A. K. (Compiler); Venkayya, V. B. (Compiler)

    1983-01-01

    Topics concerning the modeling, analysis, and optimization of large space structures are discussed including structure-control interaction, structural and structural dynamics modeling, thermal analysis, testing, and design.

  17. A Critical Analysis of Chromotherapy and Its Scientific Evolution

    PubMed Central

    2005-01-01

    Chromotherapy is a method of treatment that uses the visible spectrum (colors) of electromagnetic radiation to cure diseases. It is a centuries-old concept used successfully over the years to cure various diseases. We have undertaken a critical analysis of chromotherapy and documented its scientific evolution to date. A few researchers have tried to discover the underlying scientific principles, but without quantitative study. Sufficient published material can be found about the subject that provides a complete system of treatment focused on the treatment methodologies and healing characteristics of colors. A number of studies have elaborated the relationship between the human body and colors. We also show the possibility of carrying out diverse research into chromotherapy that is pertinent to deciphering the quantum mechanical dipole moment of water molecules. The quantum mechanical dipole moment as a result of the absorption of different colors, we conjecture, produces charge quantization phenomena. This review illustrates that the development of science in the field of electromagnetic radiation/energy can be very helpful in discovering new dimensions of this old theory. PMID:16322805

  18. Genome-Wide Analysis of Human Metapneumovirus Evolution

    PubMed Central

    Kim, Jin Il; Park, Sehee; Lee, Ilseob; Park, Kwang Sook; Kwak, Eun Jung; Moon, Kwang Mee; Lee, Chang Kyu; Bae, Joon-Yong; Park, Man-Seong; Song, Ki-Joon

    2016-01-01

    Human metapneumovirus (HMPV) has been described as an important etiologic agent of upper and lower respiratory tract infections, especially in young children and the elderly. Most of school-aged children might be introduced to HMPVs, and exacerbation with other viral or bacterial super-infection is common. However, our understanding of the molecular evolution of HMPVs remains limited. To address the comprehensive evolutionary dynamics of HMPVs, we report a genome-wide analysis of the eight genes (N, P, M, F, M2, SH, G, and L) using 103 complete genome sequences. Phylogenetic reconstruction revealed that the eight genes from one HMPV strain grouped into the same genetic group among the five distinct lineages (A1, A2a, A2b, B1, and B2). A few exceptions of phylogenetic incongruence might suggest past recombination events, and we detected possible recombination breakpoints in the F, SH, and G coding regions. The five genetic lineages of HMPVs shared quite remote common ancestors ranging more than 220 to 470 years of age with the most recent origins for the A2b sublineage. Purifying selection was common, but most protein genes except the F and M2-2 coding regions also appeared to experience episodic diversifying selection. Taken together, these suggest that the five lineages of HMPVs maintain their individual evolutionary dynamics and that recombination and selection forces might work on shaping the genetic diversity of HMPVs. PMID:27046055

  19. Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years

    PubMed Central

    Nicosia, Aldo; Maggio, Teresa; Costa, Salvatore; Salamone, Monica; Tagliavia, Marcello; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela

    2016-01-01

    Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations. PMID:26957029

  20. Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years.

    PubMed

    Nicosia, Aldo; Maggio, Teresa; Costa, Salvatore; Salamone, Monica; Tagliavia, Marcello; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela

    2016-01-01

    Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations. PMID:26957029

  1. Comparative Structural Models of Similarities and Differences between "Vehicle" and "Target" in Order to Teach Darwinian "Evolution"

    ERIC Educational Resources Information Center

    Marcelos, Maria Fatima; Nagem, Ronaldo L.

    2010-01-01

    Our objective is to contribute to the teaching of Classical Darwinian "Evolution" by means of a study of analogies and metaphors. Throughout the history of knowledge about "Evolution" and in Science teaching, tree structures have been used an analogs to refer to "Evolution," such as by Darwin in the "Tree of Life" passage contained in "On The…

  2. Structural evolution of the Mejerda zone, northern Tunisia

    SciTech Connect

    Baird, A.; Grocott, J. ); Grant, G. ); Moody, R.; Sandman, R. )

    1991-08-01

    The Mejerda zone lies southeast of the Tellian Atlas and has been regarded as part of the reactivated foreland to this late Palaeogene to Neogene thrust belt. Folds have a northeast-southwest (Atlas) trend to the zone contains Triassic, Jurassic, Cretaceous, and Tertiary sediments, including source and reservoir rocks. Northeast-southwest trending Miocene-Pliocene-Pleistocene basin in the zone have attracted petroleum exploration. In the Mejerda zone, Triassic rocks are generally held to have been emplaced diapirically. However, they often outcrop in thin, fault-bounded sheets and not in diapiric domelike structures. Furthermore, there is no unequivocal evidence for the existence of extensive salt deposits in the zone, either at outcrop or in boreholes. Instead, the Triassic rocks are red clastics with some gypsum and black dolomites. Balanced cross sections show that a thin-skinned thrust model with a decollement in the Triassic is consistent with the surface geology of the Mejerda zone. In this model the Triassic rocks decorate low-angle thrust faults. Shortening is estimated to be 40-50%, and the zone is part of the Atlas thrust belt and not a reactivated foreland. As well as thrust-generated old-over-young stratigraphic superpositions, many tectonic contacts in the Mejerda zone place young rocks on old. Such superpositions may be caused by out-of-sequence thrusts but more likely reflect northwest-southeast extension following thrusting. This extension formed the longitudinal Miocene-Pliocene-Pleistocene basins which conceal thrust-belt structures.

  3. Structure and Function Evolution of Thiolate Monolayers on Gold

    SciTech Connect

    Grant Alvin Edwards

    2006-05-01

    The use of n-alkanethiolate self-assembled monolayers on gold has blossomed in the past few years. These systems have functioned as models for common interfaces. Thiolate monolayers are ideal because they are easily modified before or after deposition. The works contained within this dissertation include interfacial characterization (inbred reflection absorption spectroscopy, ellipsometry, contact angle, scanning probe microscopy, and heterogeneous electron-transfer kinetics) and various modeling scenarios. The results of these characterizations present ground-breaking insights into the structure, function, and reproducible preparation of these monolayers. Surprisingly, three interfacial properties (electron-transfer, contact angle, and ellipsometry) were discovered to depend directly on the odd-even character of the monolayer components. Molecular modeling was utilized to investigate adlayer orientation, and suggests that these effects are adlayer structure specific. Finally, the electric force microscopy and theoretical modeling investigations of monolayer samples are presented, which show that the film dielectric constant, thickness, and dipole moment directly affect image contrast. In addition, the prospects for utilization of this emerging technique are outlined.

  4. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity. PMID:26627128

  5. Amino acid repeats and the structure and evolution of proteins.

    PubMed

    Albà, M M; Tompa, P; Veitia, R A

    2007-01-01

    Many proteins have repeats or runs of single amino acids. The pathogenicity of some repeat expansions has fueled proteomic, genomic and structural explorations of homopolymeric runs not only in human but in a wide variety of other organisms. Other types of amino acid repetitive structures exhibit more complex patterns than homopeptides. Irrespective of their precise organization, repetitive sequences are defined as low complexity or simple sequences, as one or a few residues are particularly abundant. Prokaryotes show a relatively low frequency of simple sequences compared to eukaryotes. In the latter the percentage of proteins containing homopolymeric runs varies greatly from one group to another. For instance, within vertebrates, amino acid repeat frequency is much higher in mammals than in amphibians, birds or fishes. For some repeats, this is correlated with the GC-richness of the regions containing the corresponding genes. Homopeptides tend to occur in disordered regions of transcription factors or developmental proteins. They can trigger the formation of protein aggregates, particularly in 'disease' proteins. Simple sequences seem to evolve more rapidly than the rest of the protein/gene and may have a functional impact. Therefore, they are good candidates to promote rapid evolutionary changes. All these diverse facets of homopolymeric runs are explored in this review. PMID:18753788

  6. Impact origin of the Sudbury structure: Evolution of a theory

    NASA Technical Reports Server (NTRS)

    Lowman, Paul D., Jr.

    1992-01-01

    This paper reviews the origin, development, and present status of the widely accepted theory, proposed by Robert S. Dietz in 1962, that the Sudbury structure was formed by meteoritic or asteroidal impact. The impact theory for the origin of the Sudbury structure seems supported by a nearly conclusive body of evidence. However, even assuming an impact origin to be correct, at least three major questions require further study: (1) the original size and shape of the crater, before tectonic deformation and erosion; (2) the source of the melt now forming the Sudbury Igneous Complex; and (3) the degree, if any, to which the Ni-Cu-platinum group elements are meteoritic. The history of the impact theory illustrates several under-appreciated aspects of scientific research: (1) the importance of cross-fertilization between space research and terrestrial geology; (2) the role of the outsider in stimulating thinking by insiders; (3) the value of small science, at least in the initial stages of an investigation, Dietz's first field work having been at his own expense; and (4) the value of analogies (here, between the Sudbury Igneous Complex and the maria), which although incorrect in major aspects, may trigger research on totally new lines. Finally, the Sudbury story illustrates the totally unpredictable and, by implication, unplannable nature of basic research, in that insight to the origin of the world's then-greatest Ni deposit came from the study of tektites and the Moon.

  7. Rifting to India-Asia Reactivation: Multi-phase Structural Evolution of the Barmer Basin, Rajasthan, northwest India

    NASA Astrophysics Data System (ADS)

    Kelly, M. J.; Bladon, A.; Clarke, S.; Najman, Y.; Copley, A.; Kloppenburg, A.

    2015-12-01

    The Barmer Basin, situated within the West Indian Rift System, is an intra-cratonic rift basin produced during Gondwana break-up. Despite being a prominent oil and gas province, the structural evolution and context of the rift within northwest India remains poorly understood. Substantial subsurface datasets acquired during hydrocarbon exploration provide an unrivalled tool to investigate the tectonic evolution of the Barmer Basin rift and northwest India during India-Asia collision. Here we present a structural analysis using seismic datasets to investigate Barmer Basin evolution and place findings within the context of northwest India development. Present day rift structural architectures result from superposition of two non-coaxial extensional events; an early mid-Cretaceous rift-oblique event (NW-SE), followed by a main Paleocene rifting phase (NE-SW). Three phases of fault reactivation follow rifting: A transpressive, Late Paleocene inversion along localised E-W and NNE-SSW-trending faults; a widespread Late Paleocene-Early Eocene inversion and Late Miocene-Present Day transpressive strike-slip faulting along NW-SE-trending faults and isolated inversion structures. A major Late Eocene-Miocene unconformity in the basin is also identified, approximately coeval with those identified within the Himalayan foreland basin, suggesting a common cause related to India-Asia collision, and calling into question previous explanations that are not compatible with spatial extension of the unconformity beyond the foreland basin. Although, relatively poorly age constrained, extensional and compressional events within the Barmer Basin can be correlated with regional tectonic processes including the fragmentation of Gondwana, the rapid migration of the Greater Indian continent, to subsequent collision with Asia. New insights into the Barmer Basin development have important implications not only for ongoing hydrocarbon exploration but the temporal evolution of northwest India.

  8. Tectonic evolution and mantle structure of the Caribbean

    NASA Astrophysics Data System (ADS)

    Benthem, Steven; Govers, Rob; Spakman, Wim; Wortel, Rinus

    2013-06-01

    investigate whether predictions of mantle structure from tectonic reconstructions are in agreement with a detailed tomographic image of seismic P wave velocity structure under the Caribbean region. In the upper mantle, positive seismic anomalies are imaged under the Lesser Antilles and Puerto Rico. These anomalies are interpreted as remnants of Atlantic lithosphere subduction and confirm tectonic reconstructions that suggest at least 1100 km of convergence at the Lesser Antilles island arc during the past ~45 Myr. The imaged Lesser Antilles slab consists of a northern and southern anomaly, separated by a low-velocity anomaly across most of the upper mantle, which we interpret as the subducted North America-South America plate boundary. The southern edge of the imaged Lesser Antilles slab agrees with vertical tearing of South America lithosphere. The northern Lesser Antilles slab is continuous with the Puerto Rico slab along the northeastern plate boundary. This results in an amphitheater-shaped slab, and it is interpreted as westward subducting North America lithosphere that remained attached to the surface along the northeastern boundary of the Caribbean plate. At the Muertos Trough, however, material is imaged until a depth of only 100 km, suggesting a small amount of subduction. The location and length of the imaged South Caribbean slab agrees with proposed subduction of Caribbean lithosphere under the northern South America plate. An anomaly related to proposed Oligocene subduction at the Nicaragua rise is absent in the tomographic model. Beneath Panama, a subduction window exists across the upper mantle, which is related to the cessation of subduction of the Nazca plate under Panama since 9.5 Ma and possibly the preceding subduction of the extinct Cocos-Nazca spreading center. In the lower mantle, two large anomaly patterns are imaged. The westernmost anomaly agrees with the subduction of Farallon lithosphere. The second lower mantle anomaly is found east of

  9. Patterning and evolution of floral structures - marking time.

    PubMed

    McKim, Sarah; Hay, Angela

    2010-08-01

    The diversity of flowering structures dazzles the eye, dominates the landscape, and invites evolutionary questions regarding the development of such variety. Comparative work in a number of genetically tractable plant species has addressed how diverse floral architectures develop, and started to reveal the balance between conservation and divergence of the patterning mechanisms responsible for when and where flowers form on a plant. We highlight findings from Petunia where conserved LFY/UFO function is under species-specific regulation, and a novel mechanism involving WOX homeodomain proteins for modulating cyme development in diverse nightshades. We also draw attention to recent findings in Arabidopsis of miRNA and chromatin-based timing mechanisms controlling floral development, and illustrate how genetic studies in Arabidopsis relatives can reveal how evolutionary changes in such mechanisms generate diversity in form. PMID:20452201

  10. Halo formation and evolution: unification of structure and physical properties

    NASA Astrophysics Data System (ADS)

    Ernest, Allan D.; Collins, Matthew P.

    2016-08-01

    The assembly of matter in the universe proliferates a wide variety of halo structures, often with enigmatic consequences. Giant spiral galaxies, for example, contain both dark matter and hot gas, while dwarf spheroidal galaxies, with weaker gravity, contain much larger fractions of dark matter, but little gas. Globular clusters, superficially resembling these dwarf spheroidals, have little or no dark matter. Halo temperatures are also puzzling: hot cluster halos contain cooler galaxy halos; dwarf galaxies have no hot gas at all despite their similar internal processes. Another mystery is the origin of the gas that galaxies require to maintain their measured star formation rates (SFRs). We outline how gravitational quantum theory solves these problems, and enables baryons to function as weakly-interacting-massive-particles (WIMPs) in Lambda Cold Dark Matter (LCDM) theory. Significantly, these dark-baryon ensembles may also be consistent with primordial nucleosynthesis (BBN) and cosmic microwave background (CMB) anisotropies.

  11. Structure and evolution of the Phasianidae mitochondrial DNA control region.

    PubMed

    Huang, Zuhao; Ke, Dianhua

    2016-01-01

    The mitochondrial DNA control region is an area of the mitochondrial genome which is non-coding DNA. To infer the structural and evolutionary characteristics of Phasianidae mitochondrial DNA control region, the entire control region sequences of 34 species were analyzed. The length of the control region sequences ranged from 1144 bp (Phasianus colchicus) to 1555 bp (Coturnix japonica) and can be separated into three domains. The average genetic distances among the species within the genera varied from 1.96% (Chrysolophus) to 12.05% (Coturnix). The average genetic distances showed significantly negative correlation with ts/tv. In most genera (except Coturnix), domain I is the most variable among the three domains. However, the first 150 nucleotides apparently evolved at unusually low rates. Four conserved sequence boxes in the domain II of Phasianidae sequences were identified. The alignment of the Phasianidae four boxes and CSB-1 sequences showed considerable sequence variation. PMID:24617466

  12. Structure, function and evolution of the gas exchangers: comparative perspectives

    PubMed Central

    Maina, JN

    2002-01-01

    Over the evolutionary continuum, animals have faced similar fundamental challenges of acquiring molecular oxygen for aerobic metabolism. Under limitations and constraints imposed by factors such as phylogeny, behaviour, body size and environment, they have responded differently in founding optimal respiratory structures. A quintessence of the aphorism that ‘necessity is the mother of invention’, gas exchangers have been inaugurated through stiff cost–benefit analyses that have evoked transaction of trade-offs and compromises. Cogent structural–functional correlations occur in constructions of gas exchangers: within and between taxa, morphological complexity and respiratory efficiency increase with metabolic capacities and oxygen needs. Highly active, small endotherms have relatively better-refined gas exchangers compared with large, inactive ectotherms. Respiratory structures have developed from the plain cell membrane of the primeval prokaryotic unicells to complex multifunctional ones ofthe modern Metazoa. Regarding the respiratory medium used to extract oxygen from, animal life has had only two choices – water or air – within the biological range of temperature and pressure the only naturally occurring respirable fluids. In rarer cases, certain animalshave adapted to using both media. Gills (evaginated gas exchangers) are the primordial respiratory organs: they are the archetypal water breathing organs. Lungs (invaginated gas exchangers) are the model air breathing organs. Bimodal (transitional) breathers occupy the water–air interface. Presentation and exposure of external (water/air) and internal (haemolymph/blood) respiratory media, features determined by geometric arrangement of the conduits, are important features for gas exchange efficiency: counter-current, cross-current, uniform pool and infinite pool designs have variably developed. PMID:12430953

  13. Structure and Evolution of Chlorate Reduction Composite Transposons

    PubMed Central

    Clark, Iain C.; Melnyk, Ryan A.; Engelbrektson, Anna; Coates, John D.

    2013-01-01

    ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration. PMID:23919996

  14. Structural analysis considerations for wind turbine blades

    NASA Technical Reports Server (NTRS)

    Spera, D. A.

    1979-01-01

    Approaches to the structural analysis of wind turbine blade designs are reviewed. Specifications and materials data are discussed along with the analysis of vibrations, loads, stresses, and failure modes.

  15. A numerical model for the evolution of internal structure of cavitation cloud

    NASA Astrophysics Data System (ADS)

    Du, Tezhuan; Wang, Yiwei; Liao, Lijuan; Huang, Chenguang

    2016-07-01

    Bubble size distributions in cloud cavitation are important in cavitating flows. In this study, a numerical model was developed to study the evolution of the internal structure of cloud cavitation. The model includes (1) an evolution equation of bubble number density, which considers the bubble breakup effect and (2) the multiphase Reynolds-averaged Navier-Stokes equations with a modified cavitation model for background cavitating flows. The proposed model was validated with a flow over a projectile. Results show that the numerical model can predict the evolution of the internal structure of cloud cavitation. Comparisons of the proposed model and Singhal model were discussed. The effects of re-entrant jet and bubble number density on cavitating flows were also investigated.

  16. Structure and Evolution of Mediterranean Forest Research: A Science Mapping Approach

    PubMed Central

    Nardi, Pierfrancesco; Di Matteo, Giovanni; Palahi, Marc; Scarascia Mugnozza, Giuseppe

    2016-01-01

    This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier’s Scopus database over the period 1980–2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1% (N = 17) during the period 1980–1989 and they reached 3% (N = 69) in the time slice 1990–1994. Since 1995, the number of publications increased exponentially, thus reaching 55% (N = 1,476) during the period 2010–2014. Within the thirty-four years considered, the retrieved publications were published by 88 countries. Among them, Spain was the most productive country, publishing 44% (N = 1,178) of total publications followed by Italy (18%, N = 482) and France (12%, N = 336). These countries also host the ten most productive scientific institutions in terms of number of publications in Mediterranean forest subjects. Forest Ecology and Management and Annals of Forest Science were the most active journals in publishing research in Mediterranean forest. During the period 1980–1994, the research topics were poorly characterized, but they become better defined during the time slice 1995–1999. Since 2000s, the clusters become well defined by research topics. Current status of Mediterranean forest research (20092014) was represented by four clusters, in which different research topics such as biodiversity and conservation, land-use and degradation, climate change effects on ecophysiological responses and soil were identified. Basic research in Mediterranean forest ecosystems is mainly conducted by ecophysiological research. Applied research was mainly represented by land-use and degradation, biodiversity and conservation and fire research topics. The citation analyses

  17. Structure and Evolution of Mediterranean Forest Research: A Science Mapping Approach.

    PubMed

    Nardi, Pierfrancesco; Di Matteo, Giovanni; Palahi, Marc; Scarascia Mugnozza, Giuseppe

    2016-01-01

    This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier's Scopus database over the period 1980-2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1% (N = 17) during the period 1980-1989 and they reached 3% (N = 69) in the time slice 1990-1994. Since 1995, the number of publications increased exponentially, thus reaching 55% (N = 1,476) during the period 2010-2014. Within the thirty-four years considered, the retrieved publications were published by 88 countries. Among them, Spain was the most productive country, publishing 44% (N = 1,178) of total publications followed by Italy (18%, N = 482) and France (12%, N = 336). These countries also host the ten most productive scientific institutions in terms of number of publications in Mediterranean forest subjects. Forest Ecology and Management and Annals of Forest Science were the most active journals in publishing research in Mediterranean forest. During the period 1980-1994, the research topics were poorly characterized, but they become better defined during the time slice 1995-1999. Since 2000s, the clusters become well defined by research topics. Current status of Mediterranean forest research (20092014) was represented by four clusters, in which different research topics such as biodiversity and conservation, land-use and degradation, climate change effects on ecophysiological responses and soil were identified. Basic research in Mediterranean forest ecosystems is mainly conducted by ecophysiological research. Applied research was mainly represented by land-use and degradation, biodiversity and conservation and fire research topics. The citation analyses revealed highly

  18. AfricaArray seismological studies of the structure and evolution of the African continent

    NASA Astrophysics Data System (ADS)

    Durrheim, Raymond; Nyblade, Andrew; Brandt, Martin; Tugume, Fred; Mulibo, Gabriel; Kgaswane, Eldridge; Mangongolo, Azangi; Manzi, Musa; El Tahir, Nada; Loots, Letticia

    2014-05-01

    The AfricaArray programme was launched in 2005 to conduct research that promotes development in Africa by building human and infrastructural capacity in support of the mineral exploration, mining, geohazard and environmental sectors. The AfricaArray "backbone" network now consists of 51 geophysical observatories in 20 sub-Saharan countries. Most stations are equipped with broadband seismometers, while 25 stations have continuous GPS sensors and 22 stations have meteorological packs. In addition, several temporary seismic arrays have been deployed to investigate the seismotectonics of the East African Rift System, the extent of the Congo craton, and the rifting of Mozambique and Madagascar. In this paper we will present results pertinent to large-scale crustal and mantle geodynamic processes that have been obtained by AfricaArray researchers. Brandt and Mulibo elucidated the relationship between the African Superplume, Superswell and the East African Rift System by studying the seismic velocity structure of the mantle. Kgaswane jointly inverted P-wave receiver functions (PRFs) and surface waves, and found that the Kalahari Craton lower crust is largely mafic, except for a few terrains such as the Kimberley. Kgaswane also produced evidence that supports a link between the eastern and western lobes of the Bushveld Complex. Mangongolo used surface wave tomography to define the south-western boundary of the Congo Craton. El Tahir used PRFs to investigate the crustal structure of the Khartoum Basin, while Tugume determined the Moho depths and Poisson's ratios of the Precambrian crust in East Africa. Manzi reprocessed 3D reflection seismic data covering part of the Witwatersrand goldfields using seismic attribute analysis methods, and has provided new constraints on the evolution of the Basin during the Neoarchean. Loots interpreted a 105 km 2D seismic reflection profile immediately to the north of the Cape Fold Belt, imaging the Karoo and Cape Supergroup rocks and the

  19. The evolution of the human mind and logic--mathematics structures.

    PubMed

    Yunes, Rosendo A

    2005-09-01

    The evolution of the human mind is discussed based on: (i) the fact that living beings interchange matter, energy and information with their environment, (ii) an ontological interpretation of the "reality" of the quantum world, of which logic-mathematics structures are considered constitutive parts, (iii) recent theories according to which living beings are considered as dynamic complex systems organized by information, and (iv) the fact that the evolution of living beings is guided by information about the environment and by intrinsic information on living systems (auto-organization). Assuming the evolution of vision as a model we observe that the driving forces that directed the evolution of the eyes, as dynamic complex systems, are the information about the environment supplied by sunlight and the intrinsic information-gaining mechanism of living organisms. Thus, there exists a convergence toward a visual system with the greatest ability to obtain light information, like the human eye, and also a divergence that leads to the development of specific qualities in some species. As in the case of vision the evolution of the human mind-brain cannot be a consequence of factors unrelated to the object of its own functioning. The human mind was structured for the acquisition from reality of the logic-mathematics structures that underlie the whole universe and consequently of an internal representation of the external world and of its own self. Thus, these structures are, together with the intrinsic capacity for auto-organization of the human brain, the predominant driving force of the human mind evolution. Both factors are complementary. PMID:15967187

  20. Truncated Moment Analysis of Nucleon Structure Functions

    SciTech Connect

    A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel

    2007-11-16

    We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.

  1. Models of planetary structure and evolution: The case of Io

    NASA Technical Reports Server (NTRS)

    Spohn, T.

    1985-01-01

    The interior structure of Jupiter's satellite Io is probably layered with a liquid core surrounded by a rigid mantle, a partially molten asthenosphere and a thin rigid lithosphere. The core radius could roughly equal half the planetary radius if the core is mostly FeS and if the mantle's compressibility is close to that of Earth's upper mantle rocks. The lithosphere thickness is controlled by the balance of the heat flux q sub e across the lithosphere with the tidal heating rate H within the lithosphere and the heat flux q; from the interior into the lithosphere. The maximum thickness determined by a balance of q sub e with H is probably much smaller than the lithosphere thickness that maximizes H. Thus, if Io's interior was once melted and if it's resonant orbital state is ancient it will freeze from the inside out. The time scale of internal and latent heat removal in a molten Io is 10 to the eighth power. Io's strong volcanic activity suggests the persistence of a partially molten asthenosphere to the present time.

  2. Surnames and dialects in France: population structure and cultural evolution.

    PubMed

    Scapoli, C; Goebl, H; Sobota, S; Mamolini, E; Rodriguez-Larralde, A; Barrai, I

    2005-11-01

    To study the isonymy structure of France as related to local language variations, the surname distributions of 6.03 million telephone users registered for the year 2002 were analysed in the 21 conterminous regions, their 94 departments and in 809 towns of the Country. For regions and departments the differences among local dialects were quantified according to the dialecto-metrization of the Atlas Linguistique Français. We found that Lasker's distance between regions was correlated with geographic distance with r=0.692+/-0.040, while Euclidean (r=0.546+/-0.058) and Nei's (r=0.610+/-0.048) distances were less correlated. Slightly lower correlations were observed for departments. Also, dialectometric distance was correlated with geography (r=0.582+/-0.069 for regions and r=0.617+/-0.015 for departments). The correlations between Lasker and dialectometric matrix distances for regions and departments are r=0.625+/-0.046 and 0.544+/-0.014, respectively, indicating that the common cause generating surname and language diversity accounts for about 35% of the differentiation. Both Lasker and dialectometric distances identify very similar boundaries between Poitou, Centre, Bourgogne and Franche Comptée at the North, and Aquitaine, Limousin, Auvergne, Rhône-Alpes in the South. Average Fisher's alpha for France was 7877 the highest value observed for the European countries studied to date. The size of alpha in most French towns indicates considerable recent immigration. PMID:15935393

  3. Evolution of vortical structures in Newtonian and viscoelastic turbulent flows

    NASA Astrophysics Data System (ADS)

    Kim, Kyoungyoun; Sureshkumar, Radhakrishna

    2010-11-01

    To study the influence of dynamical interactions between turbulent vortical structures and polymer stress on turbulent friction drag reduction, a series of simulations were performed for channel flow at Reτ=395. The initial eddy extracted by the conditional averages for the Q2 event from fully turbulent Newtonian flow is self-consistently evolved in the presence of polymer stresses by utilizing the FENE-P model (finitely extensible nonlinear elastic-Peterlin). The initial polymer conformation fields are given by the solutions of FENE- P model equations for the Newtonian mean shear. For a relatively low Weissenberg number, defined as the ratio of fluid relxation time to the time scale of viscous diffusion, (Weτ=50) the generation of new vortices is inhibited by polymer-induced counter torques, which results in fewer vortices in the buffer layer. However, the head of primary hairpin unaffected by the polymer stress. For larger values of Weτ (>=100), the hairpin head becomes weaker and vortex auto-generation and Reynolds stress growth are almost entirely suppressed.

  4. Fine Structure of Flare Ribbons and Evolution of Electric Currents

    NASA Astrophysics Data System (ADS)

    Sharykin, I. N.; Kosovichev, A. G.

    2014-06-01

    Emission of solar flares across the electromagnetic spectrum is often observed in the form of two expanding ribbons. The standard flare model explains flare ribbons as footpoints of magnetic arcades, emitting due to interaction of energetic particles with the chromospheric plasma. However, the physics of this interaction and properties of the accelerated particles are still unknown. We present results of multiwavelength observations of the C2.1 flare of 2013 August 15, observed with the New Solar Telescope of the Big Bear Solar Observatory, and the Solar Dynamics Observatory, GOES, and Fermi spacecraft. The observations reveal previously unresolved sub-arcsecond structure of flare ribbons in regions of strong magnetic field consisting from numerous small-scale bright knots. We observe a red-blue asymmetry of Hα flare ribbons with a width as small as ~100 km. We discuss the relationship between the ribbons and vertical electric currents estimated from vector magnetograms, and show that Joule heating can be responsible for energization of Hα knots in the ribbons.

  5. Structural and functional evolution of vertebrate neuroendocrine stress systems.

    PubMed

    Denver, Robert John

    2009-04-01

    The vertebrate hypothalamus-pituitary-adrenal (HPA; or interrenal) axis plays pivotal roles in animal development and in physiological and behavioral adaptation to environmental change. The HPA, or stress axis, is organized in a hierarchical manner, with feedback operating at several points along the axis. Recent findings suggest that the proteins, gene structures, and signaling pathways of the HPA axis were present in the earliest vertebrates and have been maintained by natural selection owing to their critical adaptive roles. In all vertebrates studied, the HPA axis is activated in response to stressors and is controlled centrally by peptides of the corticotropin-releasing factor (CRF) family of which four paralogous members have been identified. Signaling by CRF-like peptides is mediated by at least two distinct G protein-coupled receptors and modulated by a secreted binding protein. These neuropeptides function as hypophysiotropins and as neurotransmitters/neuromodulators, influencing stress-related behaviors, such as anxiety and fear. In addition to modulating HPA activity and behavioral stress responses, CRF-like peptides are implicated in timing key life history transitions, such as metamorphosis in amphibians and birth in mammals. CRF-like peptides and signaling components are also expressed outside of the central nervous system where they have diverse physiological functions. Glucocorticoids are the downstream effectors of the HPA axis, playing essential roles in development, energy balance and behavior, and feedback actions on the activity of the HPA axis. PMID:19456324

  6. FINE STRUCTURE OF FLARE RIBBONS AND EVOLUTION OF ELECTRIC CURRENTS

    SciTech Connect

    Sharykin, I. N.; Kosovichev, A. G.

    2014-06-10

    Emission of solar flares across the electromagnetic spectrum is often observed in the form of two expanding ribbons. The standard flare model explains flare ribbons as footpoints of magnetic arcades, emitting due to interaction of energetic particles with the chromospheric plasma. However, the physics of this interaction and properties of the accelerated particles are still unknown. We present results of multiwavelength observations of the C2.1 flare of 2013 August 15, observed with the New Solar Telescope of the Big Bear Solar Observatory, and the Solar Dynamics Observatory, GOES, and Fermi spacecraft. The observations reveal previously unresolved sub-arcsecond structure of flare ribbons in regions of strong magnetic field consisting from numerous small-scale bright knots. We observe a red-blue asymmetry of H{sub α} flare ribbons with a width as small as ∼100 km. We discuss the relationship between the ribbons and vertical electric currents estimated from vector magnetograms, and show that Joule heating can be responsible for energization of H{sub α} knots in the ribbons.

  7. Kinematic morphology of large-scale structure: evolution from potential to rotational flow

    SciTech Connect

    Wang, Xin; Szalay, Alex; Aragón-Calvo, Miguel A.; Neyrinck, Mark C.; Eyink, Gregory L.

    2014-09-20

    As an alternative way to describe the cosmological velocity field, we discuss the evolution of rotational invariants constructed from the velocity gradient tensor. Compared with the traditional divergence-vorticity decomposition, these invariants, defined as coefficients of the characteristic equation of the velocity gradient tensor, enable a complete classification of all possible flow patterns in the dark-matter comoving frame, including both potential and vortical flows. We show that this tool, first introduced in turbulence two decades ago, is very useful for understanding the evolution of the cosmic web structure, and in classifying its morphology. Before shell crossing, different categories of potential flow are highly associated with the cosmic web structure because of the coherent evolution of density and velocity. This correspondence is even preserved at some level when vorticity is generated after shell crossing. The evolution from the potential to vortical flow can be traced continuously by these invariants. With the help of this tool, we show that the vorticity is generated in a particular way that is highly correlated with the large-scale structure. This includes a distinct spatial distribution and different types of alignment between the cosmic web and vorticity direction for various vortical flows. Incorporating shell crossing into closed dynamical systems is highly non-trivial, but we propose a possible statistical explanation for some of the phenomena relating to the internal structure of the three-dimensional invariant space.

  8. Kinematic Morphology of Large-scale Structure: Evolution from Potential to Rotational Flow

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Szalay, Alex; Aragón-Calvo, Miguel A.; Neyrinck, Mark C.; Eyink, Gregory L.

    2014-09-01

    As an alternative way to describe the cosmological velocity field, we discuss the evolution of rotational invariants constructed from the velocity gradient tensor. Compared with the traditional divergence-vorticity decomposition, these invariants, defined as coefficients of the characteristic equation of the velocity gradient tensor, enable a complete classification of all possible flow patterns in the dark-matter comoving frame, including both potential and vortical flows. We show that this tool, first introduced in turbulence two decades ago, is very useful for understanding the evolution of the cosmic web structure, and in classifying its morphology. Before shell crossing, different categories of potential flow are highly associated with the cosmic web structure because of the coherent evolution of density and velocity. This correspondence is even preserved at some level when vorticity is generated after shell crossing. The evolution from the potential to vortical flow can be traced continuously by these invariants. With the help of this tool, we show that the vorticity is generated in a particular way that is highly correlated with the large-scale structure. This includes a distinct spatial distribution and different types of alignment between the cosmic web and vorticity direction for various vortical flows. Incorporating shell crossing into closed dynamical systems is highly non-trivial, but we propose a possible statistical explanation for some of the phenomena relating to the internal structure of the three-dimensional invariant space.

  9. Evolution of Novice Programming Environments: The Structure Editors of Carnegie Mellon University.

    ERIC Educational Resources Information Center

    Miller, Philip; And Others

    1994-01-01

    Describes three projects at Carnegie Mellon University (Pennsylvania) that developed novice programming environments based on structure editors: GNOME, MacGNOME and ACSE (Advanced Computing for Science Education). Tracks the evolution of the programming environments and courses, documenting important lessons and discoveries about novice…

  10. Star counts as an indicator of galactic structure and quasar evolution

    NASA Technical Reports Server (NTRS)

    Bahcall, J. N.; Soneira, R. M.

    1980-01-01

    A detailed model of the stellar content of the Galaxy is described briefly. Illustrative applications of the model are made, using existing data, to indicate how star counts can be used to determine some parameters of galactic structure, to detect a massive (stellar) halo, and to constrain models of quasar evolution.

  11. Assessing the impact of secondary structure and solvent accessibility on protein evolution.

    PubMed Central

    Goldman, N; Thorne, J L; Jones, D T

    1998-01-01

    Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized. PMID:9584116

  12. Evolution of the structure of iron meteorites under terrestrial climate

    NASA Astrophysics Data System (ADS)

    Yakovlev, G.; Grokhovsky, V.

    2014-07-01

    Introduction: Meteoritic iron is affected by many factors in terrestrial conditions. First of all, abundance of water induces an oxidization process. Despite rather high nickel concentration in meteoritic iron, rust is forming on a surface of extraterrestrial matter. But also transformation processes occur inside meteorites at rather low climatic temperatures (0.15 of the melting temperature). Such reaction has been observed for the first time in the Bilibino meteorite [1]. Experiments: Structural changes in kamacite were investigated in ancient iron meteorite falls (Aliskerovo IIIAB, Bilibino IIAB). All of them demonstrate uncompleted recrystallization. Polished sections were analyzed using inverted optical microscope Axiovert 40 MAT and SEM SIGMA VP with EDS and EBSD units. Results: Different percentage of recrystallization was found in Aliskerovo and Bilibino meteorites. 4 % of the section surface in Aliskerovo is occupied by recrystallization products. This value for Bilibino is equal to 80 %. It was noticed that recrystallization started from the kamacite-rhabdite boundaries in the Bilibino meteorite and from the kamacite-schreibersite boundaries in the Aliskerovo meteorite. There are strongly-etched sites in the recrystallized zones. One can suggest that these sites are traces of former boundaries. It is possible to think that the boundaries were moving with jumps because of the position of these sites in the recrystallized zone. Also it was noticed that there is a net of cracks before the recrystallization reaction front. A possible reason for this phenomenon is a wedge of extra material which generates an elastic stress field in the vicinity of the grain boundary [2]. All these phenomena can be explained using the Kirkendall effect on the grain boundary: the boundary shift is the result of the different concentrations of vacancies between the boundary sides.

  13. Tertiary structural evolution of the Gangdese thrust system southeastern Tibet

    SciTech Connect

    Yin, An; Harrison, M.; Ryerson, F.J.; Wenji, Chen; Kidd, W.S.F.; Copeland, P.

    1994-09-10

    Structural and thermochronological investigations of southern Tibet (Xizang) suggest that intracontinental thrusting has been the dominant cause for formation of thickened crust in the southernmost Tibetan plateau since late Oligocene. Two thrust systems are documented in this study: the north dipping Gangdese system (GTS) and the younger south dipping Renbu-Zedong system (RZT). West of Lhasa, the Gangdese thrust juxtaposes the Late Cretaceous forearc basin deposits of the Lhasa Block (the Xigaze Group) over the Tethyan sedimentary rocks of the Indian plate, whereas east of Lhasa, the fault juxtaposes the Late Cretaceous-Eocene, Andean-type arc (the Gangdese batholith) over Tethyan sedimentary rocks. Near Zedong, 150 km southeast of Lhasa, the Gangdese thrust is marked by a >200-m-thick mylonitic shear zone that consists of deformed granite and metasedimentary rocks. A major south dipping backthrust in the hanging wall of the Gangdese thrust puts the Xigaze Group over Tertiary conglomerates and the Gangdese plutonics north of Xigaze and west of Lhasa. A lower age bound for the Gangdese thrust of 18.3{+-}0.5 Ma is given by crosscutting relationships. The timing of slip on the Gangdese thrust is estimate to be 27-23 Ma from {sup 40}Ar/{sup 39}Ar thermochronology, and a displacement of at least 46{+-}9 km is indicated near Zedong. The age of the Gangdese thrust (GT) is consistent with an upper age limit of {approximately}24 Ma for the initiation of movement on the Main Central thrust. In places, the younger Renbu-Zedong fault is thrust over the trace of the GT, obscuring its exposure. The RZT appears to have been active at circa 18 Ma but had ceased movement by 8{+-}1 Ma. The suture between India and Asia has been complexely modified by development of the GTS, RZT, and, locally, strike-slip and normal fault systems. 64 refs., 14 figs., 2 tabs.

  14. Structure and evolution of the heliospheric magnetic field

    NASA Astrophysics Data System (ADS)

    Erdos, Geza

    Global structure of the heliospheric magnetic field is investigated through several solar cycles. The study includes magnetic field measurements by space probes located in various spaces in the heliosphere. The latitudinal extent of the heliospheric current sheet is determined from the off-ecliptic observation by Ulysses during the declining phase of solar cycles 22 and 23. The results are compared to the latitudinal excursion of the neutral line on the source surface maps, the deviations are interpreted in relation with the characteristics of the solar cycles. The open magnetic flux of the sun, as determined from interplanetary measurements is best characterized by the radial component of the magnetic field. It is shown that the distribution of the radial component is a complex function of the location in the heliosphere, of the type of solar wind (i.e., slow or fast), and of the phase of the solar cycle. We demonstrate that this complexity is due to fluctuations of the magnetic field, the effect of which can be largely reduced by exploiting the symmetry features of the waves. Two methods are presented for the corrections of the interplanetary flux measurements. It is shown that the corrected magnetic flux density measured by the Ulysses around its solar polar orbit from 1990 to 2009 matches that calculated from the OMNI in-ecliptic, 1 AU data set over the same interval. This result shows that the sun's magnetic flux is generally distributed uniformly in the heliosphere and depends only on the total open magnetic flux of the sun. We calculate the open magnetic flux of the sun from the OMNI data base covering four solar cycles and the values are compared to the total open magnetic flux of the sun as determined from source surface models. The match is fairly good except for the raising phase of the solar cycles. The possible reasons are discussed.

  15. Population structure and recent evolution of Plasmodium falciparum

    PubMed Central

    Rich, Stephen M.; Ayala, Francisco J.

    2000-01-01

    Plasmodium falciparum is the agent of malignant malaria, one of mankind's most severe maladies. The parasite exhibits antigenic polymorphisms that have been postulated to be ancient. We have proposed that the extant world populations of P. falciparum have derived from one single parasite, a cenancestor, within the last 5,000–50,000 years. This inference derives from the virtual or complete absence of synonymous nucleotide polymorphisms at genes not involved in immune or drug responses. Seeking to conciliate this claim with extensive antigenic polymorphism, we first note that allele substitutions or polymorphisms can arise very rapidly, even in a single generation, in large populations subject to strong natural selection. Second, new alleles can arise not only by single-nucleotide mutations, but also by duplication/deletion of short simple-repeat DNA sequences, a process several orders of magnitude faster than single-nucleotide mutation. We analyze three antigenic genes known to be extremely polymorphic: Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes. PMID:10860962

  16. Structural evolution of gold nanorods during controlled secondary growth.

    PubMed

    Keul, Heidrun A; Möller, Martin; Bockstaller, Michael R

    2007-09-25

    Single-crystalline gold nanorods synthesized by the Ag(I)-mediated seeded-growth method (see: El-Sayed, M. A.; Nikoobakht, B. Chem. Mater. 2003, 15, 1957) were used as seeds for the preferential overgrowth of gold on particular crystallographic facets by systematic variation of the conditions during overgrowth. The results support previous reports about the relevance of the cationic surfactant cetyltrimethylammonium bromide (CTAB) and Ag(I) in stabilizing anisotropic particle shapes and demonstrate that the regulation of the amount of ascorbic acid facilitates the preferential overgrowth of {111} crystal facets to form Xi-type particle shapes. Interestingly, secondary overgrowth is found to inevitably result in a loss of particle shape anisotropy. A mechanism based on surface reconstruction is proposed to rationalize the "shape-reversal" that is generally observed in the nanorod growth process, that is, the initial increase and subsequent decrease of particle anisotropy with increasing reaction time. High-resolution electron microscopy analysis of gold nanorods reveals clear evidence for (1 x 2) missing row surface reconstruction of high energetic {110} facets that form during the initial phase during particle growth. PMID:17713936

  17. Dating tectonic structures on Mercury: new clues to understand the planet's thermal evolution

    NASA Astrophysics Data System (ADS)

    Giacomini, Lorenza; Massironi, Matteo; Marchi, Simone; Fassett, Caleb I.; Di Achille, Gaetano; Cremonese, Gabriele

    2014-05-01

    The global tectonic scenario of Mercury is dominated by contractional features mainly represented by lobate scarps and related to planetary cooling (Watters et al., 1998, Geology, 26, 991-994). Topography of lobate scarps on Mercury: New constraints on the planet's contraction. These structures are the expression of surface-breaking thrust faults and are linear or arcuate features widely distributed on Mercury. Since they display a broad distribution of orientations, lobate scarps are thought to be related to a global contractional strain. The MESSENGER MDIS camera (with a wide-angle and a narrow-angle channels), acquired images of new regions of the Mercury surface that allowed us to detect several new lobate scarps especially where the illumination geometry is more favorable for structural analysis. Among them a 2000-km long thrust system, located between 80° and 100°E of longitude, has been detected. This system consists of several lobate scarps all exhibiting a N-S orientation and a westward vergence. Due to its considerable extension, this feature can give clues to the stress field affecting the surface in a wide sector of the planet. Dating these features and comparing the results with independent age determinations, and structural and stratigraphic evidences might concur to further constrain the age of tectonic deformation on Mercury and possibly increase our knowledge on the thermal evolution of the planet. The dating of the system was performed with different methods. Indeed, traditional stratigraphic study was accompanied by crater counts of geological units overlapping the thrust and the buffered crater counting technique, allowing us to determine an absolute model age determination for the tectonic feature. The employment of these different methods gave consistent results suggesting that thrust activity ended between 3.7-3.8 Ga, with Neukum Production Function (NPF), and 3.5-3.7 Ga, with Model Production Function (MPF), respectively.

  18. High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

    SciTech Connect

    Wagner, Jeremiah R.; Zhang, Junrui; Brunzelle, Joseph S.; Vierstra, Richard D.; Forest, Katrina T.

    2010-03-08

    Phytochromes are red/far red light photochromic photoreceptors that direct many photosensory behaviors in the bacterial, fungal, and plant kingdoms. They consist of an N-terminal domain that covalently binds a bilin chromophore and a C-terminal region that transmits the light signal, often through a histidine kinase relay. Using x-ray crystallography, we recently solved the first three-dimensional structure of a phytochrome, using the chromophore-binding domain of Deinococcus radiodurans bacterial phytochrome assembled with its chromophore, biliverdin IX{alpha}. Now, by engineering the crystallization interface, we have achieved a significantly higher resolution model. This 1.45 {angstrom} resolution structure helps identify an extensive buried surface between crystal symmetry mates that may promote dimerization in vivo. It also reveals that upon ligation of the C3{sup 2} carbon of biliverdin to Cys{sup 24}, the chromophore A-ring assumes a chiral center at C2, thus becoming 2(R),3(E)-phytochromobilin, a chemistry more similar to that proposed for the attached chromophores of cyanobacterial and plant phytochromes than previously appreciated. The evolution of bacterial phytochromes to those found in cyanobacteria and higher plants must have involved greater fitness using more reduced bilins, such as phycocyanobilin, combined with a switch of the attachment site from a cysteine near the N terminus to one conserved within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. From analysis of site-directed mutants in the D. radiodurans phytochrome, we show that this bilin preference was partially driven by the change in binding site, which ultimately may have helped photosynthetic organisms optimize shade detection. Collectively, these three-dimensional structural results better clarify bilin/protein interactions and help explain how higher plant phytochromes evolved from prokaryotic progenitors.

  19. Gene structure and evolution of transthyretin in the order Chiroptera.

    PubMed

    Khwanmunee, Jiraporn; Leelawatwattana, Ladda; Prapunpoj, Porntip

    2016-02-01

    Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested. PMID:26681450

  20. Evolution of the Exon-Intron Structure in Ciliate Genomes.

    PubMed

    Bondarenko, Vladyslav S; Gelfand, Mikhail S

    2016-01-01

    A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in

  1. Quantifying Selective Pressures Driving Bacterial Evolution Using Lineage Analysis

    NASA Astrophysics Data System (ADS)

    Lambert, Guillaume; Kussell, Edo

    2015-01-01

    Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population's rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages—i.e., the life histories of individuals and their ancestors—to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to Escherichia coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems.

  2. Design sensitivity analysis of nonlinear structural response

    NASA Technical Reports Server (NTRS)

    Cardoso, J. B.; Arora, J. S.

    1987-01-01

    A unified theory is described of design sensitivity analysis of linear and nonlinear structures for shape, nonshape and material selection problems. The concepts of reference volume and adjoint structure are used to develop the unified viewpoint. A general formula for design sensitivity analysis is derived. Simple analytical linear and nonlinear examples are used to interpret various terms of the formula and demonstrate its use.

  3. The IQD Gene Family in Soybean: Structure, Phylogeny, Evolution and Expression

    PubMed Central

    Ma, Hui; Chen, Xue; Li, Yuan; Wang, Yiyi; Xiang, Yan

    2014-01-01

    Members of the plant-specific IQ67-domain (IQD) protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum), Brachypodium distachyon and rice (Oryza sativa), systematic analysis and expression profiling of this gene family in soybean (Glycine max) have not previously been reported. In this study, we identified and structurally characterized IQD genes in the soybean genome. A complete set of 67 soybean IQD genes (GmIQD1–67) was identified using Blast search tools, and the genes were clustered into four subfamilies (IQD I–IV) based on phylogeny. These soybean IQD genes are distributed unevenly across all 20 chromosomes, with 30 segmental duplication events, suggesting that segmental duplication has played a major role in the expansion of the soybean IQD gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the GmIQD family primarily underwent purifying selection. Microsynteny was detected in most pairs: genes in clade 1–3 might be present in genome regions that were inverted, expanded or contracted after the divergence; most gene pairs in clade 4 showed high conservation with little rearrangement among these gene-residing regions. Of the soybean IQD genes examined, six were most highly expressed in young leaves, six in flowers, one in roots and two in nodules. Our qRT-PCR analysis of 24 soybean IQD III genes confirmed that these genes are regulated by MeJA stress. Our findings present a comprehensive overview of the soybean IQD gene family and provide insights into the evolution of this family. In addition, this work lays a solid foundation for further experiments aimed at determining the biological functions of soybean IQD genes in growth and development. PMID:25343341

  4. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  5. Computer applications for engineering/structural analysis

    NASA Astrophysics Data System (ADS)

    Zaslawsky, M.; Samaddar, S. K.

    1991-10-01

    Analysts and organizations have a tendency to lock themselves into specific codes with the obvious consequence of not addressing the real problem and thus reaching the wrong conclusion. This paper discusses the role of the analyst in selecting computer codes. The participation and support of a computation division in modifying the source program, configuration management, and pre- and post-processing of codes are among the subjects discussed. Specific examples illustrating the computer code selection process are described in the following problem areas: soil structure interaction, structural analysis of nuclear reactors, analysis of waste tanks where fluid structure interaction is important, analysis of equipment, structure-structure interaction, analysis of the operation of the superconductor supercollider which includes friction and transient temperature, and 3D analysis of the 10-meter telescope being built in Hawaii. Validation and verification of computer codes and their impact on the selection process are also discussed.

  6. Computer applications for engineering/structural analysis

    SciTech Connect

    Zaslawsky, M.; Samaddar, S.K.

    1991-01-01

    Analysts and organizations have a tendency to lock themselves into specific codes with the obvious consequences of not addressing the real problem and thus reaching the wrong conclusion. This paper discusses the role of the analyst in selecting computer codes. The participation and support of a computation division in modifying the source program, configuration management, and pre- and post-processing of codes are among the subjects discussed. Specific examples illustrating the computer code selection process are described in the following problem areas: soil structure interaction, structural analysis of nuclear reactors, analysis of waste tanks where fluid structure interaction is important, analysis of equipment, structure-structure interaction, analysis of the operation of the superconductor supercollider which includes friction and transient temperature, and 3D analysis of the 10-meter telescope being built in Hawaii. Validation and verification of computer codes and their impact on the selection process are also discussed.

  7. Modal analysis of jointed structures

    NASA Astrophysics Data System (ADS)

    Quinn, D. Dane

    2012-01-01

    Structural systems are often composed of multiple components joined together at localized interfaces. Compared to a corresponding monolithic system these interfaces are designed to have little influence on the load carrying capability of the system, and the resulting change in the overall system mass and stiffness is minimal. Hence, under nominal operating conditions the mode shapes and frequencies of the dominant structural modes are relatively insensitive to the presence of the interfaces. However, the energy dissipation in such systems is strongly dependent on the joints. The microslip that occurs at each interface couples together the structural modes of the system and introduces nonlinear damping into the system, effectively altering the observed damping of the structural modes, which can then significantly alter the amplitude of the response at the resonant modal frequencies. This work develops equations of motion for a jointed structure in terms of the structural modal coordinates and implements a reduced-order description of the microslip that occurs at the interface between components. The interface is incorporated into the modal description of the system through an existing decomposition of a series-series Iwan interface model and a continuum approximation for microslip of an elastic rod. The developed framework is illustrated on several examples, including a discrete three degree-of-freedom system as well as the longitudinal deformation of a continuum beam.

  8. Fast Approximate Analysis Of Modified Antenna Structure

    NASA Technical Reports Server (NTRS)

    Levy, Roy

    1991-01-01

    Abbreviated algorithms developed for fast approximate analysis of effects of modifications in supporting structures upon root-mean-square (rms) path-length errors of paraboloidal-dish antennas. Involves combination of methods of structural-modification reanalysis with new extensions of correlation analysis to obtain revised rms path-length error. Full finite-element analysis, usually requires computer of substantial capacity, necessary only to obtain responses of unmodified structure to known external loads and to selected self-equilibrating "indicator" loads. Responses used in shortcut calculations, which, although theoretically "exact", simple enough to be performed on hand-held calculator. Useful in design, design-sensitivity analysis, and parametric studies.

  9. Morphological diversity and evolution of egg and clutch structure in amphibians

    USGS Publications Warehouse

    Altig, R.; McDiarmid, R.W.

    2007-01-01

    The first part of this synthesis summarizes the morphology of the jelly layers surrounding an amphibian ovum. We propose a standard terminology and discuss the evolution of jelly layers. The second part reviews the morphological diversity and arrangement of deposited eggs?the ovipositional mode; we recognize 5 morphological classes including 14 modes. We discuss some of the oviductal, ovipositional, and postovipositional events that contribute to these morphologies. We have incorporated data from taxa from throughout the world but recognize that other types will be discovered that may modify understanding of these modes. Finally, we discuss the evolutionary context of the diversity of clutch structure and present a first estimate of its evolution.

  10. The Nonlinear Evolution of the Inviscid Secondary Instability of Streamwise Vortex Structures

    NASA Technical Reports Server (NTRS)

    Blackaby, Nicholas D.; Hall, Philip

    1994-01-01

    The weakly nonlinear evolution of an inviscid marginally unstable wave growing on a boundary layer supporting a streamwise vortex structure is investigated. The nonlinear growth of the wave is found to be controlled by the diffusion layer located at the edge of the critical layer associated with the wave. The evolution equation is found to depend on the upstream history of the wave and the solution of the equation suggests that the wave either restructures the mean state so as to make it stable or develops a singularity at a finite distance downstream of the point of neutral stability.

  11. Technology for Space Station Evolution. Volume 5: Structures and Materials/Thermal Control System

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Office of Aeronautics and Space Technology (OAST) conducted a workshop on technology for space station evolution on 16-19 Jan. 1990. The purpose of this workshop was to collect and clarify Space Station Freedom technology requirements for evolution and to describe technologies that can potentially fill those requirements. These proceedings are organized into an Executive Summary and Overview and five volumes containing the Technology Discipline Presentations. Volume 5 consists of the technology discipline sections for Structures/Materials and the Thermal Control System. For each technology discipline, there is a level 3 subsystem description, along with papers.

  12. Climate-dependent evolution of Antarctic ectotherms: An integrative analysis

    NASA Astrophysics Data System (ADS)

    Pörtner, Hans O.

    2006-04-01

    The paper explores the climate-dependent evolution of marine Antarctic fauna and tries to identify key mechanisms involved as well as the driving forces that have caused the physiological and life history characteristics observed today. In an integrative approach it uses the recent concept of oxygen and capacity limited thermal tolerance to identify potential links between molecular, cellular, whole-organism, and ecological characteristics of marine animal life in the Antarctic. As a generalized pattern, minimization of baseline energy costs, for the sake of maximized growth in the cold, appears as one over-arching principle shaping the evolution and functioning of Antarctic marine ectotherms. This conclusion is supported by recent comparisons with (sub-) Arctic ectotherms, where elevated levels of energy turnover result at unstable, including cold temperatures, and are related to wide windows of thermal tolerance and associated metabolic features. At biochemical levels, metabolic regulation at low temperatures in general, is supported by the cold compensation of enzyme kinetic parameters like substrate affinities and turnover numbers, through minute structural modifications of the enzyme molecule. These involve a shift in protein folding, sometimes supported by the replacement of individual amino acids. The hypothesis is developed that efficient metabolic regulation at low rates in Antarctic marine stenotherms occurs through high mitochondrial densities at low capacities and possibly enhanced levels of Arrhenius activation energies or activation enthalpies. This contrasts the more costly patterns of metabolic regulation at elevated rates in cold-adapted eurytherms. Energy savings in Antarctic ectotherms, largely exemplified in fish, typically involve low-cost, diffusive oxygen distribution due to high density of lipid membranes, loss of haemoglobin, myoglobin and the heat shock response, reduced anaerobic capacity, large myocytes with low ion exchange activities

  13. Large-scale structure evolution in axisymmetric, compressible free-shear layers

    SciTech Connect

    Aeschliman, D.P.; Baty, R.S.

    1997-05-01

    This paper is a description of work-in-progress. It describes Sandia`s program to study the basic fluid mechanics of large-scale mixing in unbounded, compressible, turbulent flows, specifically, the turbulent mixing of an axisymmetric compressible helium jet in a parallel, coflowing compressible air freestream. Both jet and freestream velocities are variable over a broad range, providing a wide range mixing layer Reynolds number. Although the convective Mach number, M{sub c}, range is currently limited by the present nozzle design to values of 0.6 and below, straightforward nozzle design changes would permit a wide range of convective Mach number, to well in excess of 1.0. The use of helium allows simulation of a hot jet due to the large density difference, and also aids in obtaining optical flow visualization via schlieren due to the large density gradient in the mixing layer. The work comprises a blend of analysis, experiment, and direct numerical simulation (DNS). There the authors discuss only the analytical and experimental efforts to observe and describe the evolution of the large-scale structures. The DNS work, used to compute local two-point velocity correlation data, will be discussed elsewhere.

  14. Defect structural evolution in high purity tungsten irradiated with electrons using high voltage electron microscope

    NASA Astrophysics Data System (ADS)

    Fukuzumi, S.; Yoshiie, T.; Satoh, Y.; Xu, Q.; Mori, H.; Kawai, M.

    2005-08-01

    Four types of high purity tungsten were irradiated with 2 MeV electrons to 5 dpa using a high voltage electron microscope, and defect structural evolutions were examined as a function of the irradiation temperature and the concentration of impurity atoms. Three of materials were made by sintering of tungsten powder with purity of 99.999% (5N-W), 99.99% (PF-W) and 99.95% (N-W), and one was a chemical vapor deposited tungsten of 99.9999% (CVD-W) purity. The formation of interstitial type dislocation loops is observed above room temperature by electron irradiation. In sintered tungsten, the number density of loops increases with increasing density of impurity atoms, i.e., N-W > PF-W > 5N-W. The density of loops in CVD-W is relatively high, contrary to its purity. In CVD-W, a heterogeneous formation of loops is observed at above 573 K. Loops are aligned on layers, and no loops are formed between the layers. All four types of specimens have a change in slop of the temperature dependence of loop number density at around 500 K which is caused by impurity atoms. Results of radioactivation analysis and hardness testing are also presented.

  15. Evolution of basin and range structure in the Ruby Mountains and vicinity, Nevada

    NASA Technical Reports Server (NTRS)

    Blackwell, D. D.; Reese, N. M.; Kelley, S. A.

    1985-01-01

    Results from various age dating techniques, seismic reflection profiling hydrocarbon maturation studies, and structural analysis were used to evaluate the Cenozoic deformation in the Ruby Mountains and adjoining ranges (pinyon Range and Cortez Range) in Elko and Eureka Counties, Nevada. Age dating techniques used include potassium-argon ages of biotites from granites published by Kistler et al. (1981) and fission track ages from apatite and zircon. Fission track ages from apatite reflect a closing temperature of 100 plus or minus 20 deg C. Zircon fission track ages reflect a closing temperature of 175 plus or minus 25 deg C and potassium-argon ages from brotite reflect a closing temperature of 250 plus or minus 30 deg C. Thus these results allow a reasonably precise tracking of the evolution of the ranges during the Cenozoic. Seismic reflection data are available from Huntington Valley. Access to seismic reflection data directly to the west of the Harrison Pass Pluton in the central Ruby Mountains was obtained. In addition results are available from several deep exploration holes in Huntington Valley.

  16. Structural analysis techniqes for remote sensing

    NASA Technical Reports Server (NTRS)

    Shapiro, L. G.

    1982-01-01

    The structural analysis of remotely sensed imagery is defined and basic techniques for implementing the process are described. Structural analysis uses knowledge of the properties of an entity, its parts and their relationships, and the relationships in which it participates at a higher level to locate and recognize objects in a visual scene. The representation of structural knowledge, the development of algorithms for using the knowledge to help analyze an image, and techniques for storage and retrieval of relational models are addressed.

  17. Structure and evolution of irradiated accretion disks. I - Static thermal equilibrium structure. II - Dynamical evolution of a thermally unstable torus

    NASA Technical Reports Server (NTRS)

    Tuchman, Y.; Mineshige, S.; Wheeler, J. C.

    1990-01-01

    The thermal equilibrum structure and dynamical behavior of externally irradiated accretion disks are investigated. For radiative disks only the surface layer is heated, while for convective disks the heat penetrates deeply into the disk. For sufficiently strong radiation and given irradiation flux F(irr), the disk is completely stabilized against thermal instabilities of the sort invoked to explain dwarf novae. For moderately strong irradiation there is still an unstable branch in the thermal equilibrium curve. In typical soft X-ray transients, the disk is unstable against the dwarf-nova type instability. Fixed F(irr) on accretion disk annuli reduces the amplitude and the quiescent times and increases the outburst duration of the resultant light curves. Varying F(irr) in proportion to the mass accretion rate at the disks's inner edge results in light curves with a plateau in the decay from outbursts. In the case when irradiation is suddenly switched on, a temperature inversion results which leads to the formation of an accretion corona.

  18. Structure analysis methods for crystalline solids and supercooled liquids

    NASA Astrophysics Data System (ADS)

    Yu, Da-Qi; Chen, Min; Han, Xiu-Jun

    2005-11-01

    The three most widely used methods for analyzing atomic structures are evaluated by simulating crystalline solids and supercooled liquids. The local order parameter approach due to Volkov [Phys. Rev. E 66, 061401 (2002)] fails in randomly perturbed body-centered-cubic environments, while the pair analysis method behaves as an approximate approach depending on how the neighborhood is defined. As to the Voronoi analysis method, we improve the procedure of Brostow [Phys. Rev. B 57, 13448 (1998)] to eliminate distorted Voronoi faces and edges which originate from thermal vibrations and computational rounding errors. The improved procedure works robustly in face-centered-cubic, body-centered-cubic, and hexagonal close-packed environments. When the pair analysis technique and the Voronoi analysis method are applied to detect the microstructure and its evolution in supercooled liquids, qualitatively consistent results are attained.

  19. SEASONAL EFFECTS ON COMET NUCLEI EVOLUTION: ACTIVITY, INTERNAL STRUCTURE, AND DUST MANTLE FORMATION

    SciTech Connect

    De Sanctis, M. C.; Capria, M. T.; Lasue, J.

    2010-07-15

    Rotational properties can strongly influence a comet's evolution in terms of activity, dust mantling, and internal structure. In this paper, we investigate the effects of various rotation axis directions on the activity, internal structure, and dust mantling of cometary nuclei. The numerical code developed is able to reproduce different shapes and spin axis inclinations, taking into account both the latitudinal and the longitudinal variations of illumination, using a quasi-three-dimensional approach. The results obtained show that local variations in the dust and gas fluxes can be induced by the different spin axis directions and completely different behaviors of the comet evolution can result in the same cometary shape by using different obliquities of the models. The internal structures of cometary nuclei are also influenced by comet obliquity, as well as dust mantling. Gas and dust production rates show diversities related to the comet seasons.

  20. On the role of physics and evolution in dictating protein structure and function.

    PubMed

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2014-08-01

    How many of the structural and functional properties of proteins are inherent? Computer simulations provide a powerful tool to address this question. A series of studies on QS, quasi-spherical, compact polypeptides which lack any secondary structure; ART, artificial, proteins comprised of compact homopolypeptides with protein-like secondary structure; and PDB, native, single domain proteins shows that essentially all native global folds, pockets and protein-protein interfaces are in the ART library. This suggests that many protein properties are inherent and that evolution is involved in fine-tuning. The completeness of the space of ligand binding pockets and protein-protein interfaces suggests that promiscuous interactions are intrinsic to proteins and that the capacity to perform the biochemistry of life at low level does not require evolution. If so, this has profound consequences for the origin of life. PMID:25484448

  1. On the role of physics and evolution in dictating protein structure and function

    PubMed Central

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2014-01-01

    How many of the structural and functional properties of proteins are inherent? Computer simulations provide a powerful tool to address this question. A series of studies on QS, quasi-spherical, compact polypeptides which lack any secondary structure; ART, artificial, proteins comprised of compact homopolypeptides with protein-like secondary structure; and PDB, native, single domain proteins shows that essentially all native global folds, pockets and protein-protein interfaces are in the ART library. This suggests that many protein properties are inherent and that evolution is involved in fine-tuning. The completeness of the space of ligand binding pockets and protein-protein interfaces suggests that promiscuous interactions are intrinsic to proteins and that the capacity to perform the biochemistry of life at low level does not require evolution. If so, this has profound consequences for the origin of life. PMID:25484448

  2. Valence-band electronic structure evolution of graphene oxide upon thermal annealing for optoelectronics

    DOE PAGESBeta

    Yamaguchi, Hisato; Ogawa, Shuichi; Watanabe, Daiki; Hozumi, Hideaki; Gao, Yongqian; Eda, Goki; Mattevi, Cecilia; Fujita, Takeshi; Yoshigoe, Akitaka; Ishizuka, Shinji; et al

    2016-04-08

    We report valence band electronic structure evolution of graphene oxide (GO) upon its thermal reduction. Degree of oxygen functionalization was controlled by annealing temperatures, and an electronic structure evolution was monitored using real-time ultraviolet photoelectron spectroscopy. We observed a drastic increase in density of states around the Fermi level upon thermal annealing at ~600 °C. The result indicates that while there is an apparent band gap for GO prior to a thermal reduction, the gap closes after an annealing around that temperature. This trend of band gap closure was correlated with electrical, chemical, and structural properties to determine a setmore » of GO material properties that is optimal for optoelectronics. The results revealed that annealing at a temperature of ~500 °C leads to the desired properties, demonstrated by a uniform and an order of magnitude enhanced photocurrent map of an individual GO sheet compared to as-synthesized counterpart.« less

  3. Probabilistic structural analysis by extremum methods

    NASA Technical Reports Server (NTRS)

    Nafday, Avinash M.

    1990-01-01

    The objective is to demonstrate discrete extremum methods of structural analysis as a tool for structural system reliability evaluation. Specifically, linear and multiobjective linear programming models for analysis of rigid plastic frames under proportional and multiparametric loadings, respectively, are considered. Kinematic and static approaches for analysis form a primal-dual pair in each of these models and have a polyhedral format. Duality relations link extreme points and hyperplanes of these polyhedra and lead naturally to dual methods for system reliability evaluation.

  4. Evolution of Yield Stress during Structural Relaxation for the Epoxy 828DEA

    NASA Astrophysics Data System (ADS)

    Arechederra, Gabriel; McCoy, John; Kropka, Jamie

    The evolution of yield stress from structural relaxation of diethanolamine cured diglycidyl ether of bisphenol-A, 828DEA, was tracked using uniaxial compression experiments. Samples were aged isothermally for up to 3 months at 5 temperatures ranging from deep in the glass to above Tg. Since 828DEA has remaining reactive potential, it is anticipated that the Tg will continue to evolve throughout the course of the study as new chemical crosslinks are formed. Consequently, it is important to track the evolution of Tg as well as the progression of the fictive temperature in order to interpret the evolution of yield stress. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE.

  5. Structural analysis of ultra-high speed aircraft structural components

    NASA Technical Reports Server (NTRS)

    Lenzen, K. H.; Siegel, W. H.

    1977-01-01

    The buckling characteristics of a hypersonic beaded skin panel were investigated under pure compression with boundary conditions similar to those found in a wing mounted condition. The primary phases of analysis reported include: (1) experimental testing of the panel to failure; (2) finite element structural analysis of the beaded panel with the computer program NASTRAN; and (3) summary of the semiclassical buckling equations for the beaded panel under purely compressive loads. A comparison of each of the analysis methods is also included.

  6. Modeling and structural analysis of honeycomb structure mirror

    NASA Astrophysics Data System (ADS)

    Li, Yeping

    2012-09-01

    In development of large-scale astronomical telescopes, some promising new technology and method such as honeycomb structure mirrors and silicon carbide mirrors are applied for primary mirrors. Especially in space telescopes, the mirror lightweight design is becoming the key technology and honeycomb structure mirrors are normally required more and more to reduce the cost and increase the feasibility of the telescopes system. In this paper, a parameter FEA model of a two meters honeycomb structure mirror has been built, by using the engineering analysis software ANSYS. Through this model, the structural analysis, thermal deformation analysis and the simulation active correction of low-order frequency aberration by the finite element method have been presented.

  7. A kinetic model based on experimental study of structural evolution of natural carbonaceous material to graphite

    NASA Astrophysics Data System (ADS)

    Nakamura, Y.; Yoshino, T.; Satish-Kumar, M.

    2015-12-01

    We report here new experimental kinetic data on the structural evolution of carbonaceous materials (CM) to graphite in a wide range of temperature conditions (1000 and 1450 °C) and treatment time (10 min to 115 hrs) under a pressure condition of 1GPa. The morphologies and crystallinities of natural CM, extracted from sediments in the Shimanto accretionary complex and Hidaka metamorphic belt, transformed to fully ordered graphite with increasing temperature and annealing duration. The time-temperature relations of each crystal parameter obtained using XRD analysis and micro-Raman spectroscopy demonstrated sigmoidal transformations from amorphous to graphitic structure, suggesting the complexity of chemical reactions undergoing during graphitization. To assess these kinetic processes, the results were analyzed using a superposition method in which the crystal parameters were superposed to reference temperature with non-linear regression curves. The master curves fitted by sigmoidal and power functions exhibited very good correlation coefficients of 0.940 to 0.991, suggesting the Arrhenian relation between temperature and time. On the basis of master curves and shift values, we obtained the effective activation energies of 274 +/- 9 kJmol-1 and 339 +/- 6 kJmol-1 for two different natural CM. When compared with the previous studies, our data gave remarkably low activation energies for natural graphitization, which can be represented in a time-temperature relation. In addition, the sigmoidal functions obtained from time-temperature relations can be extrapolated for low temperature condition at 1GPa. Our kinetic model predicts that if the CM underwent metamorphism for about one million years, it begins to crystallize at ≈ 420 °C and transform to fully ordered graphite at over ≈ 510 °C. Thus, natural graphitization could be discussed by the laboratory experiments using natural precursor materials under realistic pressure condition and time span in the Earth's crust.

  8. Dawn mission to constrain interior structure and thermal evolution of protoplanet Vesta

    NASA Astrophysics Data System (ADS)

    Raymond, C. A.; Asmar, S. W.; Konopliv, A. S.; McSween, H. Y.; Prettyman, T. H.; Russell, C. T.; Smith, D. E.; Zuber, M. T.

    2010-12-01

    The Dawn spacecraft will reach Vesta in mid-2011 and begin a comprehensive geological and geophysical characterization to investigate the geologic history, interior structure, and evolution of this minor planet in the Main Asteroid Belt. Analysis of the suite of basaltic achondrite howardite-eucrite-diogenite (HED) meteorites, linked spectrally to Vesta, indicate that Vesta underwent igneous differentiation and has a metallic core. As such, Vesta represents a diminutive end-member of the differentiated terrestrial planets. Recent work by Weiss et al. (Science, 322, 2008) on the angrite (basaltic achondrite) meteorites suggests that planetesimal differentiation and short-lived planetesimal dynamos were likely common in the early solar system. Thus, Vesta may be representative of a class of objects that differentiated early, and were later incorporated into the terrestrial planets or shattered by impacts. The geochemical and geophysical data that Dawn will obtain at Vesta aims to test whether Vesta’s crust and mantle formed by the fractional crystallization of a magma ocean or by serial magmatism. To characterize the magmatic processes that shaped Vesta’s surface and interior, Dawn will map the morphology, surface age, and surface mineralogical composition of Vesta using its Framing Cameras and Visible-Infrared Mapping Spectrometer, and map elemental composition using its Gamma Ray and Neutron Detector (GRaND). Radio science will determine the gravity field to constrain the crustal structure, the core radius/core and mantle density tradeoff, and the compensation state of the south polar crater to estimate roughly its age. The large south polar crater on Vesta is the likely source of many HED meteorites, and existing spectral data suggest it may be floored by olivine-rich material, either mantle rocks or cumulates of the lower crust. The degree to which the material excavated from the south polar crater (Vestoids and HEDs meteorites) is representative of the

  9. Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization

    PubMed Central

    Kwon, Annie; Byrne, Dominic P.; Ferries, Samantha; Ruan, Zheng; Hanold, Laura E.; Katiyar, Samiksha; Kennedy, Eileen J.; Eyers, Patrick A.; Kannan, Natarajan

    2016-01-01

    Protein tyrosine kinases (PTKs) are a group of closely related enzymes that have evolutionarily diverged from serine/threonine kinases (STKs) to regulate pathways associated with multi-cellularity. Evolutionary divergence of PTKs from STKs has occurred through accumulation of mutations in the active site as well as in the commonly conserved hydrophobic core. While the functional significance of active site variations is well understood, relatively little is known about how hydrophobic core variations contribute to PTK evolutionary divergence. Here, using a combination of statistical sequence comparisons, molecular dynamics simulations, mutational analysis and in vitro thermostability and kinase assays, we investigate the structural and functional significance of key PTK-specific variations in the kinase core. We find that the nature of residues and interactions in the hydrophobic core of PTKs is strikingly different from other protein kinases, and PTK-specific variations in the core contribute to functional divergence by altering the stability and dynamics of the kinase domain. In particular, a functionally critical STK-conserved histidine that stabilizes the regulatory spine in STKs is selectively mutated to an alanine, serine or glutamate in PTKs, and this loss-of-function mutation is accommodated, in part, through compensatory PTK-specific interactions in the core. In particular, a PTK-conserved phenylalanine in the I-helix appears to structurally and functionally compensate for the loss of STK-histidine by interacting with the regulatory spine, which has far-reaching effects on enzyme activity, inhibitor sensing, and stability. We propose that hydrophobic core variations provide a selective advantage during PTK evolution by increasing the conformational flexibility, and therefore the allosteric potential of the kinase domain. Our studies also suggest that Tyrosine Kinase Like kinases such as RAF are intermediates in PTK evolutionary divergence inasmuch as they

  10. Formation and evolution of tweed structures on high-purity aluminum polycrystalline foils under cyclic tension

    SciTech Connect

    Kuznetsov, P. V.; Vlasov, I. V.; Sklyarova, E. A.; Smekalina, T. V.

    2015-10-27

    Peculiarities of formation and evolution of tweed structures on the surface of high-purity aluminum polycrystalline foils under cyclic tension were studied using an atom force microscope and a white light interferometer. Tweed structures of micron and submicron sizes were found on the foils at different number of cycles. In the range of 42,000 < N < 95,000 cycles destruction of tweed patterns is observed, which leads to their disappearance from the surface of the foils. Formation of tweed structures of various scales is discussed in terms of the Grinfeld instability.

  11. Structural evolution and electronic properties of n-type doped hydrogenated amorphous silicon thin films

    NASA Astrophysics Data System (ADS)

    He, Jian; Li, Wei; Xu, Rui; Qi, Kang-Cheng; Jiang, Ya-Dong

    2011-12-01

    The relationship between structure and electronic properties of n-type doped hydrogenated amorphous silicon (a-Si:H) thin films was investigated. Samples with different features were prepared by plasma enhanced chemical vapor deposition (PECVD) at various substrate temperatures. Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy were used to evaluate the structural evolution, meanwhile, electronic-spin resonance (ESR) and optical measurement were applied to explore the electronic properties of P-doped a-Si:H thin films. Results reveal that the changes in materials structure affect directly the electronic properties and the doping efficiency of dopant.

  12. Mass spectrometry for pectin structure analysis.

    PubMed

    Ralet, Marie-Christine; Lerouge, Patrice; Quéméner, Bernard

    2009-09-28

    Pectin are extremely complex biopolymers made up of different structural domains. Enzymatic degradation followed by purification and structural analysis of the degradation products proved to be efficient tools for the understanding of pectin fine structure, including covalent interactions between pectic structural domains or with other cell wall polysaccharides. Due to its high sensitivity, high throughput and capacity to analyze mixtures, mass spectrometry has gained more and more importance as a tool for oligosaccharides structural characterization in the past 10 years. This review will focus on the combined use of mass spectrometry and enzymatic digestion for pectins structural characterization. PMID:19058795

  13. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.

    PubMed

    Xia, Xuhua

    2013-07-01

    Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013). PMID:23564938

  14. Structural analysis consultation using artificial intelligence

    NASA Technical Reports Server (NTRS)

    Melosh, R. J.; Marcal, P. V.; Berke, L.

    1978-01-01

    The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

  15. Structural style and tectonic evolution of the easternmost Gulf of Aden conjugate margins (Socotra - Southern Oman)

    NASA Astrophysics Data System (ADS)

    Nonn, Chloe; Leroy, Sylvie; Castilla, Raymi; de Clarens, Philippe; Lescanne, Marc

    2016-04-01

    domains, syn-tectonic structures and oblique accommodation zones to highlighted asymmetrical margins, characterized by strong lateral variability of crustal domains along and across strike. From external to internal domains of the margins and in between SHFZ and EGAFZ (first-order segment), this study details sharp necking domain and complex transition from hyperextended to oceanic crust characterized by: (i) hyperextended crust affected by volcanic extrusions; (ii) detachment faulting in the distal part of the margins allowing exhumation; (iii) volcanic constructions in the exhumation domain; (iv) a complex proto-oceanic crust. We highlight a significant second-order segmentation characterized by six N20°E trending transfer zones, limiting seven 25 - 60 km length segments and affecting necking domain as well as the ocean-continent transition. Based on interpretative cross-sections and detailed stratigraphic analysis, we discuss the complex temporal and spatial evolution of conjugate margins: (i) the margins segmentation and the relationship with structural inheritance (ii) the set-up of a long-offset detachment fault and the nature of the exhumed basement (iv) the origin and timing of magmatic events and the onset of proto-oceanic crust.

  16. Numerical modelling of the evolution of the salt diapiric internal structure

    NASA Astrophysics Data System (ADS)

    Adamuszek, Marta; Dabrowski, Marcin

    2014-05-01

    Evaporate series are composed of a range of interbedded rock types such as carbonates (calcite, dolomite), sulphates (anhydrite, gypsum), and chlorides (rock salt, potassium and magnesium salt). The presence of evaporates particularly with thick salt layers within sedimentary basins significantly influences their tectonic evolution. This is due to unique properties of salt, which cause that salt buried under sediments becomes buoyant and migrates towards the surface promoting development of diapiric structures. The intensive complex deformation that operates on the layered evaporates sequence leads to the development of a complicated diapir internal architecture. Varying material properties such as viscosity and density of different rock types in the evaporate series contribute to the complexity of the formed structures. We numerically investigate the initiation and evolution of tectonic structures within the salt diapirs comprising mechanically stratified evaporate series. We analyse the role of parameters such as mechanical properties of the layered evaporate series and the overburden rocks, the initial spatial arrangement of different rock types, the rate of sedimentation of the overburden rocks, and various deformation regimes. In the study, we focus on the relationship between the structures such as folds and boudinage structures that develop on a small-scale (corresponding to the outcrop scale in the salt mine galleries) and a large-scale (corresponding to the whole diapir scale). Additionally, the influence of the internal structure development on the evolution of the overall diapir shape is examined. In the numerical model, we use non-linear viscous rheology for the evaporate series and the overburden. We solve an incompressible Stokes equation in the presence of the gravity using the finite element method solver MILAMIN [1]. The diapir evolution is simulated in two dimensions. The development of complex structures is analysed using the resolved interface

  17. The co-