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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.

    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

  7. 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.

  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 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

  18. 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

  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. 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.

  10. 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.

  11. 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.

  12. 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…

  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. 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

  1. 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

  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

    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

  11. 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

  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. 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.

  10. 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

  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. 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.

  1. 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

  2. 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

  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. 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

  8. 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

  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. 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.

  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. 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.

  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. 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).

  13. 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.

  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. 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.

  6. 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.

  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. 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

  11. 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.

  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. 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

  16. 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.

  17. 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.

  18. 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

  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. 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

  2. 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.

  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. 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

  13. 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.

  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. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  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. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  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. 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.

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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