Science.gov

Sample records for asymmetry-driven structure formation

  1. Geometric asymmetry driven Janus micromotors

    NASA Astrophysics Data System (ADS)

    Zhao, Guanjia; Pumera, Martin

    2014-09-01

    The production and application of nano-/micromotors is of great importance. In order for the motors to work, asymmetry in their chemical composition or physical geometry must be present if no external asymmetric field is applied. In this paper, we present a ``coconut'' micromotor made of platinum through the partial or complete etching of the silica templates. It was shown that although both the inner and outer surfaces are made of the same material (Pt), motion of the structure can be observed as the convex surface is capable of generating oxygen bubbles. This finding shows that not only the chemical asymmetry of the micromotor, but also its geometric asymmetry can lead to fast propulsion of the motor. Moreover, a considerably higher velocity can be seen for partially etched coconut structures than the velocities of Janus or fully etched, shell-like motors. These findings will have great importance on the design of future micromotors.The production and application of nano-/micromotors is of great importance. In order for the motors to work, asymmetry in their chemical composition or physical geometry must be present if no external asymmetric field is applied. In this paper, we present a ``coconut'' micromotor made of platinum through the partial or complete etching of the silica templates. It was shown that although both the inner and outer surfaces are made of the same material (Pt), motion of the structure can be observed as the convex surface is capable of generating oxygen bubbles. This finding shows that not only the chemical asymmetry of the micromotor, but also its geometric asymmetry can lead to fast propulsion of the motor. Moreover, a considerably higher velocity can be seen for partially etched coconut structures than the velocities of Janus or fully etched, shell-like motors. These findings will have great importance on the design of future micromotors. Electronic supplementary information (ESI) available: Additional SEM images, data analysis, Videos S

  2. Cosmological structure formation

    NASA Technical Reports Server (NTRS)

    Schramm, David N.

    1991-01-01

    A summary of the current forefront problem of physical cosmology, the formation of structures (galaxies, clusters, great walls, etc.) in the universe is presented. Solutions require two key ingredients: (1) matter; and (2) seeds. Regarding the matter, it now seems clear that both baryonic and non-baryonic matter are required. Whether the non-baryonic matter is hot or cold depends on the choice of seeds. Regarding the seeds, both density fluctuations and topological defects are discussed. The combination of isotropy of the microwave background and the recent observations indicating more power on large scales have severly constrained, if not eliminated, Gaussian fluctuations with equal power on all scales, regardless of the eventual resolution of both the matter and seed questions. It is important to note that all current structure formation ideas require new physics beyond SU(3) x SU(2) x U(1).

  3. Kinetically guided colloidal structure formation

    PubMed Central

    Hecht, Fabian M.; Bausch, Andreas R.

    2016-01-01

    The self-organization of colloidal particles is a promising approach to create novel structures and materials, with applications spanning from smart materials to optoelectronics to quantum computation. However, designing and producing mesoscale-sized structures remains a major challenge because at length scales of 10–100 μm equilibration times already become prohibitively long. Here, we extend the principle of rapid diffusion-limited cluster aggregation (DLCA) to a multicomponent system of spherical colloidal particles to enable the rational design and production of finite-sized anisotropic structures on the mesoscale. In stark contrast to equilibrium self-assembly techniques, kinetic traps are not avoided but exploited to control and guide mesoscopic structure formation. To this end the affinities, size, and stoichiometry of up to five different types of DNA-coated microspheres are adjusted to kinetically control a higher-order hierarchical aggregation process in time. We show that the aggregation process can be fully rationalized by considering an extended analytical DLCA model, allowing us to produce mesoscopic structures of up to 26 µm in diameter. This scale-free approach can easily be extended to any multicomponent system that allows for multiple orthogonal interactions, thus yielding a high potential of facilitating novel materials with tailored plasmonic excitation bands, scattering, biochemical, or mechanical behavior. PMID:27444018

  4. Controlled formation of biosilica structures in vitro.

    PubMed

    Naik, Rajesh R; Whitlock, Patrick W; Rodriguez, Francisco; Brott, Lawrence L; Glawe, Diana D; Clarson, Stephen J; Stone, Morley O

    2003-01-21

    Herein we describe the controlled formation of biosilica structures by manipulation of the physical reaction environment; we were able to synthesize arched and elongated silica structures using a synthetic peptide; the results presented here are evidence that in vitro biocatalysis may be controlled in order to form desired silica structures.

  5. Unravelling lignin formation and structure

    SciTech Connect

    Lewis, N.G. . Inst. of Biological Chemistry)

    1991-01-01

    During this study, we established that the Fagaceae exclusively accumulate Z-monolignois/glucosides, and not the E-isomers. Evidence for the presence of a novel E{yields}Z isomerse has been obtained. Our pioneering work in lignin biosynthesis and structure in situ has also progressed smoothly. We established the bonding environments of a woody angiosperm, Leucanea leucocephala, as well as wheat (T. aestivum) and tobacco (N. tabacum). A cell culture system from Pinus taeda was developed which seems ideal for investigating the early stages of lignification. These cultures excrete peroxidase isozymes, considered to be specifically involved in lignin deposition. We also studied the effect of the putative lignin-degrading enzyme, lignin peroxidase, on monolignols and dehydropolymerisates therefrom. In all cases, polymerization was observed, and not degradation; these polymers are identical to that obtained with horseradish peroxidases/H{sub 2}O{sub 2}. It seems inconceivable that these enzymes can be considered as being primarily responsible for lignin biodegradation.

  6. Instabilities and structure formation in laser processing

    SciTech Connect

    Baeuerle, D.; Arenholz, E.; Arnold, N.; Heitz, J.; Kargl, P.B.

    1996-12-31

    This paper gives an overview on different types of instabilities and structure formation in various fields of laser processing. Among the examples discussed in detail are non-coherent structures observed in laser-induced chemical vapor deposition (LCVD), in laser-induced surface modifications, and in laser ablation of polymers.

  7. The Biermann Battery and Early Structure Formation

    NASA Astrophysics Data System (ADS)

    Zhao, Fen; Alvarez, Marcelo; Abel, Tom

    2008-03-01

    Using ENZO, a 3D adaptive mesh cosmological simulation code, we look at the characteristics of magnetic fields generated in early structure formation by the Biermann battery process. Tracking six species (H, H+, He, He+, He++ and e-), we follow the formation of structure from multiple independent realizations of cosmological initial conditions to better understand how magnetic fields are generated by non aligned pressure and density gradients. These efforts aim at adding ideal MHD to the ENZO framework which will enable the study of the build up and evolution of cosmic magnetic fields.

  8. Structure formation in the quasispherical Szekeres model

    SciTech Connect

    Bolejko, Krzysztof

    2006-06-15

    Structure formation in the Szekeres model is investigated. Since the Szekeres model is an inhomogeneous model with no symmetries, it is possible to examine the interaction of neighboring structures and its impact on the growth of a density contrast. It has been found that the mass flow from voids to clusters enhances the growth of the density contrast. In the model presented here, the growth of the density contrast is almost 8 times faster than in the linear approach.

  9. Early structure formation from cosmic string loops

    SciTech Connect

    Shlaer, Benjamin; Vilenkin, Alexander; Loeb, Abraham E-mail: vilenkin@cosmos.phy.tufts.edu

    2012-05-01

    We examine the effects of cosmic strings on structure formation and on the ionization history of the universe. While Gaussian perturbations from inflation are known to provide the dominant contribution to the large scale structure of the universe, density perturbations due to strings are highly non-Gaussian and can produce nonlinear structures at very early times. This could lead to early star formation and reionization of the universe. We improve on earlier studies of these effects by accounting for high loop velocities and for the filamentary shape of the resulting halos. We find that for string energy scales Gμ∼>10{sup −7}, the effect of strings on the CMB temperature and polarization power spectra can be significant and is likely to be detectable by the Planck satellite. We mention shortcomings of the standard cosmological model of galaxy formation which may be remedied with the addition of cosmic strings, and comment on other possible observational implications of early structure formation by strings.

  10. 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.

  11. 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

  12. Understanding cochleate formation: insights into structural development.

    PubMed

    Nagarsekar, Kalpa; Ashtikar, Mukul; Steiniger, Frank; Thamm, Jana; Schacher, Felix; Fahr, Alfred

    2016-04-20

    Understanding the structure and the self-assembly process of cochleates has become increasingly necessary considering the advances of this drug delivery system towards the pharmaceutical industry. It is well known that the addition of cations like calcium to a dispersion of anionic lipids such as phosphatidylserines results in stable, multilamellar cochleates through a spontaneous assembly. In the current investigation we have studied the intermediate structures generated during this self-assembly of cochleates. To achieve this, we have varied the process temperature for altering the rate of cochleate formation. Our findings from electron microscopy studies showed the formation of ribbonlike structures, which with proceeding interaction associate to form lipid stacks, networks and eventually cochleates. We also observed that the variation in lipid acyl chains did not make a remarkable difference to the type of structure evolved during the formation of cochleates. More generally, our observations provide a new insight into the self-assembly process of cochleates based on which we have proposed a pathway for cochleate formation from phosphatidylserine and calcium. This knowledge could be employed in using cochleates for a variety of possible biomedical applications in the future.

  13. The structure and formation of natural categories

    NASA Technical Reports Server (NTRS)

    Fisher, Douglas; Langley, Pat

    1990-01-01

    Categorization and concept formation are critical activities of intelligence. These processes and the conceptual structures that support them raise important issues at the interface of cognitive psychology and artificial intelligence. The work presumes that advances in these and other areas are best facilitated by research methodologies that reward interdisciplinary interaction. In particular, a computational model is described of concept formation and categorization that exploits a rational analysis of basic level effects by Gluck and Corter. Their work provides a clean prescription of human category preferences that is adapted to the task of concept learning. Also, their analysis was extended to account for typicality and fan effects, and speculate on how the concept formation strategies might be extended to other facets of intelligence, such as problem solving.

  14. Nano hydroxyapatite structures influence early bone formation.

    PubMed

    Meirelles, Luiz; Arvidsson, Anna; Andersson, Martin; Kjellin, Per; Albrektsson, Tomas; Wennerberg, Ann

    2008-11-01

    In a study model that aims to evaluate the effect of nanotopography on bone formation, micrometer structures known to alter bone formation, should be removed. Electropolished titanium implants were prepared to obtain a surface topography in the absence of micro structures, thereafter the implants were divided in two groups. The test group was modified with nanosize hydroxyapatite particles; the other group was left uncoated and served as control for the experiment. Topographical evaluation demonstrated increased nanoroughness parameters for the nano-HA implant and higher surface porosity compared to the control implant. The detected features had increased size and diameter equivalent to the nano-HA crystals present in the solution and the relative frequency of the feature size and diameter was very similar. Furthermore, feature density per microm(2) showed a decrease of 13.5% on the nano-HA implant. Chemical characterization revealed calcium and phosphorous ions on the modified implants, whereas the control implants consisted of pure titanium oxide. Histological evaluation demonstrated significantly increased bone formation to the coated (p < 0.05) compared to uncoated implants after 4 weeks of healing. These findings indicate for the first time that early bone formation is dependent on the nanosize hydroxyapatite features, but we are unaware if we see an isolated effect of the chemistry or of the nanotopography or a combination of both.

  15. Simulating the formation of cosmic structure.

    PubMed

    Frenk, C S

    2002-06-15

    A timely combination of new theoretical ideas and observational discoveries has brought about significant advances in our understanding of cosmic evolution. Computer simulations have played a key role in these developments by providing the means to interpret astronomical data in the context of physical and cosmological theory. In the current paradigm, our Universe has a flat geometry, is undergoing accelerated expansion and is gravitationally dominated by elementary particles that make up cold dark matter. Within this framework, it is possible to simulate in a computer the emergence of galaxies and other structures from small quantum fluctuations imprinted during an epoch of inflationary expansion shortly after the Big Bang. The simulations must take into account the evolution of the dark matter as well as the gaseous processes involved in the formation of stars and other visible components. Although many unresolved questions remain, a coherent picture for the formation of cosmic structure is now beginning to emerge.

  16. Simulating the formation of cosmic structure.

    PubMed

    Frenk, C S

    2002-06-15

    A timely combination of new theoretical ideas and observational discoveries has brought about significant advances in our understanding of cosmic evolution. Computer simulations have played a key role in these developments by providing the means to interpret astronomical data in the context of physical and cosmological theory. In the current paradigm, our Universe has a flat geometry, is undergoing accelerated expansion and is gravitationally dominated by elementary particles that make up cold dark matter. Within this framework, it is possible to simulate in a computer the emergence of galaxies and other structures from small quantum fluctuations imprinted during an epoch of inflationary expansion shortly after the Big Bang. The simulations must take into account the evolution of the dark matter as well as the gaseous processes involved in the formation of stars and other visible components. Although many unresolved questions remain, a coherent picture for the formation of cosmic structure is now beginning to emerge. PMID:12804279

  17. General relativity and cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Adamek, Julian; Daverio, David; Durrer, Ruth; Kunz, Martin

    2016-04-01

    Numerical simulations are a versatile tool for providing insight into the complicated process of structure formation in cosmology. This process is mainly governed by gravity, which is the dominant force on large scales. At present, a century after the formulation of general relativity, numerical codes for structure formation still employ Newton’s law of gravitation. This approximation relies on the two assumptions that gravitational fields are weak and that they originate from non-relativistic matter. Whereas the former seems well justified on cosmological scales, the latter imposes restrictions on the nature of the `dark’ components of the Universe (dark matter and dark energy), which are, however, poorly understood. Here we present the first simulations of cosmic structure formation using equations consistently derived from general relativity. We study in detail the small relativistic effects for a standard lambda cold dark matter cosmology that cannot be obtained within a purely Newtonian framework. Our particle-mesh N-body code computes all six degrees of freedom of the metric and consistently solves the geodesic equation for particles, taking into account the relativistic potentials and the frame-dragging force. This conceptually clean approach is very general and can be applied to various settings where the Newtonian approximation fails or becomes inaccurate, ranging from simulations of models with dynamical dark energy or warm/hot dark matter to core collapse supernova explosions.

  18. Secondary structure formation in peptide amphiphile micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew

    2012-02-01

    Peptide amphiphiles (PAs) are capable of self-assembly into micelles for use in the targeted delivery of peptide therapeutics and diagnostics. PA micelles exhibit a structural resemblance to proteins by having folded bioactive peptides displayed on the exterior of a hydrophobic core. We have studied two factors that influence PA secondary structure in micellar assemblies: the length of the peptide headgroup and amino acids closest to the micelle core. Peptide length was systematically varied using a heptad repeat PA. For all PAs the addition of a C12 tail induced micellization and secondary structure. PAs with 9 amino acids formed beta-sheet interactions upon aggregation, whereas the 23 and 30 residue peptides were displayed in an apha-helical conformation. The 16 amino acid PA experienced a structural transition from helix to sheet, indicating that kinetics play a role in secondary structure formation. A p53 peptide was conjugated to a C16 tail via various linkers to study the effect of linker chemistry on PA headgroup conformation. With no linker the p53 headgroup was predominantly alpha helix and a four alanine linker drastically changed the structure of the peptide headgroup to beta-sheet, highlighting the importance of hydrogen boding potential near the micelle core.

  19. High-Temperature Structure Formation in Metals

    NASA Astrophysics Data System (ADS)

    Filippov, E. S.

    2014-04-01

    Using a non-conventional theoretical approach relying on the electronic density (its probability) distribution in the coordinate space between ion cores rather than on the analysis of P = hk in the momentum space, volumetric and linear atomic relations are formulated, which control the mechanisms of structure formation (bcc, fcc, hcp, hexagonal, etc.) at Т ≈ Т melt. Based on an assumption of electronic density fluctuation in the course of energy gap smearing, the design variable (radius) of the half width value of the probability distribution is derived using coordinate R for the maximum electronic density fluctuation (at the maximum of the Gaussian function).

  20. Cosmological structure formation from soft topological defects

    NASA Technical Reports Server (NTRS)

    Hill, Christopher T.; Schramm, David N.; Fry, J. N.

    1988-01-01

    Some models have extremely low-mass pseudo-Goldstone bosons that can lead to vacuum phase transitions at late times, after the decoupling of the microwave background.. This can generate structure formation at redshifts z greater than or approx 10 on mass scales as large as M approx 10 to the 18th solar masses. Such low energy transitions can lead to large but phenomenologically acceptable density inhomogeneities in soft topological defects (e.g., domain walls) with minimal variations in the microwave anisotropy, as small as delta Y/T less than or approx 10 to the minus 6 power. This mechanism is independent of the existence of hot, cold, or baryonic dark matter. It is a novel alternative to both cosmic string and to inflationary quantum fluctuations as the origin of structure in the Universe.

  1. Structure Formation Cosmic Rays: Identifying Observational Constraints

    NASA Astrophysics Data System (ADS)

    Prodanovic, T.; Fields, B. D.

    2005-06-01

    Shocks that arise from baryonic in-fall and merger events during the structure formation are believed to be a source of cosmic rays. These "structure formation cosmic rays" (SFCRs) would essentially be primordial in composition, namely, mostly made of protons and alpha particles. However, very little is known about this population of cosmic rays. One way to test the level of its presence is to look at the products of hadronic reactions between SFCRs and the ISM. A perfect probe of these reactions would be 6Li. The rare isotope 6Li is produced only by cosmic rays, dominantly in alpha alpha rightarrow 6Li fusion reactions with the ISM helium. Consequently, this nuclide provides a unique diagnostic of the history of cosmic rays. Exactly because of this unique property is 6Li affected most by the presence of an additional cosmic ray population. In turn, this could have profound consequences for the Big-Bang nucleosynthesis: cosmic rays created during cosmic structure formation would lead to pre-Galactic Li production, which would act as a "contaminant" to the primordial 7Li content of metal-poor halo stars. Given the already existing problem of establishing the concordance between 7Li observed in halo stars and primordial 7Li as predicted by the WMAP, it is crucial to set limits to the level of this "contamination". However, the history of SFCRs is not very well known. Thus we propose a few model- independent ways of testing the SFCR species and their history, as well as the existing lithium problem: 1) we establish the connection between gamma-ray and 6Li production, which enables us to place constraints on the SFCR-made lithium by using the observed Extragalactic Gamma-Ray Background (EGRB); 2) we propose a new site for testing the primordial and SFCR-made lithium, namely, low-metalicity High-Velocity Clouds (HVCs), which retain the pre-Galactic composition without any significant depletion. Although using one method alone may not give us strong constraints, using

  2. Formation of Structure in the Universe

    NASA Technical Reports Server (NTRS)

    Bahcall, John; Fisher, Karl; Miralda-Escude, Jordi; Strauss, Michael; Weinberg, David

    1997-01-01

    This grant supported research by the investigators through summer salary support for Strauss and Weinberg, support for graduate students at Princeton University and Ohio State University, and travel, visitor, and publication support for the investigators. The grant originally had a duration of 1 year, and it was extended (without additional funding) for an additional year. The impact of the grant was considerable given its relatively modest duration and funding level, in part because it provided 'seed' funding to get Strauss and Weinberg started at new institutions, and in part because it was combined with support from subsequent grants. Here we summarize progress in the three general areas described in the grant proposal: Lyman alpha absorbers and the intergalactic medium, galaxy formation; and large scale structure.

  3. Structural control on karst collapse sinkhole formation

    NASA Astrophysics Data System (ADS)

    Santo, Antonio; Ascione, Alessandra; Mazzoli, Stefano; Santangelo, Nicoletta

    2013-04-01

    Collapse sinkholes owing their formation to erosion and deformation phenomena caused by subsurface karstification are widespread in the carbonate massifs of peninsular Italy. In contrast with solution dolines, which are densely distributed on the subplanar top surfaces of the carbonate massifs, the collapse sinkholes (hereinafter labelled karst collapse sinkholes) generally occur as isolated landforms and mostly affect the slopes and piedmont areas. In the latter instances, the sinkholes also affect alluvial fan conglomerates, or slope debris, overlying the carbonate rocks. We investigated the karst collapse sinkholes of the southern-central Apennines mountain belt (Italy), which is representative of a young orogenic system, characterised by recent tectonic activity and strong seismicity. The aim of the study is the identification of the causative factors which control the occurrence of such hazardous phenomena. The study was based on a regional scale analysis on sinkhole distribution in relation to the local geological-structural, geomorphological and hydrogeological contexts, and was paralleled with field analysis of some selected areas. The regional scale analysis indicates that the karst collapse sinkholes are not the mere response to the concurrence of the climatic and lithological conditions which commonly favour the development of karst processes, the occurrence of such landforms appearing strongly influenced by distinctive structural and hydrogeological conditions. In particular, a close relationship between the karst collapse sinkholes and the main extensional faults showing evidence of late Quaternary activity may be envisaged. This is inferred from the spatial distribution of the karst collapse sinkholes, which is strikingly uneven, the sinkholes generally occurring in alignments following large late Quaternary fault zones, or being clustered at the terminations of those faults. In addition, areas affected by the occurrence of groups of sinkholes, are

  4. Silicene oxides: formation, structures and electronic properties.

    PubMed

    Wang, Rong; Pi, Xiaodong; Ni, Zhenyi; Liu, Yong; Lin, Shisheng; Xu, Mingsheng; Yang, Deren

    2013-12-16

    Understanding the oxidation of silicon has been critical to the success of all types of silicon materials, which are the cornerstones of modern silicon technologies. For the recent experimentally obtained two-dimensional silicene, oxidation should also be addressed to enable the development of silicene-based devices. Here we focus on silicene oxides (SOs) that result from the partial or full oxidation of silicene in the framework of density functional theory. It is found that the formation of SOs greatly depends on oxidation conditions, which concern the oxidizing agents of oxygen and hydroxyl. The honeycomb lattice of silicene may be preserved, distorted or destroyed after oxidation. The charge state of Si in partially oxidized silicene ranges from +1 to +3, while that in fully oxidized silicene is +4. Metals, semimetals, semiconductors and insulators can all be found among the SOs, which show a wide spectrum of electronic structures. Our work indicates that the oxidation of silicene should be exquisitely controlled to obtain specific SOs with desired electronic properties.

  5. Non-standard structure formation scenarios

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Little, Brett; Islam, Ranty; Devriendt, Julien; Mahmood, Asim; Silk, Joe

    2003-04-01

    Observations on galactic scales seem to be in contradiction with recent high resolution N-body simulations. This so-called cold dark matter (CDM) crisis has been addressed in several ways, ranging from a change in fundamental physics by introducing self-interacting cold dark matter particles to a tuning of complex astrophysical processes such as global and/or local feedback. All these efforts attempt to soften density profiles and reduce the abundance of satellites in simulated galaxy halos. In this contribution we are exploring the differences between a Warm Dark Matter model and a CDM model where the power on a certain scale is reduced by introducing a narrow negative feature (`dip'). This dip is placed in a way so as to mimic the loss of power in the WDM model: both models have the same integrated power out to the scale where the power of the Dip model rises to the level of the unperturbed CDM spectrum again. Using N-body simulations we show that that the new Dip model appears to be a viable alternative to WDM while being based on different physics: where WDM requires the introduction of a new particle species the Dip stems from anon-standard inflationary period. If we are looking for an alternative to the currently challenged standard ΛCDM structure formation scenario, neither the ΛWDM nor the new Dip model can be ruled out with respect to the analysis presented in this contribution. They both make very similar predictions and the degeneracy between them can only be broken with observations yet to come.

  6. Structural Analysis of Dusty Plasma Formations Based on Spatial Spectra

    SciTech Connect

    Khakhaev, A. D.; Luizova, L. A.; Piskunov, A. A.; Podryadchikov, S. F.; Soloviev, A. V.

    2008-09-07

    Some advantages of studying the structure of dusty plasma formations using spatial spectra are illustrated by simulated experiments and by processing actual images of dusty structures in dc glow discharge in inert and molecular gases.

  7. Structure and formation of ant transportation networks

    PubMed Central

    Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

    2011-01-01

    Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

  8. Multilayer structure formation via homophily and homeostasis

    NASA Astrophysics Data System (ADS)

    Makarov, Vladimir V.; Koronovskii, Alexey A.; Maksimenko, Vladimir A.; Khramova, Marina V.; Hramov, Alexander E.; Pavlov, Alexey N.; Moskalenko, Olga I.; Buldú, Javier M.; Boccaletti, Stefano

    2016-03-01

    The competition of homophily and homeostasis mechanisms taking place in the multilayer network where several layers of connection topologies are simultaneously present as well as the interaction between layers is considered. We have shown that the competition of homophily and homeostasis leads in such networks to the formation of synchronous patterns within the different layers of the network, which may be both the distinct and identical.

  9. On the importance of cotranscriptional RNA structure formation.

    PubMed

    Lai, Daniel; Proctor, Jeff R; Meyer, Irmtraud M

    2013-11-01

    The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

  10. Discovery during Hydrogen Annealing: Formation of Nanoscale Fluorocarbon Tubular Structures

    NASA Astrophysics Data System (ADS)

    Hao, Xiuchun; Tanaka, Sinya; Masuda, Atsuhiko; Maenaka, Kazusuke; Higuchi, Kohei

    2013-09-01

    A novel fabrication method for nanoscale tubular structures is presented in this paper. The tubular structures can be obtained by heating single-crystal silicon trenches or pillars formed by the inductively coupled plasma reactive-ion etching (ICP-RIE) Bosch process in hydrogen ambient. The importance of initial vacuum in the reaction chamber for tube formation and the tube formation mechanism were discussed. The components and sidewall size of the tubular structure were also studied to verify that the tube is made of the fluorocarbon (CF) passivation layer deposited by the Bosch process. The CF tubular structure would be a promising structure for BioMEMS.

  11. Formation of bulk refractive index structures

    DOEpatents

    Potter, Jr., Barrett George; Potter, Kelly Simmons; Wheeler, David R.; Jamison, Gregory M.

    2003-07-15

    A method of making a stacked three-dimensional refractive index structure in photosensitive materials using photo-patterning where first determined is the wavelength at which a photosensitive material film exhibits a change in refractive index upon exposure to optical radiation, a portion of the surfaces of the photosensitive material film is optically irradiated, the film is marked to produce a registry mark. Multiple films are produced and aligned using the registry marks to form a stacked three-dimensional refractive index structure.

  12. Structure and Mechanism of a Pentameric Formate Channel

    SciTech Connect

    Waight, A.; Love, J; Wang, D

    2010-01-01

    Formate transport across the inner membrane is a critical step in anaerobic bacterial respiration. Members of the formate/nitrite transport protein family function to shuttle substrate across the cytoplasmic membrane. In bacterial pathogens, the nitrite transport protein is involved in protecting bacteria from peroxynitrite released by host macrophages. We have determined the 2.13-{angstrom} structure of the formate channel FocA from Vibrio cholerae, which reveals a pentamer in which each monomer possesses its own substrate translocation pore. Unexpectedly, the fold of the FocA monomer resembles that found in water and glycerol channels. The selectivity filter in FocA consists of a cytoplasmic slit and a central constriction ring. A 2.5-{angstrom} high-formate structure shows two formate ions bound to the cytoplasmic slit via both hydrogen bonding and van der Waals interactions, providing a structural basis for the substrate selectivity of the channel.

  13. Structuring Classroom Discourse Using Formative Assessment Rubrics

    NASA Astrophysics Data System (ADS)

    Brookes, David T.; Lin, Yuhfen

    2010-10-01

    There has been substantial attention paid to students' abilities to engage in a scientific discussion and think critically in a science class. But what constitutes critical thinking in physics? We will discuss a view that critical thinking involves participants (students) becoming increasingly involved in a specialized form of argument that has fixed epistemic rules, but whose rules are seldom made explicit within the physics community that uses them. We will then discuss one method of making the epistemic rules of physics explicit for students by using formative assessment rubrics. We will provide some examples of how these rubrics can be implemented in a physics class and how students were able to transfer critical thinking abilities beyond the physics classroom.

  14. The Temporal Structure of Scientific Consensus Formation.

    PubMed

    Shwed, Uri; Bearman, Peter S

    2010-12-01

    This article engages with problems that are usually opaque: What trajectories do scientific debates assume, when does a scientific community consider a proposition to be a fact, and how can we know that? We develop a strategy for evaluating the state of scientific contestation on issues. The analysis builds from Latour's black box imagery, which we observe in scientific citation networks. We show that as consensus forms, the importance of internal divisions to the overall network structure declines. We consider substantive cases that are now considered facts, such as the carcinogenicity of smoking and the non-carcinogenicity of coffee. We then employ the same analysis to currently contested cases: the suspected carcinogenicity of cellular phones, and the relationship between vaccines and autism. Extracting meaning from the internal structure of scientific knowledge carves a niche for renewed sociological commentary on science, revealing a typology of trajectories that scientific propositions may experience en route to consensus. PMID:21886269

  15. The Temporal Structure of Scientific Consensus Formation

    PubMed Central

    Shwed, Uri; Bearman, Peter S.

    2011-01-01

    This article engages with problems that are usually opaque: What trajectories do scientific debates assume, when does a scientific community consider a proposition to be a fact, and how can we know that? We develop a strategy for evaluating the state of scientific contestation on issues. The analysis builds from Latour’s black box imagery, which we observe in scientific citation networks. We show that as consensus forms, the importance of internal divisions to the overall network structure declines. We consider substantive cases that are now considered facts, such as the carcinogenicity of smoking and the non-carcinogenicity of coffee. We then employ the same analysis to currently contested cases: the suspected carcinogenicity of cellular phones, and the relationship between vaccines and autism. Extracting meaning from the internal structure of scientific knowledge carves a niche for renewed sociological commentary on science, revealing a typology of trajectories that scientific propositions may experience en route to consensus. PMID:21886269

  16. Coherent structure formation in turbulent thermal superfluids.

    PubMed

    Kivotides, Demosthenes

    2006-05-01

    By means of numerical calculations, we show that in turbulent thermal superfluids the normal fluid induces coherent bundles of quantized line vortices in the superfluid. These filamentary structures are formed in between the normal fluid vortices, acquiring eventually comparable circulation. They are self-stretched and evolve according to self-regulating dynamics. Their spectrum mimics the normal fluid spectrum with the mutual friction force exciting the large scales and damping the small scales. Strongly interacting triads of them merge sporadically into stronger, braided vortex filaments, inducing strong fluctuations in the system's energetics. A theoretical account of the system's statistical mechanics is proposed. PMID:16712309

  17. Formation of cosmic structure by Doppler instability

    NASA Technical Reports Server (NTRS)

    Hogan, Craig J.

    1991-01-01

    A new mechanism is described which can create an instability in homogeneous gaseous matter at very low density. When an isotropic background radiation field has, near an electronic resonance, a spectral feature for which photon occupation number increases with frequency, moving atoms increase their speed by taking energy from the photon distribution. In a cosmological setting, a sufficiently intense spectral feature can interact with neutral atomic gas, after recombination, to generate protogalactic perturbations of the scale and magnitude needed to explain large-scale cosmic structure.

  18. Structural template formation with discovery of subclasses

    NASA Astrophysics Data System (ADS)

    Long, Xiaojing; Wyatt, Chris

    2010-03-01

    A major focus of computational anatomy is to extract the most relevant information to identify and characterize anatomical variability within a group of subjects as well as between different groups. The construction of atlases is central to this effort. An atlas is a deterministic or probabilistic model with intensity variance, structural, functional or biochemical information over a population. To date most algorithms to construct atlases have been based on a single subject assuming that the population is best described by a single atlas. However, we believe that in a population with a wide range of subjects multiple atlases may be more representative since they reveal the anatomical differences and similarities within the group. In this work, we propose to use the K-means clustering algorithm to partition a set of images into several subclasses, based on a joint distance which is composed of a distance quantifying the deformation between images and a dissimilarity measured from the registration residual. During clustering, the spatial transformations are averaged rather than images to form cluster centers, to ensure a crisp reference. At the end of this algorithm, the updated centers of the k clusters are our atlases. We demonstrate this algorithm on a subset of a public available database with whole brain volumes of subjects aged 18-96 years. The atlases constructed by this method capture the significant structural differences across the group.

  19. Competing stability modes in vortex structure formation

    NASA Astrophysics Data System (ADS)

    Garrett, Stephen; Gostelow, J. Paul; Rona, Aldo; McMullan, W. Andrew

    2015-11-01

    Nose cones and turbine blades have rotating components and represent very practical geometries for which the behavior of vortex structures is not completely understood. These two different physical cases demonstrate a common theme of competition between mode and vortex types. The literature concerning boundary-layer transition over rotating cones presents clear evidence of an alternative instability mode leading to counter-rotating vortex pairs, consistent with a centrifugal instability. This is in contrast to co-rotating vortices present over rotating disks that arise from crossflow effects. It is demonstrated analytically that this mode competes with the crossflow mode and is dominant only over slender cones. Predictions are aligned with experimental measurements over slender cones. Concurrent experimental work on the flow over swept cylinders shows that organized fine-scale streamwise vorticity occurs more frequently on convex surfaces than is appreciated. The conventional view of purely two-dimensional laminar boundary layers following blunt leading edges is not realistic and such boundary layers need to be treated three-dimensionally, particularly when sweep is present. The vortical structures are counter-rotating for normal cylinders and co-rotating under high sweep conditions. Crossflow instabilities may have a major role to play in the transition process but the streamline curvature mode is still present, and seemingly unchanged, when the boundary layer becomes turbulent.

  20. Nonthermal histories and implications for structure formation

    NASA Astrophysics Data System (ADS)

    Fan, JiJi; Özsoy, Ogan; Watson, Scott

    2014-08-01

    We examine the evolution of cosmological perturbations in a nonthermal inflationary history with a late-time matter domination period prior to big bang nucleosynthesis. Such a cosmology could arise naturally in the well-motivated moduli scenario in the context of supersymmetry (SUSY)—in particular in models of split SUSY. Subhorizon dark matter perturbations grow linearly during the matter dominated phase before reheating and can lead to an enhancement in the growth of substructure on small scales, even in the presence of dark matter annihilations. This suggests that a new scale (the horizon size at reheating) could be important for determining the primordial matter power spectrum. However, we find that in many nonthermal models free-streaming effects or kinetic decoupling after reheating can completely erase the enhancement leading to small-scale structures. In particular, in the moduli scenario with wino or Higgsino dark matter we find that the dark matter particles produced from moduli decays would thermalize with radiation and kinetically decouple below the reheating temperature. Thus, the growth of dark matter perturbations is not sustained, and the predictions for the matter power spectrum are similar to a standard thermal history. We comment on possible exceptions, but these appear difficult to realize within standard moduli scenarios. We conclude that although enhanced structure does not provide a new probe for investigating the cosmic dark ages within these models, it does suggest that nonthermal histories offer a robust alternative to a strictly thermal post inflationary history.

  1. Structural Basis for Glycyl Radical Formation By Pyruvate Formate-Lyase Activating Enzyme

    SciTech Connect

    Vey, J.L.; Yang, J.; Li, M.; Broderick, W.E.; Broderick, J.B.; Drennan, C.L.

    2009-05-26

    Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G{sup 734} of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G{sup 734}. Our structures provide fundamental insights into the interactions between the activase and the G{sup 734} loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G{sup 734}4 of pyruvate formate-lyase.

  2. Nonlinear structure formation in nonlocal gravity

    SciTech Connect

    Barreira, Alexandre; Li, Baojiu; Hellwing, Wojciech A.; Baugh, Carlton M.; Pascoli, Silvia E-mail: baojiu.li@durham.ac.uk E-mail: c.m.baugh@durham.ac.uk

    2014-09-01

    We study the nonlinear growth of structure in nonlocal gravity models with the aid of N-body simulation and the spherical collapse and halo models. We focus on a model in which the inverse-squared of the d'Alembertian operator acts on the Ricci scalar in the action. For fixed cosmological parameters, this model differs from ΛCDM by having a lower late-time expansion rate and an enhanced and time-dependent gravitational strength ∼ 6% larger today). Compared to ΛCDM today, in the nonlocal model, massive haloes are slightly more abundant (by ∼ 10% at M ∼ 10{sup 14} M{sub ⊙}/h) and concentrated ≈ 8% enhancement over a range of mass scales), but their linear bias remains almost unchanged. We find that the Sheth-Tormen formalism describes the mass function and halo bias very well, with little need for recalibration of free parameters. The fitting of the halo concentrations is however essential to ensure the good performance of the halo model on small scales. For k ∼> 1 h/Mpc, the amplitude of the nonlinear matter and velocity divergence power spectra exhibits a modest enhancement of ∼ 12% to 15%, compared to ΛCDM today. This suggests that this model might only be distinguishable from ΛCDM by future observational missions. We point out that the absence of a screening mechanism may lead to tensions with Solar System tests due to local time variations of the gravitational strength, although this is subject to assumptions about the local time evolution of background averaged quantities.

  3. Femtosecond laser-induced periodic surface structure formation on tungsten

    SciTech Connect

    Vorobyev, A. Y.; Guo Chunlei

    2008-09-15

    In this paper, we demonstrate the generation of periodic surface structures on a technologically important material, tungsten, at both 400 and 800 nm, despite that the table values of dielectric constants for tungsten at these two wavelengths suggest the absence of surface plasmons, a wave necessary for forming periodic structures on metals. Furthermore, we find that the structure periods formed on tungsten are significantly less than the laser wavelengths. We believe that the dielectric constants of tungsten change significantly due to intense laser pulse heating and surface structuring and roughening at nanometer scales, permitting surface plasmon excitation and periodic structure formation.

  4. Formation of coherent structures in 3D laminar mixing flows

    NASA Astrophysics Data System (ADS)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  5. The probabilistic mechanism of formation of block structures

    NASA Astrophysics Data System (ADS)

    Ivanov, V. I.

    2012-03-01

    Questions on the formation of block structures are considered. It is shown that the block structure is characteristic of bodies in a wide range of scales from microscopic to astronomic and from the bodies of nonliving nature to living organisms and communities. A scheme of the mechanism of the probabilistic formation of block structures is suggested. The characteristics general for structures of all scales are revealed. Evidence is presented that the hierarchical pattern of element sizes is characteristic of natural structures in which the ratio of linear sizes of elements neighboring by hierarchy is 2-5, while the characteristic scale coefficient is √ N , where N is the total number of elements of which the system is formed. The block-probabilistic approach ensures knowledge of rare catastrophic events, including earthquakes, market crashes, floods, and industrial catastrophes, or creative events such as the formation of hypercomplex systems similar to organisms and communities. The statistics of rare events follows the power distribution (the distribution with a "heavy tail") rather than the exponential one and especially the Poisson distribution, the Gaussian distribution, or the distributions with "light tails" close to them. The expression for the factor of increasing the formation probability of the systems, which is of many orders of magnitude even for the simplest systems, is acquired.

  6. Bifurcation of learning and structure formation in neuronal maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Faust-Ellsässer, Carmen; Starke, Jens; van Hemmen, J. Leo

    2014-11-01

    Most learning processes in neuronal networks happen on a much longer time scale than that of the underlying neuronal dynamics. It is therefore useful to analyze slowly varying macroscopic order parameters to explore a network's learning ability. We study the synaptic learning process giving rise to map formation in the laminar nucleus of the barn owl's auditory system. Using equation-free methods, we perform a bifurcation analysis of spatio-temporal structure formation in the associated synaptic-weight matrix. This enables us to analyze learning as a bifurcation process and follow the unstable states as well. A simple time translation of the learning window function shifts the bifurcation point of structure formation and goes along with traveling waves in the map, without changing the animal's sound localization performance.

  7. Food Composition Database Format and Structure: A User Focused Approach.

    PubMed

    Clancy, Annabel K; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user's regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User's also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user's understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered.

  8. Food Composition Database Format and Structure: A User Focused Approach

    PubMed Central

    Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

  9. Personality Development at Preadolescence; Explorations of Structure Formation.

    ERIC Educational Resources Information Center

    Gardner, Riley W.; Moriarty, Alice

    Personality development and structure formation were studied in 60 preadolescent children (aged 9 to 13). Six major aspects of preadolescent individuality were assessed: cognitive controls, performance on the Holtzman Inkblot Test, intellectual abilities, general response to clinical testing, general response to laboratory testing, and defense…

  10. Orogenic structural inheritance and rifted passive margin formation

    NASA Astrophysics Data System (ADS)

    Salazar Mora, Claudio A.; Huismans, Ritske S.

    2016-04-01

    Structural inheritance is related to mechanical weaknesses in the lithosphere due to previous tectonic events, e.g. rifting, subduction and collision. The North and South Atlantic rifted passive margins that formed during the breakup of Western Gondwana, are parallel to the older Caledonide and the Brasiliano-Pan-African orogenic belts. In the South Atlantic, 'old' mantle lithospheric fabric resulting from crystallographic preferred orientation of olivine is suggested to play a role during rifted margin formation (Tommasi and Vauchez, 2001). Magnetometric and gravimetric mapping of onshore structures in the Camamu and Almada basins suggest that extensional faults are controlled by two different directions of inherited older Brasiliano structures in the upper lithosphere (Ferreira et al., 2009). In the South Atlantic Campos Basin, 3D seismic data indicate that inherited basement structures provide a first order control on basin structure (Fetter, 2009). Here we investigate the role of structural inheritance on the formation of rifted passive margins with high-resolution 2D thermo-mechanical numerical experiments. The numerical domain is 1200 km long and 600 km deep and represents the lithosphere and the sublithospheric mantle. Model experiments were carried out by creating self-consistent orogenic inheritance where a first phase of orogen formation is followed by extension. We focus in particular on the role of varying amount of orogenic shortening, crustal rheology, contrasting styles of orogen formation on rifted margin style, and the time delay between orogeny and subsequent rifted passive formation. Model results are compared to contrasting structural styles of rifted passive margin formation as observed in the South Atlantic. Ferreira, T.S., Caixeta, J.M., Lima, F.D., 2009. Basement control in Camamu and Almada rift basins. Boletim de Geociências da Petrobrás 17, 69-88. Fetter, M., 2009. The role of basement tectonic reactivation on the structural evolution

  11. Mechanisms underlying structural variant formation in genomic disorders

    PubMed Central

    Carvalho, Claudia M. B.; Lupski, James R.

    2016-01-01

    With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility. PMID:26924765

  12. Hysteresis-driven structure formation in biochemical networks

    PubMed

    Klein

    1998-09-21

    A mechanism of structure formation, based on hysteresis behaviour is presented. A bisubstrate kinetic system with substrate inhibition, discussed previously in the context of Turing structure formation, may show hysteresis behaviour, when embedded in a metabolic network: the system may possess multiple steady states and may be switched from one stable fixpoint to the other. When cells containing this type of system are diffusively coupled, under certain conditions patterns result, which, as is demonstrated, are not of the Turing type. The main difference to diffusion-driven (Turing) structures is the fact that the hysteresis-driven patterns emerge under diffusive conditions, under which both the homogeneous and the asymmetrical steady state is stable. The resulting special properties and biological implications are discussed.Copyright 1998 Academic Press Limited PMID:9778438

  13. Hierarchical Structure Formation of Nanoparticulate Spray-Dried Composite Aggregates.

    PubMed

    Zellmer, Sabrina; Garnweitner, Georg; Breinlinger, Thomas; Kraft, Torsten; Schilde, Carsten

    2015-11-24

    The design of hierarchically structured nano- and microparticles of different sizes, porosities, surface areas, compositions, and internal structures from nanoparticle building blocks is important for new or enhanced application properties of high-quality products in a variety of industries. Spray-drying processes are well-suited for the design of hierarchical structures of multicomponent products. This structure design using various nanoparticles as building blocks is one of the most important challenges for the future to create products with optimized or completely new properties. Furthermore, the transfer of designed nanomaterials to large-scale products with favorable handling and processing can be achieved. The resultant aggregate structure depends on the utilized nanoparticle building blocks as well as on a large number of process and formulation parameters. In this study, structure formation and segregation phenomena during the spray drying process were investigated to enable the synthesis of tailor-made nanostructures with defined properties. Moreover, a theoretical model of this segregation and structure formation in nanosuspensions is presented using a discrete element method simulation. PMID:26505280

  14. Excitonic gap formation and condensation in the bilayer graphene structure

    NASA Astrophysics Data System (ADS)

    Apinyan, V.; Kopeć, T. K.

    2016-09-01

    We have studied the excitonic gap formation in the Bernal Stacked, bilayer graphene (BLG) structures at half-filling. Considering the local Coulomb interaction between the layers, we calculate the excitonic gap parameter and we discuss the role of the interlayer and intralayer Coulomb interactions and the interlayer hopping on the excitonic pair formation in the BLG. Particularly, we predict the origin of excitonic gap formation and condensation, in relation to the furthermost interband optical transition spectrum. The general diagram of excitonic phase transition is given, explaining different interlayer correlation regimes. The temperature dependence of the excitonic gap parameter is shown and the role of the chemical potential, in the BLG, is discussed in details.

  15. Neural pattern formation in networks with dendritic structure

    NASA Astrophysics Data System (ADS)

    Bressloff, P. C.; De Souza, B.

    1998-04-01

    We present a detailed analysis of a recently proposed model of neural pattern formation that is based on the combined effect of diffusion along a neuron's dendritic tree and recurrent interactions along axo-dendritic synaptic connections. For concreteness, we consider a one-dimensional array of analog neurons with the dendritic tree idealized as a one-dimensional cable. Linear stability analysis and bifurcation theory together with numerical simulations are used to establish conditions for the onset of a Turing instability leading to the formation of stable spatial patterns of network output activity. It is shown that the presence of dendritic structure can induce dynamic (time-periodic) spatial pattern formation. Moreover, correlations between the dendritic location of a synapse and the relative positions of neurons in the network are shown to result in spatially oscillating patterns of activity along the dendrites of each neuron.

  16. Analysis of the Particle Formation Process of Structured Microparticles.

    PubMed

    Baldelli, Alberto; Boraey, Mohammed A; Nobes, David S; Vehring, Reinhard

    2015-08-01

    The particle formation process for microparticles of cellulose acetate butyrate dried from an acetone solution was investigated experimentally and theoretically. A monodisperse droplet chain was used to produce solution microdroplets in a size range of 55-70 μm with solution concentrations of 0.37 and 10 mg/mL. As the droplets dried in a laminar air flow with a temperature of 30, 40, or 55 °C, the particle formation process was recorded by two independent optical methods. Dried particles in a size range of 10-30 μm were collected for morphology analysis, showing hollow, elongated particles whose structure was dependent on the drying gas temperature and initial solution concentration. The setup allowed comprehensive measurements of the particle formation process to be made, including the period after initial shell formation. The early particle formation process for this system was controlled by the diffusion of cellulose acetate butyrate in the liquid phase, whereas later stages of the process were dominated by shell buckling and folding. PMID:25685865

  17. Gravitationally induced particle production and its impact on structure formation

    NASA Astrophysics Data System (ADS)

    Nunes, Rafael C.

    2016-08-01

    In this paper we investigate the influence of a continuous particles creation processes on the linear and nonlinear matter clustering, and its consequences on the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole l, showing that the scale where the nonlinear growth overcomes the linear effect depends strongly of particles creation rate.

  18. Nonlinear structure formation in gravity theories beyond general relativity

    NASA Astrophysics Data System (ADS)

    Mota, David F.

    2016-07-01

    We investigate the effects of modified gravity theories, in particular, the symmetron and f(R) gravity, on the nonlinear regime of structure formation. In particular, we investigate the velocity dispersion of galaxy clusters as a function of the halo masses, how the matter power spectra depend on the coupling, range and screening scale of the fifth force, and on possible ways of detecting violations of the equivalence principle using the mass inferred via lensing methods versus the mass inferred via dynamical methods.

  19. Hierarchical structure formation of cylindrical brush polymer-surfactant complexes.

    PubMed

    Cong, Yang; Gunari, Nikhil; Zhang, Bin; Janshoff, Andreas; Schmidt, Manfred

    2009-06-01

    The complex formation of cylindrical brush polymers with poly(l-lysine) side chains (PLL) and sodium dodecyl sulfate (SDS) can induce a helical conformation of the cylindrical brush polymer in aqueous solution (Gunari, N.; Cong, Y.; Zhang, B.; Fischer, K.; Janshoff, A.; Schmidt, M. Macromol. Rapid Commun. 2008, 29, 821-825). Herein, we have systematically investigated the influence of surfactant, salt, and pH on the supramolecular structure formation. The cylindrical brush polymers and their complexes with surfactants were directly visualized by atomic force microscopy in air and in aqueous solution. The alkyl chain length (measured by the carbon number, n) of the surfactant plays a key role. While helical structures were formed with n=10, 11, and 12, no helices were observed with n<10 and n>13. Addition of salt destroys the helical structures as do pH conditions below 4 and above 6, most probably because the polymer-surfactant complexes start to disintegrate. Circular dichroism was utilized to monitor the PLL side chain conformation and clearly revealed that beta-sheet formation of the side chains induces the helical conformation of the atactic main chain. PMID:19326944

  20. Structure Formation in Planetary Disk and Laboratory Plasma

    NASA Astrophysics Data System (ADS)

    Noguchi, Koichi; Tajima, Toshiki; Horton, Wendell

    2000-10-01

    The shear flow instabilities under the presence of magnetic fields in the protoplanetary disk can greatly facilitate the formation of density structures that serve prior to the onset of the gravitational Jeans instability as a seed for the faster formation of planetesimals. Such a process may explain several puzzles in the planetary genesis. We evaluate the effects of the Parker, magnetorotational, and kinematic dynamo instabilities, and calculate the mass spectra of coagulated density structures by the above mechanism in the radial direction for two typical models. The mass spectrum of the magnetorotational instability may describe the origin of giant planets away from central star. Our local three-dimentional MHD simulation indicates that the coupling of those instabilities creates spiral arms and gas blobs in the accretion disk, reinforcing our theory. Such a mechanism for the early structure formation may be tested in a laboratory. The recent progress in experiments invloving shear flows in tokamak and laser plasmas may become a key in this regard. * The work is supported by NSF and DoE.

  1. Chinese lexical networks: The structure, function and formation

    NASA Astrophysics Data System (ADS)

    Li, Jianyu; Zhou, Jie; Luo, Xiaoyue; Yang, Zhanxin

    2012-11-01

    In this paper Chinese phrases are modeled using complex networks theory. We analyze statistical properties of the networks and find that phrase networks display some important features: not only small world and the power-law distribution, but also hierarchical structure and disassortative mixing. These statistical traits display the global organization of Chinese phrases. The origin and formation of such traits are analyzed from a macroscopic Chinese culture and philosophy perspective. It is interesting to find that Chinese culture and philosophy may shape the formation and structure of Chinese phrases. To uncover the structural design principles of networks, network motif patterns are studied. It is shown that they serve as basic building blocks to form the whole phrase networks, especially triad 38 (feed forward loop) plays a more important role in forming most of the phrases and other motifs. The distinct structure may not only keep the networks stable and robust, but also be helpful for information processing. The results of the paper can give some insight into Chinese language learning and language acquisition. It strengthens the idea that learning the phrases helps to understand Chinese culture. On the other side, understanding Chinese culture and philosophy does help to learn Chinese phrases. The hub nodes in the networks show the close relationship with Chinese culture and philosophy. Learning or teaching the hub characters, hub-linking phrases and phrases which are meaning related based on motif feature should be very useful and important for Chinese learning and acquisition.

  2. Electron microscopic examination of wastewater biofilm formation and structural components.

    PubMed Central

    Eighmy, T T; Maratea, D; Bishop, P L

    1983-01-01

    This research documents in situ wastewater biofilm formation, structure, and physiochemical properties as revealed by scanning and transmission electron microscopy. Cationized ferritin was used to label anionic sites of the biofilm glycocalyx for viewing in thin section. Wastewater biofilm formation paralleled the processes involved in marine biofilm formation. Scanning electron microscopy revealed a dramatic increase in cell colonization and growth over a 144-h period. Constituents included a variety of actively dividing morphological types. Many of the colonizing bacteria were flagellated. Filaments were seen after primary colonization of the surface. Transmission electron microscopy revealed a dominant gram-negative cell wall structure in the biofilm constituents. At least three types of glycocalyces were observed. The predominant glycocalyx possessed interstices and was densely labeled with cationized ferritin. Two of the glycocalyces appeared to mediate biofilm adhesion to the substratum. The results suggest that the predominant glycocalyx of this thin wastewater biofilm serves, in part, to: (i) enclose the bacteria in a matrix and anchor the biofilm to the substratum and (ii) provide an extensive surface area with polyanionic properties. Images PMID:6881965

  3. Structure and formation of the lunar farside highlands.

    PubMed

    Garrick-Bethell, Ian; Nimmo, Francis; Wieczorek, Mark A

    2010-11-12

    The formation of the lunar farside highlands has long been an open problem in lunar science. We show that much of the topography and crustal thickness in this terrain can be described by a degree-2 harmonic. No other portion of the Moon exhibits comparable degree-2 structure. The quantified structure of the farside highlands unites them with the nearside and suggests a relation between lunar crustal structure, nearside volcanism, and heat-producing elements. The farside topography cannot be explained by a frozen-in tidal bulge. However, the farside crustal thickness and the topography it produces may have been caused by spatial variations in tidal heating when the ancient crust was decoupled from the mantle by a liquid magma ocean, similar to Europa's present ice shell. PMID:21071665

  4. Formation of electrostatic solitons and hole structures in pair plasmas.

    PubMed

    Jao, C-S; Hau, L-N

    2012-11-01

    In an electron-proton plasma, electrostatic solitary waves and hole structures can easily be generated by streaming instability due to the asymmetric inertia between ions and electrons. It has been argued theoretically whether electrostatic solitons and/or hole structures can form in a pair plasma. This paper presents results on the formation of pair electrostatic hole structure in an electron-positron plasma based on one-dimensional electrostatic particle-in-cell simulations. In particular, we show the feature of interlacing electron and positron holes in phase space generated by current-free electron and positron beams streaming in a stationary electron-positron background plasma. The coexistent electron and positron holes are associated with periodic interlacing of positive and negative potentials, respectively. Detailed comparisons between simulation results and linear theory of streaming instability in pair plasmas are made and the thermodynamic state is inferred. PMID:23214890

  5. FORMATION OF COLD FILAMENTARY STRUCTURE FROM WIND-BLOWN SUPERBUBBLES

    SciTech Connect

    Ntormousi, Evangelia; Burkert, Andreas; Fierlinger, Katharina; Heitsch, Fabian

    2011-04-10

    The expansion and collision of two wind-blown superbubbles is investigated numerically. Our models go beyond previous simulations of molecular cloud formation from converging gas flows by exploring this process with realistic flow parameters, sizes, and timescales. The superbubbles are blown by time-dependent winds and supernova explosions, calculated from population synthesis models. They expand into a uniform or turbulent diffuse medium. We find that dense, cold gas clumps and filaments form naturally in the compressed collision zone of the two superbubbles. Their shapes resemble the elongated, irregular structure of observed cold, molecular gas filaments, and clumps. At the end of the simulations, between 65% and 80% of the total gas mass in our simulation box is contained in these structures. The clumps are found in a variety of physical states, ranging from pressure equilibrium with the surrounding medium to highly underpressured clumps with large irregular internal motions and structures which are rotationally supported.

  6. Constraints on the Cosmic Structure Formation Models from Early Formation of Giant Galaxies

    NASA Astrophysics Data System (ADS)

    Mo, H. J.; Fukugita, M.

    1996-08-01

    A recent observation of Steidel and coworkers indicates that a substantial fraction of giant galaxies were formed at an epoch as early as redshift z > 3--3.5. We show that this early formation gives strong constraints on models of cosmic structure formation. Adopting the COBE normalization for the density perturbation spectrum, we argue that the following models do not have large enough power on galactic scales to yield the observed abundance: (1) standard cold dark matter (CDM) models (where mass density Omega 0 = 1 and power index n = 1) with the Hubble constant h <~ 0.35; (2) tilted CDM models with h = 0.5 and n <~ 0.75; (3) open CDM models with h <~ 0.8 and Omega 0 <~ 0.3; and (4) mixed dark matter models with h = 0.5 and Omega nu >~ 0.2. Flat CDM models with a cosmological constant lambda 0 ~ 0.7 are consistent with the observation, provided that h >~ 0.6. Combined with constraints from large-scale structure formation, these results imply that the flat CDM model with a low Omega 0 is the one fully consistent with observations. We predict that these high-redshift galaxies are more strongly clustered today than normal galaxies.

  7. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented. PMID:27100912

  8. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.

  9. Formation of plasma dust structures at atmospheric pressure

    SciTech Connect

    Filippov, A. V. Babichev, V. N.; Dyatko, N. A.; Pal', A. F.; Starostin, A. N.; Taran, M. D.; Fortov, V. E.

    2006-02-15

    The formation of strongly coupled stable dust structures in the plasma produced by an electron beam at atmospheric pressure was detected experimentally. Analytical expressions were derived for the ionization rate of a gas by an electron beam in an axially symmetric geometry by comparing experimental data with Monte Carlo calculations. Self-consistent one-dimensional simulations of the beam plasma were performed in the diffusion drift approximation of charged plasma particle transport with electron diffusion to determine the dust particle levitation conditions. Since almost all of the applied voltage drops on the cathode layer in the Thomson glow regime of a non-self-sustained gas discharge, a distribution of the electric field that grows toward the cathode is produced in it; this field together with the gravity produces a potential well in which the dust particles levitate to form a stable disk-shaped structure. The nonideality parameters of the dust component in the formation region of a highly ordered quasi-crystalline structure calculated using computational data for the dust particle charging problem were found to be higher than the critical value after exceeding which an ensemble of particles with a Yukawa interaction should pass to the crystalline state.

  10. Improving the Factor Structure of Psychological Scales: The Expanded Format as an Alternative to the Likert Scale Format

    ERIC Educational Resources Information Center

    Zhang, Xijuan; Savalei, Victoria

    2016-01-01

    Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format,…

  11. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2008-01-01

    Intense structure formation and reionization occur at high redshift, yet there is currently little observational information about this very important epoch. Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the formation of structures in the early universe. Past efforts have been limited to calculating merger rates using different models in which many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span a very wide range (0.1 - 104 mergers/year). Here we develop a semi-analytical, phenomenological model of MBH mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z 5 - 30 structure formation era. We do this by generating synthetic LISA observable data (total BH mass, BH mass ratio, redshift, merger rates), which are then analyzed using a Markov Chain Monte Carlo method. This allows us to constrain the physical parameters of the mergers. We find that our methodology works well at estimating merger parameters, consistently giving results within 1- of the input parameter values. We also discover that the number of merger events is a key discriminant among models. This helps our method be robust against observational uncertainties. Our approach, which at this stage constitutes a proof of principle, can be readily extended to physical models and to more general problems in cosmology and gravitational wave astrophysics.

  12. Star formation along the Hubble sequence. Radial structure of the star formation of CALIFA galaxies

    NASA Astrophysics Data System (ADS)

    González Delgado, R. M.; Cid Fernandes, R.; Pérez, E.; García-Benito, R.; López Fernández, R.; Lacerda, E. A. D.; Cortijo-Ferrero, C.; de Amorim, A. L.; Vale Asari, N.; Sánchez, S. F.; Walcher, C. J.; Wisotzki, L.; Mast, D.; Alves, J.; Ascasibar, Y.; Bland-Hawthorn, J.; Galbany, L.; Kennicutt, R. C.; Márquez, I.; Masegosa, J.; Mollá, M.; Sánchez-Blázquez, P.; Vílchez, J. M.

    2016-05-01

    The spatially resolved stellar population content of today's galaxies holds important information for understanding the different processes that contribute to the star formation and mass assembly histories of galaxies. The aim of this paper is to characterize the radial structure of the star formation rate (SFR) in galaxies in the nearby Universe as represented by a uniquely rich and diverse data set drawn from the CALIFA survey. The sample under study contains 416 galaxies observed with integral field spectroscopy, covering a wide range of Hubble types and stellar masses ranging from M⋆ ~ 109 to 7 × 1011 M⊙. Spectral synthesis techniques are applied to the datacubes to derive 2D maps and radial profiles of the intensity of the star formation rate in the recent past (ΣSFR), as well as related properties, such as the local specific star formation rate (sSFR), defined as the ratio between ΣSFR and the stellar mass surface density (μ⋆). To emphasize the behavior of these properties for galaxies that are on and off the main sequence of star formation (MSSF), we stack the individual radial profiles in seven bins of galaxy morphology (E, S0, Sa, Sb, Sbc, Sc, and Sd), and several stellar masses. Our main results are: (a) the intensity of the star formation rate shows declining profiles that exhibit very small differences between spirals with values at R = 1 half light radius (HLR) within a factor two of ΣSFR ~ 20 M⊙Gyr-1pc-2. The dispersion in the ΣSFR(R) profiles is significantly smaller in late type spirals (Sbc, Sc, Sd). This confirms that the MSSF is a sequence of galaxies with nearly constant ΣSFR. (b) sSFR values scale with Hubble type and increase radially outward with a steeper slope in the inner 1 HLR. This behavior suggests that galaxies are quenched inside-out and that this process is faster in the central, bulge-dominated part than in the disks. (c) As a whole and at all radii, E and S0 are off the MSSF with SFR much smaller than spirals of the

  13. Fractal structure formation from Ag nanoparticle films on insulating substrates.

    PubMed

    Tang, Jing; Li, Zhiyong; Xia, Qiangfei; Williams, R Stanley

    2009-07-01

    Two dimensional (2D) fractal structures were observed to form from fairly uniform Ag island films (equivalent mass thicknesses of 1.5 and 5 nm) on insulating silicon dioxide surfaces (thermally grown silicon oxide on Si or quartz) upon immersion in deionized water. This result is distinctly different from the previously observed three-dimensional (3D) growth of faceted Ag nanocrystals on conductive surfaces (ITO and graphite) as the result of an electrochemical Ostwald ripening process, which also occurs on native oxide covered silicon surfaces as reported here. The fractal structures formed by diffusion-limited aggregation (DLA) of Ag species on the insulating surfaces. We present the experimental observation of this phenomenon and discuss some possible mechanisms for the DLA formation. PMID:19496573

  14. Giant planet formation in radially structured protoplanetary discs

    NASA Astrophysics Data System (ADS)

    Coleman, Gavin A. L.; Nelson, Richard P.

    2016-08-01

    Our recent N-body simulations of planetary system formation, incorporating models for the main physical processes thought to be important during the building of planets (i.e. gas disc evolution, migration, planetesimal/boulder accretion, gas accretion on to cores, etc.), have been successful in reproducing some of the broad features of the observed exoplanet population (e.g. compact systems of low-mass planets, hot Jupiters), but fail completely to form any surviving cold Jupiters. The primary reason for this failure is rapid inward migration of growing protoplanets during the gas accretion phase, resulting in the delivery of these bodies on to orbits close to the star. Here, we present the results of simulations that examine the formation of gas giant planets in protoplanetary discs that are radially structured due to spatial and temporal variations in the effective viscous stresses, and show that such a model results in the formation of a population of cold gas giants. Furthermore, when combined with models for disc photoevaporation and a central magnetospheric cavity, the simulations reproduce the well-known hot-Jupiter/cold-Jupiter dichotomy in the observed period distribution of giant exoplanets, with a period valley between 10 and 100 d.

  15. Modulation of nanotube formation by structural modifications of sphingolipids.

    PubMed Central

    Kulkarni, V S; Boggs, J M; Brown, R E

    1999-01-01

    Galactosylceramides (GalCers) containing nervonoyl (24:1(Delta15(cis))) acyl chains have the capacity to assemble into nanotubular microstructures in excess water (. Biophys. J. 69:1976-1986). To define the structural parameters that modulate nanotube formation, GalCer derivatives were synthesized that contained cis monounsaturated acyl chains with the formula X:1((X-9)). X indicates the total acyl carbon number (24, 22, 20, or 18), and 1 indicates a single cis double bond, the location of which is designated by the superscript (X-9). Deep etching of freeze-fractured 24:1(Delta15(cis)) GalCer dispersions followed by replica production and transmission electron microscopic analysis confirmed nanotube morphology (25-30-nm diameter). Control experiments revealed that tubule formation was promoted by cooling through the main enthalpic phase transition coupled with repetitive freeze-thaw cycling. Imparting a negative charge to the sugar headgroup of 24:1(Delta15)GalCer via sulfate dramatically altered mesomorpholgy and resulted in myelinic-like, multilamellar structures. Removal of the sugar headgroup (24:1(Delta15)Cer) resulted in flattened cylindrical structures with a cochleate appearance. Compared to these large-scale changes in morphology, more subtle changes were induced by structural changes in the acyl chain of 24:1(Delta15)GalCer. 22:1(Delta13)GalCer dispersions consisted of long, smooth tubules (35-40-nm diameters) with a strong tendency to self-align into bundle-like aggregates. In contrast, the microstructures formed by 20:1(Delta11)GalCer resembled helical ribbons with a right-handed twist. Ribbon widths averaged 30-35 nm, with helical pitches of 80-90 nm. 18:1(Delta9)GalCer displayed a variety of morphologies, including large-diameter multilamellar cylinders and liposome-like structures, as well as stacked, plate-like arrays. The results are discussed within the context of current theories of lipid tubule formation. PMID:10388760

  16. Formation of Coronae Structures on Venus by Thermochemical Diapirs

    NASA Astrophysics Data System (ADS)

    Golabek, G. J.; Kaus, B. J. P.; Tackley, P. J.

    2009-04-01

    One of the most prominent features on the surface of Venus are the coronae. They are large scale volcano-tectonic structures, which are approximately circular with a mean diameter of 200 - 300 km [Dombard et al., 2007], with extrema ranging from 60 km to about 2000 km diameter. A total of 515 coronae were found on Venus in the Magellan data [Stofan et al., 2001]. The intruiging point about corona is that there is no counterpart on the other terrestrial planets for these structures. Nine different groups of coronae have been observed on Venus [Smrekar and Stofan, 1997]. Smrekar and Stofan [1997] suggested that these different groups can stand for different steps in the time evolution of coronae. Several mechanisms have been proposed to explain their formation: Dombard et al. [2007] suggested that coronae form in response to magmatic loading of the crust over zones of partial melting above thermally buoyant heads of transient mantle plumes that impinge on the base of the thermal lithosphere. On the other side, the potential importance of crust delamination induced by mantle upwellings as formation mechanisms for coronae was pointed out by Smrekar and Stofan [1997]. Here, we present results on coronae formation using the recently developed 2D finite element code MILAMIN_VEP, which employs MILAMIN technology [Dabrowski et al., 2008]. We apply a temperature and stress-dependent visco-elasto-plastic rheology in a rectangular box, which includes a rising thermochemical diapir beneath the Venusian crust and lithosphere. The rheological parameters are taken from results inferred for Venusian materials [Mackwell et al., 1998]. A free surface is used in our calculations, which allows for the self-consistent computation of topography induced by the buoyant diapir. A hybrid particle-in-cell approach allows remeshing of strongly deformed grid cells. A systematic investigation of the physical conditions under which coronae can form is being performed in 2D. Initial results

  17. Perineuronal net formation and structure in aggrecan knockout mice.

    PubMed

    Giamanco, K A; Morawski, M; Matthews, R T

    2010-11-10

    Perineuronal nets (PNNs) are specialized substructures of the neural extracellular matrix (ECM) which envelop the cell soma and proximal neurites of particular sets of neurons with apertures at sites of synaptic contact. Previous studies have shown that PNNs are enriched with chondroitin sulfate proteoglycans (CSPGs) and hyaluronan, however, a complete understanding of their precise molecular composition has been elusive. In addition, identifying which specific PNN components are critical to the formation of this structure has not been demonstrated. Previous work in our laboratory has demonstrated that the CSPG, aggrecan, is a key activity-dependent component of PNNs in vivo. In order to assess the contribution of aggrecan to PNN formation, we utilized cartilage matrix deficiency (cmd) mice, which lack aggrecan. Herein, we utilized an in vitro model, dissociated cortical culture, and an ex vivo model, organotypic slice culture, to specifically investigate the role aggrecan plays in PNN formation. Our work demonstrates that staining with the lectin, Wisteria floribunda agglutinin (WFA), considered a broad PNN marker, is eliminated in the absence of aggrecan, suggesting the loss of PNNs. However, in contrast, we found that the expression patterns of other PNN markers, including hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R, brevican, and hyaluronan are unaffected by the absence of aggrecan. Lastly, we determined that while all PNN components are bound to the surface in a hyaluronan-dependent manner, only HAPLN1 remains attached to the cell surface when neurons are treated with chondroitinase. These results suggest a different model for the molecular association of PNNs to the cell surface. Together our work has served to assess the contribution of aggrecan to PNN formation while providing key evidence concerning the molecular composition of PNNs in addition to determining how these components ultimately form PNNs.

  18. Perineuronal net formation and structure in aggrecan knockout mice.

    PubMed

    Giamanco, K A; Morawski, M; Matthews, R T

    2010-11-10

    Perineuronal nets (PNNs) are specialized substructures of the neural extracellular matrix (ECM) which envelop the cell soma and proximal neurites of particular sets of neurons with apertures at sites of synaptic contact. Previous studies have shown that PNNs are enriched with chondroitin sulfate proteoglycans (CSPGs) and hyaluronan, however, a complete understanding of their precise molecular composition has been elusive. In addition, identifying which specific PNN components are critical to the formation of this structure has not been demonstrated. Previous work in our laboratory has demonstrated that the CSPG, aggrecan, is a key activity-dependent component of PNNs in vivo. In order to assess the contribution of aggrecan to PNN formation, we utilized cartilage matrix deficiency (cmd) mice, which lack aggrecan. Herein, we utilized an in vitro model, dissociated cortical culture, and an ex vivo model, organotypic slice culture, to specifically investigate the role aggrecan plays in PNN formation. Our work demonstrates that staining with the lectin, Wisteria floribunda agglutinin (WFA), considered a broad PNN marker, is eliminated in the absence of aggrecan, suggesting the loss of PNNs. However, in contrast, we found that the expression patterns of other PNN markers, including hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R, brevican, and hyaluronan are unaffected by the absence of aggrecan. Lastly, we determined that while all PNN components are bound to the surface in a hyaluronan-dependent manner, only HAPLN1 remains attached to the cell surface when neurons are treated with chondroitinase. These results suggest a different model for the molecular association of PNNs to the cell surface. Together our work has served to assess the contribution of aggrecan to PNN formation while providing key evidence concerning the molecular composition of PNNs in addition to determining how these components ultimately form PNNs. PMID:20732394

  19. Towards the mathematical model of rim structure formation

    NASA Astrophysics Data System (ADS)

    Kinoshita, M.

    1997-09-01

    The high burnup LWR UO 2 fuels show a notable micro-structural change around the pellet outer zone which is called the rim structure. It is observed at temperatures as low as 400°C so that fission track and cascade mixing could be the key mechanism. SEM observation revealed that the structure primarily appears on free surfaces of UO 2, indicating that strong sink for point defects may play a big role. And as generic observations, increase of lattice parameter indicates extensive amounts of vacancies are stored in high burnup fuel, which may induce the restructuring interacting with dislocations of high density at high burnup. Considering these observations a model of reaction-diffusion process of defects with irradiation induced transport is proposed. The equations are investigated numerically. The model indicates that an instability starts when the dislocation network starts intensive interaction with vacancy flux which is modified by interstitial diffusion between spatial segments. It appeared to be similar to the Turing type instability which indicates that the rim structure formation is one kind of the self-organizing processes of open reaction-diffusion systems.

  20. The Large-scale Structure of the Universe: Probes of Cosmology and Structure Formation

    NASA Astrophysics Data System (ADS)

    Noh, Yookyung

    The usefulness of large-scale structure as a probe of cosmology and structure formation is increasing as large deep surveys in multi-wavelength bands are becoming possible. The observational analysis of large-scale structure guided by large volume numerical simulations are beginning to offer us complementary information and crosschecks of cosmological parameters estimated from the anisotropies in Cosmic Microwave Background (CMB) radiation. Understanding structure formation and evolution and even galaxy formation history is also being aided by observations of different redshift snapshots of the Universe, using various tracers of large-scale structure. This dissertation work covers aspects of large-scale structure from the baryon acoustic oscillation scale, to that of large scale filaments and galaxy clusters. First, I discuss a large- scale structure use for high precision cosmology. I investigate the reconstruction of Baryon Acoustic Oscillation (BAO) peak within the context of Lagrangian perturbation theory, testing its validity in a large suite of cosmological volume N-body simulations. Then I consider galaxy clusters and the large scale filaments surrounding them in a high resolution N-body simulation. I investigate the geometrical properties of galaxy cluster neighborhoods, focusing on the filaments connected to clusters. Using mock observations of galaxy clusters, I explore the correlations of scatter in galaxy cluster mass estimates from multi-wavelength observations and different measurement techniques. I also examine the sources of the correlated scatter by considering the intrinsic and environmental properties of clusters.

  1. Locally Biased Galaxy Formation and Large-Scale Structure

    NASA Astrophysics Data System (ADS)

    Narayanan, Vijay K.; Berlind, Andreas A.; Weinberg, David H.

    2000-01-01

    We examine the influence of the morphology-density relation and a wide range of simple models for biased galaxy formation on statistical measures of large-scale structure. We contrast the behavior of local biasing models, in which the efficiency of galaxy formation is determined by the density, geometry, or velocity dispersion of the local mass distribution, with that of nonlocal biasing models, in which galaxy formation is modulated coherently over scales larger than the galaxy correlation length. If morphological segregation of galaxies is governed by a local morphology-density relation, then the correlation function of E/S0 galaxies should be steeper and stronger than that of spiral galaxies on small scales, as observed, while on large scales the E/S0 and spiral galaxies should have correlation functions with the same shape but different amplitudes. Similarly, all of our local bias models produce scale-independent amplification of the correlation function and power spectrum in the linear and mildly nonlinear regimes; only a nonlocal biasing mechanism can alter the shape of the power spectrum on large scales. Moments of the biased galaxy distribution retain the hierarchical pattern of the mass moments, but biasing alters the values and scale dependence of the hierarchical amplitudes S3 and S4. Pair-weighted moments of the galaxy velocity distribution are sensitive to the details of the bias prescription even if galaxies have the same local velocity distribution as the underlying dark matter. The nonlinearity of the relation between galaxy density and mass density depends on the biasing prescription and the smoothing scale, and the scatter in this relation is a useful diagnostic of the physical parameters that determine the bias. While the assumption that galaxy formation is governed by local physics leads to some important simplifications on large scales, even local biasing is a multifaceted phenomenon whose impact cannot be described by a single parameter or

  2. Changes in protein structure at the interface accompanying complex formation.

    PubMed

    Chakravarty, Devlina; Janin, Joël; Robert, Charles H; Chakrabarti, Pinak

    2015-11-01

    Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

  3. Innovative design of composite structures: The use of curvilinear fiber format in composite structure design

    NASA Technical Reports Server (NTRS)

    Hyer, M. W.; Charette, R. F.

    1990-01-01

    The gains in structural efficiency are investigated that can be achieved by aligning the fibers in some or all of the layers in a laminate with the principal stress directions in those layers. The name curvilinear fiber format is given to this idea. The problem studied is a plate with a central circular hole subjected to a uniaxial tensile load. An iteration scheme is used to find the fiber directions at each point in the laminate. Two failure criteria are used to evaluate the tensile load capacity of the plates with a curvilinear format, and for comparison, counterpart plates with a conventional straightline fiber format. The curvilinear designs for improved tensile capacity are then checked for buckling resistance. It is concluded that gains in efficiency can be realized with the curvilinear format.

  4. Structural basis of complement membrane attack complex formation

    NASA Astrophysics Data System (ADS)

    Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen

    2016-02-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a `multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a `split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.

  5. Numerical models of sunspot formation and fine structure.

    PubMed

    Rempel, Matthias

    2012-07-13

    Sunspots are central to our understanding of solar (and stellar) magnetism in many respects. On the large scale, they link the magnetic field observable in the photosphere to the dynamo processes operating in the solar interior. Properly interpreting the constraints that sunspots impose on the dynamo process requires a detailed understanding of the processes involved in their formation, dynamical evolution and decay. On the small scale, they give an insight into how convective energy transport interacts with the magnetic field over a wide range of field strengths and inclination angles, leading to sunspot fine structure observed in the form of umbral dots and penumbral filaments. Over the past decade, substantial progress has been made on both observational and theoretical sides. Advanced ground- and space-based observations have resolved, for the first time, the details of umbral dots and penumbral filaments and discovered similarities in their substructures. Numerical models have advanced to the degree that simulations of entire sunspots with sufficient resolution to resolve sunspot fine structure are feasible. A combination of improved helioseismic inversion techniques with seismic forward modelling provides new views on the subsurface structure of sunspots. In this review, we summarize recent progress, with particular focus on numerical modelling. PMID:22665895

  6. Formation, structure and morphology of polyurethane-metal interphases

    NASA Astrophysics Data System (ADS)

    Wehlack, C.; Possart, W.

    2009-09-01

    Thin films (few 10 nm to some μm) of different two-part polyurethane adhesive systems (polyether resins and aromatic isocyanate hardener) are characterised on the native metal surfaces of gold, aluminium, copper and steel, thus acting as a model for the interphase in technically relevant material compounds. It is investigated in how far the curing processes, the resulting chemical structure and the morphology of the polymer films differ from the bulk. The comparison of films on the different metals and with the bulk provides conclusions on the properties of the interphase at polymer-metal contacts. The variation of the film thickness gives access to microstructure gradients. The chemical structure of the films is characterised by IR spectroscopy during curing at room temperature (RT kinetics) and in the cured state. Furthermore, microscopic (e.g. SFM) and additional spectroscopic techniques (e.g. XPS) characterise the films and their surface with respect to morphology, composition, homogeneity and topography. The results reveal specific features in the interphase caused by adhesive interactions, catalysis, phase separation and transport phenomena on the different metal surfaces. Remarkable quantitative differences can be seen in the chemical structure formation of thin PU films with respect to reaction rate and final degree of cure.

  7. Investigation of Laser Induced Structure formation and resultant fluorescence

    NASA Astrophysics Data System (ADS)

    Kandpal, Sanjeev Kumar; Otterson, Samantha L.; Bousfield, Douglas W.; Neivandt, David J.; Mason, Michael D.

    2015-04-01

    The formation mechanism of 3D micron-sized fluorescent structures generated in silver nanoparticle containing sodium citrate dihydrate films, during exposure to focused laser radiation, was investigated. Microscopic and thermochemical data indicate that heat accumulates at the nanoparticle surface. The heat causes local melting and an increase in temperature beyond the decomposition point of the immediate surrounding layer. In turn this leads to the rapid release of volatile gases (H2O and CO2). These expanding gases push the melted liquid pool outward, from the center of the focal volume, leaving behind a trough-like structure with elevated edges. It was observed that the edges of the structures were fluorescent. The fluorescence mechanism was investigated using atomic force, scanning electron and Confocal Fluorescence Microscopy. The observed fluorescence was attributed to the decomposition of sodium citrate dihydrate to sodium citrate. The presence of water acts to quench fluorescence in the bulk film, but near regions that experienced heat, the water is driven off.

  8. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  9. Magnetic Structure and Formation of On-disk Coronal Plumes

    NASA Astrophysics Data System (ADS)

    Antonsson, S.; Tiwari, S. K.; Moore, R. L.; Winebarger, A. R.

    2015-12-01

    "Plumes" are feather-like features found on the solar disk, in the plage-like field concentrations of quiet regions. On-disk plumes are analogous to polar/coronal-hole plumes but have not been studied in detail in the past. We research their formation and characteristics, such as lifetime, intensity and magnetic setting at the feet. Atmospheric Imaging Assembly (AIA) images in the 171 Å filter and Helioseismic and Magnetic Imager (HMI) line-of-sight magnetograms, both from the Solar Dynamics Observatory (SDO), are analyzed with the IDL SolarSoftWare package and used to study the plumes. We find that on-disk plumes form at the places of converging magnetic fields, and disappear when those fields disperse. However, plumes disappear after nearby events, such as flares, or with the emergence of opposite polarity. The lifetime of each plume tends to be several days, although some appear and disappear within several hours. On-disk plumes outline magnetic fields close to the sun, allowing a better understanding of fine magnetic structures than before. Additionally, since plumes must be heated to around 600,000 K to be visible in 171 Å, their formation and characteristics could tell about how they, and therefore the corona, are heated.

  10. Formation of RNA Beads from Various DNA Nanoring Structures.

    PubMed

    Kim, Hyejin; Lee, Jong Bum

    2016-05-01

    By taking advantages of rolling circle transcription, one of the powerful methods to overcome the instability of RNA, we successfully synthesized RNA particles having high copy numbers of RNA strands. To examine dependence of RNA particle formation to template circular DNA strands, we synthesized RNA beads with 65-nt, 92-nt and 200-nt DNA nanoring structures as template circular DNA. Our conclusion is that characteristics of RNA beads could be controlled with various template circular DNA for RCT. It is feasible that our RNA beads could be used for RNAzyme-based metal sensors such as aqueous lead ion sensing. In this case, we expect that multi-metal ion detection would be possible by using 200-nt circular DNA bearing multiple desired functions as a template for RNA bead formation. Furthermore, certain features of RNA beads such as sensitivity to nuclease digestion and maximum loading amount of drugs when used as a carrier are expected to be further adjusted by choosing appropriate porosity and size.

  11. Halo formation and evolution: unification of structure and physical properties

    NASA Astrophysics Data System (ADS)

    Ernest, Allan D.; Collins, Matthew P.

    2016-08-01

    The assembly of matter in the universe proliferates a wide variety of halo structures, often with enigmatic consequences. Giant spiral galaxies, for example, contain both dark matter and hot gas, while dwarf spheroidal galaxies, with weaker gravity, contain much larger fractions of dark matter, but little gas. Globular clusters, superficially resembling these dwarf spheroidals, have little or no dark matter. Halo temperatures are also puzzling: hot cluster halos contain cooler galaxy halos; dwarf galaxies have no hot gas at all despite their similar internal processes. Another mystery is the origin of the gas that galaxies require to maintain their measured star formation rates (SFRs). We outline how gravitational quantum theory solves these problems, and enables baryons to function as weakly-interacting-massive-particles (WIMPs) in Lambda Cold Dark Matter (LCDM) theory. Significantly, these dark-baryon ensembles may also be consistent with primordial nucleosynthesis (BBN) and cosmic microwave background (CMB) anisotropies.

  12. Statistics of Caustics in Large-Scale Structure Formation

    NASA Astrophysics Data System (ADS)

    Feldbrugge, Job L.; Hidding, Johan; van de Weygaert, Rien

    2016-10-01

    The cosmic web is a complex spatial pattern of walls, filaments, cluster nodes and underdense void regions. It emerged through gravitational amplification from the Gaussian primordial density field. Here we infer analytical expressions for the spatial statistics of caustics in the evolving large-scale mass distribution. In our analysis, following the quasi-linear Zel'dovich formalism and confined to the 1D and 2D situation, we compute number density and correlation properties of caustics in cosmic density fields that evolve from Gaussian primordial conditions. The analysis can be straightforwardly extended to the 3D situation. We moreover, are currently extending the approach to the non-linear regime of structure formation by including higher order Lagrangian approximations and Lagrangian effective field theory.

  13. Structural modification in the formation of starch - silver nanocomposites

    NASA Astrophysics Data System (ADS)

    Begum, S. N. Suraiya; Aswal, V. K.; Ramasamy, Radha Perumal

    2016-05-01

    Polymer based nanocomposites have gained wide applications in field of battery technology. Starch is a naturally occurring polysaccharide with sustainable properties such as biodegradable, non toxic, excellent film forming capacity and it also act as reducing agent for the metal nanoparticles. In our research various concentration of silver nitrate (AgNO3) was added to the starch solution and films were obtained using solution casting method. Surface electron microscope (SEM) of the films shows modifications depending upon the concentration of AgNO3. Small angle neutron scattering (SANS) analysis showed that addition of silver nitrate modifies the starch to disc like structures and with increasing the AgNO3 concentration leads to the formation of fractals. This research could benefit battery technology where solid polymer membranes using starch is used.

  14. Structure formation in inhomogeneous Early Dark Energy models

    SciTech Connect

    Batista, R.C.; Pace, F. E-mail: francesco.pace@port.ac.uk

    2013-06-01

    We study the impact of Early Dark Energy fluctuations in the linear and non-linear regimes of structure formation. In these models the energy density of dark energy is non-negligible at high redshifts and the fluctuations in the dark energy component can have the same order of magnitude of dark matter fluctuations. Since two basic approximations usually taken in the standard scenario of quintessence models, that both dark energy density during the matter dominated period and dark energy fluctuations on small scales are negligible, are not valid in such models, we first study approximate analytical solutions for dark matter and dark energy perturbations in the linear regime. This study is helpful to find consistent initial conditions for the system of equations and to analytically understand the effects of Early Dark Energy and its fluctuations, which are also verified numerically. In the linear regime we compute the matter growth and variation of the gravitational potential associated with the Integrated Sachs-Wolf effect, showing that these observables present important modifications due to Early Dark Energy fluctuations, though making them more similar to the ΛCDM model. We also make use of the Spherical Collapse model to study the influence of Early Dark Energy fluctuations in the nonlinear regime of structure formation, especially on δ{sub c} parameter, and their contribution to the halo mass, which we show can be of the order of 10%. We finally compute how the number density of halos is modified in comparison to the ΛCDM model and address the problem of how to correct the mass function in order to take into account the contribution of clustered dark energy. We conclude that the inhomogeneous Early Dark Energy models are more similar to the ΛCDM model than its homogeneous counterparts.

  15. 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

  16. Cosmological Structure Formation Shocks and Cosmic Rays in Hydrodynamical Simulations

    NASA Astrophysics Data System (ADS)

    Pfrommer, C.; Springel, V.; Enβlin, T. A.; Jubelgas, M.

    Cosmological shock waves during structure formation not only play a decisive role for the thermalization of gas in virializing structures but also for the acceleration of relativistic cosmic rays (CRs) through diffusive shock acceleration. We discuss a novel numerical treatment of the physics of cosmic rays in combination with a formalism for identifying and measuring the shock strength on-the-fly during a smoothed particle hydrodynamics simulation. In our methodology, the non-thermal CR population is treated self-consistently in order to assess its dynamical impact on the thermal gas as well as other implications on cosmological observables. Using this formalism, we study the history of the thermalization process in high-resolution hydrodynamic simulations of the Lambda cold dark matter model. Collapsed cosmological structures are surrounded by shocks with high Mach numbers up to 1000, but they play only a minor role in the energy balance of thermalization. However, this finding has important consequences for our understanding of the spatial distribution of CRs in the large-scale structure. In high resolution simulations of galaxy clusters, we find a low contribution of the averaged CR pressure, due to the small acceleration efficiency of lower Mach numbers of flow shocks inside halos and the softer adiabatic index of CRs. These effects disfavour CRs when a composite of thermal gas and CRs is adiabatically compressed. However, within cool core regions, the CR pressure reaches equipartition with the thermal pressure leading, to a lower effective adiabatic index and thus to an enhanced compressibility of the central intracluster medium. This effect increases the central density and pressure of the cluster, and thus the resulting X-ray emission and the central Sunyaev-Zel'dovich flux decrement. The integrated Sunyaev-Zel'dovich effect, however, is only slightly changed.

  17. Structure Formation through Magnetohydrodynamical Instabilities in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Noguchi, K.; Tajima, T.; Horton, W.

    2000-12-01

    The shear flow instabilities under the presence of magnetic fields in the protoplanetary disk can greatly facilitate the formation of density structures that serve as seeds prior to the onset of the gravitational Jeans instability. Such a seeding process may explain several outstanding puzzles in the planetary genesis that are further compounded by the new discoveries of extrasolar planets and a new insight into the equation of state of dense matter. This puzzle also includes the apparent narrow window of the age difference of the Sun and the Earth. We evaluate the effects of the Parker, magnetorotational(Balbus-Hawley), and kinematic dynamo instabilities by comparing the properties of these instabilities. We calculate the mass spectra of aggregated density structures by the above mechanism in the radial direction for an axisymmetric magnetohydrodynamic(MHD) torus equiblium and power-law density profile models. The mass spectrum of the magnetorotational instability may describe the origin of giant planets away from the central star such as Jupiter. Our local three-dimentional MHD simulation indicates that the coupling of the Parker and magnetorotational instabilities creates spiral arms and gas blobs in the accretion disk, reinforcing the theory and model.

  18. Linear and nonlinear effects in detonation wave structure formation

    NASA Astrophysics Data System (ADS)

    Borisov, S. P.; Kudryavtsev, A. N.

    2016-06-01

    The role of linear and nonlinear effects in the process of formation of detonation wave structure is investigated using linear stability analysis and direct numerical simulation. A simple model with a one-step irreversible chemical reaction is considered. For linear stability computations, both the local iterative shooting procedure and the global Chebyshev pseudospectral method are employed. Numerical simulations of 1D pulsating instability are performed using a shock fitting approach based on a 5th order upwind-biased compact-difference discretization and a shock acceleration equation deduced from the Rankine-Hugoniot conditions. A shock capturing WENO scheme of the 5th order is used to simulate propagation of detonation wave in a plane channel. It is shown that the linear analysis predicts correctly the mode dominating on early stages of flow evolution and the size of detonation cells which emerge during these stages. Later, however, when a developed self-reproducing cellular structure forms, the cell size is approximately doubled due to nonlinear effects.

  19. CdTe film structure formation in layerwise component sorption

    SciTech Connect

    Murashev, S.V.; Denisova, A.T.; Ezhovskii, Yu.K.

    1988-04-10

    Aleskovskii's insular hypothesis has been used in a new approach to film synthesis, where irreversible reactions occur at surfaces on sequential component treatment, where the components contain the compound units. One can synthesize a film of a strictly defined composition on the basis of the critical condensation temperatures T/sub A/ and T/sub B/ together with the compound decomposition temperature T/sub AB/, i.e., it is necessary to have T/sub A/, T/sub B/ < T/sub s/ < T/sub AB/, where T/sub s/ is substrate temperature. The authors used AGChT-23-17 single-crystal gallium arsenide substrates having (100) orientation. Films up to 15 nm thick were measured by ellipsometry, while thicker films were assessed with an interferometer. The cadmium telluride films were made by alternating treatment in cadmium and tellurium beams made by evaporation from Knudsen cells. The lower limit to monolayer growth is set by the onset of tellurium condensation, and the upper by the transition from irreversible chemisorption to reversible. The growth constant and the diffraction data indicate the mode of film formation, the growth direction, and the relationship to the structure, which is related to the temperature. Films with the best structure are made at substrate temperatures of 498-535 K.

  20. Turbulence driven by structure formation in the circumgalactic medium

    NASA Astrophysics Data System (ADS)

    Iapichino, L.; Viel, M.; Borgani, S.

    2013-07-01

    The injection of turbulence in the circumgalactic medium at redshift z = 2 is investigated using the mesh-based hydrodynamic code ENZO and a sub-grid-scale (SGS) model for unresolved turbulence. Radiative cooling and heating by a uniform Ultraviolet (UV) background are included in our runs and compared with the effect of turbulence modelling. Mechanisms of gas exchange between galaxies and the surrounding medium, as well as metal enrichment, are not taken into account, and turbulence is here driven solely by structure formation (mergers and shocks). We find that turbulence, both at resolved and SGS scales, impacts mostly the warm-hot intergalactic medium (WHIM), with temperature between 105 and 107 K, mainly located around collapsed and shock-heated structures, and in filaments. Typical values of the ratio of turbulent to thermal pressure is 0.1 in the WHIM, corresponding to a volume-weighted average of the SGS turbulent to thermal Doppler broadening bt/btherm = 0.26, on length scales below the grid resolution of 25 kpc h- 1. In the diffuse intergalactic medium, defined in a range of baryon overdensity δ between 1 and 50, the importance of turbulence is smaller, but grows as a function of gas density, and the Doppler broadening ratio is fitted by the function bt/btherm = 0.023 × δ0.58.

  1. FORMATION AND STRUCTURE OF LOW-DENSITY EXO-NEPTUNES

    SciTech Connect

    Rogers, Leslie A.; Seager, Sara; Bodenheimer, Peter

    2011-09-01

    Kepler has found hundreds of Neptune-size (2-6 R{sub +}) planet candidates within 0.5 AU of their stars. The nature of the vast majority of these planets is not known because their masses have not been measured. Using theoretical models of planet formation, evolution, and structure, we explore the range of minimum plausible masses for low-density exo-Neptunes. We focus on highly irradiated planets with T{sub eq} {>=} 500 K. We consider two separate formation pathways for low-mass planets with voluminous atmospheres of light gases: core-nucleated accretion and outgassing of hydrogen from dissociated ices. We show that Neptune-size planets at T{sub eq} = 500 K with masses as small as a few times that of Earth can plausibly be formed by core-nucleated accretion coupled with subsequent inward migration. We also derive a limiting low-density mass-radius relation for rocky planets with outgassed hydrogen envelopes but no surface water. Rocky planets with outgassed hydrogen envelopes typically have computed radii well below 3 R{sub +}. For both planets with H/He envelopes from core-nucleated accretion and planets with outgassed hydrogen envelopes, we employ planet interior models to map the range of planet mass-envelope mass-equilibrium temperature parameter space that is consistent with Neptune-size planet radii. Atmospheric mass loss mediates which corners of this parameter space are populated by actual planets and ultimately governs the minimum plausible mass at a specified transit radius. We find that Kepler's 2-6 R{sub +} planet candidates at T{sub eq} = 500-1000 K could potentially have masses {approx}< 4 M{sub +}. Although our quantitative results depend on several assumptions, our qualitative finding that warm Neptune-size planets can have masses substantially smaller than those given by interpolating the masses and radii of planets within our Solar System is robust.

  2. Formation and Internal Structure of Terrestrial Planets, and Atmospheric Escape

    NASA Astrophysics Data System (ADS)

    Jin, S.

    2014-11-01

    As of 2014 April 21, over 1490 confirmed exoplanets and 3705 Kepler candidates have been detected. This implies that exoplanets may be ubiquitous in the universe. In this paper, we focus on the formation, evolution, and internal structure of terrestrial planets, and the atmospheric escape of close-in planets. In chapter 2, we investigate the dynamical evolution of planetary system after the protoplanetary disk has dissipated. We find that in the final assembly stage, the occurrence of terrestrial planets is quite common and in 40% of our simulations finally at least one planet is formed in the habitable zone. We also find that if there is a highly-inclined giant planet in the system, a great many bodies will be either driven out of the system, or collide with the giant planet or the central star. This will lead to the difficulty in planetary accretion. Moreover, our results show that planetary migration can lead to the formation of close-in planets. Besides migration, close-in terrestrial planets can also be formed by a collision-merger mechanism, which means that planetary embryos can kick terrestrial planets directly into orbits that are extremely close to their parent stars. In chapter 3, we construct numerically an internal structure model for terrestrial planets, and provide three kinds of possible internal structures of Europa (Jupiter's moon) based on this model. Then, we calculate the radii of low-mass exoplanets for various mass combinations of core and mantle, and find that some of them are inconsistent with the observed radius of rocky planets. This phenomenon can be explained only if there exists a large amount of water in the core, or they own gaseous envelopes. In chapter 4, we improve our planetary evolution codes using the semi-gray model of Guillot (2010), which includes the incident flux from the host star as a heating source in planetary atmosphere. The updated codes can solve the structure of the top radiative zone of intensely irradiated

  3. Plasma Suppression of Large Scale Structure Formation in the Universe

    SciTech Connect

    Chen, Pisin; Lai, Kwang-Chang

    2007-12-10

    We point out that during the reionization epoch of the cosmic history, the plasma collective effect among the ordinary matter would suppress the large scale structure formation. The imperfect Debye shielding at finite temperature would induce a residual long-range electrostatic potential which, working together with the baryon thermal pressure, would counter the gravitational collapse. As a result the effective Jean's length, {tilde {lambda}}{sub J}, is increased by a factor, {tilde {lambda}}{sub J}/{lambda}{sub J} = {radical}8/5, relative to the conventional one. For scales smaller than the effective Jean's scale the plasma would oscillate at the ion-acoustic frequency. The modes that would be influenced by this effect depend on the starting time and the initial temperature of reionization, but roughly lie in the range 0.5hMpc{sup -1} < k, which corresponds to the region of the Lyman-{alpha} forest from the inter-galactic medium. We predict that in the linear regime of density-contrast growth, the plasma suppression of the matter power spectrum would approach 1 - ({Omega}{sub dm}/{Omega}{sub m}){sup 2} {approx} 1 -(5/6){sup 2} {approx} 30%.

  4. Using Black Hole Mergers to Explore Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2009-01-01

    Observations of gravitational waves from massive black hole mergers will open a new window into the era of structure formation in the early universe. Past efforts have concentrated on calculating merger rates using different physical assumptions, resulting in merger rate estimates that span a wide range (0.1 - 10(exp 4) mergers/year). We develop a semi-analytical, phenomenological model of massive black hole mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 epoch. Our approach involves generating synthetic LISA observable data (total BH masses, BH mass ratios, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo method, thus finding constraints for the physical parameters of the mergers. We find that our method works well at estimating merger parameters and that the number of merger events is a key discriminant among models, therefore making our method robust against observational uncertainties. Our approach can also be extended to more physically-driven models and more general problems in cosmology. This work is supported in part by the Cooperative Education Program at NASA/GSFC.

  5. Using Black Hole Mergers to Explore Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2008-01-01

    Observations of gravitational waves from massive black hole mergers will open a new window into the era of structure formation in the early universe. Past efforts have concentrated on calculating merger rates using different physical assumptions, resulting in merger rate estimates that span a wide range (0.1 - 1 0A4 mergers/year). We develop a semi-analytical, phenomenological model of massive black hole mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z approx. 5 - 30 epoch. Our approach involves generating synthetic LISA observable data (total BH masses, BH mass ratios, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo method, thus finding constraints for the physical parameters of the mergers. We find that our method works well at estimating merger parameters and that the number of merger events is a key discriminant among models, therefore making our method robust against observational uncertainties. Our approach can also be extended to more physically-driven models and more general problems in cosmology.

  6. Renormalizing a viscous fluid model for large scale structure formation

    NASA Astrophysics Data System (ADS)

    Führer, Florian; Rigopoulos, Gerasimos

    2016-02-01

    Using the Stochastic Adhesion Model (SAM) as a simple toy model for cosmic structure formation, we study renormalization and the removal of the cutoff dependence from loop integrals in perturbative calculations. SAM shares the same symmetry with the full system of continuity+Euler equations and includes a viscosity term and a stochastic noise term, similar to the effective theories recently put forward to model CDM clustering. We show in this context that if the viscosity and noise terms are treated as perturbative corrections to the standard eulerian perturbation theory, they are necessarily non-local in time. To ensure Galilean Invariance higher order vertices related to the viscosity and the noise must then be added and we explicitly show at one-loop that these terms act as counter terms for vertex diagrams. The Ward Identities ensure that the non-local-in-time theory can be renormalized consistently. Another possibility is to include the viscosity in the linear propagator, resulting in exponential damping at high wavenumber. The resulting local-in-time theory is then renormalizable to one loop, requiring less free parameters for its renormalization.

  7. Generation of Hierarchically Ordered Structures on a Polymer Film by Electrohydrodynamic Structure Formation.

    PubMed

    Tian, Hongmiao; Shao, Jinyou; Hu, Hong; Wang, Li; Ding, Yucheng

    2016-06-29

    The extensive applications of hierarchical structures in optoelectronics, micro/nanofluidics, energy conservation, etc., have led to the development of a variety of approaches for their fabrication, which can be categorized as bottom-up or top-down strategies. Current bottom-up and top-down strategies bear a complementary relationship to each other due to their processing characteristics, i.e., the advantages of one method correspond to the disadvantages of the other, and vice versa. Here we propose a novel method based on electrohydrodynamic structure formation, aimed at combining the main advantages of the two strategies. The method allows the fabrication of a hierarchically ordered structure with well-defined geometry and high mechanical durability on a polymer film, through a simple and low-cost process also suitable for mass-production. In this approach, upon application of an electric field between a template and a substrate sandwiching an air gap and a polymer film, the polymer is pulled toward the template and further flows into the template cavities, resulting in a hierarchical structure with primary and secondary patterns determined by electrohydrodynamic instability and by the template features, respectively. In this work, the fabrication of a hierarchical structure by electrohydrodynamic structure formation is studied using numerical simulations and experimental tests. The proposed method is then employed for the one-step fabrication of a hierarchical structure exhibiting a gradual transition in the periodicity of the primary structure using a slant template and a flat polymer film, which presents an excellent performance on controllable wettability.

  8. Generation of Hierarchically Ordered Structures on a Polymer Film by Electrohydrodynamic Structure Formation.

    PubMed

    Tian, Hongmiao; Shao, Jinyou; Hu, Hong; Wang, Li; Ding, Yucheng

    2016-06-29

    The extensive applications of hierarchical structures in optoelectronics, micro/nanofluidics, energy conservation, etc., have led to the development of a variety of approaches for their fabrication, which can be categorized as bottom-up or top-down strategies. Current bottom-up and top-down strategies bear a complementary relationship to each other due to their processing characteristics, i.e., the advantages of one method correspond to the disadvantages of the other, and vice versa. Here we propose a novel method based on electrohydrodynamic structure formation, aimed at combining the main advantages of the two strategies. The method allows the fabrication of a hierarchically ordered structure with well-defined geometry and high mechanical durability on a polymer film, through a simple and low-cost process also suitable for mass-production. In this approach, upon application of an electric field between a template and a substrate sandwiching an air gap and a polymer film, the polymer is pulled toward the template and further flows into the template cavities, resulting in a hierarchical structure with primary and secondary patterns determined by electrohydrodynamic instability and by the template features, respectively. In this work, the fabrication of a hierarchical structure by electrohydrodynamic structure formation is studied using numerical simulations and experimental tests. The proposed method is then employed for the one-step fabrication of a hierarchical structure exhibiting a gradual transition in the periodicity of the primary structure using a slant template and a flat polymer film, which presents an excellent performance on controllable wettability. PMID:27268135

  9. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    NASA Astrophysics Data System (ADS)

    Filippova, E. V.; Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-01

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD+). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD+-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 Å resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  10. Crystal structures of complexes of NAD{sup +}-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    SciTech Connect

    Filippova, E. V. Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-15

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI{sub 2} with the coupled reduction of nicotinamide adenine dinucleotide (NAD{sup +}). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD{sup +}-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  11. Structure and Soot Formation Properties of Laminar Flames

    NASA Technical Reports Server (NTRS)

    El-Leathy, A. M.; Xu, F.; Faeth, G. M.

    2001-01-01

    Soot formation within hydrocarbon-fueled flames is an important unresolved problem of combustion science for several reasons: soot emissions are responsible for more deaths than any other combustion-generated pollutant, thermal loads due to continuum radiation from soot limit the durability of combustors, thermal radiation from soot is mainly responsible for the growth and spread of unwanted fires, carbon monoxide emissions associated with soot emissions are responsible for most fire deaths, and limited understanding of soot processes in flames is a major impediment to the development of computational combustion. Motivated by these observations, soot processes within laminar premixed and nonpremixed (diffusion) flames are being studied during this investigation. The study is limited to laminar flames due to their experimental and computational tractability, noting the relevance of these results to practical flames through laminar flamelet concepts. Nonbuoyant flames are emphasized because buoyancy affects soot processes in laminar diffusion flames whereas effects of buoyancy are small for most practical flames. This study involves both ground- and space-based experiments, however, the following discussion will be limited to ground-based experiments because no space-based experiments were carried out during the report period. The objective of this work was to complete measurements in both premixed and nonpremixed flames in order to gain a better understanding of the structure of the soot-containing region and processes of soot nucleation and surface growth in these environments, with the latter information to be used to develop reliable ways of predicting soot properties in practical flames. The present discussion is brief, more details about the portions of the investigation considered here can be found in refs. 8-13.

  12. Hikurangi Plateau: Crustal structure, rifted formation, and Gondwana subduction history

    NASA Astrophysics Data System (ADS)

    Davy, Bryan; Hoernle, Kaj; Werner, Reinhard

    2008-07-01

    Seismic reflection profiles across the Hikurangi Plateau Large Igneous Province and adjacent margins reveal the faulted volcanic basement and overlying Mesozoic-Cenozoic sedimentary units as well as the structure of the paleoconvergent Gondwana margin at the southern plateau limit. The Hikurangi Plateau crust can be traced 50-100 km southward beneath the Chatham Rise where subduction cessation timing and geometry are interpreted to be variable along the margin. A model fit of the Hikurangi Plateau back against the Manihiki Plateau aligns the Manihiki Scarp with the eastern margin of the Rekohu Embayment. Extensional and rotated block faults which formed during the breakup of the combined Manihiki-Hikurangi plateau are interpreted in seismic sections of the Hikurangi Plateau basement. Guyots and ridge-like seamounts which are widely scattered across the Hikurangi Plateau are interpreted to have formed at 99-89 Ma immediately following Hikurangi Plateau jamming of the Gondwana convergent margin at ˜100 Ma. Volcanism from this period cannot be separately resolved in the seismic reflection data from basement volcanism; hence seamount formation during Manihiki-Hikurangi Plateau emplacement and breakup (125-120 Ma) cannot be ruled out. Seismic reflection data and gravity modeling suggest the 20-Ma-old Hikurangi Plateau choked the Cretaceous Gondwana convergent margin within 5 Ma of entry. Subsequent uplift of the Chatham Rise and slab detachment has led to the deposition of a Mesozoic sedimentary unit that thins from ˜1 km thickness northward across the plateau. The contrast with the present Hikurangi Plateau subduction beneath North Island, New Zealand, suggests a possible buoyancy cutoff range for LIP subduction consistent with earlier modeling.

  13. Merger histories in warm dark matter structure formation scenarios

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Devriendt, Julien E. G.; Mahmood, Asim; Silk, Joseph

    2002-02-01

    Observations on galactic scales seem to be in contradiction with recent high-resolution N-body simulations. This so-called cold dark matter (CDM) crisis has been addressed in several ways, ranging from a change in fundamental physics by introducing self-interacting cold dark matter particles to a tuning of complex astrophysical processes such as global and/or local feedback. All these efforts attempt to soften density profiles and reduce the abundance of satellites in simulated galaxy haloes. In this paper, we explore a different approach that consists of filtering the dark matter power spectrum on small scales, thereby altering the formation history of low-mass objects. The physical motivation for damping these fluctuations lies in the possibility that the dark matter particles have a different nature, i.e. are warm (WDM) rather than cold. We show that this leads to some interesting new results in terms of the merger history and large-scale distribution of low-mass haloes, compared with the standard CDM scenario. However, WDM does not appear to be the ultimate solution, in the sense that it is not able to fully solve the CDM crisis, even though one of the main drawbacks, namely the abundance of satellites, can be remedied. Indeed, the cuspiness of the halo profiles still persists, at all redshifts, and for all haloes and sub-haloes that we investigated. Despite the persistence of the cuspiness problem of DM haloes, WDM seems to be still worth taking seriously, as it alleviates the problems of over-abundant sub-structures in galactic haloes and possibly the lack of angular momentum of simulated disc galaxies. WDM also lessens the need to invoke strong feedback to solve these problems, and may provide a natural explanation of the clustering properties and ages of dwarfs.

  14. Topics in cosmology: Structure formation, dark energy and recombination

    NASA Astrophysics Data System (ADS)

    Alizadeh, Esfandiar

    The field of theoretical cosmology consists of numerous, inter-related branches, whose ambitious goal is to uncover the history of the universe from its beginning to its future. Achieving this, no doubt, requires a deep understanding of many areas of physics. In this thesis I touch upon a few of these areas in which I worked during my PhD studies. Chapter (2) describes our work in finding the accretion and merger history of dark matter halos. Dark matter halos are the collapsed dark matter structures in the late time evolution of the universe, whose existence is vital for the formation of galaxies in the Universe as they act as the potential wells where normal matter (collectively called Baryons) can accumulate, cool, and form stars. It is then no surprise that the properties of galaxies depends on the properties of the dark matter halo in which it resides, including its merger history, i.e. the number of times it merged with other halos. Even though these merger rates can be calculated theoretically for infinitesimal time steps, in order to find the merger history over an extended period of time one had to use either Monte-Carlo simulations to build up the total rates of merging and accreting from the infinitesimal rates or use N-body simulations. In chapter (2) we show how we used random walk formalism to write down an analytical (integral) equation for the merger history of halos. We have solved this equation numerically and find very good agreement with Monte-Carlo simulations. This work can be used in theories of galaxy formation and evolution. We then switch from the overdense regions of the Universe, halos, to the underdense ones, voids. These structures have not attracted as much attention from cosmologists as their overdense counterparts in probing the cosmological models. We show here that the shapes of voids as a probe can be of use for future surveys to pin down the equation of state of the dark energy, i.e. the ratio of its pressure to its energy

  15. Flexible Virtual Structure Consideration in Dynamic Modeling of Mobile Robots Formation

    NASA Astrophysics Data System (ADS)

    El Kamel, A. Essghaier; Beji, L.; Lerbet, J.; Abichou, A.

    2009-03-01

    In cooperative mobile robotics, we look for formation keeping and maintenance of a geometric configuration during movement. As a solution to these problems, the concept of a virtual structure is considered. Based on this idea, we have developed an efficient flexible virtual structure, describing the dynamic model of n vehicles in formation and where the whole formation is kept dependant. Notes that, for 2D and 3D space navigation, only a rigid virtual structure was proposed in the literature. Further, the problem was limited to a kinematic behavior of the structure. Hence, the flexible virtual structure in dynamic modeling of mobile robots formation presented in this paper, gives more capabilities to the formation to avoid obstacles in hostile environment while keeping formation and avoiding inter-agent collision.

  16. Star Formation Histories of Dwarf Galaxies: Keys to Galaxy Formation and Dark Matter Structure

    NASA Astrophysics Data System (ADS)

    Boylan-Kolchin, Michael

    2014-10-01

    We propose to perform a suite of hydrodynamical simulations in order to understand the connection between dwarf galaxy star formation histories, stellar content, and central dark matter densities. This will leverage one of HST's unique and enduring scientific contributions, deep and uniform photometry of nearby dwarf galaxies that enables reconstructions of their ancient {z 6-10} star formation histories, to shed light on some of the main problems in galaxy formation and cosmology.Analysis of HST observations has definitively shown that dwarfs exhibit a surprising variety of star formation histories: some dwarfs host nearly purely ancient populations, while others have formed 90% of their stars after redshift 1. This diversity is unexpected in current theoretical models, which predict primarily old stellar populations in low-mass objects. The topic of star formation histories of dwarfs has also received significant attention recently in the context of possible small-scale problems of the LCDM model: if episodic bursts of star formation inject energy into dwarfs' dark matter halos, it may provide a natural explanation of the observed low densities of dwarf galaxies within LCDM.Our simulations will adopt physically-motivated, explicit feedback prescriptions that are fixed by our knowledge of stellar evolution. We will choose halos having diverse mass assembly histories within a narrow range of mass and compare their star formation histories to HST observations of nearby isolated dwarf galaxies, thereby testing fundamental aspects of galaxy formation modeling and dark matter astrophysics. Data from our simulations will be publicly released via a dedicated website.

  17. Chirality as a physical aspect of structure formation in biological macromolecular systems

    NASA Astrophysics Data System (ADS)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  18. Dissipative structure formation in lipid/lipopolymer monolayers.

    PubMed

    Seitz, Peter C; Reif, Michael; Yoshikawa, Kenichi; Jordan, Rainer; Tanaka, Motomu

    2011-03-17

    We study the formation of dissipative microstructures in monomolecular films of surfactant mixtures, which occur near the three-phase contact line during Langmuir-Blodgett transfer onto a solid substrate. Continuous stripes parallel to the transfer direction are generated over several centimeters, indicating the phase separation of phospholipids and lipids with polymer head groups (lipopolymers). The systematic variation of transfer conditions revealed that transfer speed and subphase viscosity determine the stripe-to-stripe distance from several micrometers to submicrometers. To account for the physical mechanism of such pattern formation, we characterize the local film thickness and the membrane composition in the vicinity of the three-phase contact line using imaging ellipsometry and fluorescence microscopy. At relatively slow rates of substrate lifting, the power law exponent that we found between the interstripe distance and the transfer speed suggests that the stripe formation is due to spinodal decomposition, which can be accounted under the framework of the Cahn-Hilliard equation, whereas at relatively high rates, the distance is found to be proportional to the substrate speed, suggesting a dominant effect of the shear force on the stripe formation.

  19. Competition and Diversity among Radio Formats: Legal and Structural Issues.

    ERIC Educational Resources Information Center

    Glasser, Theodore L.

    That competition in broadcasting may not bring about sufficiently heterogeneous programing has long been the subject of debate among policymakers, and nowhere has that debate been more acrimonious than in its application to the diversification of radio formats. While the Federal Communications Commission (FCC) prefers to leave questions of…

  20. Dissipative structure formation in lipid/lipopolymer monolayers.

    PubMed

    Seitz, Peter C; Reif, Michael; Yoshikawa, Kenichi; Jordan, Rainer; Tanaka, Motomu

    2011-03-17

    We study the formation of dissipative microstructures in monomolecular films of surfactant mixtures, which occur near the three-phase contact line during Langmuir-Blodgett transfer onto a solid substrate. Continuous stripes parallel to the transfer direction are generated over several centimeters, indicating the phase separation of phospholipids and lipids with polymer head groups (lipopolymers). The systematic variation of transfer conditions revealed that transfer speed and subphase viscosity determine the stripe-to-stripe distance from several micrometers to submicrometers. To account for the physical mechanism of such pattern formation, we characterize the local film thickness and the membrane composition in the vicinity of the three-phase contact line using imaging ellipsometry and fluorescence microscopy. At relatively slow rates of substrate lifting, the power law exponent that we found between the interstripe distance and the transfer speed suggests that the stripe formation is due to spinodal decomposition, which can be accounted under the framework of the Cahn-Hilliard equation, whereas at relatively high rates, the distance is found to be proportional to the substrate speed, suggesting a dominant effect of the shear force on the stripe formation. PMID:21338143

  1. Formation, structure, and orientation of gold silicide on gold surfaces

    NASA Technical Reports Server (NTRS)

    Green, A. K.; Bauer, E.

    1976-01-01

    The formation of gold silicide on Au films evaporated onto Si(111) surfaces is studied by Auger electron spectroscopy (AES) and low-energy electron diffraction (LEED). Surface condition, film thickness, deposition temperature, annealing temperature, and heating rate during annealing are varied. Several oriented crystalline silicide layers are observed.

  2. Formation of copper porous structures under near-equilibrium chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Kornyushchenko, A. S.; Natalich, V. V.; Perekrestov, V. I.

    2016-05-01

    The mechanism of copper structure formation under near-equilibrium conditions in a chemically-active medium-condensate system has been investigated. The desired conditions have been implemented using CVD system. Copper chloride CuCl2 was used as a source material, and mixture of hydrogen with nitrogen served as a working gas. The influence of the evaporation temperature, condensation temperature and state of the growth surface on the porous structures formation has been investigated. It has been established, that the structure formation mechanism is determined by layer-by-layer or normal crystal growth, nucleation and growth of whiskers, and also by partial intergrowth of structural elements.

  3. Laser-induced structure formation on stretched polymer foils

    SciTech Connect

    Bityurin, Nikita; Arnold, Nikita; Baeuerle, Dieter; Arenholz, Enno

    2007-04-15

    Noncoherent structures that develop during UV laser ablation of stretched semicrystalline polymer foils are a very general phenomenon. A thermodynamic model based on stress relaxation within the modified layer of the polymer surface describes the main features of the observed phenomena, and, in particular, the dependence of the period of structures on laser wavelength, fluence, and number of laser pulses.

  4. BOOK REVIEW: Transport and Structural Formation in Plasmas

    NASA Astrophysics Data System (ADS)

    Thyagaraja, A.

    1999-06-01

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

  5. Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

    PubMed Central

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-01-01

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. PMID:22303014

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

    PubMed

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

    2016-12-01

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

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

    PubMed

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

    2016-12-01

    Engineering materials with nanocrystalline structure could be exploited under simultaneous action of mechanical loading and corrosion environments; therefore, their corrosion resistance is important. Surface nanocrystalline structure was generated on middle carbon steels by severe plastic deformation using the method of mechanical pulse friction treatment. This treatment additionally includes high temperature phase transformation and alloying. Using a complex of the corrosive, electrochemical and physical investigations, it was established that nanocrystalline structures can be characterized by lower or increased corrosion resistance in comparison with the reference material. It is caused by the action of two confronting factors: arising energy level and anticorrosive alloying of the surface layer. PMID:26831689

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  9. Energy minimization for self-organized structure formation and actuation

    NASA Astrophysics Data System (ADS)

    Kofod, Guggi; Wirges, Werner; Paajanen, Mika; Bauer, Siegfried

    2007-02-01

    An approach for creating complex structures with embedded actuation in planar manufacturing steps is presented. Self-organization and energy minimization are central to this approach, illustrated with a model based on minimization of the hyperelastic free energy strain function of a stretched elastomer and the bending elastic energy of a plastic frame. A tulip-shaped gripper structure illustrates the technological potential of the approach. Advantages are simplicity of manufacture, complexity of final structures, and the ease with which any electroactive material can be exploited as means of actuation.

  10. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

    PubMed

    Bose, Tungadri; Dutta, Anirban; Mh, Mohammed; Gandhi, Hemang; Mande, Sharmila S

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  11. Regulatory effects of cotranscriptional RNA structure formation and transitions.

    PubMed

    Liu, Sheng-Rui; Hu, Chun-Gen; Zhang, Jin-Zhi

    2016-09-01

    RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website. PMID:27028291

  12. STRUCTURE AND FORMATION OF ELLIPTICAL AND SPHEROIDAL GALAXIES

    SciTech Connect

    Kormendy, John; Fisher, David B.; Cornell, Mark E.; Bender, Ralf E-mail: dbfisher@astro.as.utexas.edu E-mail: bender@usm.uni-muenchen.de

    2009-05-15

    New surface photometry of all known elliptical galaxies in the Virgo cluster is combined with published data to derive composite profiles of brightness, ellipticity, position angle, isophote shape, and color over large radius ranges. These provide enough leverage to show that Sersic log I {proportional_to} r {sup 1/n} functions fit the brightness profiles I(r) of nearly all ellipticals remarkably well over large dynamic ranges. Therefore, we can confidently identify departures from these profiles that are diagnostic of galaxy formation. Two kinds of departures are seen at small radii. All 10 of our ellipticals with total absolute magnitudes M{sub VT} {<=} -21.66 have cuspy cores-'missing light'-at small radii. Cores are well known and naturally scoured by binary black holes (BHs) formed in dissipationless ('dry') mergers. All 17 ellipticals with -21.54 {<=} M{sub VT} {<=} -15.53 do not have cores. We find a new distinct component in these galaxies: all coreless ellipticals in our sample have extra light at the center above the inward extrapolation of the outer Sersic profile. In large ellipticals, the excess light is spatially resolved and resembles the central components predicted in numerical simulations of mergers of galaxies that contain gas. In the simulations, the gas dissipates, falls toward the center, undergoes a starburst, and builds a compact stellar component that, as in our observations, is distinct from the Sersic-function main body of the elliptical. But ellipticals with extra light also contain supermassive BHs. We suggest that the starburst has swamped core scouring by binary BHs. That is, we interpret extra light components as a signature of formation in dissipative ('wet') mergers. Besides extra light, we find three new aspects to the ('E-E') dichotomy into two types of elliptical galaxies. Core galaxies are known to be slowly rotating, to have relatively anisotropic velocity distributions, and to have boxy isophotes. We show that they have

  13. Lipid Microdomains: Structural Correlations, Fluctuations, and Formation Mechanisms

    NASA Astrophysics Data System (ADS)

    Fan, Jun; Sammalkorpi, Maria; Haataja, Mikko

    2010-03-01

    Compositional lipid microdomains (“lipid rafts”) in mammalian plasma membranes are believed to facilitate many important cellular processes. While several physically distinct scenarios predicting the presence of finite-sized microdomains in vivo have been proposed in the past, direct experimental verification or falsification of model predictions has remained elusive. Herein, we demonstrate that the combination of the spatial correlation and temporal fluctuation spectra of the lipid domains can be employed to unambiguously differentiate between the existing theoretical scenarios. Furthermore, the differentiation of the raft formation mechanisms using this methodology can be achieved by collecting data at physiologically relevant conditions without the need to tune control parameters.

  14. Block-copolymer-induced structure formation in microemulsions

    SciTech Connect

    Hilfiker, R.; Eicke, H.F.; Steeb, C.; Hofmeier, U. )

    1991-02-07

    Transient electric birefringence measurements were performed on water/AOT (sodium bis(2-ethylhexyl) sulfosuccinate)/isooctane microemulsions with various amounts of block-copoly(oxyethylene/isoprene/oxyethylene) added. The authors could show that addition of the copolymer leads to a formation of nanodroplet (ND)-copolymer-aggregates. The contributions of NDs and aggregates to the induced birefringence could easily be separated because the NDs exhibited a negative and the aggregates a positive induced birefringence and because the time scales corresponding to the two processes were different.

  15. Note on structure formation from cosmic string wakes

    SciTech Connect

    Duplessis, Francis; Brandenberger, Robert E-mail: rhb@physics.mcgill.ca

    2013-04-01

    The search for cosmic strings has been of renewed interest with the advent of precision cosmology. In this note we give a quantitative description of the nonlinear matter density fluctuations that can form from a scaling network of cosmic string wakes. Specifically, we compute the distribution of dark matter halos. These halos would possess strong correlations in position space that should have survived until today. We also discuss the challenges involved in their detection due to their small size and the complex dynamics of their formation.

  16. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  17. Formation and structural characteristics of thermosensitive multiblock copolymer vesicles.

    PubMed

    Ma, Shiying; Xiao, Mengying; Wang, Rong

    2013-12-23

    The spontaneous vesicle formation of ABABA-type amphiphilic multiblock copolymers bearing thermosensitive hydrophilic A-block in a selective solvent is studied using dissipative particle dynamics (DPD) approach. The formation process of vesicle through nucleation and growth pathway is observed by varying the temperature. The simulation results show that spherical micelle takes shape at high temperature. As temperature decreases, vesicles with small aqueous cavity appear and the cavity expands as well as the membrane thickness decreases with the temperature further decreasing. This finding is in agreement with the experimental observation. Furthermore, by continuously varying the temperature and the length of the hydrophobic block, a phase diagram is constructed, which can indicate the thermodynamically stable region for vesicles. The morphological phase diagram shows that vesicles can form in a larger parameter scope. The relationship between the hydrophilic and hydrophobic block length versus the aqueous cavity size and vesicle size are revealed. Simulation results demonstrate that the copolymers with shorter hydrophobic blocks length or the higher hydrophilicity are more likely to form vesicles with larger aqueous cavity size and vesicle size as well as thinner wall thickness. However, the increase in A-block length results to form vesicles with smaller aqueous cavity size and larger vesicle size. PMID:24304193

  18. Processes of ordered structure formation in polypeptide thin film solutions.

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G.

    2010-06-17

    An experimental study is presented on the hierarchical assembly of {alpha}-helical block copolymers polystyrene-poly({gamma}-benzyl-L-glutamate) into anisotropic ordered structures. We transformed thin solid films into solutions through exposure to solvent vapor and studied the nucleation and growth of ordered three-dimensional structures in such solutions, with emphasis on the dependence of these processes on supersaturation with respect to the solubility limit. Interestingly, polymer solubility could be significantly influenced via variation of humidity in the surrounding gas phase. It is concluded that the interfacial tension between the ordered structures and the solution increased with humidity. The same effect was observed for other protic non-solvents in the surrounding gas phase and is attributed to a complexation of poly({gamma}-benzyl-L-glutamate) by protic non-solvent molecules (via hydrogen-bonding interactions). This change of polymer solubility was demonstrated to be reversible by addition or removal of small amounts of protic non-solvent in the surrounding gas phase. At a constant polymer concentration, ordered ellipsoidal structures could be dissolved by removing water or methanol present in the solution. Such structures formed once again when water or methanol was reintroduced via the vapor phase.

  19. Formation of micro/nano structures out of soap bubbles

    NASA Astrophysics Data System (ADS)

    Bai, Xiao-Dan; Liu, Jing

    2007-07-01

    We proposed to synthesize, etch and construct micro/nano structures through manipulating the large-scale bubbles composed of specific chemical compounds. The core of the method lies in the chemical reaction occurred at the interfaces between two or more soap bubbles. A unique virtue of the bubble is that it can have a rather large diameter however an extremely small membrane thickness, whose smallest size could reach nano scale. Therefore, the chemical reaction and synthesis occurred in the common interface of such contacting bubbles would lead to products with very small size. Several typical micro structures were fabricated to demonstrate the feasibility of the new method. Being flexible, easily controllable and environment friendly, the present concept may open a straightforward low-cost way for making micro/nano structures.

  20. Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

    PubMed Central

    Braun, Hans-Georg; Meyer, Evelyn

    2013-01-01

    The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm) result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

  1. How chemistry influences cloud structure, star formation, and the IMF

    NASA Astrophysics Data System (ADS)

    Hocuk, S.; Cazaux, S.; Spaans, M.; Caselli, P.

    2016-03-01

    In the earliest phases of star-forming clouds, stable molecular species, such as CO, are important coolants in the gas phase. Depletion of these molecules on dust surfaces affects the thermal balance of molecular clouds and with that their whole evolution. For the first time, we study the effect of grain surface chemistry (GSC) on star formation and its impact on the initial mass function (IMF). We follow a contracting translucent cloud in which we treat the gas-grain chemical interplay in detail, including the process of freeze-out. We perform 3D hydrodynamical simulations under three different conditions, a pure gas-phase model, a freeze-out model, and a complete chemistry model. The models display different thermal evolution during cloud collapse as also indicated in Hocuk, Cazaux & Spaans, but to a lesser degree because of a different dust temperature treatment, which is more accurate for cloud cores. The equation of state (EOS) of the gas becomes softer with CO freeze-out and the results show that at the onset of star formation, the cloud retains its evolution history such that the number of formed stars differ (by 7 per cent) between the three models. While the stellar mass distribution results in a different IMF when we consider pure freeze-out, with the complete treatment of the GSC, the divergence from a pure gas-phase model is minimal. We find that the impact of freeze-out is balanced by the non-thermal processes; chemical and photodesorption. We also find an average filament width of 0.12 pc (±0.03 pc), and speculate that this may be a result from the changes in the EOS caused by the gas-dust thermal coupling. We conclude that GSC plays a big role in the chemical composition of molecular clouds and that surface processes are needed to accurately interpret observations, however, that GSC does not have a significant impact as far as star formation and the IMF is concerned.

  2. Formation of the internal structure of solids under severe load.

    PubMed

    Metlov, Leonid S

    2010-05-01

    An alternative form of kinetic equations, involving the internal and free energies symmetrically, has been derived in the framework of the theory of vacancies. Dynamical nature of irreversible phenomena during formation and motion of defects (dislocations) has been analyzed by a computer experiment. Results of this simulation are then extended into a thermodynamic identity, involving the law of conservation of energy at interaction with an environment (the first law of thermodynamics) and the law of energy transformation in the internal degrees of freedom (relaxation). This identity is compared to the analogous Jarzynski identity. The approach is illustrated by simulation of processes during severe plastic deformation; the Rybin kinetic equation for this case has been derived.

  3. Turbulence and Vorticity in Galaxy Clusters Generated by Structure Formation

    NASA Astrophysics Data System (ADS)

    Vazza, F.; Jones, T. W.; Brüggen, M.; Brunetti, G.; Gheller, C.; Porter, D.; Ryu, D.

    2016-09-01

    Turbulence is a key ingredient for the evolution of the intracluster medium, whose properties can be predicted with high resolution numerical simulations. We present initial results on the generation of solenoidal and compressive turbulence in the intracluster medium during the formation of a small-size cluster using highly resolved, non-radiative cosmological simulations, with a refined monitoring in time. In this first of a series of papers, we closely look at one simulated cluster whose formation was distinguished by a merger around z ˜ 0.3. We separate laminar gas motions, turbulence and shocks with dedicated filtering strategies and distinguish the solenoidal and compressive components of the gas flows using Hodge-Helmholtz decomposition. Solenoidal turbulence dominates the dissipation of turbulent motions (˜95%) in the central cluster volume at all epochs. The dissipation via compressive modes is found to be more important (˜30% of the total) only at large radii (≥0.5~rvir) and close to merger events. We show that enstrophy (vorticity squared) is good proxy of solenoidal turbulence. All terms ruling the evolution of enstrophy (i.e. baroclinic, compressive, stretching and advective terms) are found to be significant, but in amounts that vary with time and location. Two important trends for the growth of enstrophy in our simulation are identified: first, enstrophy is continuously accreted into the cluster from the outside, and most of that accreted enstrophy is generated near the outer accretion shocks by baroclinic and compressive processes. Second, in the cluster interior vortex stretching is dominant, although the other terms also contribute substantially.

  4. Microstructure of polycrystalline PBTTT films: domain mapping and structure formation.

    PubMed

    Schuettfort, Torben; Watts, Benjamin; Thomsen, Lars; Lee, Mijung; Sirringhaus, Henning; McNeill, Christopher R

    2012-02-28

    We utilize near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and scanning transmission X-ray microscopy (STXM) to study the microstructure and domain structure of polycrystalline films of the semiconducting polymer poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). Total electron yield NEXAFS spectroscopy is used to examine the surface structure of the first 1-2 molecular layers, while bulk-sensitive STXM is used to produce maps of domain orientation and order sampled through the entire film thickness. We study different phases of PBTTT including as-cast, terraced and nanoribbon morphologies produced via spin-coating as well as aligned films of as-cast and nanoribbon morphologies produced by zone-casting. For the terraced morphology, domains are observed that are larger than the size of the terraced surface features, and the calculated degree of order is reduced compared to the nanoribbon morphology. For zone-cast films, we find that, although little optical anisotropy is observed in the bulk of as-cast films, a high degree of surface structural anisotropy is observed with NEXAFS spectroscopy, similar to what is observed in annealed nanoribbon films. This observation indicates that the aligned surface structure in unannealed zone-cast films templates the bulk ordering of the aligned nanoribbon phase. STXM domain mapping of aligned nanoribbon films reveals elongated, micrometer-wide domains with each domain misoriented with respect to its neighbor by up to 45°, but with broad domain boundaries. Within each nanoribbon domain, a high degree of X-ray dichroism is observed, indicating correlated ordering throughout the bulk of the film.

  5. Structural Insights into Clostridium perfringens Delta Toxin Pore Formation

    PubMed Central

    Huyet, Jessica; Naylor, Claire E.; Savva, Christos G.; Gibert, Maryse; Popoff, Michel R.; Basak, Ajit K.

    2013-01-01

    Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins. PMID:23805259

  6. Unconstrained Structure Formation in Coarse-Grained Protein Simulations

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan

    The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid

  7. Structure formation in a nonlocally modified gravity model

    SciTech Connect

    Park, Sohyun; Dodelson, Scott

    2013-01-01

    We study a nonlocally modified gravity model proposed by Deser and Woodard which gives an explanation for current cosmic acceleration. By deriving and solving the equations governing the evolution of the structure in the Universe, we show that this model predicts a pattern of growth that differs from standard general relativity (+dark energy) at the 10-30% level. These differences will be easily probed by the next generation of galaxy surveys, so the model should be tested shortly.

  8. Vortex ring structure at late stages of formation

    SciTech Connect

    Fabris, D.; Liepmann, D.

    1997-09-01

    High resolution DPIV measurements are made of a vortex ring formed by a piston/cylinder mechanism (Reynolds number 3700 and 7500). A complex ring structure is identified. The stopping condition of the piston leads to vortical fluid collecting near the forward stagnation point of the ring. In addition, the roll-up of the core produces a vorticity distribution that departs from a simple Gaussian profile. {copyright} {ital 1997 American Institute of Physics.}

  9. Investigation of hierarchical structure formation in ceramics with invar effect

    NASA Astrophysics Data System (ADS)

    Dedova, Elena S.; Shadrin, Vladimir S.; Shutilova, Ekaterina S.; Kulkov, Sergei N.

    2015-10-01

    The structure, phase composition and thermal properties of (Al2O3-20 wt % ZrO2)-ZrW2O8 ceramic composites obtained using nanosized, finely dispersed and coarse-grained initial powders were investigated. On the polished surface of composites homogeneously distributed white particles were observed. The chemical composition of the particles was determined. The phase composition of the composites was represented with corundum, monoclinic ZrO2 and two modifications of ZrW2O8 (tetragonal and cubic) regardless of initial powders morphology. Crystal structure parameters of the material obtained were determined. Linear thermal expansion coefficient values of the composites were determined and compared with those calculated using the mixture rule. The experimental data correlated well with the calculated values of CTE for Al2O3-20 wt % ZrO2 ceramics. The difference in thermal expansion values for composites obtained using initial components with different morphology may be attributed to phase transformations, features of hierarchical structures, internal stresses due to thermal expansion mismatch, which contribute significantly to thermal expansion of the ceramic composites.

  10. Terasaki Ramps in the Endoplasmic Reticulum: Structure, Function and Formation

    NASA Astrophysics Data System (ADS)

    Huber, Greg; Guven, Jemal; Valencia, Dulce-Maria

    2015-03-01

    The endoplasmic reticulum (ER) has long been considered an exceedingly important and complex cellular organelle in eukaryotes (like you). It is a membrane structure, part folded lamellae, part tubular network, that both envelopes the nucleus and threads its way outward, all the way to the cell's periphery. Despite the elegant mechanics of bilayer membranes offered by the work of Helfrich and Canham, as far as the ER is concerned, theory has mostly sat on the sidelines. However, refined imaging of the ER has recently revealed beautiful and subtle geometrical forms - simple geometries, from the mathematical point of view - which some have called a ``parking garage for ribosomes.'' I'll review the discovery and physics of Terasaki ramps and discuss their relation to cell-biological questions, such as ER and nuclear-membrane re-organization during mitosis. Rather than being a footnote in a textbook on differential geometry, these structures suggest answers to a number of the ER's structure-function problems.

  11. Dynamically-induced structures formation in congested magma

    NASA Astrophysics Data System (ADS)

    Petford, N.

    2008-12-01

    Crystal fabrics preserved in igneous rocks offer a glimpse into the magma emplacement process. Detailed field mapping, in combination with AMS studies, seem to provide the best available data for unravelling intrusion architecture on the decimetre scale. However, a full and proper understanding of the fluid dynamics of congested fluid-particle mixtures during shear remains elusive. This is a shame as without recourse to such fundamental understanding, the interpretation of structural field data in the context of magma flow remains problematic. One way to gain insight into the process is to treat flowing magma as a dynamic material with a rheology similar to sheared, congested slurries. The fancy that dense magma equates to a high temperature slurry is an attractive one, and opens up a way to examine the emplacement process that does not rely exclusively on equilibrium thermodynamics as a final explanation of commonly observed igneous structures. Instead, using examples from mafic rocks where cooling has been rapid, the idea is put forward that in high Peclet number suspensions (where particle diffusion is negligible), shearing and non- Newtonian behaviour imparts a rich diversity of structures including layering, grading and flow segregation. Key to understanding the rheology, hence flow dynamics of congested magma, is the particle microstructure, a still poorly known essence of suspension flows. Where magma transport is continental in scale and long lived (e.g. Large Igneous Provinces), rotation of the earth may in theory endow a small but potentially measurable imprint on the preserved flow fabric.

  12. Structural ensembles of the north belt of Venus deformations and possible mechanisms of their formation

    NASA Technical Reports Server (NTRS)

    Markov, M. S.

    1986-01-01

    The author discusses structural formations in the northern deformation belt of Venus, studied according to the data of the radar pictures obtained with the Venera 15 and 16 probes. He shows that it consists of regions of compression with submeridional orientation, regions of displacement, extending in the sublatitudinal direction and individual slightly deformed blocks. He puts forward the hypothesis that the formation of these structures is related with horizontal movements in the mantle in the sublatitudinal direction.

  13. Foreign body impact event damage formation in composite structures

    NASA Technical Reports Server (NTRS)

    Bucinell, Ronald B.

    1994-01-01

    This report discusses a methodology that can be used to assess the effect of foreign body impacts on composite structural integrity. The described effort focuses on modeling the effect of a central impact on a 5 3/4 inch filament wound test article. The discussion will commence with details of the material modeling that was used to establish the input properties for the analytical model. This discussion is followed by an overview of the impact assessment methodology. The progress on this effort to date is reviewed along with a discussion of tasks that have yet to be completed.

  14. Disentangling effects of nuclear structure in heavy element formation.

    PubMed

    Hinde, D J; Thomas, R G; du Rietz, R; Diaz-Torres, A; Dasgupta, M; Brown, M L; Evers, M; Gasques, L R; Rafiei, R; Rodriguez, M D

    2008-05-23

    Forming the same heavy compound nucleus with different isotopes of the projectile and target elements allows nuclear structure effects in the entrance channel (resulting in static deformation) and in the dinuclear system to be disentangled. Using three isotopes of Ti and W, forming 232Cm, with measurement spanning the capture barrier energies, alignment of the heavy prolate deformed nucleus is shown to be the main reason for the broadening of the mass distribution of the quasifission fragments as the beam energy is reduced. The complex, consistently evolving mass-angle correlations that are observed carry more information than the integrated mass or angular distributions, and should severely test models of quasifission.

  15. Disentangling Effects of Nuclear Structure in Heavy Element Formation

    SciTech Connect

    Hinde, D. J.; Thomas, R. G.; Rietz, R. du; Diaz-Torres, A.; Dasgupta, M.; Brown, M. L.; Evers, M.; Gasques, L. R.; Rafiei, R.; Rodriguez, M. D.

    2008-05-23

    Forming the same heavy compound nucleus with different isotopes of the projectile and target elements allows nuclear structure effects in the entrance channel (resulting in static deformation) and in the dinuclear system to be disentangled. Using three isotopes of Ti and W, forming {sup 232}Cm, with measurement spanning the capture barrier energies, alignment of the heavy prolate deformed nucleus is shown to be the main reason for the broadening of the mass distribution of the quasifission fragments as the beam energy is reduced. The complex, consistently evolving mass-angle correlations that are observed carry more information than the integrated mass or angular distributions, and should severely test models of quasifission.

  16. Simulations of the formation of large-scale structure

    NASA Astrophysics Data System (ADS)

    White, S. D. M.

    Numerical studies related to the simulation of structure growth are examined. The linear development of fluctuations in the early universe is studied. The research of Aarseth, Gott, and Turner (1979) based on N-body integrators that obtained particle accelerations by direct summation of the forces due to other objects is discussed. Consideration is given to the 'pancake theory' of Zel'dovich (1970) for the evolution from adiabatic initial fluctuation, the neutrino-dominated universe models of White, Frenk, and Davis (1983), and the simulations of Davis et al. (1985).

  17. Modelling the structural controls of primary kaolinite formation

    NASA Astrophysics Data System (ADS)

    Tierney, R. L.; Glass, H. J.

    2016-09-01

    An abundance of kaolinite was formed within the St. Austell outcrop of the Cornubian batholith in Cornwall, southwest England, by the hydrous dissolution of feldspar crystals. The permeability of Cornish granites is low and alteration acts pervasively from discontinuity features, with montmorillonite recognised as an intermediate assemblage in partially kaolinised material. Structural features allowed fluids to channel through the impermeable granite and pervade deep into the rock. Areas of high structural control are hypothesised to link well with areas of advanced alteration. As kaolinisation results in a loss of competence, we present a method of utilising discontinuity orientations from nearby unaltered granites alongside the local tectonic history to calculate strain rates and delineate a discrete fracture network. Simulation of the discrete fracture network is demonstrated through a case study at Higher Moor, where kaolinite is actively extracted from a pit. Reconciliation of fracture connectivity and permeability against measured subsurface data show that higher values of modelled properties match with advanced kaolinisation observed in the field. This suggests that the technique may be applicable across various industries and disciplines.

  18. Dynamics of structure formation in crystallizable block copolymers

    SciTech Connect

    Rangarajan, P.; Register, R.A.; Adamson, D.H.

    1995-12-31

    Isothermal crystallization of polyolefin diblock copolymers from homogeneous and weakly segregated melts has been tracked using simultaneous, synchrotron-based small and wide-angle x-ray scattering (SAXS and WAXS). The polymers are prepared by hydrogenating polydiene diblocks, and contain crystallizable polyethylene ({open_quotes}E{close_quotes}; hydrogenated high 1,4-polybutadiene) blocks and a variety of amorphous polyolefin blocks. All polymers exhibit a well-ordered lamellar morphology at room temperature, as evidenced by 2-3 clear SAXS reflections, even for compositions containing as little as 12% E. In polymers crystallizing from homogeneous melts, the WAXS reflections from the E crystallites grow in parallel with the 3-4 SAXS reflections, so microphase separation is driven by crystallization. These structures, which are reminiscent of strong segregation (as indicated by the multiple SAXS reflections), are obtained by cooling only 20{degrees}C below the melting point. For a polymer having a weakly segregated melt, crystallization eradicates the melt morphology, but larger domain spacings were observed for higher crystallization temperatures, unlike the path-independent values obtained on crystallization from single-phase melts, suggesting that melt segregation hinders the development of the equilibrium crystallization-driven structure.

  19. Minimal continuum theories of structure formation in dense active fluids

    NASA Astrophysics Data System (ADS)

    Dunkel, Jörn; Heidenreich, Sebastian; Bär, Markus; Goldstein, Raymond E.

    2013-04-01

    Self-sustained dynamical phases of living matter can exhibit remarkable similarities over a wide range of scales, from mesoscopic vortex structures in microbial suspensions and motility assays of biopolymers to turbulent large-scale instabilities in flocks of birds or schools of fish. Here, we argue that, in many cases, the phenomenology of such active states can be efficiently described in terms of fourth- and higher-order partial differential equations. Structural transitions in these models can be interpreted as Landau-type kinematic transitions in Fourier (wavenumber) space, suggesting that microscopically different biological systems can share universal long-wavelength features. This general idea is illustrated through numerical simulations for two classes of continuum models for incompressible active fluids: a Swift-Hohenberg-type scalar field theory, and a minimal vector model that extends the classical Toner-Tu theory and appears to be a promising candidate for the quantitative description of dense bacterial suspensions. We discuss how microscopic symmetry-breaking mechanisms can enter macroscopic continuum descriptions of collective microbial motion near surfaces, and conclude by outlining future applications.

  20. Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

    SciTech Connect

    Kryzhevich, Dmitrij S. E-mail: kost@ispms.ru; Zolnikov, Konstantin P. E-mail: kost@ispms.ru; Abdrashitov, Andrei V.; Lerner, Marat I.; Psakhie, Sergey G.

    2014-11-14

    A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

  1. Distributed attitude synchronization of formation flying via consensus-based virtual structure

    NASA Astrophysics Data System (ADS)

    Cong, Bing-Long; Liu, Xiang-Dong; Chen, Zhen

    2011-06-01

    This paper presents a general framework for synchronized multiple spacecraft rotations via consensus-based virtual structure. In this framework, attitude control systems for formation spacecrafts and virtual structure are designed separately. Both parametric uncertainty and external disturbance are taken into account. A time-varying sliding mode control (TVSMC) algorithm is designed to improve the robustness of the actual attitude control system. As for the virtual attitude control system, a behavioral consensus algorithm is presented to accomplish the attitude maneuver of the entire formation and guarantee a consistent attitude among the local virtual structure counterparts during the attitude maneuver. A multiple virtual sub-structures (MVSSs) system is introduced to enhance current virtual structure scheme when large amounts of spacecrafts are involved in the formation. The attitude of spacecraft is represented by modified Rodrigues parameter (MRP) for its non-redundancy. Finally, a numerical simulation with three synchronization situations is employed to illustrate the effectiveness of the proposed strategy.

  2. Structural Basis of Vesicle Formation at the Inner Nuclear Membrane.

    PubMed

    Hagen, Christoph; Dent, Kyle C; Zeev-Ben-Mordehai, Tzviya; Grange, Michael; Bosse, Jens B; Whittle, Cathy; Klupp, Barbara G; Siebert, C Alistair; Vasishtan, Daven; Bäuerlein, Felix J B; Cheleski, Juliana; Werner, Stephan; Guttmann, Peter; Rehbein, Stefan; Henzler, Katja; Demmerle, Justin; Adler, Barbara; Koszinowski, Ulrich; Schermelleh, Lothar; Schneider, Gerd; Enquist, Lynn W; Plitzko, Jürgen M; Mettenleiter, Thomas C; Grünewald, Kay

    2015-12-17

    Vesicular nucleo-cytoplasmic transport is becoming recognized as a general cellular mechanism for translocation of large cargoes across the nuclear envelope. Cargo is recruited, enveloped at the inner nuclear membrane (INM), and delivered by membrane fusion at the outer nuclear membrane. To understand the structural underpinning for this trafficking, we investigated nuclear egress of progeny herpesvirus capsids where capsid envelopment is mediated by two viral proteins, forming the nuclear egress complex (NEC). Using a multi-modal imaging approach, we visualized the NEC in situ forming coated vesicles of defined size. Cellular electron cryo-tomography revealed a protein layer showing two distinct hexagonal lattices at its membrane-proximal and membrane-distant faces, respectively. NEC coat architecture was determined by combining this information with integrative modeling using small-angle X-ray scattering data. The molecular arrangement of the NEC establishes the basic mechanism for budding and scission of tailored vesicles at the INM.

  3. Structural characterization of a karstified limestone formation using GPR

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Sénéchal, G.; Gaffet, S.

    2009-12-01

    The Laboratoire Souterrain à Bas Bruit (LSBB) at Rustrel - Pays d'Apt, France, is an Inter-disciplinary Underground Science and Technology Laboratory buried in a karstified limestone formation. A multidisciplinary program focused on water circulation monitoring is presently performed inside the tunnels. This program comprises the investigation of faults, fractures, karstification and stratigraphy ofthe limestone massif using GPR. We present the main results obtained from these data. The tunnel has been dug in lower cretaceous limestone which is characterized by a low clay content, high electrical resistivity which results in generally very low attenuation of electro-magnetic waves. 90% of the tunnels floor are made of concrete whereas other are made of bare limestone. This experimental site offers a unique opportunity of perfoming measurements within an unweathered limestone massif. The whole 3km long tunnel has been investigated using single offset shielded 250 MHz antennas in May 2009. Processing includes : DC and very low frequency removal, amplitude compensation preserving lateral variations, migration and time to depth conversion. When necessary predictive deconvolution has been applied to remove ringing effects. These data sets are characterized by good signal to noise ratio and a signal penetration down to 18 meters. These data allow us to accurately map the stratigraphy of the surrounding rocks across the concrete walls of the tunnel. Some 20 m deep vertical wells have been drilled inside the tunnel through observed reflectors. This is a strong validation of the GPR images. The estimated resolution is centimetric to decimetric and matches the required geologic accuracy. The GPR data set allows to extend previous geological results in depth, particularly in the concrete coated parts of the tunnel where conventional geological surveying is impossible. Thanks to the processing which preserves lateral amplitude variations, GPR sections exhibit prominent

  4. Identification of formation of initial native structure in onconase from an unfolded state.

    PubMed

    Gahl, Robert F; Oswald, Robert E; Scheraga, Harold A

    2012-01-10

    In the oxidative folding of onconase, the stabilization of intermediates early in the folding process gives rise to efficient formation of its biologically active form. To identify the residues responsible for the initial formation of structured intermediates, the transition from an ensemble of unstructured three-disulfide species, 3S(U), to a single structured three-disulfide intermediate species, des-[30-75] or 3S(F), at pH 8.0 and 25 °C was examined. This transition was first monitored by far-UV circular dichroism spectroscopy at pH 8.0 and 25 °C, showing that it occurs with the formation of secondary structure, presumably because of native interactions. The time dependence of formation of nativelike structure was then followed by nuclear magnetic resonance spectroscopy after we had arrested the transition at different times by lowering the pH to 3 and then acquiring (1)H-(15)N heteronuclear single-quantum coherence spectra at pH 3 and 16 °C to identify amide hydrogens that become part of nativelike structure. H/D exchange was utilized to reduce the intensity of resonances from backbone amide hydrogens not involved in structure, without allowing exchange of backbone amide hydrogens involved in initial structure. Six hydrogen-bonding residues, namely, Tyr38, Lys49, Ser82, Cys90, Glu91, and Ala94, were identified as being involved in the earliest detectable nativelike structure before complete formation of des-[30-75] and are further stabilized later in the formation of this intermediate through S-S/SH interchange. By observing the stabilization of the structures of these residues by their neighboring residues, we have identified the initial, nativelike structural elements formed in this transition, providing details of the initial events in the oxidative folding of onconase. PMID:22142378

  5. Structure formation constraints on Sommerfeld-enhanced dark matter annihilation

    SciTech Connect

    Armendariz-Picon, Cristian; Neelakanta, Jayanth T. E-mail: jtneelak@syr.edu

    2012-12-01

    We study the growth of cosmic structure in a ΛCDM universe under the assumption that dark matter self-annihilates with an averaged cross section times relative velocity that grows with the scale factor, an increase known as Sommerfeld-enhancement. Such an evolution is expected in models in which a light force carrier in the dark sector enhances the annihilation cross section of dark matter particles, and has been invoked, for instance, to explain anomalies in cosmic ray spectra reported in the past. In order to make our results as general as possible, we assume that dark matter annihilates into a relativistic species that only interacts gravitationally with the standard model. This assumption also allows us to test whether the additional relativistic species mildly favored by cosmic-microwave background data could originate from dark matter annihilation. We do not find evidence for Sommerfeld-enhanced dark matter annihilation and derive the corresponding upper limits on the annihilation cross-section.

  6. Structural Basis of Clostridium perfringens Toxin Complex Formation

    SciTech Connect

    Adams,J.; Gregg, K.; Bayer, E.; Boraston, A.; Smith, S.

    2008-01-01

    The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between the X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.

  7. Modulation of crystal formation by bone phosphoproteins: structural specificity of the osteopontin-mediated inhibition of hydroxyapatite formation.

    PubMed

    Hunter, G K; Kyle, C L; Goldberg, H A

    1994-06-15

    Osteopontin is a phosphorylated sialoprotein containing a conserved sequence of contiguous aspartic acid residues. This protein is expressed at high levels in mineralized tissues and has previously been shown to inhibit the in vitro formation of hydroxyapatite (HA). In the present study, protein modification and model compound studies have been used to identify the structural features of osteopontin that are responsible for its crystal-modulating properties. Using metastable calcium phosphate solutions buffered by autotitration, osteopontin caused half-maximal inhibition of HA formation at a concentration (IC50) of 0.06 microgram/ml. The hen egg yolk phosphoprotein phosvitin was a much weaker inhibitor, while dextran sulphate had no effect. The synthetic polypeptide poly(aspartic acid) was almost as effective an inhibitor of HA formation as osteopontin (IC50 0.11 microgram/ml), whereas poly(glutamic acid) was more than a thousand times less potent (IC50 155 micrograms/ml). In a steady-state agarose gel system, much higher polypeptide concentrations were required for inhibition of HA formation, but a similar relative order of inhibitory effectiveness was observed. Treatment of osteopontin with alkaline phosphatase removed 84% of the covalently bound phosphate and reduced its HA-inhibiting activity by more than 40-fold. Treatment with glycine ethyl ester in the presence of carbodi-imide modified 86% of the carboxylate groups in osteopontin and reduced its inhibitory activity by 6-fold. These findings indicate that osteopontin is a potent inhibitor of HA formation. This activity requires phosphate and carboxylate groups, possibly including the conserved sequence of contiguous aspartic acid residues. Osteopontin may act as an inhibitor of phase separation in physiological fluids of high supersaturation.

  8. Formation and finite element analysis of tethered bilayer lipid structures.

    PubMed

    Kwak, Kwang Joo; Valincius, Gintaras; Liao, Wei-Ching; Hu, Xin; Wen, Xuejin; Lee, Andrew; Yu, Bo; Vanderah, David J; Lu, Wu; Lee, L James

    2010-12-01

    Rapid solvent exchange of an ethanolic solution of diphytanoyl phosphatidylcholine (DPhyPC) in the presence of a mixed self-assembled monolayer (SAM) [thiolipid/β-mercaptoethanol (βME) (3/7 mol/mol) on Au] shows a transition from densely packed tethered bilayer lipid membranes [(dp)tBLMs], to loosely packed tethered bilayer lipid membranes [(lp)tBLMs], and tethered bilayer liposome nanoparticles (tBLNs) with decreasing DPhyPC concentration. The tethered lipidic constructs in the aqueous medium were analyzed by atomic force microscopy (AFM) and electrochemical impedance spectroscopy (EIS). Finite element analysis (FEA) was applied to interpret spectral EIS features without referring to equivalent circuit modeling. Using structural data obtained earlier from neutron reflectometry and dielectric constants of lipid bilayers, we reproduced experimentally observed features of the electrochemical impedance (EI) spectra of complex surface constructs involving small pinhole defects, large membrane-free patches, and bound liposomes. We demonstrated by FEA that highly insulating (dp)tBLMs with low-defect density exhibit EI spectra in the shape of a perfect semicircle with or without low-frequency upward "tails" in the Cole-Cole representation. Such EI spectra were observed at DPhyPC concentrations of >5 × 10(-3) mol L(-1). While AFM was not able to visualize very small lateral defects in such films, EI spectra unambiguously signaled their presence by increased low frequency "tails". Using FEA we demonstrate that films with large diameter visible defects (>25 nm by AFM) produce EI spectral features consisting of two semicircles of comparable size. Such films were typically obtained at DPhyPC concentrations of <5 × 10(-3) mol L(-1). At DPhyPC concentrations of <1.0 × 10(-3) mol L(-1) the planar bilayer structures were replaced by ellipsoidal liposomes with diameters ranging from 50 to 500 nm as observed in AFM images. Despite the distinct surface morphology change, the EI

  9. Formation and finite element analysis of tethered bilayer lipid structures.

    PubMed

    Kwak, Kwang Joo; Valincius, Gintaras; Liao, Wei-Ching; Hu, Xin; Wen, Xuejin; Lee, Andrew; Yu, Bo; Vanderah, David J; Lu, Wu; Lee, L James

    2010-12-01

    Rapid solvent exchange of an ethanolic solution of diphytanoyl phosphatidylcholine (DPhyPC) in the presence of a mixed self-assembled monolayer (SAM) [thiolipid/β-mercaptoethanol (βME) (3/7 mol/mol) on Au] shows a transition from densely packed tethered bilayer lipid membranes [(dp)tBLMs], to loosely packed tethered bilayer lipid membranes [(lp)tBLMs], and tethered bilayer liposome nanoparticles (tBLNs) with decreasing DPhyPC concentration. The tethered lipidic constructs in the aqueous medium were analyzed by atomic force microscopy (AFM) and electrochemical impedance spectroscopy (EIS). Finite element analysis (FEA) was applied to interpret spectral EIS features without referring to equivalent circuit modeling. Using structural data obtained earlier from neutron reflectometry and dielectric constants of lipid bilayers, we reproduced experimentally observed features of the electrochemical impedance (EI) spectra of complex surface constructs involving small pinhole defects, large membrane-free patches, and bound liposomes. We demonstrated by FEA that highly insulating (dp)tBLMs with low-defect density exhibit EI spectra in the shape of a perfect semicircle with or without low-frequency upward "tails" in the Cole-Cole representation. Such EI spectra were observed at DPhyPC concentrations of >5 × 10(-3) mol L(-1). While AFM was not able to visualize very small lateral defects in such films, EI spectra unambiguously signaled their presence by increased low frequency "tails". Using FEA we demonstrate that films with large diameter visible defects (>25 nm by AFM) produce EI spectral features consisting of two semicircles of comparable size. Such films were typically obtained at DPhyPC concentrations of <5 × 10(-3) mol L(-1). At DPhyPC concentrations of <1.0 × 10(-3) mol L(-1) the planar bilayer structures were replaced by ellipsoidal liposomes with diameters ranging from 50 to 500 nm as observed in AFM images. Despite the distinct surface morphology change, the EI

  10. Biological pattern formation: from basic mechanisms to complex structures

    NASA Astrophysics Data System (ADS)

    Koch, A. J.; Meinhardt, H.

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  11. Nonlinear structure formation in the cubic Galileon gravity model

    SciTech Connect

    Barreira, Alexandre; Li, Baojiu; Hellwing, Wojciech A.; Baugh, Carlton M.; Pascoli, Silvia E-mail: baojiu.li@durham.ac.uk E-mail: c.m.baugh@durham.ac.uk

    2013-10-01

    We model the linear and nonlinear growth of large scale structure in the Cubic Galileon gravity model, by running a suite of N-body cosmological simulations using the ECOSMOG code. Our simulations include the Vainshtein screening effect, which reconciles the Cubic Galileon model with local tests of gravity. In the linear regime, the amplitude of the matter power spectrum increases by ∼ 20% with respect to the standard ΛCDM model today. The modified expansion rate accounts for ∼ 15% of this enhancement, while the fifth force is responsible for only ∼ 5%. This is because the effective unscreened gravitational strength deviates from standard gravity only at late times, even though it can be twice as large today. In the nonlinear regime (k∼>0.1h Mpc{sup −1}), the fifth force leads to only a modest increase (∼<8%) in the clustering power on all scales due to the very efficient operation of the Vainshtein mechanism. Such a strong effect is typically not seen in other models with the same screening mechanism. The screening also results in the fifth force increasing the number density of halos by less than 10%, on all mass scales. Our results show that the screening does not ruin the validity of linear theory on large scales which anticipates very strong constraints from galaxy clustering data. We also show that, whilst the model gives an excellent match to CMB data on small angular scales (l∼>50), the predicted integrated Sachs-Wolfe effect is in tension with Planck/WMAP results.

  12. Biological pattern formation: from basic mechanisms to complex structures

    SciTech Connect

    Koch, A.J.; Meinhardt, H. )

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  13. Formation and evolution of tweed structures on high-purity aluminum polycrystalline foils under cyclic tension

    NASA Astrophysics Data System (ADS)

    Kuznetsov, P. V.; Vlasov, I. V.; Sklyarova, E. A.; Smekalina, T. V.

    2015-10-01

    Peculiarities of formation and evolution of tweed structures on the surface of high-purity aluminum polycrystalline foils under cyclic tension were studied using an atom force microscope and a white light interferometer. Tweed structures of micron and submicron sizes were found on the foils at different number of cycles. In the range of 42,000 < N < 95,000 cycles destruction of tweed patterns is observed, which leads to their disappearance from the surface of the foils. Formation of tweed structures of various scales is discussed in terms of the Grinfeld instability.

  14. Formation and evolution of tweed structures on high-purity aluminum polycrystalline foils under cyclic tension

    SciTech Connect

    Kuznetsov, P. V.; Vlasov, I. V.; Sklyarova, E. A.; Smekalina, T. V.

    2015-10-27

    Peculiarities of formation and evolution of tweed structures on the surface of high-purity aluminum polycrystalline foils under cyclic tension were studied using an atom force microscope and a white light interferometer. Tweed structures of micron and submicron sizes were found on the foils at different number of cycles. In the range of 42,000 < N < 95,000 cycles destruction of tweed patterns is observed, which leads to their disappearance from the surface of the foils. Formation of tweed structures of various scales is discussed in terms of the Grinfeld instability.

  15. Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism.

    PubMed

    Tong, Chunfa; Shen, Lianying; Lv, Yafei; Wang, Zhong; Wang, Xiaoling; Feng, Sisi; Li, Xin; Sui, Yihan; Pang, Xiaoming; Wu, Rongling

    2014-01-01

    Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation.

  16. Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

    PubMed

    Shu, Qin; Krezel, Andrzej M; Cusumano, Zachary T; Pinkner, Jerome S; Klein, Roger; Hultgren, Scott J; Frieden, Carl

    2016-06-28

    Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation. PMID:27298344

  17. FORMATION OF A PROPELLER STRUCTURE BY A MOONLET IN A DENSE PLANETARY RING

    SciTech Connect

    Michikoshi, Shugo; Kokubo, Eiichiro E-mail: kokubo@th.nao.ac.jp

    2011-05-10

    The Cassini spacecraft discovered a propeller-shaped structure in Saturn's A. This propeller structure is thought to be formed by gravitational scattering of ring particles by an unseen embedded moonlet. Self-gravity wakes are prevalent in dense rings due to gravitational instability. Strong gravitational wakes affect the propeller structure. Here, we derive the condition for the formation of a propeller structure by a moonlet embedded in a dense ring with gravitational wakes. We find that a propeller structure is formed when the wavelength of the gravitational wakes is smaller than the Hill radius of the moonlet. We confirm this formation condition by performing numerical simulations. This condition is consistent with observations of propeller structures in Saturn's A.

  18. Innovative design of composite structures: The use of curvilinear fiber format in structural design of composites

    NASA Technical Reports Server (NTRS)

    Charette, R. F.; Hyer, M. W.

    1990-01-01

    The influence is investigated of a curvilinear fiber format on load carrying capacity of a layered fiber reinforced plate with a centrally located hole. A curvilinear fiber format is descriptive of layers in a laminate having fibers which are aligned with the principal stress directions in those layers. Laminates of five curvilinear fiber format designs and four straightline fiber format designs are considered. A quasi-isotropic laminate having a straightline fiber format is used to define a baseline design for comparison with the other laminate designs. Four different plate geometries are considered and differentiated by two values of hole diameter/plate width equal to 1/6 and 1/3, and two values of plate length/plate width equal to 2 and 1. With the plates under uniaxial tensile loading on two opposing edges, alignment of fibers in the curvilinear layers with the principal stress directions is determined analytically by an iteration procedure. In-plane tensile load capacity is computed for all of the laminate designs using a finite element analysis method. A maximum strain failure criterion and the Tsai-Wu failure criterion are applied to determine failure loads and failure modes. Resistance to buckling of the laminate designs to uniaxial compressive loading is analyzed using the commercial code Engineering Analysis Language. Results indicate that the curvilinear fiber format laminates have higher in-plane tensile load capacity and comparable buckling resistance relative to the straightline fiber format laminates.

  19. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

    SciTech Connect

    Sievers, Stuart A.; Karanicolas, John; Chang, Howard W.; Zhao, Anni; Jiang, Lin; Zirafi, Onofrio; Stevens, Jason T.; Münch, Jan; Baker, David; Eisenberg, David

    2011-09-20

    Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-{beta}-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.

  20. The evolution of galaxies at constant number density: a less biased view of star formation, quenching, and structural formation

    NASA Astrophysics Data System (ADS)

    Ownsworth, Jamie R.; Conselice, Christopher J.; Mundy, Carl J.; Mortlock, Alice; Hartley, William G.; Duncan, Kenneth; Almaini, Omar

    2016-09-01

    Due to significant galaxy contamination and impurity in stellar mass selected samples (up to 95 per cent from z = 0-3), we examine the star formation history, quenching time-scales, and structural evolution of galaxies using a constant number density selection with data from the United Kingdom Infra-Red Deep Sky Survey Ultra-Deep Survey field. Using this methodology, we investigate the evolution of galaxies at a variety of number densities from z = 0-3. We find that samples chosen at number densities ranging from 3 × 10-4 to 10-5 galaxies Mpc-3 (corresponding to z ˜ 0.5 stellar masses of M* = 1010.95-11.6 M0) have a star-forming blue fraction of ˜50 per cent at z ˜ 2.5, which evolves to a nearly 100 per cent quenched red and dead population by z ˜ 1. We also see evidence for number density downsizing, such that the galaxies selected at the lowest densities (highest masses) become a homogeneous red population before those at higher number densities. Examining the evolution of the colours for these systems furthermore shows that the formation redshift of galaxies selected at these number densities is zform > 3. The structural evolution through size and Sérsic index fits reveal that while there remains evolution in terms of galaxies becoming larger and more concentrated in stellar mass at lower redshifts, the magnitude of the change is significantly smaller than for a mass-selected sample. We also find that changes in size and structure continues at z < 1, and is coupled strongly to passivity evolution. We conclude that galaxy structure is driving the quenching of galaxies, such that galaxies become concentrated before they become passive.

  1. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a

  2. Neotectonic stage in the formation of the Khokhlovskoe uranium deposit, eastern Transural region: Structural, hydrochemical, mineralogical, and geochemical formation conditions

    NASA Astrophysics Data System (ADS)

    Vinokurov, S. F.; Prokof'ev, V. Yu.; Malkovsky, V. I.; Dymkov, Yu. M.; Chugaev, A. V.; Nesterova, M. V.

    2013-11-01

    The structural, hydrochemical, mineralogical, and geochemical features of the Khokhlovskoe uranium deposit related to neotectonic processes are considered. The structural feature is expressed in neotectonic dislocations in the form of overall intense fragmentation of host rocks and widespread low-amplitude strike-slip faulting. The hydrochemical specificity is determined by the appearance of thermal carbonated formation water in ore-bearing aquifers. This water is similar in chemical and gas composition to hydrothermal solutions in fluid inclusions and mineral waters abundant in this district. The mineralogical and geochemical features comprise the occurrence of newly formed ferroan carbonates and late iron hydroxides in altered (bleached) pelitic rocks; the formation of silicic opal segregations in ore-bearing sand and sandstone; late sulfides, arsenides, and selenides of iron and other metals; and multiphase gel-pitchblende enriched in Zr especially typical of high-grade uranium ore. The age of high-grade ore determined by a precision uranium-ionium method coincides with the time when thermal carbonated water appeared in the host rocks. This time was estimated from a mathematical model of heat transfer and regional dynamics of underground water. This coincidence clearly indicates that the aforementioned processes are related to the late Quaternary neotectonic reactivation of the eastern Transural region.

  3. Revised age and structural interpretations of Nuka Formation at Nuka Ridge, northwestern Alaska

    USGS Publications Warehouse

    Tailleur, I.L.; Mamet, B.L.; Dutro, J.T.

    1973-01-01

    New collections of foraminifers and macrofossils from Nuka Ridge, the type area of the enigmatic Nuka Formation, demonstrate that the type Nuka Formation is not a continuous stratigraphic sequence as originally described. Paleontologic evidence indicates the presence of a structurally repeated sequence at Nuka Ridge consisting of Upper Mississippian (Meramec and younger) strata overlain by Permian beds which, in turn, are succeeded by Triassic(?) and Cretaceous rocks. Mississippian calcareous mudstone and limestone units are correlated with the Lisburne Group; microcline-bearing arkose units with Mississippian and Permian macrofossils and microfossils represent the Nuka Formation; units of chert are inferred to be of Permian and Triassic age; and wacke at the top of the sequence resembles unnamed wacke assigned to the Cretaceous elsewhere. These new data and their interpretations indicate that the type section of the Nuka Formation is inadequate. The standard for the Nuka Formation is therefore referred to a newly measured section of the middle arkosic unit of the old section.

  4. Formation of chain structures in systems of charged grains interacting via isotropic pair potentials

    SciTech Connect

    Vaulina, O. S.; Lisina, I. I.; Koss, K. G.

    2013-05-15

    Conditions for the formation of chain structures of charged grains confined in the gravitational field by external electric fields are studied analytically and numerically. The relationships between the parameters of the pair interaction potential, the number of grains, and the electric field gradient in the trap are found. A criterion for the violation of stable equilibrium in a quasi-one-dimensional chain of grains and the formation of a new configuration in the system is proposed.

  5. Formation of large-scale structure from cosmic strings and massive neutrinos

    NASA Technical Reports Server (NTRS)

    Scherrer, Robert J.; Melott, Adrian L.; Bertschinger, Edmund

    1989-01-01

    Numerical simulations of large-scale structure formation from cosmic strings and massive neutrinos are described. The linear power spectrum in this model resembles the cold-dark-matter power spectrum. Galaxy formation begins early, and the final distribution consists of isolated density peaks embedded in a smooth background, leading to a natural bias in the distribution of luminous matter. The distribution of clustered matter has a filamentary appearance with large voids.

  6. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN

    1989-01-01

    The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

  7. Structural Complexities Influencing Biostratigraphic Interpretations of the Permian Nansen Formation type-section, Ellesmere Island, Canada

    NASA Astrophysics Data System (ADS)

    Hill, M.; Guest, B.

    2011-12-01

    The Carboniferous to Permian aged Nansen Formation is a cyclic carbonate shelf deposit and potential hydrocarbon reservoir. This formation is the thickest, most widespread carbonate sequence in the Sverdrup Basin. Deformed during the Eurekan Orogeny, the Nansen Fm. is topographically prominent and responsible for the rugged topography on Axel Heiburg and Ellesmere Island. The type-section for the Nansen Fm. is located on the north side of Hare Fiord, along Girty Creek. At this location there is an estimated stratigraphic thickness of 2 km. Due to easier access most of the stratigraphic work has been completed on nearby glacially exposed sections that traverse parallel to Girty Creek along glacial margins. Extensive biostratigraphy was completed on a glacier section to the west, however, in a glacier section to the east of Girty Creek, structural complexities appear to be repeating sections of the formation. Here, the Nansen formation is bounded by two regional reverse faults. This has produced duplex structures, with clearly exposed stacked horses, footwall synclines, and truncations. By projecting the structures observed along the eastern glacier section to the western glacier section that was used for biostratigraphic studies, it is clear that these structures would affect biostratigraphic interpretations. It was previously noted by biostratigraphers that thrust faults appear to be repeating sections of the Nansen formation. However by correlating all observed faults with the biostratigraphy, we can determine the extent to which the faulting has affected the interpretations, and whether all faults or stratigraphic repetitions are accounted for.

  8. Introducing a more realistic model for opinion formation considering instability in social structure

    NASA Astrophysics Data System (ADS)

    Salehi, Sajjad; Taghiyareh, Fattaneh

    2016-06-01

    Opinion formation is a process through which interactions of individuals and dynamism of their opinions in effect of neighbors are modeled. In this paper, in an effort to model the opinion formation more realistically, we have introduced a model that considers the role of network structure in opinion dynamics. In this model, each individual changes his opinion in a way so as to decrease its difference with the opinion of trusted neighbors while he intensifies his dissention with the untrusted ones. Considering trust/distrust relations as a signed network, we have defined a structural indicator which shows the degree of instability in social structure and is calculated based on the structural balance theory. It is also applied as feedback to the opinion formation process affecting its dynamics. Our simulation results show formation of a set of clusters containing individuals holding opinions having similar values. Also, the opinion value of each individual is far from the ones of distrusted neighbors. Since this model considers distrust and instability of relations in society, it can offer a more realistic model of opinion formation.

  9. CO mapping of the Orion molecular cloud: The influence of star formation on cloud structure

    NASA Technical Reports Server (NTRS)

    Schloerb, F. P.; Snell, R. L.; Goldsmith, P. F.; Morgan, J. A.

    1986-01-01

    Regions of massive star formation have long been believed to have a profound influence on the structure of their surrounding molecular clouds. The ways in which massive star formation has altered the structure and kinematics of the Orion Molecular Cloud are discussed. The data to be discussed consists of a large scale map of the CO J=1-0 emission from approximately 3 square degrees of OMC-1. During 1985, the Five College Radio Astronomy Observatory 14M antenna was used to map a 2 deg x 1 deg region centered on alpha(1950) = 5(h)33(m)00(s) delta(1950) = -5 deg 30 min. The region mapped in 1985 covers the well known HII regions M42, M43, and NGC1977, and the CO map contains abundant evidence of the interaction between these regions and the molecular cloud. Indeed, the global structure of the cloud appears to have been strongly influenced by the continuous formation of massive stars within the cloud. Individual instances of some of these features are discussed. There appear to be two classes of features which are indicative of this interaction: CO bright rims and CO holes. During 1986, we have undertaken further mapping of OMC-1 to the south of the region covered by the 1985 map. This portion of the cloud contains significant regions of star formation, but O star formation has not occured and large HII regions have not developed to alter the appearance of the cloud. A detailed map of this region is thus an opportunity to view the structure of the molecular cloud before it has been altered by massive star formation. Preliminary analysis of data obtained in this region suggests that the structure and kinematics of the southern portion of the Orion cloud are indeed dramatically different from those of the region previously mapped. Comparison of the two regions thus supports models of the development of structure in molecular clouds through interaction with the HII regions formed within them.

  10. Structural Mapping of the Tunnunik Impact Structure, NWT, Canada: Insights in to Central Uplift Formation

    NASA Astrophysics Data System (ADS)

    Osinski, G. R.; Francis, R.; Hansen, J.; Marion, C. L.; Pickersgill, A. E.; Tornabene, L. L.

    2013-08-01

    We report on structural mapping of the newly discovered Tunnunik impact structure, a 28 km diameter structure in the Canadian Arctic. The central uplift is exposed in a 2 km long canyon and features thrust-faulted blocks and outwards dipping strata.

  11. Microsized structures assisted nanostructure formation on ZnSe wafer by femtosecond laser irradiation

    SciTech Connect

    Wang, Shutong; Feng, Guoying E-mail: zhoush@scu.edu.cn

    2014-12-22

    Micro/nano patterning of ZnSe wafer is demonstrated by femtosecond laser irradiation through a diffracting pinhole. The irradiation results obtained at fluences above the ablation threshold are characterized by scanning electron microscopy. The microsized structure with low spatial frequency has a good agreement with Fresnel diffraction theory. Laser induced periodic surface structures and laser-induced periodic curvelet surface structures with high spatial frequency have been found on the surfaces of microsized structures, such as spikes and valleys. We interpret its formation in terms of the interference between the reflected laser field on the surface of the valley and the incident laser pulse.

  12. Probing Distinct Fullerene Formation Processes from Carbon Precursors of Different Sizes and Structures.

    PubMed

    Han, Jong Yoon; Choi, Tae Su; Kim, Soyoung; Lee, Jong Wha; Ha, Yoonhoo; Jeong, Kwang Seob; Kim, Hyungjun; Choi, Hee Cheul; Kim, Hugh I

    2016-08-16

    Fullerenes, cage-structured carbon allotropes, have been the subject of extensive research as new materials for diverse purposes. Yet, their formation process is still not clearly understood at the molecular level. In this study, we performed laser desorption ionization-ion mobility-mass spectrometry (LDI-IM-MS) of carbon substrates possessing different molecular sizes and structures to understand the formation process of fullerene. Our observations show that the formation process is strongly dependent on the size of the precursor used, with small precursors yielding small fullerenes and large graphitic precursors generally yielding larger fullerenes. These results clearly demonstrate that fullerene formation can proceed via both bottom-up and top-down processes, with the latter being favored for large precursors and more efficient at forming fullerenes. Furthermore, we observed that specific structures of carbon precursors could additionally affect the relative abundance of C60 fullerene. Overall, this study provides an advanced understanding of the mechanistic details underlying the formation processes of fullerene.

  13. Probing Distinct Fullerene Formation Processes from Carbon Precursors of Different Sizes and Structures.

    PubMed

    Han, Jong Yoon; Choi, Tae Su; Kim, Soyoung; Lee, Jong Wha; Ha, Yoonhoo; Jeong, Kwang Seob; Kim, Hyungjun; Choi, Hee Cheul; Kim, Hugh I

    2016-08-16

    Fullerenes, cage-structured carbon allotropes, have been the subject of extensive research as new materials for diverse purposes. Yet, their formation process is still not clearly understood at the molecular level. In this study, we performed laser desorption ionization-ion mobility-mass spectrometry (LDI-IM-MS) of carbon substrates possessing different molecular sizes and structures to understand the formation process of fullerene. Our observations show that the formation process is strongly dependent on the size of the precursor used, with small precursors yielding small fullerenes and large graphitic precursors generally yielding larger fullerenes. These results clearly demonstrate that fullerene formation can proceed via both bottom-up and top-down processes, with the latter being favored for large precursors and more efficient at forming fullerenes. Furthermore, we observed that specific structures of carbon precursors could additionally affect the relative abundance of C60 fullerene. Overall, this study provides an advanced understanding of the mechanistic details underlying the formation processes of fullerene. PMID:27434606

  14. Formation of a submicrocrystalline structure in metastable austenitic steels during severe plastic deformation and subsequent heating

    NASA Astrophysics Data System (ADS)

    Mal'tseva, L. A.; Mal'tseva, T. V.; Yurovskikh, A. S.; Raab, G. I.; Sharapova, V. A.; Vakhonina, K. D.

    2016-03-01

    The structure and the mechanical properties of metastable austenitic steels after severe plastic deformation by four or six passes of equal-channel angular pressing (ECAP) at a temperature of 400°C are studied. It is shown that ECAP results in strain hardening mainly due to the formation of a submicrocrystalline structure, which is retained after subsequent heating to 500°C.

  15. The formation of tin oxides in thin-film Sn/C/KCl(100) structures

    SciTech Connect

    Yurakov, Yu. A. Ryabtsev, S. V.; Chuvenkova, O. A.; Domashevskaya, E. P.; Nikitenko, A. S.; Kannykin, S. V.; Kushchev, S. B.

    2009-01-15

    The formation of oxides upon the thermal annealing (both in air and vacuum) of island tin films grown on a KCl(100) substrate, which was coated by a thin layer of amorphous carbon, has been investigated by transmission electron microscopy. It is established that thermal annealing at temperatures below the tin melting point (T{sub m}) does not lead to phase transitions with the formation of new crystalline oxide phases. At the same time, the films undergo structural changes: the average size of blocks in the substrate plane decreases compared to those in an as-deposited film. Thermal annealing in air at temperatures above the tin melting point leads to the formation of multiphase oxide structures and increases the average size of blocks and islands in the substrate plane. It is shown that preliminary thermal annealing in air at temperatures below T{sub m} hinders oxidation upon subsequent heat treatment.

  16. Geologic structure and altitude of the top of the Minnelusa Formation, northeastern Black Hills, South Dakota

    USGS Publications Warehouse

    Peter, Kathy D.; Kyllonen, David P.; Mills, Kathy R.

    1988-01-01

    This map shows the altitude of the top of the Permian--and Pennsylvanian age Minnelusa Formation, the deepest aquifer in the northeastern Black Hills for which there is sufficient data available to construct a structural map. The Minnelusa Formation outcrops in the western part of the map area and is more than 3 ,600 ft below land surface in the northeastern corner of the area. The formation consists of interbedded sandstone, sandy dolomite and limestone, shale, siltstone, gypsum, and anhydrite. The upper beds are an aquifer and the lower beds are a confining or semi-confining unit. Small anticlines and synclines parallel the Minnelusa outcrop. Domal structures and peaks in the study area are the result of Tertiary-age intrusions. (USGS)

  17. Nanoscale Control of Silks for Nanofibrous Scaffold Formation with Improved Porous Structure.

    PubMed

    Lin, Shasha; Lu, Guozhong; Liu, Shanshan; Bai, Shumeng; Liu, Xi; Lu, Qiang; Zuo, Baoqi; Kaplan, David L; Zhu, Hesun

    2014-05-01

    Silk-based porous scaffolds have been used extensively in tissue engineering because of their excellent biocompatibility, tunable biodegradability and robust mechanical properties. Although many silk-based scaffolds have been prepared through freeze-drying, a challenge remains to effectively control porous structures during this process. In the present study silk fibroin with different nanostructures were self-assembled in aqueous solution by repeated drying-dissolving process and then used to improve porous structure formation in lyophilization process. Viscosity, secondary structures and water interactions were also studied to exclude their influence on the formation and control of porous structures. Following nanofiber formation in aqueous solution, silk scaffolds with improved porous structure were directly formed after lyophilization and then stabilized with water or methanol annealing treatments. Compared to silk scaffolds derived from fresh solution, the nanofibrous scaffolds showed significantly better cell compatibility in vitro. Therefore, this nanoscale control of silk offers feasible way to regulate the matrix features including porous structure and nanostructure, which are important in regulating cell and tissue outcomes in tissue engineering and regeneration, and then achieve silk-based scaffolds with improved properties. PMID:24949200

  18. How relevant are assembled equilibrium samples in understanding structure formation during lipid digestion?

    PubMed

    Phan, Stephanie; Salentinig, Stefan; Hawley, Adrian; Boyd, Ben J

    2015-10-01

    Lipid-based formulations are gaining interest for use as drug delivery systems for poorly water-soluble drug compounds. During digestion, the lipolysis products self-assemble with endogenous surfactants in the gastrointestinal tract to form colloidal structures, enabling enhanced drug solubilisation. Although earlier studies in the literature focus on assembled equilibrium systems, little is known about structure formation under dynamic lipolysis conditions. The purpose of this study was to investigate the likely colloidal structure formation in the small intestine after the ingestion of lipids, under equilibrium and dynamic conditions. The structural aspects were studied using small angle X-ray scattering and dynamic light scattering, and were found to depend on lipid composition, lipid chain length, prandial state and emulsification. Incorporation of phospholipids and lipolysis products into bile salt micelles resulted in swelling of the structure. At insufficient bile salt concentrations, a co-existing lamellar phase was observed, due to a reduction in the solubilisation capacity for lipolysis products. Emulsification accelerated the rate of lipolysis and structure formation.

  19. Structure formation during the sintering of powder steels alloyed with copper, chromium, and phosphorous

    SciTech Connect

    Romanov, S.M.

    1995-11-01

    The process of structure formation during the sintering of powder steels alloyed with copper, chromium, and phosphorous was investigated. The microstructure of the materials, and distribution of alloying elements in the iron grains, were studied by the methods of electron and scanning electron microscopy. The effect of dispersion of the ferrochromium powder on its solubility in iron was examined.

  20. Fibronectin alters the rate of formation and structure of the fibrin matrix.

    PubMed

    Ramanathan, Anand; Karuri, Nancy

    2014-01-10

    Plasma fibronectin is a vital component of the fibrin clot; however its role on clot structure is not clearly understood. The goal of this study was to examine the influence of fibronectin on the kinetics of formation, structural characteristics and composition of reconstituted fibrin clots or fibrin matrices. Fibrin matrices were formed by adding thrombin to 1, 2 or 4 mg/ml fibrinogen supplemented with 0-0.4 mg/ml fibronectin. The rate of fibrin matrix formation was then monitored by measuring light absorbance properties at different time points. Confocal microscopy of fluorescein conjugated fibrinogen was used to visualize the structural characteristics of fibrin matrices. The amount of fibronectin in fibrin matrices was determined through electrophoresis and immunoblotting of solubilized matrices. Fibronectin concentration positively correlated with the initial rate of fibrin matrix formation and with steady state light absorbance values of fibrin matrices. An increase in fibronectin concentration resulted in thinner and denser fibers in the fibrin matrices. Electrophoresis and immunoblotting showed that fibronectin was covalently and non-covalently bound to fibrin matrices and in the form of high molecular weight multimers. The formation of fibronectin multimers was attributed to cross-linking of fibronectin by trace amounts Factor XIIIa. These findings are novel because they link results from light absorbance studies to microcopy analyses and demonstrate an influence of fibronectin on fibrin matrix structural characteristics. This data is important in developing therapies that destabilize fibrin clots.

  1. Formative Evaluation of the Structured Language Improvement Project for Deaf Adolescents. Lesson I: Round I.

    ERIC Educational Resources Information Center

    Rudner, Lawrence M.

    This report outlines the formative evaluation of the first lesson in the Structured Language Improvement Project (SLIP) - an English language instructional program being developed at the Model Secondary School for the Deaf, Washington, D.C. The theme of this first lesson is the distinction between the simple present (e.g. He eats lunch every day.)…

  2. Formation of pseudotachylitic breccias in the central uplifts of very large impact structures: Scaling the melt formation

    NASA Astrophysics Data System (ADS)

    Mohr-Westheide, Tanja; Reimold, Wolf Uwe

    2011-04-01

    The processes leading to formation of sometimes massive occurrences of pseudotachylitic breccia (PTB) in impact structures have been strongly debated for decades. Variably an origin of these pseudotachylite (friction melt)-like breccias by (1) shearing (friction melting); (2) so-called shock compression melting (with or without a shear component) immediately after shock propagation through the target; (3) decompression melting related to rapid uplift of crustal material due to central uplift formation; (4) combinations of these processes; or (5) intrusion of allochthonous impact melt from a coherent melt body has been advocated. Our investigations of these enigmatic breccias involve detailed multidisciplinary analysis of millimeter- to meter-sized occurrences from the type location, the Vredefort Dome. This complex Archean to early Proterozoic terrane constitutes the central uplift of the originally >250 km diameter Vredefort impact structure in South Africa. Previously, results of microstructural and microchemical investigations have indicated that formation of very small veinlets involved local melting, likely during the early shock compression phase. However, for larger veins and networks it was so far not possible to isolate a specific melt-forming mechanism. Macroscopic to microscopic evidence for friction melting is very limited, and so far chemical results have not directly supported PTB generation by intrusion of impact melt. On the other hand, evidence for filling of dilational sites with melt is abundant. Herein, we present a new approach to the mysterium of PTB formation based on volumetric melt breccia calculations. The foundation for this is the detailed analysis of a 1.5 × 3 × 0.04 m polished granite slab from a dimension-stone quarry in the core of the Vredefort Dome. This slab contains a 37.5 dm3 breccia zone. The pure melt volume in 0.1 m3 PTB-bearing granitic target rock outside of the several-decimeter-wide breccia zone in the granite slab was

  3. EGCG Inhibited Lipofuscin Formation Based on Intercepting Amyloidogenic β-Sheet-Rich Structure Conversion

    PubMed Central

    Cai, Shuxian; Yang, Heng; Zeng, Kewu; Zhang, Jing; Zhong, Ni; Wang, Yingzi; Ye, Jing; Tu, Pengfei; Liu, Zhonghua

    2016-01-01

    Background Lipofuscin (LF) is formed during lipid peroxidation and sugar glycosylation by carbonyl-amino crosslinks with biomacrolecules, and accumulates slowly within postmitotic cells. The environmental pollution, modern dietary culture and lifestyle changes have been found to be the major sources of reactive carbonyl compounds in vivo. Irreversible carbonyl-amino crosslinks induced by carbonyl stress are essentially toxiferous for aging-related functional losses in modern society. Results show that (-)-epigallocatechin gallate (EGCG), the main polyphenol in green tea, can neutralize the carbonyl-amino cross-linking reaction and inhibit LF formation, but the underlying mechanism is unknown. Methods and Results We explored the mechanism of the neutralization process from protein, cell, and animal levels using spectrofluorometry, infrared spectroscopy, conformation antibodies, and electron microscopy. LF demonstrated an amyloidogenic β-sheet-rich with antiparallel structure, which accelerated the carbonyl-amino crosslinks formation and disrupted proteolysis in both PC12 cells and D-galactose (D-gal)-induced brain aging mice models. Additionally, EGCG effectively inhibited the formation of the amyloidogenic β-sheet-rich structure of LF, and prevented its conversion into toxic and on-pathway aggregation intermediates, thereby cutting off the carbonyl-amino crosslinks. Conclusions Our study indicated that the amyloidogenic β-sheet structure of LF may be the core driving force for carbonyl-amino crosslinks further formation, which mediates the formation of amyloid fibrils from native state of biomacrolecules. That EGCG exhibits anti-amyloidogenic β-sheet-rich structure properties to prevent the LF formation represents a novel strategy to impede the development of degenerative processes caused by ageing or stress-induced premature senescence in modern environments. PMID:27030967

  4. Soft sediment deformation structures in the Maastrichtian Ajali Formation Western Flank of Anambra Basin, Southern Nigeria

    NASA Astrophysics Data System (ADS)

    Olabode, Solomon Ojo

    2014-01-01

    Soft sediment deformation structures were recognized in the Maastrichtian shallow marine wave to tide influenced regressive sediments of Ajali Formation in the western flank of Anambra basin, southern Nigerian. The soft sediment deformation structures were in association with cross bedded sands, clay and silt and show different morphological types. Two main types recognised are plastic deformations represented by different types of recumbent folds and injection structure represented by clastic dykes. Other structures in association with the plastic deformation structures include distorted convolute lamination, subsidence lobes, pillars, cusps and sand balls. These structures are interpreted to have been formed by liquefaction and fluidization mechanisms. The driving forces inferred include gravitational instabilities and hydraulic processes. Facies analysis, detailed morphologic study of the soft sediment deformation structures and previous tectonic history of the basin indicate that the main trigger agent for deformation is earthquake shock. The soft sediment deformation structures recognised in the western part of Anambra basin provide a continuous record of the tectonic processes that acted on the regressive Ajali Formation during the Maastrichtian.

  5. Pressure-dependent formation of i-motif and G-quadruplex DNA structures.

    PubMed

    Takahashi, S; Sugimoto, N

    2015-12-14

    Pressure is an important physical stimulus that can influence the fate of cells by causing structural changes in biomolecules such as DNA. We investigated the effect of high pressure on the folding of duplex, DNA i-motif, and G-quadruplex (G4) structures; the non-canonical structures may be modulators of expression of genes involved in cancer progression. The i-motif structure was stabilized by high pressure, whereas the G4 structure was destabilized. The melting temperature of an intramolecular i-motif formed by 5'-dCGG(CCT)10CGG-3' increased from 38.8 °C at atmospheric pressure to 61.5 °C at 400 MPa. This effect was also observed in the presence of 40 wt% ethylene glycol, a crowding agent. In the presence of 40 wt% ethylene glycol, the G4 structure was less destabilized than in the absence of the crowding agent. P-T stability diagrams of duplex DNA with a telomeric sequence indicated that the duplex is more stable than G4 and i-motif structures under low pressure, but the i-motif dominates the structural composition under high pressure. Under crowding conditions, the P-T diagrams indicated that the duplex does not form under high pressure, and i-motif and G4 structures dominate. Our findings imply that temperature regulates the formation of the duplex structure, whereas pressure triggers the formation of non-canonical DNA structures like i-motif and G4. These results suggest that pressure impacts the function of nucleic acids by stabilizing non-canonical structures; this may be relevant to deep sea organisms and during evolution under prebiotic conditions.

  6. Soft-sediment deformation structures interpreted as seismites in the Kolankaya Formation, Denizli Basin (SW Turkey).

    PubMed

    Topal, Savaş; Özkul, Mehmet

    2014-01-01

    The NW-trending Denizli basin of the SW Turkey is one of the neotectonic grabens in the Aegean extensional province. It is bounded by normal faults on both southern and northern margins. The basin is filled by Neogene and Quaternary terrestrial deposits. Late Miocene- Late Pliocene aged Kolankaya formation crops out along the NW trending Karakova uplift in the Denizli basin. It is a typical fluviolacustrine succession that thickens and coarsens upward, comprising poorly consolidated sand, gravelly sand, siltstone and marl. Various soft-sediment deformation structures occur in the formation, especially in fine- to medium grained sands, silts and marls: load structures, flame structures, clastic dikes (sand and gravely-sand dike), disturbed layers, laminated convolute beds, slumps and synsedimentary faulting. The deformation mechanism and driving force for the soft-sediment deformation are related essentially to gravitational instability, dewatering, liquefaction-liquidization, and brittle deformation. Field data and the wide lateral extent of the structures as well as regional geological data show that most of the deformation is related to seismicity and the structures are interpreted as seismites. The existence of seismites in the Kolankaya Formation is evidence for continuing tectonic activity in the study area during the Neogene and is consistent with the occurrence of the paleoearthquakes of magnitude >5.

  7. Formation, molecular structure, and morphology of humins in biomass conversion: influence of feedstock and processing conditions.

    PubMed

    van Zandvoort, Ilona; Wang, Yuehu; Rasrendra, Carolus B; van Eck, Ernst R H; Bruijnincx, Pieter C A; Heeres, Hero J; Weckhuysen, Bert M

    2013-09-01

    Neither the routes through which humin byproducts are formed, nor their molecular structure have yet been unequivocally established. A better understanding of the formation and physicochemical properties of humins, however, would aid in making biomass conversion processes more efficient. Here, an extensive multiple-technique-based study of the formation, molecular structure, and morphology of humins is presented as a function of sugar feed, the presence of additives (e.g., 1,2,4-trihydroxybenzene), and the applied processing conditions. Elemental analyses indicate that humins are formed through a dehydration pathway, with humin formation and levulinic acid yields strongly depending on the processing parameters. The addition of implied intermediates to the feedstocks showed that furan and phenol compounds formed during the acid-catalyzed dehydration of sugars are indeed included in the humin structure. IR spectra, sheared sum projections of solid-state 2DPASS (13) C NMR spectra, and pyrolysis GC-MS data indicate that humins consist of a furan-rich polymer network containing different oxygen functional groups. The structure is furthermore found to strongly depend on the type of feedstock. A model for the molecular structure of humins is proposed based on the data presented. PMID:23836679

  8. Ionic liquid-induced formation of the α-helical structure of β-lactoglobulin.

    PubMed

    Takekiyo, Takahiro; Koyama, Yoshihiro; Yamazaki, Kumiko; Abe, Hiroshi; Yoshimura, Yukihiro

    2013-09-01

    Structural modification of bovine milk β-lactoglobulin (β-LG) in aqueous 1-butyl-3-methylimidazolium nitrate ([bmim][NO3]) and ethylammonium nitrate ([EAN][NO3]) solutions has been investigated by Fourier transform infrared and circular dichroism spectroscopy. Remarkably, high ionic liquid (IL) concentrations (>15 mol %IL) caused formation of a non-native α-helical structure of β-LG and disruption of its tertiary structure. Furthermore, while [bmim][NO3] promoted protein aggregation, [EAN][NO3] inhibited it probably owing to differences in the unique solution structure (nanoheterogeneity) of the ILs by the different cationic species. The IL-induced α-helical formation of β-LG shows a behavior similar to the alcohol denaturation, but a disordered structure-rich state was observed in the β-α transition process by adding IL, in contrast to the case of an aqueous alcohol solution of protein. We propose that the molten salt-like property of aqueous IL solutions strongly support α-helical formation of proteins.

  9. Soft-Sediment Deformation Structures Interpreted as Seismites in the Kolankaya Formation, Denizli Basin (SW Turkey)

    PubMed Central

    Topal, Savaş; Özkul, Mehmet

    2014-01-01

    The NW-trending Denizli basin of the SW Turkey is one of the neotectonic grabens in the Aegean extensional province. It is bounded by normal faults on both southern and northern margins. The basin is filled by Neogene and Quaternary terrestrial deposits. Late Miocene- Late Pliocene aged Kolankaya formation crops out along the NW trending Karakova uplift in the Denizli basin. It is a typical fluviolacustrine succession that thickens and coarsens upward, comprising poorly consolidated sand, gravelly sand, siltstone and marl. Various soft-sediment deformation structures occur in the formation, especially in fine- to medium grained sands, silts and marls: load structures, flame structures, clastic dikes (sand and gravely-sand dike), disturbed layers, laminated convolute beds, slumps and synsedimentary faulting. The deformation mechanism and driving force for the soft-sediment deformation are related essentially to gravitational instability, dewatering, liquefaction-liquidization, and brittle deformation. Field data and the wide lateral extent of the structures as well as regional geological data show that most of the deformation is related to seismicity and the structures are interpreted as seismites. The existence of seismites in the Kolankaya Formation is evidence for continuing tectonic activity in the study area during the Neogene and is consistent with the occurrence of the paleoearthquakes of magnitude >5. PMID:25152909

  10. Formation of periodic structures upon laser ablation of metal targets in liquids

    SciTech Connect

    Kazakevich, Pavel V; Simakin, Aleksandr V; Shafeev, Georgii A

    2005-09-30

    Experimental data on the formation of ordered microstructures produced upon ablation of metal targets in liquids irradiated by a copper vapour laser or a pulsed Nd:YAG laser are presented. The structures were obtained on brass, bronze, copper, and tungsten substrates immersed in distilled water or ethanol. As a result of multiple-pulse laser ablation by a scanning beam, ordered microcones with pointed vertexes are formed on the target surface. The structures are separated by deep narrow channels. The structure period was experimentally shown to increase linearly with diameter of the laser spot on the target surface. (interaction of laser radiation with matter)

  11. Structure formation in fibrous materials based on poly-3-hydroxybutyrate for traumatology

    NASA Astrophysics Data System (ADS)

    Olkhov, A. A.; Sklyanchuk, E. D.; Staroverova, O. V.; Abbasov, T. A.; Guryev, V. V.; Akatov, V. S.; Fadeyeva, I. S.; Fesenko, N. I.; Filatov, Yu. N.; Iordanskii, A. L.

    2015-10-01

    The paper reviews the structure formation of fibrous materials based on poly-3-hydroxybutyrate depending on parameters of electrospinning and characteristics of polymer solution. Fiber structure was studied by DSC, ESR and SEM. The molecular weight affects the diameter and uniformity of the fiber. An electromechanical impact leads to an orientation of crystalline structure in the fiber. The design of an artificial bioresorbable implant based on nano- and microfibers of poly-3-hydroxybutyrate is created. Dynamics of growth of mesenchymal stem cells on poly-3-hydroxybutyrate scaffolds is studied. Successful field tests of implants of the Achilles tendon in Wistar rats are conducted.

  12. Using Structured e-Forum to Support the Legislation Formation Process

    NASA Astrophysics Data System (ADS)

    Xenakis, Alexandros; Loukis, Euripides

    Many public policy problems are 'wicked', being characterised by high complexity, many heterogeneous views and conflicts among various stakeholders, and also lack of mathematically 'optimal' solutions and predefined algorithms for calculating them. The best approach for addressing such problems is through consultation and argumentation among stakeholders. The e-participation research has investigated and suggested several ICT tools for this purpose, such as e-forum, e-petition and e-community tools. This paper investigates the use of an advanced ICT tool, the structured e-forum, for addressing such wicked problems associated with the legislation formation. For this purpose we designed, implemented and evaluated two pilot e-consultations on legislation under formation in the Parliaments of Austria and Greece using a structured e-forum tool based on the Issue Based Information Systems (IBIS) framework. The conclusions drawn reveal the advantages offered by the structured e-forum, but also its difficulties as well.

  13. Galaxy Structure as a Driver of the Star Formation Sequence Slope and Scatter

    NASA Astrophysics Data System (ADS)

    Whitaker, Katherine E.; Franx, Marijn; Bezanson, Rachel; Brammer, Gabriel B.; van Dokkum, Pieter G.; Kriek, Mariska T.; Labbé, Ivo; Leja, Joel; Momcheva, Ivelina G.; Nelson, Erica J.; Rigby, Jane R.; Rix, Hans-Walter; Skelton, Rosalind E.; van der Wel, Arjen; Wuyts, Stijn

    2015-09-01

    It is well established that (1) star-forming galaxies follow a relation between their star formation rate (SFR) and stellar mass ({M}\\star ), the “star formation sequence,” and (2) the SFRs of galaxies correlate with their structure, where star-forming galaxies are less concentrated than quiescent galaxies at fixed mass. Here, we consider whether the scatter and slope of the star formation sequence is correlated with systematic variations in the Sérsic indices, n, of galaxies across the SFR-{M}\\star plane. We use a mass-complete sample of 23,848 galaxies at 0.5 < z < 2.5 selected from the 3D-HST photometric catalogs. Galaxy light profiles parameterized by n are based on Hubble Space Telescope Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey near-infrared imaging. We use a single SFR indicator empirically calibrated from stacks of Spitzer/MIPS 24 μm imaging, adding the unobscured and obscured star formation. We find that the scatter of the star formation sequence is related in part to galaxy structure; the scatter due to variations in n at fixed mass for star-forming galaxies ranges from 0.14 ± 0.02 dex at z ˜ 2 to 0.30 ± 0.04 dex at z < 1. While the slope of the {log} {SFR}-{log} {M}\\star relation is of order unity for disk-like galaxies, galaxies with n > 2 (implying more dominant bulges) have significantly lower {SFR}/{M}\\star than the main ridgeline of the star formation sequence. These results suggest that bulges in massive z ˜ 2 galaxies are actively building up, where the stars in the central concentration are relatively young. At z < 1, the presence of older bulges within star-forming galaxies lowers global {SFR}/{M}\\star , decreasing the slope and contributing significantly to the scatter of the star formation sequence.

  14. Biofunctionalized Microfiber-Assisted Formation of Intrinsic Three-Dimensional Capillary-Like Structures

    PubMed Central

    Weinandy, Stefan; Laffar, Simone; Unger, Ronald E.; Flanagan, Thomas C.; Loesel, Robert; Kirkpatrick, C. James; van Zandvoort, Marc; Hermanns-Sachweh, Benita; Dreier, Agnieszka; Klee, Doris

    2014-01-01

    Objectives: A vascular supply network is essential in engineered tissues >100–200-μm thickness. To control vascular network formation in vitro, we hypothesize that capillarization can be achieved locally by using fibers to position and guide vessel-forming endothelial cells within a three-dimensional (3D) matrix. Materials and Methods: Biofunctionalization of poly-(L-lactic acid) (PLLA) fibers was performed by amino-functionalization and covalent binding of RGD peptides. Human foreskin fibroblasts (HFFs) and human umbilical vein endothelial cells (HUVECs) were seeded on the fibers in a mould and subsequently embedded in fibrin gel. After 9–21 days of coculture, constructs were fixed and immunostained (PECAM-1). Capillary-like structures with lumen in the 3D fibrin matrix were verified and quantified using two-photon microscopy and image analysis software. Results: Capillary-like networks with lumen formed adjacent to the PLLA fibers. Increased cell numbers were observed to attach to RGD-functionalized fibers, resulting in enhanced formation of capillary-like structures. Cocultivation of HFFs sufficiently supported HUVECs in the formation of capillary-like structures, which persisted for at least 21 days of coculture. Conclusions: The guidance of vessel growth within tissue-engineered constructs can be achieved using biofunctionalized PLLA microfibers. Further methods are warranted to perform specified spatial positioning of fibers within 3D formative scaffolds to enhance the applicability of the concept. PMID:24456033

  15. Spectroscopic study on formation of aggregated structures by carotenoids: Role of water

    NASA Astrophysics Data System (ADS)

    Adamkiewicz, Przemysław; Sujak, Agnieszka; Gruszecki, Wiesław I.

    2013-08-01

    Formation of molecular aggregate structures of β-carotene and zeaxanthin, by means of evaporation from pigment solutions in organic solvent was studied with UV-Vis absorption, FTIR and resonance Raman techniques. Pigment solutions were prepared in CHCl3 and CCl4 both dehydrated and hydrated with trace amounts of water. Formation of the aggregated structures characterized by either strong-coupling (e.g. zeaxanthin in hydrated CHCl3) or weak-coupling (e.g. β-carotene in hydrated CHCl3) has been observed. FTIR analysis and molecular modeling showed that H2O molecules can be bound to the aggregated structures formed by zeaxanthin in the form of molecular bridges, predominantly between the terminal hydroxyl groups of adjacent molecules (stabilized by strong hydrogen bonds), but also between the polyene chains (by means of the π-type weak hydrogen bonds). Resonance Raman analysis revealed that the structures formed with the presence of H2O molecules are characterized by twisting of the polyene backbone. The effect of twisting is observed particularly in the case of zeaxanthin structures deposited from hydrated CHCl3 and is not observed in the case of the structures of β-carotene deposited from dehydrated CCl4. Involvement of water molecules in stabilizing aggregated structures of carotenoids is postulated.

  16. Formation of 1D adsorbed water structures on CaO(001)

    NASA Astrophysics Data System (ADS)

    Zhao, Xunhua; Bhattacharya, Saswata; Ghiringhelli, Luca M.; Levchenko, Sergey V.; Scheffler, Matthias

    2015-03-01

    Understanding the interaction of water with oxide surfaces is of fundamental importance for basic and engineering sciences. Recently, a spontaneous formation of one-dimensional (1D) adsorbed water structures have been observed on CaO(001). Interestingly, at other alkaline earth metal oxides, in particular MgO(001) and SrO(001), such structures have not been found experimentally. We calculate the relative stability of adsorbed water structures on the three oxides using density-functional theory combined with the ab initio atomistic thermodynamics. Low-energy structures at different coverages are obtained with a first-principles genetic algorithm. Finite-temperature vibrational spectra are calculated using ab initio molecular dynamics. We find a range of (T, p) conditions where 1D structures are thermodynamically stable on CaO(001). The orientation and vibrational spectra of the 1D structures are in agreement with the experiments. The formation of the 1D structures is found to be actuated by a symmetry breaking in the adsorbed water tetramer, as well as by a balance between water-water and water-substrate interactions, determined by the lattice constant of the oxide.

  17. Control globular structure formation of a copolymer chain through inverse design

    NASA Astrophysics Data System (ADS)

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-01

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  18. Control globular structure formation of a copolymer chain through inverse design.

    PubMed

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-14

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design. PMID:27306020

  19. The small and the beautiful: how the star formation law affects galactic disc structure

    NASA Astrophysics Data System (ADS)

    Braun, H.; Schmidt, W.

    2015-12-01

    We investigate the influence of different analytical parametrizations and fit functions for the local star formation rate in adaptive mesh refinement simulations of an isolated disc galaxy with the NYX code. Suchparametrizations express the star formation efficiency as function of the local turbulent Mach number and virial parameter. By employing the method of adaptively refined large eddy simulations, we are able to evaluate these physical parameters from the numerically unresolved turbulent energy associated with the grid scale. We consider both single and multi free-fall variants of star formation laws proposed by Padoan & Nordlund, Hennebelle & Chabrier, and Krumholz & McKee, summarized and tested recently with numerical simulations by Federrath & Klessen. We find that the global star formation rate and the relation between the local star formation rate and the gas column density is reproduced in agreement with observational constraints by all multi free-fall models of star formation. Some models with obsolete calibration or a single free-fall time-scale, however, result in an overly clumpy disc that does not resemble the structure of observed spirals.

  20. The Saccharomyces cerevisiae Swi/Snf complex can catalyze formation of dimeric nucleosome structures in vitro.

    PubMed

    Krajewski, Wladyslaw A; Vassiliev, Oleg L

    2010-08-10

    The Swi/Snf chromatin-remodeling complexes, human BAF/PBAF and yeast RSC, can catalyze formation of stably altered dimeric forms of nucleosomes. However, the ability to create remodeled dimers has not yet been reported for the Saccharomyces cerevisiae Swi/Snf complex. Despite its similarity with the other Swi/Snf proteins, the yeast Swi/Snf complex features certain structural and functional differences. This raises the question of whether ySwi/Snf can in fact catalyze formation of dimeric nucleosomes. Dimer formation was proposed to have a specific impact on chromatin regulatory effects. Thus, the answer to the above question may be helpful in clarifying the ySwi/Snf functions in vivo and generalizing the notions of the regulatory principles of Swi/Snf family proteins. Here we describe ySwi/Snf-catalyzed formation of nucleosome dimers using mono- and dinucleosome templates assembled from purified histones and DNA of the high-affinity (601) nucleosome positioning sequence. We evaluated effects of nucleosome template geometry on the formation of altered dimers and assayed formation of altered nucleosome pairs on reconstituted dinucleosomes.

  1. Formation of polycrystalline-silicon films with hemispherical grains for capacitor structures with increased capacitance

    SciTech Connect

    Novak, A. V.

    2014-12-15

    The effect of formation conditions on the morphology of silicon films with hemispherical grains (HSG-Si) obtained by the method of low-pressure chemical vapor deposition (LPCVD) is investigated by atomic-force microscopy. The formation conditions for HSG-Si films with a large surface area are found. The obtained HSG-Si films make it possible to fabricate capacitor structures, the electric capacitance of which is twice as large in comparison to that of capacitors with “smooth” electrodes from polycrystalline silicon.

  2. Chemical structure of vanadium-based contact formation on n-AlN

    SciTech Connect

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  3. Talking therapy groups on acute psychiatric wards: patients' experience of two structured group formats

    PubMed Central

    Radcliffe, Jonathan; Bird, Laura

    2016-01-01

    Aims and method We report the results of a clinical audit of patients' reactions to two types of talking therapy groups facilitated by assistant psychologists and psychology graduates on three acute wards. Patients' experiences of problem-solving and interpersonal group formats were explored via focus groups and structured interviews with 29 group participants. Results Both group formats generated high satisfaction ratings, with benefits related mostly to generic factors. Clinical implications Adequately trained and supported assistant psychologists and psychology graduates can provide supportive talking groups that patients find helpful. PMID:27512586

  4. Surface structures induced by ultrashort laser pulses: Formation mechanisms of ripples and grooves

    NASA Astrophysics Data System (ADS)

    He, Shutong; Nivas, Jijil JJ; Anoop, K. K.; Vecchione, Antonio; Hu, Minglie; Bruzzese, Riccardo; Amoruso, Salvatore

    2015-10-01

    We report a detailed theoretical and experimental analysis of the surface structures induced by ultrashort laser pulses on silicon. We address two issues seldom considered in the literature: i) bending and bifurcation of surface ripples and ii) the mechanism of microgrooves formation. Our experimental results illustrate the diverse morphological features of surface structures, which are explained by taking into account the variation of the dielectric constant of the target surface at different excitation levels, by means of a theoretical approach based on the combination of two-temperature model, free-carrier dynamics and Sipe model. In particular, calculated spatial distributions of the deposited laser energy on the target surface provide direct evidence of the diverse morphological characteristics of the produced structures, eventually explaining ripples bending and bifurcation phenomena, as well as grooves formation. The good agreement between model predictions and experimental findings suggests that the proposed approach ascertains the main physical mechanisms underlying both ripples and grooves formation, and influencing their fine morphological features. In addition to providing a deeper understanding of the mechanisms involved in femtosecond direct laser surface processing, our results highlight interesting ways of implementing the design of surface structures of applicative interest.

  5. Structural aspects of glass-formation in Ni-Nb melts

    SciTech Connect

    Holland-Moritz, D.; Yang, F.; Gegner, J.; Meyer, A.; Hansen, T.; Ruiz-Martín, M. D.

    2014-05-28

    We report on investigations of the static structure factors of glass-forming Ni{sub 59.5}Nb{sub 40.5} alloy melts by combination of the containerless processing technique of electrostatic levitation with neutron diffraction. By application of the isotopic substitution method, the full set of partial structure factors was determined. The short-range order in liquid Ni{sub 59.5}Nb{sub 40.5} is characterized by a large nearest neighbor coordination number of Z{sub NN} = 14.3 and a chemical short-range order with an affinity for the formation of heterogeneous Nb-Ni nearest neighbors. The structure factors observed here in the liquid state closely resemble those reported for amorphous Nb-Ni solids. The comparison with earlier results on the short-range structure in Zr-based glass-forming melts suggests that a large local density of packing, chemical order, and structural frustration are, amongst others, common structural properties of these metallic glass-forming systems, which favor glass-formation.

  6. Structure formation in metal complex/polymer hybrid nanomaterials prepared by miniemulsion.

    PubMed

    Hauser, Christoph P; Jagielski, Nicole; Heller, Jeannine; Hinderberger, Dariush; Spiess, Hans W; Lieberwirth, Ingo; Weiss, Clemens K; Landfester, Katharina

    2011-11-01

    Polymer/complex hybrid nanostructures were prepared using a variety of hydrophobic metal β-diketonato complexes. The mechanism of structure formation was investigated by electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS) in the liquid phase. Structure formation is attributed to an interaction between free coordination sites of metal β-diketonato complexes and coordinating anionic surfactants. Lamellar structures are already present in the miniemulsion. By subsequent polymerization the lamellae can be embedded in a great variety of different polymeric matrices. The morphology of the lamellar structures, as elucidated by transmission electron microscopy (TEM), can be controlled by the choice of anionic surfactant. Using sodium alkylsulfates and sodium dodecylphosphate, "nano-onions" are formed, while sodium carboxylates lead to "kebab-like" structures. The composition of the hybrid nanostructures can be described as bilayer lamellae, embedded in a polymeric matrix. The metal complexes are separated by surfactant molecules which are arranged tail-to-tail; by increasing the carbon chain length of the surfactant the layer distance of the structured nanomaterial can be adjusted between 2 and 5 nm. PMID:21977909

  7. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a

  8. Whistler wave interaction with magnetic islands and electron scale structure formation

    NASA Astrophysics Data System (ADS)

    Pathak, Neha

    2016-07-01

    The present work aims to investigate the role of whistler waves in facilitating reconnection and to explore relationship between magnetic reconnection and turbulence. The key role of the whistler waves in the formation of coherent structures during their propagation in the pre-existing fully developed chain of magnetic islands has been investigated. For this scenario, the dynamical equation of whistler wave has been derived in the presence of magnetic islands and has been solved semi-analytically as well as numerically. Due to pre-existing magnetic islands, background field gets perturbed and localization of the whistler waves and formation of current sheets of electron scale takes place, contributing to the generation of magnetic turbulence. In this way whistler wave propagating through fully developed magnetic islands may provide a physical mechanism underlying the formation of electron scale current sheet.

  9. Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

    NASA Astrophysics Data System (ADS)

    Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

    2014-04-01

    Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

  10. Polarization dependent formation of femtosecond laser-induced periodic surface structures near stepped features

    SciTech Connect

    Murphy, Ryan D.; Torralva, Ben; Adams, David P.; Yalisove, Steven M.

    2014-06-09

    Laser-induced periodic surface structures (LIPSS) are formed near 110 nm-tall Au microstructured edges on Si substrates after single-pulse femtosecond irradiation with a 150 fs pulse centered near a 780 nm wavelength. We investigate the contributions of Fresnel diffraction from step-edges and surface plasmon polariton (SPP) excitation to LIPSS formation on Au and Si surfaces. For certain laser polarization vector orientations, LIPSS formation is dominated by SPP excitation; however, when SPP excitation is minimized, Fresnel diffraction dominates. The LIPSS orientation and period distributions are shown to depend on which mechanism is activated. These results support previous observations of the laser polarization vector influencing LIPSS formation on bulk surfaces.

  11. Galaxy Structure as a Driver of the Star Formation Sequence Slope and Scatter

    NASA Astrophysics Data System (ADS)

    Whitaker, Katherine E.; 3D-HST Collaboration

    2016-01-01

    It is well established that (1) star-forming galaxies follow a relation between their star formation rate (SFR) and stellar mass (M*), the "star formation sequence," and (2) the SFRs of galaxies correlate with their structure, where star-forming galaxies are less concentrated than quiescent galaxies at fixed mass. In this talk, we consider whether the scatter and slope of the star formation sequence is correlated with systematic variations in the Sérsic indices, n, of galaxies across the SFR-M* plane. Using a mass-complete sample of 23,848 galaxies at 0.5 < z < 2.5 selected from the 3D-HST photometric catalogs, we find that the scatter of the star formation sequence is related in part to galaxy structure; the scatter due to variations in n at fixed mass for star-forming galaxies ranges from 0.14 ± 0.02 dex at z ˜ 2 to 0.30 ± 0.04 dex at z < 1. While the slope of the log(SFR)-log(M*) relation is of order unity for disk-like galaxies, galaxies with n > 2 (implying more dominant bulges) have significantly lower SFR/M* than the main ridgeline of the star formation sequence. These results suggest that bulges in massive z ˜ 2 galaxies are actively building up, where the stars in the central concentration are relatively young. At z < 1, the presence of older bulges within star-forming galaxies lowers global SFR/M*, decreasing the slope and contributing significantly to the scatter of the star formation sequence.

  12. STAR FORMATION LAWS AND THRESHOLDS FROM INTERSTELLAR MEDIUM STRUCTURE AND TURBULENCE

    SciTech Connect

    Renaud, Florent; Kraljic, Katarina; Bournaud, Frederic

    2012-11-20

    We present an analytical model of the relation between the surface density of gas and star formation rate in galaxies and clouds, as a function of the presence of supersonic turbulence and the associated structure of the interstellar medium (ISM). The model predicts a power-law relation of index 3/2, flattened under the effects of stellar feedback at high densities or in very turbulent media, and a break at low surface densities when ISM turbulence becomes too weak to induce strong compression. This model explains the diversity of star formation laws and thresholds observed in nearby spirals and their resolved regions, the Small Magellanic Cloud, high-redshift disks and starbursting mergers, as well as Galactic molecular clouds. While other models have proposed interstellar dust content and molecule formation to be key ingredients to the observed variations of the star formation efficiency, we demonstrate instead that these variations can be explained by ISM turbulence and structure in various types of galaxies.

  13. Formation of Structured Water and Gas Hydrate by the Use of Xenon Gas in Vegetable Tissue

    NASA Astrophysics Data System (ADS)

    Ando, Hiroko; Suzuki, Toru; Kawagoe, Yoshinori; Makino, Yoshio; Oshita, Seiichi

    Freezing is a valuable technique for food preservation. However, vegetables are known to be softening remarkably after freezing and thawing process. It is expected to find alternative technique instead of freezing. Recently, the application of structured water and/or gas hydrate had been attempted to prolong the preservation of vegetable. In this study, the formation process of structure water and/or gas hydrate in pure water and carrot tissue was investigated by using NMR relaxation times, T1 and T2, of which applying condition was up to 0.4MPa and 0.8MPa at 5oC. Under the pressure of 0.4MPa, no gas hydrate was appeared, however, at 0.8MPa, formation of gas hydrate was recognized in both water and carrot tissue. Once the gas hydrate formation process in carrot tissue started, T1 and T2 increased remarkably. After that, as the gas hydrate developed, then T1 and T2 turned to decrease. Since this phenomenon was not observed in pure water, it is suggested that behavior of NMR relaxation time just after the formation of gas hydrate in carrot tissue may be peculiar to compartment system such as inter and intracellular spaces.

  14. Structure and conditions for the formation of fullerite crystallites in Sn-C{sub 60} films

    SciTech Connect

    Baran, L. V.

    2009-01-15

    The structure of tin-fullerite films with different thicknesses of the Sn coating layer (50, 100, 200, 300, 450, and 700 nm) and the conditions for the formation and growth of fullerite crystallites on the tin surface during sample exposure in air have been investigated. The methods of X-ray diffraction; scanning electron, transmission electron, and atomic force microscopy; and X-ray microanalysis were used to reveal changes in the structure and phase composition of the tin-fullerite films. Fullerite crystallites in the form of plates and bolts grown under internal stress have been found on the surface of tin films with thicknesses of 50, 100, and 200 nm. The incubation period of crystallite formation is established to be 12-22 months, depending on the thickness of the tin layer.

  15. Modeling the fusion of cylindrical bioink particles in post bioprinting structure formation

    NASA Astrophysics Data System (ADS)

    McCune, Matt; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2015-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method to describe the shape evolution and biomechanical relaxation processes in multicellular systems. Thus, CPD is a useful tool to predict the outcome of post-printing structure formation in bioprinting. The predictive power of CPD has been demonstrated for multicellular systems composed of spherical bioink units. Experiments and computer simulations were related through an independently developed theoretical formalism based on continuum mechanics. Here we generalize the CPD formalism to (i) include cylindrical bioink particles often used in specific bioprinting applications, (ii) describe the more realistic experimental situation in which both the length and the volume of the cylindrical bioink units decrease during post-printing structure formation, and (iii) directly connect CPD simulations to the corresponding experiments without the need of the intermediate continuum theory inherently based on simplifying assumptions. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  16. Effect of the conditions of structure formation on the physicochemical properties of ozonated shungites

    NASA Astrophysics Data System (ADS)

    Emel'Yanova, G. I.; Gorlenko, L. E.; Rozhkova, N. N.; Rumyantseva, M. N.; Lunin, V. V.

    2010-08-01

    It was investigated the influence of ozone on the physicochemical properties of shungites (type 1) (75-98% C) from Nigozero and Chebolaksha deposits (Karelia) formed by hydrothermal (Nigozero) and high-temperature (Chebolaksha) processes. Ozonation was found to affect the specific surface and the total pore volume of shungites considerably. The pore size distribution pattern depends on the volume morphology (texture) of the sample. An increase in the temperature and pressure during the structure formation of shungite (Chebolaksha) led to a shift of the maximum on the distribution pattern towards the formation of mesopores. The size distribution of pores with the dominant contents of micro- and submesopores for both shungites correlated with the basic structural nanoelements of shungite carbon. The peculiarities of the ozonation of shungite nanocarbon found previously (the non-steady state vibrational kinetics of ozonation and the absence of carbon(II) oxide among the reaction products) were confirmed.

  17. Single- and multi-pulse formation of surface structures under static femtosecond irradiation

    NASA Astrophysics Data System (ADS)

    Guillermin, M.; Garrelie, F.; Sanner, N.; Audouard, E.; Soder, H.

    2007-07-01

    Femtosecond surface structure modifications are investigated under irradiation with laser pulses of 150 fs at 800 nm, on copper and silicon. We report sub-wavelength periodic structures formation (ripples) with a periodicity of 500 nm for both materials. These ripples are perpendicular to the laser polarization and can be obtained with only one pulse. The formation of these ripples corresponds to a fluence threshold of 1 J/cm 2 for copper and 0.15 J/cm 2 for silicon. We find several morphologies when more pulses are applied: larger ripples parallel to the polarization are formed with a periodicity of 1 μm and degenerate into a worm-like morphology with a higher number of pulses. In addition, walls of deep holes also show sub-wavelength and large ripples.

  18. Formation of gut-like structures in vitro from mouse embryonic stem cells.

    PubMed

    Torihashi, Shigeko

    2006-01-01

    Embryonic stem (ES) cells have the potential to differentiate into all cell types originating from the three germ layers; however, there are still few reports about the formation of functional organs from embryonic stem cells. Recently, we reported that by hanging drops of mouse ES cells, embryoid bodies (EBs) formed gut-like structures in vitro composed of three layers corresponding to the epithelium, lamina propria, and musculature. The morphological features and the process of formation are similar to gut and its organogenesis in vivo. Thus, this is a good model for development of the gut and a useful tool for analysis of the factors required for gut organogenesis. The protocol basically involves a method of hanging drops to make EBs, which are then plated on coated dishes for outgrowth. EBs develop to form gut-like structures when induced to spontaneously enter a program of differentiation in vitro without addition of any extrinsic factors.

  19. H5MD: A structured, efficient, and portable file format for molecular data

    NASA Astrophysics Data System (ADS)

    de Buyl, Pierre; Colberg, Peter H.; Höfling, Felix

    2014-06-01

    We propose a new file format named "H5MD" for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD files are HDF5 (Hierarchical Data Format) files with a specific hierarchy and naming scheme. Thus, H5MD inherits many benefits of HDF5, e.g., structured layout of multi-dimensional datasets, data compression, fast and parallel I/O, and portability across many programming languages and hardware platforms. H5MD files are self-contained, and foster the reproducibility of scientific data and the interchange of data between researchers using different simulation programs and analysis software. In addition, the H5MD specification can serve for other kinds of data (e.g. experimental data) and is extensible to supplemental data, or may be part of an enclosing file structure.

  20. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

    PubMed

    Kinjo, Akira R; Suzuki, Hirofumi; Yamashita, Reiko; Ikegawa, Yasuyo; Kudou, Takahiro; Igarashi, Reiko; Kengaku, Yumiko; Cho, Hasumi; Standley, Daron M; Nakagawa, Atsushi; Nakamura, Haruki

    2012-01-01

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

  1. Local formation of a Heusler structure in CoFe-Al alloys

    NASA Astrophysics Data System (ADS)

    Wurmehl, S.; Jacobs, P. J.; Kohlhepp, J. T.; Swagten, H. J. M.; Koopmans, B.; Maat, S.; Carey, M. J.; Childress, J. R.

    2011-01-01

    We systematically study the changes in the local atomic environments of Co in CoFe-Al alloys as a function of Al content by means of nuclear magnetic resonance. We find that a Co2FeAl Heusler type structure is formed on a local scale. The observed formation of a highly spin-polarized Heusler compound may explain the improved magnetotransport properties in CoFe-Al based current-perpendicular-to-the-plane spin-valves.

  2. CONNECTING LOCAL STRUCTURE TO INTERFACE FORMATION: A Molecular Scale van der Waals Theory of Nonuniform Liquids

    NASA Astrophysics Data System (ADS)

    Weeks, John D.

    2002-10-01

    This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

  3. Oxide Formation on Biological Nanostructures via a Structure-Directing Agent: Towards an Understanding of Precise Structural Transcription

    PubMed Central

    Wang, Fuke; Nimmo, Susan L.; Cao, Binrui; Mao, Chuanbin

    2012-01-01

    Biomimetic silica formation is strongly dependent on the presence of cationic amine groups which hydrolyze organosilicate precursors and bind to silicate oligomers. Since most biological species possess anionic surfaces, the dependence on amine groups limits utilization of biotemplates for fabricating materials with specific morphologies and pore structures. Here, we report a general aminopropyltriethoxysilane (APTES) directed method for preparing hollow silica with well-defined morphologies using varying biotemplates (proteins, viruses, flagella, bacteria and fungi). Control experiments, pH evolution measurements and 29Si NMR spectroscopic studies have revealed a mechanism of the assembly of APTES on bio-surfaces with subsequent nucleation and growth of silica. The APTES assembly and nuclei formation on bio-surfaces ensured precise transcription of the morphologies of biotemplates to the resulting silica. This method could be extended to the preparation of other oxides. PMID:23630644

  4. The metal site as a template for the metalloprotein structure formation.

    PubMed

    Liu, Changlin; Xu, Huibi

    2002-01-01

    Achieving a thorough explanation of the behavior of metal sites in the formation of native metalloprotein structures is an exciting challenge in the biochemistry of metallobiomacromolecules. This study presents a personal insight into the subject. It is proposed that a metal center and its exogenous ligand compose a template. A template may impose a clear stereochemical preference on the loose peptide chains, and organize them into natural stereospecificity via the metal-ligand interaction, a long-range and strong interaction. Therefore, the stable peptide conformation induced by the template effect surrounding a template polyhedron could be called a template-mediated structural motif (TMSM).

  5. Role of "magic" numbers in structure formation in small silver nanoclusters

    NASA Astrophysics Data System (ADS)

    Redel', L. V.; Gafner, Yu. Ya.; Gafner, S. L.

    2015-10-01

    The molecular dynamics method with the modified tight-binding (TB-SMA) potential has been used to study thermal stability of the initial fcc phase in perfect silver clusters to 2 nm in diameter. Dimensional boundaries of nanoparticles, at which the internal atomic configuration changes upon heating, have been determined using the molecular dynamics simulation. It has been shown that the temperature factor can cause the transition from the initial fcc phase to other structural modifications, including those with pentagonal symmetry, in small Ag clusters. It has been demonstrated that "magic" numbers play an important role in the formation of the internal structure of silver clusters.

  6. [Formation of probabilistic structure of motor behavior in bottlenose dolphins in captivity].

    PubMed

    Chechina, O N; Kondrat'eva, N L

    2009-01-01

    A probabilistic structure of the motor behavior was analyzed in dolphin calves Tursiops truncatus in the prenatal period and adult dolphins in an oceanarium. Ethograms were recorded and subjected to a computer analysis. Ranking probabilities of transitions between behavioral acts revealed a highly determined sequence of operations underlying the newborn dolphins' behavior. The principle of formation of the variation ethologic structures providing a contact between a developing organism and the environment was determined. The results are discussed in terms of the concept of the informational brain-environment interaction. PMID:19947534

  7. Low-temperature process of the formation of tubular and graphene carbon structures

    SciTech Connect

    Dubkov, S. V.; Gavrilov, S. A.; Gromov, D. G. Krasulin, G. A.

    2011-12-15

    The formation of carbon nanostructures by chemical vapor deposition enhanced by glow-discharge plasma is considered. The studies are conducted in the temperature range 300 to 700 Degree-Sign C. Dependences of the structure of the carbon deposit on the thickness of the Ni catalyst film and on the concentration of the carbon-containing component in the vapor phase are analyzed. The reproducible growth of arrays of homogeneous vertical nanotubes or graphene flakes is observed at a low temperature ({approx}350 Degree-Sign C). The electrical properties of the structures are studied.

  8. Formation and atomic structure of ordered Sr-induced nanostrips on Ge(100)

    NASA Astrophysics Data System (ADS)

    Lukanov, Boris R.; Garrity, Kevin F.; Ismail-Beigi, Sohrab; Altman, Eric I.

    2014-04-01

    The deposition of alkaline earths onto Ge(100) surfaces leads to well-ordered arrays of narrow trenches and elongated plateaus that extend for thousands of angstroms. Using scanning tunneling microscopy (STM) in conjunction with density functional theory (DFT), the atomic scale details of these nanostructures are revealed and the driving force responsible for their formation is evaluated. The STM data reveal a dramatic contrast reversal when the polarity of the imaging bias is switched. An energetically favorable structure for the plateaus was found using DFT that can reproduce all of the observed features. This structure is based upon a double dimer vacancy model in which Sr atoms displace two Ge dimers from the surface. Interestingly, the ordered plateau-trench structure is unique to Ge(100) despite the structural and chemical similarities to the Si(100) surface.

  9. Network formation of lipid membranes: Triggering structural transitions by chain melting

    PubMed Central

    Schneider, Matthias F.; Marsh, Derek; Jahn, Wolfgang; Kloesgen, Beate; Heimburg, Thomas

    1999-01-01

    Phospholipids when dispersed in excess water generally form vesicular membrane structures. Cryo-transmission and freeze-fracture electron microscopy are combined here with calorimetry and viscometry to demonstrate the reversible conversion of phosphatidylglycerol aqueous vesicle suspensions to a three-dimensional structure that consists of extended bilayer networks. Thermodynamic analysis indicates that the structural transitions arise from two effects: (i) the enhanced membrane elasticity accompanying the lipid state fluctuations on chain melting and (ii) solvent-associated interactions (including electrostatics) that favor a change in membrane curvature. The material properties of the hydrogels and their reversible formation offer the possibility of future applications, for example in drug delivery, the design of structural switches, or for understanding vesicle fusion or fission processes. PMID:10588702

  10. Spontaneous formation of complex structures made from elastic membranes in an aluminum-hydroxide-carbonate system

    NASA Astrophysics Data System (ADS)

    Kiehl, Micah; Kaminker, Vitaliy; Pantaleone, James; Nowak, Piotr; Dyonizy, Agnieszka; Maselko, Jerzy

    2015-06-01

    A popular playground for studying chemo-hydrodynamic patterns and instabilities is chemical gardens, also known as silicate gardens. In these systems, complex structures spontaneously form, driven by buoyant forces and either osmotic or mechanical pumps. Here, we report on systems that differ somewhat from classical chemical gardens in that the membranes are much more deformable and soluble. These properties lead to structures that self-construct and evolve in new ways. For example, they exhibit the formation of chemical balloons, a new growth mechanism for tubes, and also the homologous shrinking of these tubes. The stretching mechanism for the membranes is probably different than for other systems by involving membrane "self-healing." Other unusual properties are osmosis that sometimes occurs out of the structure and also small plumes that flow away from the structure, sometimes upwards, and sometimes downwards. Mathematical models are given that explain some of the observed phenomena.

  11. Structural phase transitions in trigonal Selenium induce the formation of a disordered phase

    NASA Astrophysics Data System (ADS)

    Pal, Anirban; Gohil, Smita; Sengupta, Surajit; Poswal, H. K.; Sharma, Surinder M.; Ghosh, Shankar; Ayyub, Pushan

    2015-10-01

    Arguments based on the Mermin-Wagner theorem suggest that the quasi-1D trigonal phase of Se should be unstable against long wavelength perturbations. Consisting of parallel Se-Se chains, this essentially fragile solid undergoes a partial transition to a monoclinic structure (consisting of 8-membered rings) at low temperatures (≈50 K), and to a distorted trigonal phase at moderate pressures (≈3GPa). Experimental investigations on sub-millimeter-sized single crystals provide clear evidence that these transitions occur via a novel and counter-intuitive route. This involves the reversible formation of an intermediate, disordered structure that appears as a minority phase with increasing pressure as well as with decreasing temperature. The formation of the disordered state is indicated by: (a) a ‘Boson-peak’ that appears at low temperatures in the specific heat and resonance Raman data, and (b) a decrease in the intensity of Raman lines over a relatively narrow pressure range. We complement the experimental results with a phenomenological model that illustrates how a first order structural transition may lead to disorder. Interestingly, nanocrystals of trigonal Se do not undergo any structural transition in the parameter space studied; neither do they exhibit signs of disorder, further underlining the role of disorder in this type of structural transition.

  12. Spontaneous Formation of Surface Magnetic Structure from Large-scale Dynamo in Strongly Stratified Convection

    NASA Astrophysics Data System (ADS)

    Masada, Youhei; Sano, Takayoshi

    2016-05-01

    We report the first successful simulation of spontaneous formation of surface magnetic structures from a large-scale dynamo by strongly stratified thermal convection in Cartesian geometry. The large-scale dynamo observed in our strongly stratified model has physical properties similar to those in earlier weakly stratified convective dynamo simulations, indicating that the α 2-type mechanism is responsible for the dynamo. In addition to the large-scale dynamo, we find that large-scale structures of the vertical magnetic field are spontaneously formed in the convection zone (CZ) surface only in cases with a strongly stratified atmosphere. The organization of the vertical magnetic field proceeds in the upper CZ within tens of convective turnover time and band-like bipolar structures recurrently appear in the dynamo-saturated stage. We consider several candidates to be possibly be the origin of the surface magnetic structure formation, and then suggest the existence of an as-yet-unknown mechanism for the self-organization of the large-scale magnetic structure, which should be inherent in the strongly stratified convective atmosphere.

  13. Formation of carbon nano- and micro-structures on C+1 irradiated copper surfaces

    NASA Astrophysics Data System (ADS)

    Ahmad, Shoaib

    2013-06-01

    A series of experiments has identified mechanisms of carbon nano- and micro-structure formation at room temperature, without catalyst and in the environment of immiscible metallic surroundings. The structures include threaded nano fibres, graphitic sheets and carbon onions. Copper as substrate was used due to its immiscibility with carbon. Energetic carbon ions (C+1) of 0.2-2.0 MeV irradiated Cu targets. Cu substrates, apertures and 3 mm dia TEM Cu grids were implanted with the carbon. We observed wide range of μm-size structures formed on Cu grids and along the edges of the irradiated apertures. These are shown to be threaded nano fibers (TNF) of few μm thicknesses with lengths varying from 10 to 3000 μm. Secondary electron microscopy (SEM) identifies the μm-size structures while Confocal microscopy was used to learn about the mechanisms by which C+1 irradiated Cu provides the growth environment. Huge carbon onions of diameters ranging from hundreds of nm to μm were observed in the as-grown and annealed samples. Transformations of the nanostructures were observed under prolonged electron irradiations of SEM and TEM. A mechanism for the formation of carbon nano- and micro-structures is proposed.

  14. Local structure of the metal-organic perovskite dimethylammonium manganese(ii) formate.

    PubMed

    Duncan, Helen D; Dove, Martin T; Keen, David A; Phillips, Anthony E

    2016-03-14

    We report total neutron scattering measurements on the metal-organic perovskite analogue dimethylammonium manganese(ii) formate, (CD3)2ND2[Mn(DCO2)3]. Reverse Monte Carlo modelling shows that, in both the disordered high-temperature and ordered low-temperature phases, the ammonium moiety forms substantially shorter hydrogen bonds (N...O = 2.4 Å and 2.6 Å) than are visible in the average crystal structures. These bonds result from a pincer-like motion of two adjacent formate ions about the dimethylammonium ion in such a way that the framework can adjust independently to the positions of nearest-neighbour dimethylammonium ions. At low temperatures the shortest hydrogen bond is less favourable, apparently because it involves a greater distortion of the framework. Furthermore, in the high-temperature phase, in addition to the three disordered nitrogen positions expected from the average crystal structure, there appear to be also smaller probability maxima between these positions, corresponding to orientations in which the dimethylammonium is hydrogen-bonded to the two oxygen atoms of a single formate ion. The spontaneous strain across the phase transition reveals a contraction of the framework about the dimethylammonium cation, continuing as the material is cooled below the transition temperature. These results provide direct evidence of the local atomic structure of the guest-framework hydrogen bonding, and in particular the distortions of the framework responsible for the phase transition in this system. PMID:26763144

  15. The link between galaxy structure and star formation across cosmic time

    NASA Astrophysics Data System (ADS)

    Fang, Jerome Joseph

    The processes that fuel and quench star formation in galaxies are expected to leave imprints on their structure. Moreover, these imprints can serve as signposts to identify galaxies at various stages of their evolution. In this dissertation, we describe our efforts to characterize changes in galaxy structure (1) as star formation is going out, (2) after star formation has ostensibly quenched, and (3) during active star formation, with the goal of elucidating the relevant processes that regulate star formation in each case. In Chapter 2, we use a local (z ˜ 0) sample of galaxies drawn from the Sloan Digital Sky Survey (SDSS) to investigate the first two cases. We find that, as galaxies quench, their outer stellar mass density profiles remain essentially constant. However, their inner stellar mass density (within 1 kpc) increases, even while galaxies are still star-forming, until it reaches a mass-dependent threshold, at which point quenching can occur. The existence of this threshold indicates that quenching is connected with processes that grow bulges. In Chapter 3, we then study the morphologies and color profiles of 19 z ˜ 0 early-type galaxies located in the green valley. Combining high-resolution Hubble ultraviolet images with SDSS optical photometry, we find that these objects harbor low-level star formation that is clearly detectable in the ultraviolet. Moreover, the recently formed stars are distributed in symmetric rings that often span the entire optical extent of the galaxy. The presence of an old underlying population in their outer parts suggests that star formation in these galaxies is either gradually fading out or possibly rejuvenated by smooth accretion from the intergalactic medium. Such galaxies comprise ≈13% of green valley galaxies of similar mass and color, and they may linger in the green valley for several Gyr. Finally, in Chapter 4, we focus on the evolution of star-forming galaxies since z = 2.5, leveraging the rich multi

  16. Formation of asymmetrical structured silica controlled by a phase separation process and implication for biosilicification.

    PubMed

    Shi, Jia-Yuan; Yao, Qi-Zhi; Li, Xi-Ming; Zhou, Gen-Tao; Fu, Sheng-Quan

    2013-01-01

    Biogenetic silica displays intricate patterns assembling from nano- to microsize level and interesting non-spherical structures differentiating in specific directions. Several model systems have been proposed to explain the formation of biosilica nanostructures. Of them, phase separation based on the physicochemical properties of organic amines was considered to be responsible for the pattern formation of biosilica. In this paper, using tetraethyl orthosilicate (TEOS, Si(OCH2CH3)4) as silica precursor, phospholipid (PL) and dodecylamine (DA) were introduced to initiate phase separation of organic components and influence silica precipitation. Morphology, structure and composition of the mineralized products were characterized using a range of techniques including field emission scanning electron microscopy (FESEM), transmission electron microscope (TEM), X-ray diffraction (XRD), thermogravimetric and differential thermal analysis (TG-DTA), infrared spectra (IR), and nitrogen physisorption. The results demonstrate that the phase separation process of the organic components leads to the formation of asymmetrically non-spherical silica structures, and the aspect ratios of the asymmetrical structures can be well controlled by varying the concentration of PL and DA. On the basis of the time-dependent experiments, a tentative mechanism is also proposed to illustrate the asymmetrical morphogenesis. Therefore, our results imply that in addition to explaining the hierarchical porous nanopatterning of biosilica, the phase separation process may also be responsible for the growth differentiation of siliceous structures in specific directions. Because organic amine (e.g., long-chair polyamines), phospholipids (e.g., silicalemma) and the phase separation process are associated with the biosilicification of diatoms, our results may provide a new insight into the mechanism of biosilicification.

  17. Formation of Asymmetrical Structured Silica Controlled by a Phase Separation Process and Implication for Biosilicification

    PubMed Central

    Shi, Jia-Yuan; Yao, Qi-Zhi; Li, Xi-Ming; Zhou, Gen-Tao; Fu, Sheng-Quan

    2013-01-01

    Biogenetic silica displays intricate patterns assembling from nano- to microsize level and interesting non-spherical structures differentiating in specific directions. Several model systems have been proposed to explain the formation of biosilica nanostructures. Of them, phase separation based on the physicochemical properties of organic amines was considered to be responsible for the pattern formation of biosilica. In this paper, using tetraethyl orthosilicate (TEOS, Si(OCH2CH3)4) as silica precursor, phospholipid (PL) and dodecylamine (DA) were introduced to initiate phase separation of organic components and influence silica precipitation. Morphology, structure and composition of the mineralized products were characterized using a range of techniques including field emission scanning electron microscopy (FESEM), transmission electron microscope (TEM), X-ray diffraction (XRD), thermogravimetric and differential thermal analysis (TG-DTA), infrared spectra (IR), and nitrogen physisorption. The results demonstrate that the phase separation process of the organic components leads to the formation of asymmetrically non-spherical silica structures, and the aspect ratios of the asymmetrical structures can be well controlled by varying the concentration of PL and DA. On the basis of the time-dependent experiments, a tentative mechanism is also proposed to illustrate the asymmetrical morphogenesis. Therefore, our results imply that in addition to explaining the hierarchical porous nanopatterning of biosilica, the phase separation process may also be responsible for the growth differentiation of siliceous structures in specific directions. Because organic amine (e.g., long-chair polyamines), phospholipids (e.g., silicalemma) and the phase separation process are associated with the biosilicification of diatoms, our results may provide a new insight into the mechanism of biosilicification. PMID:23585878

  18. Formation of structures around HII regions: ionization feedback from massive stars

    NASA Astrophysics Data System (ADS)

    Tremblin, P.; Audit, E.; Minier, V.; Schmidt, W.; Schneider, N.

    2015-03-01

    We present a new model for the formation of dense clumps and pillars around HII regions based on shocks curvature at the interface between a HII region and a molecular cloud. UV radiation leads to the formation of an ionization front and of a shock ahead. The gas is compressed between them forming a dense shell at the interface. This shell may be curved due to initial interface or density modulation caused by the turbulence of the molecular cloud. Low curvature leads to instabilities in the shell that form dense clumps while sufficiently curved shells collapse on itself to form pillars. When turbulence is high compared to the ionized-gas pressure, bubbles of cold gas have sufficient kinetic energy to penetrate into the HII region and detach themselves from the parent cloud, forming cometary globules. Using computational simulations, we show that these new models are extremely efficient to form dense clumps and stable and growing elongated structures, pillars, in which star formation might occur (see Tremblin et al. 2012a). The inclusion of turbulence in the model shows its importance in the formation of cometary globules (see Tremblin et al. 2012b). Globally, the density enhancement in the simulations is of one or two orders of magnitude higher than the density enhancement of the classical ``collect and collapse`` scenario. The code used for the simulation is the HERACLES code, that comprises hydrodynamics with various equation of state, radiative transfer, gravity, cooling and heating. Our recent observations with Herschel (see Schneider et al. 2012a) and SOFIA (see Schneider et al. 2012b) and additional Spitzer data archives revealed many more of these structures in regions where OB stars have already formed such as the Rosette Nebula, Cygnus X, M16 and Vela, suggesting that the UV radiation from massive stars plays an important role in their formation. We present a first comparison between the simulations described above and recent observations of these regions.

  19. Geologic Observations and Numerical Modeling: A Combined Approach to Understanding Crater and Basin Formation and Structure

    NASA Astrophysics Data System (ADS)

    Potter, R. W. K.; Head, J. W., III

    2014-12-01

    Impact cratering is a fundamental geological process throughout the Solar System. The Moon is an ideal location to document the impact cratering process due to the number and excellent state of preservation of large craters and basins, and the wide range of geological, geophysical, topographic, mineralogic, remote sensing and returned sample data. Despite the number and excellent preservation state of many large complex craters and basins, their formation and the origin of their structural features and the stages in their evolution remain contentious. To more comprehensively document the final stage of lunar impact basin formation, we have compiled detailed topographic, geological and mineralogic maps of several type examples of peak-ring and multi-ring basins, including the Orientale basin. These data include the mineralogic characteristics of basin ring structures and assist in the interpretation of the target stratigraphy, and the depth of origin of basin rings. Data for the current structure of basins is compared to numerical model outputs of basin-forming impacts, which track formation to the conclusion of dynamic processes (2 to 3 hours after impact). We use the Orientale basin as an example and provide combined correlations and interpretations that assign rings to various stages in the numerical models, and compare these candidates to crustal stratigraphy, with the ultimate aim of producing a consistent model for large crater/basin formation. The shock physics code iSALE is used to numerically model the basin-scale impacts. Constitutive equations and equations of state for materials analogous to the lunar crust (gabbroic anorthosite) and mantle (dunite) are used. Aspects of the numerically-produced lunar basins (e.g., material distribution and accumulated stress) are compared and contrasted to remote observations and geological maps of the Orientale rings and geological units, including ejecta and impact melt deposits.

  20. Supramolecular structure formation of Langmuir-Blodgett films of comblike precursor and polyimide

    SciTech Connect

    Goloudina, S. I. Luchinin, V. V.; Rozanov, V. V.; Pasyuta, V. M.; Gofman, I. V.; Sklizkova, V. P.; Kudryavtsev, V. V.

    2013-03-15

    The surface structure of Langmuir-Blodgett films of a comblike polyimide precursor-a rigid-chain polyamic acid alkylamine salt bearing multichains of tertiary amine-and films of the corresponding polyimide were studied by atomic force microscopy (AFM). An analysis of the images of the surface of three-layer films revealed a domain structure. It was found that the Langmuir-Blodgett film formation of the precursor occurs as a result of the layer-by-layer deposition of two-dimensional domains (composed of polyamic acid salt molecules on the water surface) onto a substrate. The formation of domains in a monolayer is associated with the chemical structure of the precursor, to be more precise, with the rigidity of the main chain and the presence of closely spaced aliphatic side chains in the polymer chain, whose total cross-section area is close to the surface area of the projection onto the plane of the repeating unit of the main chain. Polyimide films inherit the domain structure of the precursor films; the inhomogeneity of the film thickness substantially decreases, whereas the domain size and character of their distribution in the film remain unchanged.

  1. Recrystallized Impact Glasses of the Onaping Formation and the Sudbury Igneous Complex, Sudbury Structure, Ontario, Canada

    NASA Technical Reports Server (NTRS)

    Dressler, B. O.; Weiser, T.; Brockmeyer, P.

    1996-01-01

    The origin of the Sudbury Structure and of the associated heterolithic breccias of the Onaping Formation and the Sudbury Igneous Complex have been controversial. While an impact origin of the structure has gained wide acceptance over the last 15 years, the origin of the recrystallized Onaping Formation glasses and of the igneous complex is still being debated. Recently the interpretation of the breccias of the Onaping Formation as suevitic fall-back impact breccias has been challenged. The igneous complex is interpreted either as a differentiated impact melt sheet or as a combination of an upper impact melt represented by the granophyre, and a lower, impact-triggered magmatic body consisting of the norite-sublayer formations. The Onaping Formation contains glasses as fluidal and nonfluidal fragments of various shapes and sizes. They are recrystallized, and our research indicates that they are petrographically heterogeneous and span a wide range of chemical compositions. These characteristics are not known from glasses of volcanic deposits. This suggests an origin by shock vitrification, an interpretation consistent with their association with numerous and varied country rock clasts that exhibit microscopic shock metamorphic features. The recrystallized glass fragments represent individual solid-state and liquid-state vitrified rocks or relatively small melt pods. The basal member lies beneath the Gray and Black members of the Onaping Formation and, where not metamorphic, has an igneous matrix. Igneous-textured melt bodies occur in the upper two members and above the Basal Member. A comparison of the chemical compositions of recrystallized glasses and of the matrices of the Basal Member and the melt bodies with the components and the bulk composition of the igneous complex is inconclusive as to the origin of the igneous complex. Basal Member matrix and Melt Bodies, on average, are chemically similar to the granophyre of the Sudbury Igneous Complex, suggesting that

  2. The formation of Population III stars and their effect on cosmological structure in the early universe

    NASA Astrophysics Data System (ADS)

    O'Shea, Brian William

    2005-11-01

    The first generation of stars to form in the universe have a profound impact on their environment. These stars are responsible for beginning the universe's transition from a "cosmic dark age" where no sources of visible light existed; to the bright universe seen today. Additionally, these stars were believed to be the first sources of all elements heavier than lithium, which strongly affected the ability of gas to cool and permanently changed how star formation occurred. In this dissertation I present results from numerical simulations of the formation of the first generation of stars to form in the universe ("Population III" stars) and their effects on later structure formation. I compare Enzo, the adaptive mesh refinement cosmology code used to perform all of the simulations in this work, to GADGET, a smoothed particle hydrodynamics cosmology code. Nearly identical results can be obtained when using two extremely different numerical methods, which helps to verify the correctness of both codes and strengthen the confidence of predictions made with these tools. I perform high dynamical range calculations of the formation of an ensemble of Population III stars, varying multiple simulation parameters, in a standard cold dark matter cosmology as well as with a soft ultraviolet background and in a generic warm dark matter cosmology. I find that the accretion rates of primordial protostars have been systematically overestimated by previously published work, which has profound implications for later structure formation and the reionization of the universe. Additionally, the presence of a soft ultraviolet background and warm dark matter serves to delay the onset of star formation. I propose limits on the possible mass of a warm dark matter particle. I also present results of simulations which demonstrate the effects of the HII regions and metal enrichment from Population III stars. It appears that HII regions from these stars may hasten the formation of later generations

  3. Formation of Multicomponent Star Structures at the Liquid/Solid Interface.

    PubMed

    Tahara, Kazukuni; Kaneko, Kyohei; Katayama, Keisuke; Itano, Shintaro; Nguyen, Chi Huan; Amorim, Deborah D D; De Feyter, Steven; Tobe, Yoshito

    2015-06-30

    To demonstrate key roles of multiple interactions between multiple components and multiple phases in the formation of an uncommon self-assembling pattern, we present here the construction of a porous hexagonal star (h-star) structure using a trigonal molecular building block at the liquid/solid interface. For this purpose, self-assembly of hexaalkoxy-substituted dehydrobenzo[12]annulene derivatives DBA-OCns was investigated at the tetradecane/graphite interface by means of scanning tunneling microscopy (STM). Monolayer structures were significantly influenced by coadsorbed tetradecane molecules depending on the alkyl chains length (C13-C16) of DBA-OCn. However, none of DBA-OCn molecules formed the expected trigonal complexes, indicating that an additional driving force is necessary for the formation of the trigonal complex and its assembly into the h-star structure. As a first approach, we employed the "guest induced structural change" for the formation of the h-star structure. In the presence of two guest molecules, nonsubstituted DBA and hexakis(phenylethynyl)benzene which fit the respective pores, an h-star structure was formed by DBA-OC15 at the tetradecane/graphite interface. Moreover, a tetradecane molecule was coadsorbed between a pair of alkyl chains of DBA-OC15, thereby blocking the interdigitation of the alkyl chain pairs. Therefore, the h-star structure results from the self-assembly of the four molecular components including the solvent molecule. The second approach is based on aggregation of perfluoroalkyl chains via fluorophilicity of DBA-F, in which the perfluoroalkyl groups are substituted at the end of three alkyl chains of DBA-OCn via p-phenylene linkers. A trigonal complex consisting of DBA-F and three tetradecane molecules formed an h-star structure, in which the perfluoroalkyl groups that orient into the alkane solution phase aggregated at the hexagonal pore via fluorophilicity. The present result provides useful insight into the design and

  4. Formation of Multicomponent Star Structures at the Liquid/Solid Interface.

    PubMed

    Tahara, Kazukuni; Kaneko, Kyohei; Katayama, Keisuke; Itano, Shintaro; Nguyen, Chi Huan; Amorim, Deborah D D; De Feyter, Steven; Tobe, Yoshito

    2015-06-30

    To demonstrate key roles of multiple interactions between multiple components and multiple phases in the formation of an uncommon self-assembling pattern, we present here the construction of a porous hexagonal star (h-star) structure using a trigonal molecular building block at the liquid/solid interface. For this purpose, self-assembly of hexaalkoxy-substituted dehydrobenzo[12]annulene derivatives DBA-OCns was investigated at the tetradecane/graphite interface by means of scanning tunneling microscopy (STM). Monolayer structures were significantly influenced by coadsorbed tetradecane molecules depending on the alkyl chains length (C13-C16) of DBA-OCn. However, none of DBA-OCn molecules formed the expected trigonal complexes, indicating that an additional driving force is necessary for the formation of the trigonal complex and its assembly into the h-star structure. As a first approach, we employed the "guest induced structural change" for the formation of the h-star structure. In the presence of two guest molecules, nonsubstituted DBA and hexakis(phenylethynyl)benzene which fit the respective pores, an h-star structure was formed by DBA-OC15 at the tetradecane/graphite interface. Moreover, a tetradecane molecule was coadsorbed between a pair of alkyl chains of DBA-OC15, thereby blocking the interdigitation of the alkyl chain pairs. Therefore, the h-star structure results from the self-assembly of the four molecular components including the solvent molecule. The second approach is based on aggregation of perfluoroalkyl chains via fluorophilicity of DBA-F, in which the perfluoroalkyl groups are substituted at the end of three alkyl chains of DBA-OCn via p-phenylene linkers. A trigonal complex consisting of DBA-F and three tetradecane molecules formed an h-star structure, in which the perfluoroalkyl groups that orient into the alkane solution phase aggregated at the hexagonal pore via fluorophilicity. The present result provides useful insight into the design and

  5. Biological carbon precursor to diagenetic siderite with spherical structures in iron formations.

    PubMed

    Köhler, Inga; Konhauser, Kurt O; Papineau, Dominic; Bekker, Andrey; Kappler, Andreas

    2013-01-01

    During deposition of Precambrian iron formation, the combined sedimentation of ferrihydrite and phytoplankton biomass should have facilitated Fe(III) reduction during diagenesis. However, the only evidence for this reaction in iron formations is the iron and carbon isotope values preserved in the authigenic ferrous iron-containing minerals. Here we show experimentally that spheroidal siderite, which is preserved in many iron formation and could have been precursor to rhombohedral or massive siderite, forms by reacting ferrihydrite with glucose (a proxy for microbial biomass) at pressure and temperature conditions typical of diagenesis (170 °C and 1.2 kbar). Depending on the abundance of siderite, we found that it is also possible to draw conclusions about the Fe(III):C ratio of the initial ferrihydrite-biomass sediment. Our results suggest that spherical to rhombohedral siderite structures in deep-water, Fe-oxide iron formation can be used as a biosignature for photoferrotrophy, whereas massive siderite reflects high cyanobacterial biomass loading in highly productive shallow-waters.

  6. Biological carbon precursor to diagenetic siderite with spherical structures in iron formations.

    PubMed

    Köhler, Inga; Konhauser, Kurt O; Papineau, Dominic; Bekker, Andrey; Kappler, Andreas

    2013-01-01

    During deposition of Precambrian iron formation, the combined sedimentation of ferrihydrite and phytoplankton biomass should have facilitated Fe(III) reduction during diagenesis. However, the only evidence for this reaction in iron formations is the iron and carbon isotope values preserved in the authigenic ferrous iron-containing minerals. Here we show experimentally that spheroidal siderite, which is preserved in many iron formation and could have been precursor to rhombohedral or massive siderite, forms by reacting ferrihydrite with glucose (a proxy for microbial biomass) at pressure and temperature conditions typical of diagenesis (170 °C and 1.2 kbar). Depending on the abundance of siderite, we found that it is also possible to draw conclusions about the Fe(III):C ratio of the initial ferrihydrite-biomass sediment. Our results suggest that spherical to rhombohedral siderite structures in deep-water, Fe-oxide iron formation can be used as a biosignature for photoferrotrophy, whereas massive siderite reflects high cyanobacterial biomass loading in highly productive shallow-waters. PMID:23612282

  7. Lipid-free Apolipoprotein A-I Structure: Insights into HDL Formation and Atherosclerosis Development.

    PubMed

    Mei, Xiaohu; Atkinson, David

    2015-07-01

    Apolipoprotein A-I is the major protein in high-density lipoprotein (HDL) and plays an important role during the process of reverse cholesterol transport (RCT). Knowledge of the high-resolution structure of full-length apoA-I is vital for a molecular understanding of the function of HDL at the various steps of the RCT pathway. Due to the flexible nature of apoA-I and aggregation properties, the structure of full-length lipid-free apoA-I has evaded description for over three decades. Sequence analysis of apoA-I suggested that the amphipathic α-helix is the structural motif of exchangeable apolipoprotein, and NMR, X-ray and MD simulation studies have confirmed this. Different laboratories have used different methods to probe the secondary structure distribution and organization of both the lipid-free and lipid-bound apoA-I structure. Mutation analysis, synthetic peptide models, surface chemistry and crystal structures have converged on the lipid-free apoA-I domain structure and function: the N-terminal domain [1-184] forms a helix bundle while the C-terminal domain [185-243] mostly lacks defined structure and is responsible for initiating lipid-binding, aggregation and is also involved in cholesterol efflux. The first 43 residues of apoA-I are essential to stabilize the lipid-free structure. In addition, the crystal structure of C-terminally truncated apoA-I suggests a monomer-dimer conversation mechanism mediated through helix 5 reorganization and dimerization during the formation of HDL. Based on previous research, we have proposed a structural model for full-length monomeric apoA-I in solution and updated the HDL formation mechanism through three states. Mapping the known natural mutations on the full-length monomeric apoA-I model provides insight into atherosclerosis development through disruption of the N-terminal helix bundle or deletion of the C-terminal lipid-binding domain.

  8. THE FORMATION AND MAGNETIC STRUCTURES OF ACTIVE-REGION FILAMENTS OBSERVED BY NVST, SDO, AND HINODE

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Wang, J. C.; Xiang, Y. Y.; Kong, D. F.; Yang, L. H.; Pan, G. M.

    2015-08-15

    To better understand the properties of solar active-region filaments, we present a detailed study on the formation and magnetic structures of two active-region filaments in active region NOAA 11884 during a period of four days. It is found that the shearing motion of the opposite magnetic polarities and the rotation of the small sunspots with negative polarity play an important role in the formation of two active-region filaments. During the formation of these two active-region filaments, one foot of the filaments was rooted in a small sunspot with negative polarity. The small sunspot rotated not only around another small sunspot with negative polarity, but also around the center of its umbra. By analyzing the nonlinear force-free field extrapolation using the vector magnetic fields in the photosphere, twisted structures were found in the two active-region filaments prior to their eruptions. These results imply that the magnetic fields were dragged by the shearing motion between opposite magnetic polarities and became more horizontal. The sunspot rotation twisted the horizontal magnetic fields and finally formed the twisted active-region filaments.

  9. Nanoscale self-assembly of starch: Phase relations, formation, and structure

    NASA Astrophysics Data System (ADS)

    Creek, John A.

    This project has been undertaken to develop a fundamental understanding of the spherulitic self-assembly of starch polymers from aqueous solution, both as a model for starch granule initiation in vivo and as a biologically-inspired material with applications in the food and pharmaceutical industries. Botanical starches were observed to form semi-crystalline spherulites from aqueous solution when cooled after a high temperature treatment, and the processes resulting in spherulite formation were investigated. Based on the influence of cooling rate on spherulite formation from a botanical starch, liquid-liquid demixing in competition with crystallization was proposed as the mechanism leading to spherulite formation (summarized in a hypothetical phase diagram). Study of amylose and amylopectin self-assembly demonstrated that the linear polymer plays the primary role in forming spherulites. As a result, the roles of degree of polymerization, concentration, and thermal processing conditions on amylose self-assembly were explored. Thermal properties, final system morphology, and crystalline allomorph were characterized. In all cases the experimental findings supported the proposed phase diagram. Finally, the crystalline nanostructure of the spherulites was probed using atomic force microscopy (AFM), revealing a seemingly universal level of structure in crystalline starch materials. This was compared to an existing model of crystallization for synthetic polymers involving a transitional liquid crystalline-like ordering---a comparison that makes sense in light of the known helical structure of starch.

  10. Structural changes of tumor necrosis factor alpha associated with membrane insertion and channel formation.

    PubMed Central

    Baldwin, R L; Stolowitz, M L; Hood, L; Wisnieski, B J

    1996-01-01

    Low pH enhances tumor necrosis factor alpha (TNF)-induced cytolysis of cancer cells and TNF-membrane interactions that include binding, insertion, and ion-channel formation. We have also found that TNF increases Na+ influx in cells. Here, we examined the structural features of the TNF-membrane interaction pathway that lead to channel formation. Fluorometric studies link TNF's acid-enhanced membrane interactions to rapid but reversible acquisition of hydrophobic surface properties. Intramembranous photolabeling shows that (i) protonation of TNF promotes membrane insertion, (ii) the physical state of the target bilayer affects the kinetics and efficiency of TNF insertion, and (iii) binding and insertion of TNF are two distinct events. Acidification relaxes the trimeric structure of soluble TNF so that the cryptic carboxyl termini, centrally located at the base of the trimer cone, become susceptible to carboxypeptidase Y. After membrane insertion, TNF exhibits a trimeric configuration in which the carboxyl termini are no longer exposed; however, the proximal salt-bridged Lys-11 residues as well as regional surface amino acids (Glu-23, Arg-32, and Arg-44) are notably more accessible to proteases. The sequenced cleavage products bear the membrane-restricted photoreactive probe, proof that surface-cleaved TNF has an intramembranous disposition. In summary, the trimer's structural plasticity is a major determinant of its channel-forming ability. Channel formation occurs when cracked or partially splayed trimers bind and penetrate the bilayer. Reannealing leads to a slightly relaxed trimeric structure. The directionality of bilayer penetration conforms with x-ray data showing that receptor binding to the monomer interfaces of TNF poises the tip of the trimeric cone directly above the target cell membrane. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8577707

  11. Electrochemistry of surfactant-doped polypyrrole film(I): Formation of columnar structure by electropolymerization

    SciTech Connect

    Naoi, Katsuhiko; Oura, Yasushi; Maeda, Michiko; Nakamura, Sadako

    1995-02-01

    Electroactive polypyrrole (PPy) films have been studied widely in the field of applied material science for high energy/power storage applications. Perpendicularly oriented columnar structure was obtained for electropolymerized polypyrrole films formed from micellar solution of anionic surfactants. The surfactants used as dopants were a class of anionic surfactant, namely, Na salts of dodecyl sulfate (SDS) and dodecylbenzene sulfonate (SDBS). The formation process of polypyrrole films on electrode surfaces was studied with in situ atomic force microscopy (AFM) and electrochemical quartz crystal microbalance (EQCM) methods to monitor the structure of the grown polymers. In EQCM measurement, the frequency shift ({Delta}f) and the resonance resistance ({Delta}R) of the quartz crystal electrode were obtained simultaneously. An abrupt increase in {Delta}R was observed for both PPy/DS and PPy/DBS films at about 60--100mC/cm{sup 2}. Such a drastic change in {Delta}R, which may be associated with the emergence of the viscoelastic properties of the films, could be explained by the formation of columnar structure. In situ AFM observation clearly indicated that such a structure started to form around these critical charges. The cyclic voltammograms for the PPy/DS and PPy/DBS{sup {minus}} films showed sharp redox couples observed around {minus}0.5 to 0.6 V. The diffusion rate of cations for the resulting films was studied with ac impedance measurement as a function of the concentration of surfactant dopants. As the PPy film was prepared in higher concentration of the surfactant dopant, where the micelles are formed in solution, the resulting film showed a considerably higher (ca. 3 orders of magnitude) diffusion coefficient compared to ordinary PPy films so far reported. Such an enhanced diffusivity of ions could be attributed to a special formation process of polypyrrole in micelle solution: the mechanism is discussed here.

  12. Helix-like structure formation of a semi-flexible chain confined in a cylinder channel

    NASA Astrophysics Data System (ADS)

    Wen, Xiaohui; Sun, Tieyu; Zhang, Wei-Bing; Lam, Chi-Hang; Zhang, Linxi; Zang, Huaping

    2016-09-01

    Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel. A novel helix-like structure is found to form during the simulation. Moreover, the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated. We find that the structure is not a perfect helix, but a bundle of elliptical turns. In addition, we conduct a statistical analysis for the chain monomer distribution along the radial direction. This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent. Project supported by the National Natural Science Foundation of China (Grant Nos. 11504033 and 11404290) and the General Research Fund of Hong Kong Research Council of China (Grant No. 15301014).

  13. Structures in material transference and vitelline envelope formation in Betta splendens follicles.

    PubMed

    Genta, H D

    1996-01-01

    Structures were found by transmission electron microscopy, they were located within follicular cells and the oocyte, and in the interspace between them in follicles of the teleost fish Betta splendens. Some structures with features characteristic or lamellar bodies were found in small follicles. The possible role of these structures in the formation of the vitelline envelope as well as in the material transference is discussed. Vacuoles, vesticles and particles intensely stained were found in the microvilli and the cortical cytoplasm of the oocyte at the onset of vitellogenesis. These results suggest that different substances present in the cellular components of the follicle might be transferred from cell to cell through the extracellular space and through the prolongations that cross the extracellular space.

  14. Formation, structure, and properties of "welded" h-BN/graphene compounds

    NASA Astrophysics Data System (ADS)

    Chernozatonskii, L. A.; Demin, V. A.; Artyukh, A. A.

    2016-07-01

    Structures of h-BN/graphene with holes where atoms at the edges are bonded to each other by sp 2 hybridized C-B and C-N bonds and form continuous junctions from layer to layer with topological defects inside holes have been considered. Their formation, as well as the moiré-type stable atomic structure of such compounds (with different rotation angles of graphene with respect to the hexagonal boron nitride monolayer) with closed hexagonal holes in the AA centers of packing of the moiré superlattice, has been studied. The stability, as well as the electronic and mechanical properties, of such bilayer BN/graphene nanomeshes has been analyzed within electron density functional theory. It has been shown that they have semiconducting properties. Their electronic band structures and mechanical characteristics differ from the respective properties of separate monolayer nanomeshes with the same geometry and arrangement of holes.

  15. Formation, Structure and Properties of Amorphous Carbon Char from Polymer Materials in Extreme Atmospheric Reentry Environments

    NASA Technical Reports Server (NTRS)

    Lawson, John W.

    2010-01-01

    Amorphous carbonaceous char produced from the pyrolysis of polymer solids has many desirable properties for ablative heat shields for space vehicles. Molecular dynamics simulations are presented to study the transformation of the local atomic structure from virgin polymer to a dense, disordered char [1]. Release of polymer hydrogen is found to be critical to allow the system to collapse into a highly coordinated char structure. Mechanisms of the char formation process and the morphology of the resulting structures are elucidated. Thermal conductivity and mechanical response of the resulting char are evaluated [2]. During reenty, the optical response and oxidative reactivity of char are also important properties. Results of ab initio computations of char optical functions [3] and char reactivity [4] are also presented.

  16. Helix-like structure formation of a semi-flexible chain confined in a cylinder channel

    NASA Astrophysics Data System (ADS)

    Wen, Xiaohui; Sun, Tieyu; Zhang, Wei-Bing; Lam, Chi-Hang; Zhang, Linxi; Zang, Huaping

    2016-09-01

    Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel. A novel helix-like structure is found to form during the simulation. Moreover, the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated. We find that the structure is not a perfect helix, but a bundle of elliptical turns. In addition, we conduct a statistical analysis for the chain monomer distribution along the radial direction. This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent. Project supported by the National Natural Science Foundation of China (Grant Nos. 11504033 and 11404290) and the General Research Fund of Hong Kong Research Council of China (Grant No. 15301014).

  17. Thermodynamics of Complex Sulfide Inclusion Formation in Ca-Treated Al-Killed Structural Steel

    NASA Astrophysics Data System (ADS)

    Guo, Yin-tao; He, Sheng-ping; Chen, Gu-jun; Wang, Qian

    2016-08-01

    Controlling the morphology of the sulfide inclusion is of vital importance in enhancing the properties of structural steel. Long strip-shaped sulfides in hot-rolled steel can spherize when, instead of the inclusion of pure single-phase MnS, the guest is a complex sulfide, such as an oxide-sulfide duplex and a solid-solution sulfide particle. In this study, the inclusions in a commercial rolled structural steel were investigated. Spherical and elongated oxide-sulfide duplex as well as single-phase (Mn,Ca)S solid solution inclusions were observed in the steel. A thermodynamic equilibrium between the oxide and sulfide inclusions was proposed to understand the oxide-sulfide duplex inclusion formation. Based on the equilibrium solidification principle, thermodynamic discussions on inclusion precipitation during the solidification process were performed for both general and resulfurized structural steel. The predicted results of the present study agreed well with the experimental ones.

  18. Using laser radiation for the formation of capillary structure in flat ceramic heat pipes

    NASA Astrophysics Data System (ADS)

    Nikolaenko, Yu. E.; Rotner, S. M.

    2012-12-01

    The possibility of using laser radiation with a wavelength of 1.064 μm for the formation of a capillary structure in the evaporation zone of flat ceramic heat pipes has been experimentally confirmed. Using a technological regime with established parameters, a capillary structure was formed in AlN and Al2O3 ceramic plates with a thickness of 1-2 mm and lateral dimensions of 48 × 60 and 100 × 100 mm, which ensured absorption of heat-transfer fluids (distilled water, ethyl alcohol, acetone) to a height of 100 mm against gravity forces. The thermal resistance of flat ceramic heat pipes with this capillary structure reaches 0.07°C/W, which is quite acceptable for their use as heat sinks in systems of thermal regime control for electronic components and as heat exchange plates for large-size thermoelectric conversion units.

  19. Structures in material transference and vitelline envelope formation in Betta splendens follicles.

    PubMed

    Genta, H D

    1996-01-01

    Structures were found by transmission electron microscopy, they were located within follicular cells and the oocyte, and in the interspace between them in follicles of the teleost fish Betta splendens. Some structures with features characteristic or lamellar bodies were found in small follicles. The possible role of these structures in the formation of the vitelline envelope as well as in the material transference is discussed. Vacuoles, vesticles and particles intensely stained were found in the microvilli and the cortical cytoplasm of the oocyte at the onset of vitellogenesis. These results suggest that different substances present in the cellular components of the follicle might be transferred from cell to cell through the extracellular space and through the prolongations that cross the extracellular space. PMID:9369035

  20. Relationship between chain collapse and secondary structure formation in a partially folded protein.

    PubMed

    Nakagawa, Kanako; Yamada, Yoshiteru; Matsumura, Yoshitaka; Tsukamoto, Seiichi; Yamamoto-Ohtomo, Mio; Ohtomo, Hideaki; Okabe, Takahiro; Fujiwara, Kazuo; Ikeguchi, Masamichi

    2014-06-01

    Chain collapse and secondary structure formation are frequently observed during the early stages of protein folding. Is the chain collapse brought about by interactions between secondary structure units or is it due to polymer behavior in a poor solvent (coil-globule transition)? To answer this question, we measured small-angle X-ray scattering for a series of β-lactoglobulin mutants under conditions in which they assume a partially folded state analogous to the folding intermediates. Mutants that were designed to disrupt the secondary structure units showed the gyration radii similar to that of the wild type protein, indicating that chain collapse is due to coil-globule transitions. PMID:25100622

  1. Inert-Gas Condensed Co-W Nanoclusters: Formation, Structure and Magnetic Properties

    NASA Astrophysics Data System (ADS)

    Golkar-Fard, Farhad Reza

    Rare-earth permanent magnets are used extensively in numerous technical applications, e.g. wind turbines, audio speakers, and hybrid/electric vehicles. The demand and production of rare-earth permanent magnets in the world has in the past decades increased significantly. However, the decrease in export of rare-earth elements from China in recent time has led to a renewed interest in developing rare-earth free permanent magnets. Elements such as Fe and Co have potential, due to their high magnetization, to be used as hosts in rare-earth free permanent magnets but a major challenge is to increase their magnetocrystalline anisotropy constant, K1, which largely drives the coercivity. Theoretical calculations indicate that dissolving the 5d transition metal W in Fe or Co increases the magnetocrystalline anisotropy. The challenge, though, is in creating a solid solution in hcp Co or bcc Fe, which under equilibrium conditions have negligible solubility. In this dissertation, the formation, structure, and magnetic properties of sub-10 nm Co-W clusters with W content ranging from 4 to 24 atomic percent were studied. Co-W alloy clusters with extended solubility of W in hcp Co were produced by inert gas condensation. The different processing conditions such as the cooling scheme and sputtering power were found to control the structural state of the as-deposited Co-W clusters. For clusters formed in the water-cooled formation chamber, the mean size and the fraction crystalline clusters increased with increasing power, while the fraction of crystalline clusters formed in the liquid nitrogen-cooled formation chamber was not as affected by the sputtering power. For the low W content clusters, the structural characterization revealed clusters predominantly single crystalline hcp Co(W) structure, a significant extension of W solubility when compared to the equilibrium solubility, but fcc Co(W) and Co3W structures were observed in very small and large clusters, respectively. At high

  2. Influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures and lattice defects accumulation

    SciTech Connect

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

    2014-04-28

    The influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures (LIPSS) has been investigated on a polycrystalline nickel sample. Electron Backscatter Diffraction characterization has been exploited to provide structural information within the laser spot on irradiated samples to determine the dependence of LIPSS formation and lattice defects (stacking faults, twins, dislocations) upon the crystal orientation. Significant differences are observed at low-to-medium number of laser pulses, outstandingly for (111)-oriented surface which favors lattice defects formation rather than LIPSS formation.

  3. 3D structure and formation of hydrothermal vent complexes in the Møre Basin

    NASA Astrophysics Data System (ADS)

    Kjoberg, Sigurd; Schmiedel, Tobias; Planke, Sverre; Svensen, Henrik H.; Galland, Oliver; Jerram, Dougal A.

    2016-04-01

    The mid-Norwegian Møre margin is regarded as a type example of a volcanic rifted margin, with its formation usually related to the influence of the Icelandic plume activity. The area is characterized by the presence of voluminous basaltic complexes such as extrusive lava sequences, intrusive sills and dikes, and hydrothermal vent complexes within the Møre Basin. Emplacement of hydrothermal vent complexes is accommodated by deformation of the host rock. The edges of igneous intrusions mobilize fluids by heat transfer into the sedimentary host rock (aureoles). Fluid expansion may lead to formation of piercing structures due to upward fluid migration. Hydrothermal vent complexes induce bending of overlying strata, leading to the formation of dome structures at the paleo-surface. These dome structures are important as they indicate the accommodation created for the intrusions by deformation of the upper layers of the stratigraphy, and may form important structures in many volcanic margins. Both the morphological characteristics of the upper part and the underlying feeder-structure (conduit-zone) can be imaged and studied on 3D seismic data. Seismic data from the Tulipan prospect located in the western part of the Møre Basin have been used in this study. The investigation focusses on (1) the vent complex geometries, (2) the induced surface deformation patterns, (3) the relation to the intrusions (heat source), as well as (4) the emplacement depth of the hydrothermal vent complexes. We approach this by doing a detailed 3D seismic interpretation of the Tulipan seismic data cube. The complexes formed during the initial Eocene, and are believed to be a key factor behind the rapid warming event called the Paleocene-Eocene thermal maximum (PETM). The newly derived understanding of age, eruptive deposits, and formation of hydrothermal vent complexes in the Møre Basin enables us to contribute to the general understanding of the igneous plumbing system in volcanic basins and

  4. SrF{sub 2} hierarchical flowerlike structures: Solvothermal synthesis, formation mechanism, and optical properties

    SciTech Connect

    Quan Zewei; Yang Dongmei; Li Chunxia; Yang Piaoping; Cheng, Ziyong; Yang Jun; Kong Deyan; Lin Jun

    2009-05-06

    We present a solvothermal route to the synthesis of SrF{sub 2} hierarchical flowerlike structures based on thermal decomposition of single source precursor (SSP) of strontium trifluoroacetate in benzylamine solvent. These flowerlike superstructures are actually composed of numerous aggregated nanoplates, and the growth process involves the initial formation of spherical nanoparticles and subsequent transformation into nanoplates, which aggregated together to form microdisks and finally flowerlike superstructures. The results demonstrate the important role of benzylamine in the formation of well-defined SrF{sub 2} superstructures, not only providing size and shape control to form nanoplates but also contributing to the self-assembly behavior of nanoplates to build into flower-like superstructures. Additionally, the photoluminescence properties of the obtained SrF{sub 2} superstructures are studied.

  5. Predictive modeling of multicellular structure formation by using Cellular Particle Dynamics simulations

    NASA Astrophysics Data System (ADS)

    McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2014-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  6. Influence of dendrimer's structure on its activity against amyloid fibril formation

    SciTech Connect

    Klajnert, B. . E-mail: aklajn@biol.uni.lodz.pl; Cortijo-Arellano, M.; Cladera, J.; Bryszewska, M.

    2006-06-23

    Inhibition of fibril assembly is a potential therapeutic strategy in neurodegenerative disorders such as prion and Alzheimer's diseases. Highly branched, globular polymers-dendrimers-are novel promising inhibitors of fibril formation. In this study, the effect of polyamidoamine (PAMAM) dendrimers (generations 3rd, 4th, and 5th) on amyloid aggregation of the prion peptide PrP 185-208 and the Alzheimer's peptide A{beta} 1-28 was examined. Amyloid fibrils were produced in vitro and their formation was monitored using the dye thioflavin T (ThT). Fluorescence studies were complemented with electron microscopy. The results show that the higher the dendrimer generation, the larger the degree of inhibition of the amyloid aggregation process and the more effective are dendrimers in disrupting the already existing fibrils. A hypothesis on dendrimer-peptide interaction mechanism is presented based on the dendrimers' molecular structure.

  7. Structure and formation conditions of paleogene coal-bearing deposits of Western Kamchatka

    SciTech Connect

    Polyanskii, B.V.

    1995-03-01

    Peculiarities of lithofacial composition and cyclic structure of the Lower-Middle Paleogene volcano-terrigenous coal-bearing deposits of the Western Kamchatka marginal sedimentary basin are discussed. Unstable sedimentation under delta progradation environments is shown to be prevalent. Such conditions were favorable for coal formation of deltaic and alluvial-estuarine types. Against a background of the marine-coastal high rate (avalanche) sedimentation, short-lived conditions for dominantly allochthonous coal formation in the environment of humid, warm temperature climate and high changeable sedimentation rates were distinguished. The clastic material in the basin originates from two provenances, represented by Pre-Paleogene, mainly Cretaceous rocks. The Central Range supplied mainly coarse-grained graywacke material. The western continental denudation areas, consisting of sedimentary and igneous rocks (including granites), supplied fine-grained terrigenous graywacke-arkosic material.

  8. The Effects of Gravity on Combustion and Structure Formation During Combustion Synthesis in Gasless Systems

    NASA Technical Reports Server (NTRS)

    Varma, Arvind; Mukasyan, Alexander; Pelekh, Aleksey

    1997-01-01

    There have been relatively few publications examining the role of gravity during combustion synthesis (CS), mostly involving thermite systems. The main goal of this research was to study the influence of gravity on the combustion characteristics of heterogeneous gasless systems. In addition, some aspects of microstructure formation processes which occur during gasless CS were also studied. Four directions for experimental investigation have been explored: (1) the influence of gravity force on the characteristic features of heterogeneous combustion wave propagation (average velocity, instantaneous velocities, shape of combustion front); (2) the combustion of highly porous mixtures (with porosity greater than that for loose powders), which cannot be obtained in normal gravity; (3) the effect of gravity on sample expansion during combustion, in order to produce highly porous materials under microgravity conditions; and (4) the effect of gravity on the structure formation mechanism during the combustion synthesis of poreless composite materials.

  9. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

    PubMed Central

    Lu, Zhi John; Turner, Douglas H.; Mathews, David H.

    2006-01-01

    A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. PMID:16982646

  10. Atomic Resolution Crystal Structure of NAD+-Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1

    PubMed Central

    Shabalin, I.G.; Polyakov, K.M.; Tishkov, V.I.

    2009-01-01

    The crystal structure of the ternary complex of NAD+-dependent formate dehydrogenase from the methylotrophic bacterium Moraxella sp. C-1 with the cofactor (NAD+) and the inhibitor (azide ion) was established at 1.1 A resolution. The complex mimics the structure of the transition state of the enzymatic reaction. The structure was refined with anisotropic displacitalicents parameters for non-hydrogen atoms to a R factor of 13.4%. Most of the nitrogen, oxygen, and carbon atoms were distinguished based on the analysis of the titalicperature factors and electron density peaks, with the result that side-chain rotamers of histidine residues and most of asparagine and glutamine residues were unambiguously determined. A comparative analysis of the structure of the ternary complex determined at the atomic resolution and the structure of this complex at 1.95 A resolution was performed. In the atomic resolution structure, the covalent bonds in the nicotinamide group are somewhat changed in agreitalicent with the results of quantum mechanical calculations, providing evidence that the cofactor acquires a bipolar form in the transition state of the enzymatic reaction. PMID:22649619

  11. Deep structure of the central Lesser Antilles Island Arc: Relevance for the formation of continental crust

    NASA Astrophysics Data System (ADS)

    Kopp, H.; Weinzierl, W.; Becel, A.; Charvis, P.; Evain, M.; Flueh, E. R.; Gailler, A.; Galve, A.; Hirn, A.; Kandilarov, A.; Klaeschen, D.; Laigle, M.; Papenberg, C.; Planert, L.; Roux, E.

    2011-04-01

    Oceanic island arcs are sites of high magma production and contribute to the formation of continental crust. Geophysical studies may provide information on the configuration and composition of island arc crust, however, to date only few seismic profiles exist across active island arcs, limiting our knowledge on the deep structure and processes related to the production of arc crust. We acquired active-source wide-angle seismic data crossing the central Lesser Antilles island arc north of Dominica where the oceanic Tiburon Ridge subducts obliquely beneath the forearc. A combined analysis of wide-angle seismics and pre-stack depth migrated reflection data images the complex structure of the backstop and its segmentation into two individual ridges, suggesting an intricate relation between subducted basement relief and forearc deformation. Tomographic imaging reveals three distinct layers composing the island arc crust. A three kilometer thick upper crust of volcanogenic sedimentary rocks and volcaniclastics is underlain by intermediate to felsic middle crust and plutonic lower crust. The island arc crust may comprise inherited elements of oceanic plateau material contributing to the observed crustal thickness. A high density ultramafic cumulates layer is not detected, which is an important observation for models of continental crust formation. The upper plate Moho is found at a depth of 24 km below the sea floor. Upper mantle velocities are close to the global average. Our study provides important information on the composition of the island arc crust and its deep structure, ranging from intermediate to felsic and mafic conditions.

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

    PubMed

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

    2013-09-01

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

  13. The Deep Structure of Lunar Basins: Clues to the Understanding of Basin Formation and Modification

    NASA Technical Reports Server (NTRS)

    Bratt, S. R.; Solomon, S. C.; Head, J. W.; Thurber, C. H.

    1985-01-01

    Basin excavation has played a major role in shaping the surface and subsurface of the Moon. Though photogeologic observations provide estimates for the present volumes of lunar impact basins and their ejecta deposits, there is not sufficient information to describe completely either the geometry of the basins at the time of impact or their modification with time. Determination of the structure of the crust and upper mantle beneath large basins can provide important insight into the thermal and mechanical processes associated with basin formation and modification as well as the differences in these processes as functions of basin age and size. Using observed gravity and topography together with the seismically determined crustal thickness of the central nearside, a model for the structure of the crust and upper mantle of the nearside of the Moon is presented. With this model the deep structure of the largest lunar basins are compared. The implications for the processes of basin formation and modification at different stages in lunar history are explored.

  14. Mass Spectrometric and Spectrophotometric Analyses Reveal an Alternative Structure and a New Formation Mechanism for Melanin.

    PubMed

    Li, Yuanjiao; Liu, Jingjing; Wang, Yajie; Chan, Ho Wai; Wang, Lianrong; Chan, Wan

    2015-08-01

    In this study, we investigated the formation mechanism and chemical structure of melanin that results from the self-assembly of L-3,4-dihydroxyphenylalanine (L-DOPA). Using a combination of "top-down" and "bottom-up" approaches, and on the basis of state-of-the-art electrospray ionization mass spectrometry (ESI-MS) results, we propose a new formation mechanism and an alternative structure for melanin. Specifically, our study of the self-aggregation of L-DOPA based on L-DOPA clusters revealed that melanin is comprised partially of noncovalent supramolecular aggregate that is formed by self-aggregation of L-DOPA and with the individual monomers linked together by a combination of hydrogen bonds, π-π stacking, and ionic bonds. Furthermore, our study showed that unmodified L-DOPA may be part of the building block for melanin in addition to the previously proposed indole derivative based on L-DOPA cyclization. A similar self-aggregation phenomenon was also observed in other structurally related catecholamines, for example, adrenaline.

  15. Chitosan facilitates structure formation of the salivary gland by regulating the basement membrane components.

    PubMed

    Yang, Tsung-Lin; Hsiao, Ya-Chuan

    2015-10-01

    Tissue structure is important for inherent physiological function and should be recapitulated during tissue engineering for regenerative purposes. The salivary gland is a branched organ that is responsible for saliva secretion and regulation. The salivary glands develop from epithelial-mesenchymal interactions, and depend on the support of the basement membrane (BM). Chitosan-based biomaterials have been demonstrated to be competent in facilitating the formation of salivary gland tissue structure. However, the underlying mechanisms have remained elusive. In the developing submandibular gland (SMG), the chitosan effect was found to diminish when collagen and laminin were removed from cultured SMG explants. Chitosan increased the expression of BM components including collagen, laminin, and heparan sulfate proteoglycan, and also facilitated BM components and the corresponding receptors to be expressed in tissue-specific patterns beneficial for SMG branching. The chitosan effect decreased when either laminin components or receptors were inhibited, as well when the downstream signaling was blocked. Our results revealed that chitosan promotes salivary glands branching through the BM. By regulating BM components and receptors, chitosan efficiently stimulated downstream signaling to facilitate salivary gland branching. The present study revealed the underlying mechanism of the chitosan effect in engineering SMG structure formation.

  16. Predicting total organic halide formation from drinking water chlorination using quantitative structure-property relationships.

    PubMed

    Luilo, G B; Cabaniss, S E

    2011-10-01

    Chlorinating water which contains dissolved organic matter (DOM) produces disinfection byproducts, the majority of unknown structure. Hence, the total organic halide (TOX) measurement is used as a surrogate for toxic disinfection byproducts. This work derives a robust quantitative structure-property relationship (QSPR) for predicting the TOX formation potential of model compounds. Literature data for 49 compounds were used to train the QSPR in moles of chlorine per mole of compound (Cp) (mol-Cl/mol-Cp). The resulting QSPR has four descriptors, calibration [Formula: see text] of 0.72 and standard deviation of estimation of 0.43 mol-Cl/mol-Cp. Internal and external validation indicate that the QSPR has good predictive power and low bias (‰<‰1%). Applying this QSPR to predict TOX formation by DOM surrogates - tannic acid, two model fulvic acids and two agent-based model assemblages - gave a predicted TOX range of 136-184 µg-Cl/mg-C, consistent with experimental data for DOM, which ranged from 78 to 192 µg-Cl/mg-C. However, the limited structural variation in the training data may limit QSPR applicability; studies of more sulfur-containing compounds, heterocyclic compounds and high molecular weight compounds could lead to a more widely applicable QSPR.

  17. Structural characteristics of polysaccharides that induce protection against intra-abdominal abscess formation.

    PubMed Central

    Tzianabos, A O; Onderdonk, A B; Zaleznik, D F; Smith, R S; Kasper, D L

    1994-01-01

    Bacteroides fragilis is the anaerobe most commonly isolated from clinical cases of intra-abdominal sepsis. In a rodent model of this disease process, intraperitoneal injection of the capsular polysaccharide complex (CPC) from B. fragilis provokes abscess formation, while subcutaneous administration of this complex confers protection against B. fragilis-induced intra-abdominal abscesses. The CPC consists of two discrete polysaccharides, polysaccharides A and B (PS A and PS B), each possessing oppositely charged structural groups critical to the ability of these carbohydrates to induce the formation of abscesses. Other bacterial polysaccharides that possess oppositely charged groups (such as the group antigen or capsular polysaccharide from Streptococcus pneumoniae type 1 strains) also exhibited potent abscess-inducing capabilities. We report here that positively and negatively charged groups on polysaccharides are also essential for inducing protection against abscess formation. Vaccination of rats with B. fragilis PS A, PS B, or the S. pneumoniae type 1 capsule protected against intra-abdominal abscesses subsequent to intraperitoneal challenge with each of these polysaccharides. Chemical conversion of the free amino or carboxyl groups on PS A to uncharged N-acetyl or hydroxymethyl groups, respectively, abrogated the ability of this polymer to confer protection against polysaccharide-mediated abscess formation. Adoptive transfer of splenic T cells from polysaccharide-vaccinated rats to naive animals demonstrated that T cells mediated this protective activity. T cells transferred from animals vaccinated with a polysaccharide repeating unit (Salmonella typhi Vi antigen) that normally contains one carboxyl group but was chemically converted to a polymer that possesses both free amino and carboxyl groups (accomplished by de-N-acetylating the Vi antigen) protected naive T-cell recipients against polysaccharide-induced abscesses. These results demonstrate that a distinct

  18. Formation mechanism of orderly structures in Au films deposited on silicone oil surfaces [rapid communication

    NASA Astrophysics Data System (ADS)

    Yang, Bo

    2005-06-01

    An optical microscopy study of ordered structures, namely bands, and self-organized phenomena in a continuous gold film system deposited on silicone oil surfaces is presented. The bands are composed of a large number of parallel keys with different width w but nearly uniform length L; the characteristic length of the bands is of the order of 101 102 μm. After disturbed with an external force, the growth process of the bands is observed directly. The experiment indicates that the formation mechanism of bands can be explained in terms of the relaxation of the compressive stress, which mainly results from the characteristic boundary condition of the nearly free sustained films.

  19. Formation of periodic phase structures in a photopolymerizable layer by nonstationary light beams

    NASA Astrophysics Data System (ADS)

    Mensov, S. N.; Morozova, M. A.; Polushtaitsev, Yu. V.

    2016-09-01

    Photopolymerization of a composite containing a nonpolymerizable component under the action of nonstationary optical radiation is studied. It is shown that the diffusion displacement of the nonpolymerizable component at the illuminated region boundary is caused by the appearance of the monomer concentration gradient, which, in turn, is induced by nonuniform photoinitiation. The action of radiation with a nonstationary intensity distribution makes it possible to form a periodic refractive index structure in the volume of the photopolymerizable material. The possibility of optical formation of polymer phase gratings by moving the shadow boundary stepwise along the polymerizable layer is studied numerically and experimentally.

  20. Structures Formation on the Y-TZP-AI2O3 Ceramic Composites Surface

    NASA Astrophysics Data System (ADS)

    Kulkov, Sergei; Sevostyanova, Irina; Sablina, Tatiana; Buyakova, Svetlana; Pshenichnyy, Artem; Savchenko, Nickolai

    2016-07-01

    The paper discusses the structure of Y-TZP-Al2O3 ceramics produced from nanopowders and friction surface, wear resistance, friction coefficient of Y-TZP-AEO3 composites rubbed against a steel disk counterface at a pressure of 5 MPa in a range of sliding speeds from 0.2 to 47 m/s. Analysis by X-ray diffraction, scanning electron microscopy showed that the high wear resistance of Y-TZP-Al2O3 composites at high sliding speeds is due to high-temperature phase transitions and protective film formation on the friction surface.

  1. The effects of extended clinorotation on potato minituber formation and structure

    NASA Astrophysics Data System (ADS)

    Nedukha, O. M.; Vasyltsov, I. V.

    Formation and structure of potato minitubers grown aseptically for 30 days on a horizontal clinostat and in stationary control have been studied by light and electron microscopy. It was demonstrated that the number of plants that formed minitubers, their size and fresh weight, was higher when clino-rotated than in the stationary control. It was revealed that the amount of amyloplasts in parenchyma cell sections was doubled in minitubers formed under clino-rotation. Other factors (shape of minitubers and size of reserve parenchyma cells) did not differ from the stationary control. The changes in amyloplast ultrastructure suggest accelerated cell maturity of potato reserve parenchyma in extended clino-rotation.

  2. Formation of surface nano-structures by plasma expansion induced by highly charged ions

    SciTech Connect

    Moslem, W. M.; El-Said, A. S.

    2012-12-15

    Slow highly charged ions (HCIs) create surface nano-structures (nano-hillocks) on the quartz surface. The formation of hillocks was only possible by surpassing a potential energy threshold. By using the plasma expansion approach with suitable hydrodynamic equations, the creation mechanism of the nano-hillocks induced by HCIs is explained. Numerical analysis reveal that within the nanoscale created plasma region, the increase of the temperature causes an increase of the self-similar solution validity domain, and consequently the surface nano-hillocks become taller. Furthermore, the presence of the negative (positive) nano-dust particles would lead to increase (decrease) the nano-hillocks height.

  3. Behavior of dust particles in cylindrical discharges: Structure formation, mixture and void, effect of gravity

    NASA Astrophysics Data System (ADS)

    Totsuji, Hiroo; Totsuji

    2014-12-01

    Theoretical and numerical works on dusty plasmas with cylindrical symmetry are presented. The main purpose has been to investigate behavior of dust particles in strongly coupled dusty plasmas which are expected to be realized in the planned experiments by PK-4 on the International Space Station and experiments by PK-4J, a similar apparatus constructed in Japan. The distribution of dust particles is analyzed on the basis of the drift-diffusion equations and, with the effect of discreteness taken into account, structure formations are numerically simulated.

  4. Formation of Fragment Rich Pseudotachylite Zones During Central Uplift Formation in the Vredefort Impact Structure, South Africa

    NASA Astrophysics Data System (ADS)

    Lieger, D.; Riller, U.; Reimold, W. U.; Gibson, R. L.

    Field-based structural analysis of the Vredefort Dome focused on mapping of pre-impact planar mineral fabrics and structural properties of fragment-rich pseudotachylite zones, such as geometry, orientation, brecciation intensity of the zones.

  5. Heteroepitaxial formation of aligned mesostructured silica films with large structural periodicities from mixed surfactant systems.

    PubMed

    Hayase, Saeko; Kanno, Yosuke; Watanabe, Masatoshi; Takahashi, Masahiko; Kuroda, Kazuyuki; Miyata, Hirokatsu

    2013-06-11

    Liquid-crystal phases consisting of cylindrical micelles of amphiphilic block copolymers and silica precursors are epitaxially built up on aligned surface micelles formed by an alkyl-PEO surfactant, Brij56, irrespective of the large difference in the intrinsic structural periodicities resulting in the formation of fully aligned mesostructured silica films with large lattice constants. Brij56 works as an alignment controlling agent on rubbing-treated polyimide through selective adsorption from a precursor solution containing the two surfactants, a block copolymer and Brij56, through strong hydrophobic interactions to form an anisotropic surface micelle structure. Aligned mesostructured silica layers with larger periodicities, which dominantly consist of block copolymers, form on these aligned surface micelles by gradually changing the vertical periodicity keeping the lateral intermicelle distance constant. This can be regarded as a kind of heteroepitaxy because the lattice constant at the surface is different from that of the bulk of the film. On the basis of this new concept, highly aligned mesostructured silica films with structural periodicities as large as 10 nm are successfully formed, which has never been achieved when the block copolymers are used alone as the structure-directing agent. The periodicity of the aligned films can precisely be controlled by an appropriate choice of block copolymers and the mixing ratio of the two surfactants, which increases the opportunity for applications of these films with highly anisotropic mesoscale structure.

  6. Formation of the small-scale structure of auroral electron precipitations

    NASA Astrophysics Data System (ADS)

    Kropotkin, A. P.

    2016-10-01

    This paper is aimed at physical causes of the small-scale transverse structure in the flows of auroral electrons, generating the corresponding small-scale structure of discrete auroras. The parallel electric field existing in the lower part of the auroral magnetosphere, in the auroral cavity region, in the presence of a strong upward field-aligned current, accelerates magnetospheric electrons to energies of ∼ 1 - 10 keV. The flow of these particles while maintaining the high density of the field-aligned current, produces a current-driven instability, which generates Alfvénic turbulence at short perpendicular wavelengths ≤ 1 km. These short-wavelength inertial Alfvén disturbances possess a nonzero parallell electric field, which modulates the electron flow velocity. The modulation occurring at high altitudes ≥104 km leads to a nonlinear effect of formation of strong density peaks at low altitudes of electron precipitation. The transverse, horizontal scales of the corresponding electron flow structure coincide with the small scales of the Alfvénic turbulence; and this structuring leads to non-uniformities in the auroral luminosity on the same scales, i.e., to small-scale structure of discrete auroras.

  7. Structural formation of huntingtin-like aggregates probed by small-angle neutron scattering

    SciTech Connect

    Stanley, Christopher B; Perevozchikova, Tatiana; Berthelier-Jung, Valerie M

    2011-01-01

    In several neurodegenerative disorders, including Huntington s disease (HD), aspects concerning the earliest of protein structures that form along the aggregation pathway have increasingly gained attention since these particular species are likely to be neurotoxic. We used time-resolved small-angle neutron scattering (SANS) to probe in solution these transient structures formed by peptides having the N-terminal sequence context of mutant huntingtin (Htt) exon 1. We obtained snapshots of the formed aggregates as the kinetic reaction ensued to yield quantitative information on their size and mass. At the early stage, small precursor species with an initial radius of gyration (Rg) of 16.1 5.9 and average mass of a dimer to trimer were monitored. Structural growth was treated as two modes with a transition from three-dimensional early aggregate formation to two-dimensional fibril growth and association. Our SANS results on the internal structure of the mature fibrils demonstrate loose packing with about 1 peptide per 4.75 -sheet repeat distance, which is shown to be quantitatively consistent with a -helix model. This research provides new insights into the structures forming along the pathway of Htt exon 1 aggregation and should assist in determining the role that precursors play in neuronal toxicity.

  8. Spontaneous Formation of Eutectic Crystal Structures in Binary and Ternary Charged Colloids due to Depletion Attraction

    PubMed Central

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-01-01

    Crystallization of colloids has extensively been studied for past few decades as models to study phase transition in general. Recently, complex crystal structures in multi-component colloids, including alloy and eutectic structures, have attracted considerable attention. However, the fabrication of 2D area-filling colloidal eutectics has not been reported till date. Here, we report formation of eutectic structures in binary and ternary aqueous colloids due to depletion attraction. We used charged particles + linear polyelectrolyte systems, in which the interparticle interaction could be represented as a sum of the electrostatic, depletion, and van der Waals forces. The interaction was tunable at a lengthscale accessible to direct observation by optical microscopy. The eutectic structures were formed because of interplay of crystallization of constituent components and accompanying fractionation. An observed binary phase diagram, defined by a mixing ratio and inverse area fraction of the particles, was analogous to that for atomic and molecular eutectic systems. This new method also allows the adjustment of both the number and wavelengths of Bragg diffraction peaks. Furthermore, these eutectic structures could be immobilized in polymer gel to produce self-standing materials. The present findings will be useful in the design of the optical properties of colloidal crystals. PMID:26984298

  9. Spontaneous Formation of Eutectic Crystal Structures in Binary and Ternary Charged Colloids due to Depletion Attraction

    NASA Astrophysics Data System (ADS)

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-03-01

    Crystallization of colloids has extensively been studied for past few decades as models to study phase transition in general. Recently, complex crystal structures in multi-component colloids, including alloy and eutectic structures, have attracted considerable attention. However, the fabrication of 2D area-filling colloidal eutectics has not been reported till date. Here, we report formation of eutectic structures in binary and ternary aqueous colloids due to depletion attraction. We used charged particles + linear polyelectrolyte systems, in which the interparticle interaction could be represented as a sum of the electrostatic, depletion, and van der Waals forces. The interaction was tunable at a lengthscale accessible to direct observation by optical microscopy. The eutectic structures were formed because of interplay of crystallization of constituent components and accompanying fractionation. An observed binary phase diagram, defined by a mixing ratio and inverse area fraction of the particles, was analogous to that for atomic and molecular eutectic systems. This new method also allows the adjustment of both the number and wavelengths of Bragg diffraction peaks. Furthermore, these eutectic structures could be immobilized in polymer gel to produce self-standing materials. The present findings will be useful in the design of the optical properties of colloidal crystals.

  10. [Basic principles of structural asymmetry of cortex formations in the human brain].

    PubMed

    Bogolepova, I N; Malofeeva, L I

    2004-01-01

    Studying the cytoarchitectonical asymmetry of human brain cortex requires using the new approaches and modern quantitative methods. One of the promising ways is analyzing relation between the macroscopic and neuronal structure of the brain. The present article contains original data of histological and morphological studies. The authors develop the concept of different degree of expression of asymmetry in the cortex formations of left and right hemispheres. The data on the principal differences of topography and types of structure of fissure and gyrus in different brain hemispheres are presented. Results of the analysis carried out enable one to show the basic criteria of peculiarities of cytoarchitecture of human brain cortex in the left and right hemispheres. PMID:15455550

  11. Formation of Coherent Structures and Impact on Turbulence Scaling in Solar-Wind Plasma

    NASA Astrophysics Data System (ADS)

    Nandal, P.; Sharma, Swati; Yadav, N.; Sharma, R. P.

    2016-10-01

    The governing dynamical equations of the right-handed circularly polarized dispersive Alfvén wave (DAW), which becomes dispersive owing to the finite frequency of the wave, and the slow Alfvén wave have been obtained using a two-fluid model. The wave localization at different instants of time and its power spectrum have been investigated. The ponderomotive force associated with the pump wave results in intense localized structures. The steepening of spectra is observed from the inertial range to the dispersive range. The results imply that the DAW may play a significant role in solar-wind turbulence. In addition, the formation of DAW localized structures is further examined considering two primary approaches, parametric instability (filamentation) and the reconnection-based model, to study the impact on the turbulent spectrum in more detail.

  12. FeAs2 formation and electronic nematic ordering: Analysis in terms of structural transformations

    NASA Astrophysics Data System (ADS)

    Pishtshev, A.; Rubin, P.

    2016-02-01

    By combining DFT-based computational analysis and symmetry constraints in terms of group-subgroup relations, we analyzed the formation of the native crystalline structure of loellingite FeAs2. We showed that the ground state of the material exhibits the ordered patterns of the electronic localization which are mainly associated with iron 3 dx2-y2 orbitals and can be characterized in terms of nematiclike ordering. The ordering is the result of the close interplay of the lattice and the electron degrees of freedom. In a structural aspect, the interplay pursues an energy quest to select the orthorhombic crystal lattice attributed to the P n n m space group. In a charge aspect, the ordering is connected with the valence charge density redistribution that not only provides a high electronic polarizability but also gives rise to an extra-large magnitude of the negative component of the dynamical p -d charge transfer.

  13. Femtosecond laser-induced periodic surface structural formation on sapphire with nanolayered gold coating

    NASA Astrophysics Data System (ADS)

    Yin, Kai; Wang, Cong; Duan, Ji'an; Guo, Chunlei

    2016-09-01

    Sapphire has a potential as a new generation of electronics display. However, direct processing of sapphire surface by visible or near-IR laser light is challenging since sapphire is transparent to these wavelengths. In this study, we investigate the formation of femtosecond laser-induced periodic surface structures (LIPSSs) on sapphire coated with nanolayered gold film. We found a reduced threshold by about 25 % in generating uniform LIPSSs on sapphire due to the nanolayered gold film. Different thickness of nanolayered gold films are studied, and it is shown that the change in thickness does not significantly affect the threshold reduction. It is believed that the diffusion of hot electrons in the gold films increases interfacial carrier density and electron-phonon coupling that results in a reduced threshold and more uniform periodic surface structure generation.

  14. Stochastic formation of magnetic vortex structures in asymmetric disks triggered by chaotic dynamics

    DOE PAGESBeta

    Im, Mi-Young; Lee, Ki-Suk; Vogel, Andreas; Hong, Jung-Il; Meier, Guido; Fischer, Peter

    2014-12-17

    The non-trivial spin configuration in a magnetic vortex is a prototype for fundamental studies of nanoscale spin behaviour with potential applications in magnetic information technologies. Arrays of magnetic vortices interfacing with perpendicular thin films have recently been proposed as enabler for skyrmionic structures at room temperature, which has opened exciting perspectives on practical applications of skyrmions. An important milestone for achieving not only such skyrmion materials but also general applications of magnetic vortices is a reliable control of vortex structures. However, controlling magnetic processes is hampered by stochastic behaviour, which is associated with thermal fluctuations in general. Here we showmore » that the dynamics in the initial stages of vortex formation on an ultrafast timescale plays a dominating role for the stochastic behaviour observed at steady state. Our results show that the intrinsic stochastic nature of vortex creation can be controlled by adjusting the interdisk distance in asymmetric disk arrays.« less

  15. Electronic structure of narrow gap semiconductors: Understanding gap formation and thermoelectric properties

    NASA Astrophysics Data System (ADS)

    Larson, Paul Melvin

    Electronic band structure calculations are invaluable theoretical tools to understand structural, transport, and optical properties of materials. We have used this tool in the search for new high performance thermoelectric materials, which are usually narrow-gap semiconductors. We have studied the electronic structures of these systems both to understand which properties of the band structure are most important for thermoelectric properties and the nature of the gap formation. Narrow-gap semiconductors lie between metals and wide-gap semiconductors, so understanding the nature of the gap formation is very important. The small band gaps in the systems we have studied generally arise from hybridization between different bands. We have used the local density approximation (LDA) and the generalized gradient approximation (GGA) within density functional theory (DFT). These have been implemented using the full-potential linearized augmented planewave (FLAPW) method within the WIEN97 package. This state-of-the-art method is among the most accurate methods for calculating the electronic structure of solids. We have studied four classes of compounds. These include the half-Heusler compounds, the ternary Zintl-phase compounds, the simple chalcogenides, and the complex chalcogenides. The ternary half-Heusler compounds, considered having a stuffed NaCl structure, show promising thermoelectric properties. The band gap formation is understood by starting with the semi-metallic binary NaCl compounds from which they are formed. Adding the transition (or noble) metal atom causes a strong p-d hybridization near the Fermi energy which opens up the band gap. This hybridization also leads to highly anisotropic effective masses at the conduction band minimum which are found in the best thermoelectric materials. Similar band gap formation is found in the ternary Zintl-phase compounds which are considered a stuffed Th3P4 structure. The band gaps in these ternary compounds are larger than

  16. Formation of large-scale structure from cosmic-string loops and cold dark matter

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Scherrer, Robert J.

    1987-01-01

    Some results from a numerical simulation of the formation of large-scale structure from cosmic-string loops are presented. It is found that even though G x mu is required to be lower than 2 x 10 to the -6th (where mu is the mass per unit length of the string) to give a low enough autocorrelation amplitude, there is excessive power on smaller scales, so that galaxies would be more dense than observed. The large-scale structure does not include a filamentary or connected appearance and shares with more conventional models based on Gaussian perturbations the lack of cluster-cluster correlation at the mean cluster separation scale as well as excessively small bulk velocities at these scales.

  17. Stochastic formation of magnetic vortex structures in asymmetric disks triggered by chaotic dynamics

    SciTech Connect

    Im, Mi-Young; Lee, Ki-Suk; Vogel, Andreas; Hong, Jung-Il; Meier, Guido; Fischer, Peter

    2014-12-17

    The non-trivial spin configuration in a magnetic vortex is a prototype for fundamental studies of nanoscale spin behaviour with potential applications in magnetic information technologies. Arrays of magnetic vortices interfacing with perpendicular thin films have recently been proposed as enabler for skyrmionic structures at room temperature, which has opened exciting perspectives on practical applications of skyrmions. An important milestone for achieving not only such skyrmion materials but also general applications of magnetic vortices is a reliable control of vortex structures. However, controlling magnetic processes is hampered by stochastic behaviour, which is associated with thermal fluctuations in general. Here we show that the dynamics in the initial stages of vortex formation on an ultrafast timescale plays a dominating role for the stochastic behaviour observed at steady state. Our results show that the intrinsic stochastic nature of vortex creation can be controlled by adjusting the interdisk distance in asymmetric disk arrays.

  18. Tuning the formation and stability of microcapsules by environmental conditions and chitosan structure.

    PubMed

    Ren, Ying; Xie, Hongguo; Liu, Xiaocen; Yang, Fan; Yu, Weiting; Ma, Xiaojun

    2016-10-01

    The goal of this work is to tune the formation and stability of the alginate-chitosan (AC) polyelectrolyte complexes (PECs) and microcapsules. Particularly, we explore the role of the conformation of chitosan on its interaction with alginate to understand the mechanism underpinning their interactions at the molecular level. Reducing the charge density by increasing pH will increase the compactness of chitosan, the values of the enthalpy (H) and stoichiometry (N) of binding between chitosan and alginate. Consequently, chitosan has advantage in being adsorbed on alginate beads to form microcapsules, including the binding rate and binding amount. Though the total heat release remain similar in the range of ionic strength, chitosan diffuses much easier into alginate hydrogels when in higher ionic strength. Increasing pH and ionic strength both help AC microcapsules to have higher stability. The results indicate that the formation and stability of AC microcapsules are related to the rigidity and conformations of chitosan molecules. After increasing acetylation degree (DA) of chitosan, the binding rate of chitosan and mechanical strength of AC microcapsules are both reduced. This work demonstrates the versatility and feasibility of tuning the formation and stability of polysaccharide microcapsules by physical factors and chitosan chemical structures. PMID:27344950

  19. Formation and structural organization of the egg-sperm bundle of the scleractinian coral Montipora capitata

    NASA Astrophysics Data System (ADS)

    Padilla-Gamiño, J. L.; Weatherby, T. M.; Waller, R. G.; Gates, R. D.

    2011-06-01

    The majority of scleractinian corals are hermaphrodites that broadcast spawn their gametes separately or packaged as egg-sperm bundles during spawning events that are timed to the lunar cycle. The egg-sperm bundle is an efficient way of transporting gametes to the ocean surface where fertilization takes place, while minimizing sperm dilution and maximizing the opportunity for gamete encounters during a spawning event. To date, there are few studies that focus on the formation and structure of egg-sperm bundle. This study explores formation, ultrastructure, and longevity of the egg-sperm bundle in Montipora capitata, a major reef building coral in Hawai`i. Our results show that the egg-sperm bundle is formed by a mucus layer secreted by the oocytes. The sperm package is located at the center of each bundle, possibly reflecting the development of male and female gametes in different mesenteries. Once the egg-sperm bundle has reached the ocean surface, it breaks open within 10-35 min, depending on the environmental conditions (i.e., wind, water turbulence). Although the bundle has an ephemeral life span, the formation of an egg-sperm bundle is a fundamental part of the reproductive process that could be strongly influenced by climate change and deterioration of water quality (due to anthropogenic effects) and thus requires further investigation.

  20. Titanium-based icosahedral quasicrystals and approximants: Phase formation, cluster structure, and hydrogenation

    NASA Astrophysics Data System (ADS)

    Majzoub, Eric Hish

    Equilibrium phase formation is reported for ternary Ti-Zr-Ni alloys near the icosahedral phase (i-phase) forming composition. The i-phase forms over a small compositional range from a high-temperature equilibrium phase mixture of the Laves and alpha(Ti/Zr) solid solution phases. Additions of small amounts of Pb, 1--2 at. %, are demonstrated to substantially effect the equilibrium phase formation and extend the stability of the i-phase to nearly 700°C. An electrochemical method was used to hydrogenate Ti-based quasicrystals and their crystal approximants. This technique gives a consistently high hydrogen to metal atom ratio of 1.9, without crystal hydride formation in the quasicrystal. Nuclear Magnetic Resonance (NMR) measurements of the hydrogen dipole-dipole interaction were made using hydrided i-phase samples. Comparisons with simulations based on hydrogen filling of the approximant-phase tetrahedral interstitials reveals that any filling order is consistent with the experimental data. Studies of the atomic structure of hydrided and unhydrided i-TiZrNi quasicrystal and its approximant are reported. We construct constrained icosahedral glass models using Bergman and Mackay clusters to describe the i-phase in Ti-Zr-Ni and Ti-TM-Si-O. A comparison of simulated and experimental diffraction reveals that, the Bergman and Mackay clusters are the fundamental clusters in i-TiZrNi and i-TiMnSiO, respectively.

  1. Tuning the formation and stability of microcapsules by environmental conditions and chitosan structure.

    PubMed

    Ren, Ying; Xie, Hongguo; Liu, Xiaocen; Yang, Fan; Yu, Weiting; Ma, Xiaojun

    2016-10-01

    The goal of this work is to tune the formation and stability of the alginate-chitosan (AC) polyelectrolyte complexes (PECs) and microcapsules. Particularly, we explore the role of the conformation of chitosan on its interaction with alginate to understand the mechanism underpinning their interactions at the molecular level. Reducing the charge density by increasing pH will increase the compactness of chitosan, the values of the enthalpy (H) and stoichiometry (N) of binding between chitosan and alginate. Consequently, chitosan has advantage in being adsorbed on alginate beads to form microcapsules, including the binding rate and binding amount. Though the total heat release remain similar in the range of ionic strength, chitosan diffuses much easier into alginate hydrogels when in higher ionic strength. Increasing pH and ionic strength both help AC microcapsules to have higher stability. The results indicate that the formation and stability of AC microcapsules are related to the rigidity and conformations of chitosan molecules. After increasing acetylation degree (DA) of chitosan, the binding rate of chitosan and mechanical strength of AC microcapsules are both reduced. This work demonstrates the versatility and feasibility of tuning the formation and stability of polysaccharide microcapsules by physical factors and chitosan chemical structures.

  2. Numerical simulations of galaxy formation: Angular momentum distribution and phase space structure of galactic halos

    NASA Astrophysics Data System (ADS)

    Sharma, Sanjib

    Within the past decade, the L CDM model has emerged as a standard paradigm of structure formation. While it has been very successful in explaining the structure of the Universe on large scales, on smaller (galactic) scales problems have surfaced. In this thesis, we investigate several of these problems in more detail. The thesis is organized as follows. In Chapter 1, we give a brief introduction about structure formation in the universe and discuss some of the problems being faced by the current CDM paradigm of galaxy formation. In Chapter 2, we analyze the angular momentum properties of virialized halos obtained from hydrodynamical simulations. We describe an analytical function that can be used to describe a wide variety of angular momentum distributions (AMDs), with just one parameter a. About 90-95% of halos turn out to have a < 1.3, while exponential disks in cosmological halos would require 1.3 < a < 1.6. This implies that a typical halo in simulations has an excess of low angular momentum material as compared to that of observed exponential disks, a result which is consistent with the findings of earlier works. In Chapter 3, we perform controlled numerical experiments of merging galactic halos in order to shed light on the results obtained in cosmological simulations. We explore the properties of shape parameter a of AMDs and the spin ratio l Gas /l DM in merger remnants and also their dependence on orbital parameters. We find that the shape parameter a is typically close to 1 for a wide range of orbital parameters, less than what is needed to form an exponential disk. The last chapter of the thesis (Chapter 4) is devoted to the analysis of phase space structure of dark matter halos. We first present a method to numerically estimate the densities of discretely sampled data based on a binary space partitioning tree. We implement an entropy-based node splitting criterion that results in a significant improvement in the estimation of densities compared to

  3. Effective stiffness and formation of secondary structures in a protein-like model

    NASA Astrophysics Data System (ADS)

    Škrbić, Tatjana; Hoang, Trinh X.; Giacometti, Achille

    2016-08-01

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true.

  4. Effective stiffness and formation of secondary structures in a protein-like model.

    PubMed

    Škrbić, Tatjana; Hoang, Trinh X; Giacometti, Achille

    2016-08-28

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true. PMID:27586943

  5. Phase formation, liquid structure, and physical properties of amorphous and quasicrystal-forming alloys

    NASA Astrophysics Data System (ADS)

    Wessels, Victor Medgar

    2009-12-01

    Since the discovery of quasicrystals in 1985 and the development of commercially viable bulk metallic glasses (BMGs) in the mid 1990's a great deal of attention has been given to the characterization of new alloys with desirable properties, such as larger amorphous casting thickness, higher mechanical strength, or hydrogen storage capacity. Here, the results of a number of investigations into the structures and properties of some noncrystalline solid alloys will be presented and analyzed. Beamline electrostatic levitation (BESL), a method for determining supercooled liquid structure and phase formation in-situ, was used. Using BESL, the development of structural and chemical inhomogeneity was observed in supercooled liquid Cu46Zr 54 (a BMG when cast) with an onset at 845 +/- 5°C, providing experimental support for structural changes determined from molecular dynamics (MD) simulations of these liquids. Differing segregation of Hf and Zr atoms was observed in solidified Ti45Zr(38-x)HfxNi 17 using scanning electron microscopy (SEM), and correlated to a previously observed, sharp boundary in phase formation near x = 19 that was further investigated using BESL. In addition to the BESL studies, results will be presented and discussed on changes in microstructure and devitrification mechanisms with the addition of Ag in Mg65Cu(25-x)AgxGd 10 BMGs, interesting for their light weight and resistance to oxygen during casting, using transmission electron microscopy (TEM), SEM, and differential scanning calorimetry (DSC). Previous, preliminary results on the hydrogen storage capacity of icosahedral quasicrystal Ti45Zr38Ni 17 were re-examined, using an improved apparatus and analysis method developed as part of this work, and the previous results found to be in error.

  6. Structure and mechanism of formation of an important ion in doping control

    NASA Astrophysics Data System (ADS)

    Borges, Chad R.; Taccogno, James; Crouch, Dennis J.; Le, Ly; Truong, Thanh N.

    2005-12-01

    An ion with m/z 143 serves as a biomarker that is often continuously monitored in urine samples undergoing screening by electron ionization gas chromatography/mass spectrometry (EI GC/MS) for banned anabolic agents. The ion is known to arise from trimethylsilyl (TMS)-derivatized synthetic 17-hydroxy, 17-methyl steroids. The purpose of this work was to characterize, in detail, the origin(s), structure(s), and mechanism(s) of formation of such ions with m/z 143. High resolution mass spectrometry (HRMS) data revealed the elemental composition of the D-ring derived m/z 143 ion to be C7H15OSi. Analysis of dihydrotestosterone (DHT) and its 2-methyl substituted analog dromostanolone by HRMS revealed that an elementally equivalent ion of m/z 143 could be derived from the A-ring of TMS-derivatized 3-keto-enol steroids demonstrating that an abnormally intense peak in the m/z 143 extracted ion chromatogram of urine samples undergoing screening for banned anabolic agents does not necessarily indicate the presence of a 17-hydroxy, 17-methyl steroid. To gain information on ion structure, breakdown curves for the most abundant product ions of the m/z 143 ion were generated using both native and perdeutero-TMS derivatives, providing structures for second, third, and fourth generation product ions. An EI-mass spectrum of [16,16,17-2H3]-DHT (DHT-d3) demonstrated that one of the C-16 hydrogen atoms is removed prior to the formation of an ion that is highly analogous to the ion with m/z 143 strongly suggesting, in accord with all other evidence, one particular fragmentation pathway and resulting product: a resonance stabilized 3-(O-trimethylsilyl)but-1-ene ion.

  7. The past and the future fate of the universe and the formation of structure in it

    PubMed Central

    Rix, Hans-Walter

    1999-01-01

    The history and the ultimate future fate of the universe as a whole depend on how much the expansion of the universe is decelerated by its own mass. In particular, whether the expansion of the universe will ever come to a halt can be determined from the past expansion. However, the mass density in the universe does not only govern the expansion history and the curvature of space, but in parallel also regulates the growth of hierarchical structure, including the collapse of material into the dense, virialized regions that we identify with galaxies. Hence, the formation of galaxies and their clustered distribution in space depend not only on the detailed physics of how stars are formed but also on the overall structure of the universe. Recent observational efforts, fueled by new large, ground-based telescopes and the Hubble Space Telescope, combined with theoretical progress, have brought us to the verge of determining the expansion history of the universe and space curvature from direct observation and to linking this to the formation history of galaxies. PMID:10411874

  8. Influence of transport mechanisms on nucleation and grain structure formation in DC cast aluminium alloy ingots

    NASA Astrophysics Data System (ADS)

    Bedel, M.; Založnik, M.; Kumar, A.; Combeau, H.; Jarry, P.; Waz, E.

    2012-01-01

    The grain structure formation in direct chill (DC) casting is directly linked to nucleation, which is generally promoted by inoculation. Inoculation prevents defects, but also modifies the physical properties by changing the microstructure. We studied the coupling of the nucleation on inoculant particles and the grain growth in the presence of melt flow induced by thermosolutal convection and of the transport of free-floating equiaxed grains. We used a volume-averaged two-phase multiscale model with a fully coupled description of phenomena on the grain scale (nucleation on grain refiner particles and grain growth) and on the product scale (macroscopic transport). The transport of inoculant particles is also modeled, which accounts for the inhomogeneous distribution of inoculant particles in the melt. The model was applied to an industrial sized (350mm thick) DC cast aluminium alloy ingot. A discretised nuclei size distribution was defined and the impact of different macroscopic phenomena on the grain structure formation was studied: the zone and intensity of nucleation and the resulting grain size distribution. It is shown that nucleation in the presence of macroscopic transport cannot be explained only in terms of cooling rate, but variations of composition, nuclei density and grain density, all affected by transport, must be accounted for.

  9. The dependence of star formation on initial conditions and molecular cloud structure

    NASA Astrophysics Data System (ADS)

    Bate, Matthew R.

    2009-07-01

    We investigate the dependence of stellar properties on the initial kinematic structure of the gas in star-forming molecular clouds. We compare the results from two large-scale hydrodynamical simulations of star cluster formation that resolve the fragmentation process down to the opacity limit, the first of which was reported by Bate, Bonnell & Bromm. The initial conditions of the two calculations are identical, but in the new simulation the power spectrum of the velocity field imposed on the cloud initially and allowed to decay is biased in favour of large-scale motions. Whereas the calculation of Bate et al. began with a power spectrum P(k) ~ k-4 to match the Larson scaling relations for the turbulent motions observed in molecular clouds, the new calculation begins with a power spectrum P(k) ~ k-6. Despite this change to the initial motions in the cloud and the resulting density structure of the molecular cloud, the stellar properties resulting from the two calculations are indistinguishable. This demonstrates that the results of such hydrodynamical calculations of star cluster formation are relatively insensitive to the initial conditions. It is also consistent with the fact that the statistical properties of stars and brown dwarfs (e.g. the stellar initial mass function) are observed to be relatively invariant within our Galaxy and do not appear to depend on environment.

  10. Organization of the Pre-autophagosomal Structure Responsible for Autophagosome Formation

    PubMed Central

    Kawamata, Tomoko; Kamada, Yoshiaki; Kabeya, Yukiko; Sekito, Takayuki

    2008-01-01

    Autophagy induced by nutrient depletion is involved in survival during starvation conditions. In addition to starvation-induced autophagy, the yeast Saccharomyces cerevisiae also has a constitutive autophagy-like system, the Cvt pathway. Among 31 autophagy-related (Atg) proteins, the function of Atg17, Atg29, and Atg31 is required specifically for autophagy. In this study, we investigated the role of autophagy-specific (i.e., non-Cvt) proteins under autophagy-inducing conditions. For this purpose, we used atg11Δ cells in which the Cvt pathway is abrogated. The autophagy-unique proteins are required for the localization of Atg proteins to the pre-autophagosomal structure (PAS), the putative site for autophagosome formation, under starvation condition. It is likely that these Atg proteins function as a ternary complex, because Atg29 and Atg31 bind to Atg17. The Atg1 kinase complex (Atg1–Atg13) is also essential for recruitment of Atg proteins to the PAS. The assembly of Atg proteins to the PAS is observed only under autophagy-inducing conditions, indicating that this structure is specifically involved in autophagosome formation. Our results suggest that Atg1 complex and the autophagy-unique Atg proteins cooperatively organize the PAS in response to starvation signals. PMID:18287526

  11. The past and the future fate of the universe and the formation of structure in it.

    PubMed

    Rix, H W

    1999-07-20

    The history and the ultimate future fate of the universe as a whole depend on how much the expansion of the universe is decelerated by its own mass. In particular, whether the expansion of the universe will ever come to a halt can be determined from the past expansion. However, the mass density in the universe does not only govern the expansion history and the curvature of space, but in parallel also regulates the growth of hierarchical structure, including the collapse of material into the dense, virialized regions that we identify with galaxies. Hence, the formation of galaxies and their clustered distribution in space depend not only on the detailed physics of how stars are formed but also on the overall structure of the universe. Recent observational efforts, fueled by new large, ground-based telescopes and the Hubble Space Telescope, combined with theoretical progress, have brought us to the verge of determining the expansion history of the universe and space curvature from direct observation and to linking this to the formation history of galaxies.

  12. Influence of structural features of carrageenan on the formation of polyelectrolyte complexes with chitosan.

    PubMed

    Volod'ko, A V; Davydova, V N; Glazunov, V P; Likhatskaya, G N; Yermak, I M

    2016-03-01

    The polyelectrolyte complexes (PEC) of carrageenans (CG)-κ-, κ/β-, λ-and x-CG with chitosan were obtained. The formation of PEC was detected by Fourier-transform infrared (FTIR) spectroscopy and by centrifugation in a Percoll gradient. The influence of the structural peculiarities of CG on its interaction with chitosan was studied. The results of centrifugation showed that x-CG with a high degree of sulphation (SD) was completely bound to chitosan, unlike low SD κ-CG and κ/β-CG. Binding constant values showed there was a high affinity of CG for chitosan. CG with flexible macromolecule conformation and high SD exhibited the greatest binding affinity for chitosan. The full-atomic 3D-structures of the PEC κ-CG: chitosan in solution have been obtained by the experiments in silico for the first time. The amino groups of chitosan make the largest contribution to the energy of the complex formation by means of hydrogen and ionic bonds. The most probable complexes have stoichiometries of 1:1 and 1:1.5.

  13. Self-regulation in flow-induced structure formation of polypropylene.

    PubMed

    Roozemond, Peter C; van Drongelen, Martin; Ma, Zhe; Spoelstra, Anne B; Hermida-Merino, Daniel; Peters, Gerrit W M

    2015-02-01

    Flow-induced structure formation is investigated with in situ wide-angle X-ray diffraction with high acquisition rate (30 Hz) using isotactic polypropylene in a piston-driven slit flow with high wall shear rates (up to ≈900 s(-1) ). We focus on crystallization within the shear layers that form in the high shear rate regions near the walls. Remarkably, the kinetics of the crystallization process show no dependence on either flow rate or flow time; the crystallization progresses identically regardless. Stronger or longer flows only increase the thickness of the layers. A conceptual model is proposed to explain the phenomenon. Above a certain threshold, the number of shish-kebabs formed affects the rheology such that further structure formation is halted. The critical amount is reached already within 0.1 s under the current flow conditions. The change in rheology is hypothesized to be a consequence of the "hairy" nature of shish. Our results have large implications for process modelling, since they suggest that for injection molding type flows, crystallization kinetics can be considered independent of deformation history. PMID:25522201

  14. Notch Signalling Is Required for the Formation of Structurally Stable Muscle Fibres in Zebrafish

    PubMed Central

    Pascoal, Susana; Esteves de Lima, Joana; Leslie, Jonathan D.; Hughes, Simon M.; Saúde, Leonor

    2013-01-01

    Background Accurate regulation of Notch signalling is central for developmental processes in a variety of tissues, but its function in pectoral fin development in zebrafish is still unknown. Methodology/Principal Findings Here we show that core elements necessary for a functional Notch pathway are expressed in developing pectoral fins in or near prospective muscle territories. Blocking Notch signalling at different levels of the pathway consistently leads to the formation of thin, wavy, fragmented and mechanically weak muscles fibres and loss of stress fibres in endoskeletal disc cells in pectoral fins. Although the structural muscle genes encoding Desmin and Vinculin are normally transcribed in Notch-disrupted pectoral fins, their proteins levels are severely reduced, suggesting that weak mechanical forces produced by the muscle fibres are unable to stabilize/localize these proteins. Moreover, in Notch signalling disrupted pectoral fins there is a decrease in the number of Pax7-positive cells indicative of a defect in myogenesis. Conclusions/Significance We propose that by controlling the differentiation of myogenic progenitor cells, Notch signalling might secure the formation of structurally stable muscle fibres in the zebrafish pectoral fin. PMID:23840804

  15. The past and the future fate of the universe and the formation of structure in it.

    PubMed

    Rix, H W

    1999-07-20

    The history and the ultimate future fate of the universe as a whole depend on how much the expansion of the universe is decelerated by its own mass. In particular, whether the expansion of the universe will ever come to a halt can be determined from the past expansion. However, the mass density in the universe does not only govern the expansion history and the curvature of space, but in parallel also regulates the growth of hierarchical structure, including the collapse of material into the dense, virialized regions that we identify with galaxies. Hence, the formation of galaxies and their clustered distribution in space depend not only on the detailed physics of how stars are formed but also on the overall structure of the universe. Recent observational efforts, fueled by new large, ground-based telescopes and the Hubble Space Telescope, combined with theoretical progress, have brought us to the verge of determining the expansion history of the universe and space curvature from direct observation and to linking this to the formation history of galaxies. PMID:10411874

  16. Formation of nanoporous structures in metallic materials by pulse-periodic laser treatment

    NASA Astrophysics Data System (ADS)

    Murzin, Serguei P.

    2015-09-01

    A method of the formation of nanoporous structures in metallic materials by pulse-periodic laser treatment was developed. In this study, the multicomponent aluminum-iron brass was considered and the nanoporous structure across the entire cross section of the material with a thickness of 50 μm was formed. The method was implemented using a CO2 laser processing unit. The pulse-periodic laser treatment of the Cu-Zn-Al-Fe alloy with pulse frequency of 5 Hz has led to the formation of nanosized cavities due to accumulation of internal stresses during cyclic heating and cooling at high speeds. It was determined that the pores of a channel type with average widths of 80-100 nm are formed in the central region of the heat-affected zone during laser action with thermocycling. When implementing the chosen conditions of the pulse-periodic laser processing, the localness in depth and area of the physical processes occurring in the heat-affected zone is ensured, while maintaining the original properties of the material and the absence of significant deformations in the rest of the volume. This patented process is perspective for the production not only catalysts for chemical reactions, but for ultrafiltration and microfiltration membranes as well.

  17. Three-Coordinate Terminal Imidoiron(III) Complexes: Structure, Spectroscopy, and Mechanism of Formation

    PubMed Central

    Cowley, Ryan E.; DeYonker, Nathan J.; Eckert, Nathan A.; Cundari, Thomas R.; DeBeer, Serena; Bill, Eckhard; Ottenwaelder, Xavier; Flaschenriem, Christine; Holland, Patrick L.

    2010-01-01

    Reaction of 1-adamantyl azide with iron(I) diketiminate precursors gives metastable but isolable imidoiron(III) complexes LFe=NAd (L = bulky β-diketiminate ligand; Ad = 1-adamantyl). This paper addresses: (1) the spectroscopic and structural characterization of the Fe=N multiple bond in these interesting three-coordinate iron imido complexes, and (2) the mechanism through which the imido complexes form. The iron(III) imido complexes have been examined by 1H NMR and EPR spectroscopies and temperature-dependent magnetic susceptibility (SQUID), and structurally characterized by crystallography and/or X-ray absorption (EXAFS) measurements. These data show that the imido complexes have quartet ground states and short (1.68 ± 0.01 Å) iron-nitrogen bonds. The formation of the imido complexes proceeds through unobserved iron–RN3 intermediates, which are indicated by QM/MM computations to be best described as iron(II) with an RN3 radical anion. The radical character on the organoazide bends its NNN linkage to enable easy N2 loss and imido complex formation. The product distribution between imidoiron(III) products and hexazene-bridged diiron(II) products is solvent-dependent, and the solvent dependence can be explained by coordination of certain solvents to the iron(I) precursor prior to interaction with the organoazide. PMID:20524625

  18. EBSD analysis of magnesium addition on inclusion formation in SS400 structural steel

    SciTech Connect

    Luo, Sin-Jie; Su, Yen-Hao Frank; Lu, Muh-Jung; Kuo, Jui-Chao

    2013-08-15

    In this study, the effect of magnesium addition on the inclusion formation in SS400 steel was investigated. The experimental specimens with and without Mg addition treatment were compared. The microstructure was observed using optical microscopy after etching with 3% nital. The morphology and chemical composition of the inclusions were analyzed via scanning electron microscopy and energy dispersive spectrometry. The lattice structure and orientation of the inclusions were identified by electron backscattering diffraction. The average size of inclusions in SS400 was between 0.67 and 0.75 μm, and between 0.65 and 0.68 μm in SS400 + Mg. The 2 ppm Mg addition resulted in the oxide formation change from Al{sub 2}O{sub 3} to MgO·Al{sub 2}O{sub 3} and in the inclusion formation change from Al{sub 2}O{sub 3}–MnS to MgO·Al{sub 2}O{sub 3}–MnS. Moreover, a simple-phase MnS with an average grain size of 1 μm to 2 μm was observed in rod-like, globular, and polyhedron forms. - Highlights: • The effect of magnesium addition was investigated for SS400 steel. • 2 ppm Mg addition changes the inclusion formation from Al2O3-MnS to MgO·Al2O3-MnS. • MnS observed in inclusions exhibits rod-like, globular, and polyhedron forms.

  19. Structural insight into the role of Streptococcus parasanguinis Fap1 within oral biofilm formation

    SciTech Connect

    Garnett, James A.; Simpson, Peter J.; Taylor, Jonathan; Benjamin, Stefi V.; Tagliaferri, Camille; Cota, Ernesto; Chen, Yi-Ywan M.; Wu, Hui; Matthews, Stephen

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer Crystal structure of Streptococcus parasanguinis Fap1-NR{sub {alpha}} at pH 5.0. Black-Right-Pointing-Pointer pH-dependent conformational changes mediated through electrostatic potential of Fap1-NR{sub {alpha}}. Black-Right-Pointing-Pointer Fap1 facilitates pH-dependent biofilms. Black-Right-Pointing-Pointer We model inter-Fap1 biofilm interactions. -- Abstract: The fimbriae-associated protein 1 (Fap1) is a major adhesin of Streptococcus parasanguinis, a primary colonizer of the oral cavity that plays an important role in the formation of dental plaque. Fap1 is an extracellular adhesive surface fibre belonging to the serine-rich repeat protein (SRRP) family, which plays a central role in the pathogenesis of streptococci and staphylococci. The N-terminal adhesive region of Fap1 (Fap1-NR) is composed of two domains (Fap1-NR{sub {alpha}} and Fap1-NR{sub {beta}}) and is projected away from the bacterial surface via the extensive serine-rich repeat region, for adhesion to the salivary pellicle. The adhesive properties of Fap1 are modulated through a pH switch in which a reduction in pH results in a rearrangement between the Fap1-NR{sub {alpha}} and Fap1-NR{sub {beta}} domains, which assists in the survival of S. parasanguinis in acidic environments. We have solved the structure of Fap1-NR{sub {alpha}} at pH 5.0 at 3.0 A resolution and reveal how subtle rearrangements of the 3-helix bundle combined with a change in electrostatic potential mediates 'opening' and activation of the adhesive region. Further, we show that pH-dependent changes are critical for biofilm formation and present an atomic model for the inter-Fap1-NR interactions which have been assigned an important role in the biofilm formation.

  20. Targeting pyrimidine single strands by triplex formation: structural optimization of binding.

    PubMed

    Vo, T; Wang, S; Kool, E T

    1995-08-11

    Recent reports describe a new strategy for the binding of single-stranded pyrimidine sequences by triple helix formation. In this approach, a double-length purine-rich oligonucleotide binds a target strand, folding back to form an antiparallel pur.pur.pyr triple helix. We now describe a series of studies in which sequence and structural variations are made in such purine-rich ligands, in an effort to optimize binding properties. Comparison is made between the use of two separate strands and the use of single two-domain ligands; the latter are found to bind more tightly and to aggregate less in media containing Na+ or K+. Placement of mismatched bases in the target shows that sequence selectivity of binding is as high as that for Watson-Crick duplex formation. Variation of the lengths and sequences of loops bridging the binding domains demonstrates that dinucleotide loops composed of pyrimidines give the highest stability. Oligoethylene glycol-derived loop replacements are shown to give good binding affinity as well. The binding of an RNA target is shown to occur with the same affinity as the binding of DNA. In general, it is found that circular variants bind more tightly than do either separate strands or singly-linked ligands and unlike linear oligomers, the circular compounds do not aggregate to a large extent even in buffers containing 100 mM K+. Such structurally optimized ligands are useful in expanding the number of possible naturally-occurring sequences which can be targeted by triplex formation. PMID:7544889

  1. Phenomenological thermodynamics and the structure formation mechanism of the CuTi₂S₄ rhombohedral phase.

    PubMed

    Talanov, Michail V; Shirokov, Vladimir B; Talanov, Valery M

    2016-04-21

    The theory of structural phase transition in CuTi2S4 is proposed. The symmetry of order parameters, thermodynamics and the mechanism of the atomic structure formation of the rhombohedral Cu-Ti-thiospinel have been studied. The critical order parameter inducing the phase transition has been found. Within the Landau theory of phase transitions, it is shown that the phase state may change from the high-symmetry cubic disordered Fd3[combining macron]m phase to the low-symmetry ordered rhombohedral R3[combining macron]m phase as a result of phase transition of the first order close to the second order. It is shown that the rhombohedral structure of CuTi2S4 is formed as a result of the displacements of all types of atoms and the ordering of Cu-atoms (1 : 1 order type in tetrahedral spinel sites), Ti-atoms (1 : 1 : 6 order type in octahedral spinel sites), and S-atoms (1 : 1 : 3 : 3 order type). The Cu- and Ti-atoms form metal nanoclusters which are named a "bunch" of dimers. The "bunch" of dimers in CuTi2S4 is a new type of self-organization of atoms in frustrated spinel-like structures. It is shown that Ti-atoms also form other types of metal nanoclusters: trimers and tetrahedra. PMID:27035866

  2. Formation and prediction of structural traps in northwest Beartooth Mountains near Livingston, Montana

    SciTech Connect

    Robbins, E.A.; Erslev, E.A.

    1986-08-01

    The bounding faults on the northeastern flank of the Beartooth Mountains display a reversal of thrust vergence, with southwest-dipping thrust faults in the southeast, and northeast-dipping thrust faults in the northwest. Previous structural models of the Beartooth uplift do not explain this reversal in vergence because they do not balance by sedimentary bed length or basement block area and are not restorable to conceivable initial geometries. In addition, the models do not account for the thin-skinned deformation exposed along the northwestern corner. Restorable models for the northwest Beartooth uplift predict a blind master thrust, dipping to the southwest with wedges of basement back thrust over the main block. The basement-wedge formation is probably responsible for complex thin-skinned thrusts, duplexes, and ramp structures that fill apparent strain incompatibilities (space problems) for the southeast and northwest corners of the uplift. Estimates of 8 to 14 km (5 to 7 mi) of upper crustal shortening are consistent with published estimates from gravity modeling to the southeast. Geometric balancing techniques that conserve basement area and sediment bed length provide strong constraints on the structural geometry of foreland uplifts in the Rocky Mountain region. In the Beartooth Mountains, the complex interplay between the postulated southwest-dipping master fault, northeast-dipping back thrusts, and thin-skinned deformation allow for multiple structural traps for petroleum accumulation. The surface exposures in the Beartooth Mountain uplift do not suggest the subsurface complexity predicted by the balanced cross sections.

  3. Cyanophenyl vs. pyridine substituent: impact on the adlayer structure and formation on HOPG and Au(111).

    PubMed

    Dai, Y; Eggers, B; Metzler, M; Künzel, D; Groß, A; Jacob, T; Ziener, U

    2016-03-01

    A new cyano substituted bis(terpyridine) derivative CN-BTP was synthesized and its adsorption on highly oriented pyrolytic graphite (HOPG) and Au(111) was investigated. CN-BTP is closely related to the previously investigated 2,4'-BTP, where the cyanophenyl groups are replaced by pyridine moieties. The scanning tunneling microscopy (STM) investigation of CN-BTP at the liquid|HOPG interface shows a highly ordered herringbone structure that is stabilized by double weak intermolecular C-HN hydrogen bonds, partially through the -CN substituents, which is different from the most stable square structure of 2,4'-BTP. The adsorption processes were investigated using cyclic voltammetry (CV) on Au(111) in a neutral phosphate buffer. A fast and full adlayer formation could be observed with CN-BTP, whereas an extremely slow process with 2,4'-BTP under the same conditions was found. Our data show that the CN substituents on BTP not only change the structure of the monolayer at the liquid|HOPG interface, but also accelerate the phase transition process in the electrolyte dramatically. This could be explained by the adlayer-substrate interactions, which is supported by DFT calculations. Our findings might be extended more generally to further pyridine comprising self-assembling molecules to fine-tune the adlayer structure and phase transition/adsorption kinetics by replacing pyridine by cyanophenyl moieties.

  4. Formation of mixed-layer structures in smectites intercalated with tryptone

    NASA Astrophysics Data System (ADS)

    Block, K. A.; Trusiak, A.; Steiner, J. C.; Katz, A.; Gottlieb, P.; Alimova, A.

    2012-12-01

    Stable clay-protein complexes are fundamental to studies of the critical zone, terrestrial ecosystems, pharmacology, and industrial applications such as bioremediation. Two sets of montmorillonite clays were purified and made homoionic for Na and Mg. Mg-montmorillonite and Na-montmorillonite were mixed with tryptone (casein digest) in a 9:1 and 18:1 clay:tryptone ratio, resulting in the formation of reversible intercalated structures. X-ray diffraction analysis of the protein-clay complexes produced profiles consisting of two peaks associated with the smectite 001 reflection and a related tryptone-packet peak similar to that produced by a mixed layer clay structure. Shifts in the 002, 003, and 004 diffraction maxima are attributed to disorder caused by the interaction with the protein. Line broadening in the smectite-tryptone XRD spectra is interpreted to be the result of interlayer absorption. Adsorption produces coherent crystalline packets of regularly interbedded tryptone and smectite platelets. SEM images reveal clay platelets with upwardly rolled edges that tend toward cylindrical structures with the production of occasional tubes in the smaller platelet size range as noted for organic compound-kaolinite intercalation reported by Fenoll Hach-Ali and Weiss (1969). Reference: Fenoll Hach-Ali, P.F., Weiss, A., 1969. Estudio de la reaccion de caolinita y N-metilform- amida. Quimica LXV, 769-790. Scanning electron micrograph of tryptone-intercalated clay platelets exhibiting rolled edge structure.

  5. Mechanism for starch granule ghost formation deduced from structural and enzyme digestion properties.

    PubMed

    Zhang, Bin; Dhital, Sushil; Flanagan, Bernadine M; Gidley, Michael J

    2014-01-22

    After heating in excess water under little or no shear, starch granules do not dissolve completely but persist as highly swollen fragile forms, commonly termed granule "ghosts". The macromolecular architecture of these ghosts has not been defined, despite their importance in determining characteristic properties of starches. In this study, amylase digestion of isolated granule ghosts from maize and potato starches is used as a probe to study the mechanism of ghost formation, through microstructural, mesoscopic, and molecular scale analyses of structure before and after digestion. Digestion profiles showed that neither integral nor surface proteins/lipids were crucial for control of either ghost digestion or integrity. On the basis of the molecular composition and conformation of enzyme-resistant fractions, it was concluded that the condensed polymeric surface structure of ghost particles is mainly composed of nonordered but entangled amylopectin (and some amylose) molecules, with limited reinforcement through partially ordered enzyme-resistant structures based on amylose (for maize starch; V-type order) or amylopectin (for potato starch; B-type order). The high level of branching and large molecular size of amylopectin is proposed to be the origin for the unusual stability of a solid structure based primarily on temporary entanglements. PMID:24382148

  6. Phenomenological thermodynamics and the structure formation mechanism of the CuTi₂S₄ rhombohedral phase.

    PubMed

    Talanov, Michail V; Shirokov, Vladimir B; Talanov, Valery M

    2016-04-21

    The theory of structural phase transition in CuTi2S4 is proposed. The symmetry of order parameters, thermodynamics and the mechanism of the atomic structure formation of the rhombohedral Cu-Ti-thiospinel have been studied. The critical order parameter inducing the phase transition has been found. Within the Landau theory of phase transitions, it is shown that the phase state may change from the high-symmetry cubic disordered Fd3[combining macron]m phase to the low-symmetry ordered rhombohedral R3[combining macron]m phase as a result of phase transition of the first order close to the second order. It is shown that the rhombohedral structure of CuTi2S4 is formed as a result of the displacements of all types of atoms and the ordering of Cu-atoms (1 : 1 order type in tetrahedral spinel sites), Ti-atoms (1 : 1 : 6 order type in octahedral spinel sites), and S-atoms (1 : 1 : 3 : 3 order type). The Cu- and Ti-atoms form metal nanoclusters which are named a "bunch" of dimers. The "bunch" of dimers in CuTi2S4 is a new type of self-organization of atoms in frustrated spinel-like structures. It is shown that Ti-atoms also form other types of metal nanoclusters: trimers and tetrahedra.

  7. Crystal structures and phase formation thermodynamics of iron-gold nanoclusters

    NASA Astrophysics Data System (ADS)

    Mukherjee, Pinaki

    Alloy nanoparticles are being increasingly used in wide variety of applications (catalysis, contrast enhancement in magnetic resonance imaging, etc.). Knowledge of crystal structure and phase formation of the alloy nanoparticles is critical for these applications. Anomalous thermodynamic behavior and unusual phase formation have been reported for nanoparticles with size below 10 nm. In the present work, inert gas condensation (IGC) has been used to produce Au-Fe nanoclusters of varied compositions with a mean size between 5-10 nm. Here, the nanoclusters below 10 nm display complete solubility between Fe and Au in Fex Au1-x (0.3 < x < 0.8) alloys. The as-deposited clusters are single-crystalline but crystallinity is poor with significant disorder. New structural phases have been obtained for as-deposited clusters that are inconsistent with the equilibrium phase diagram. The as-deposited structures were either bcc for x > 0.65 and fcc for x < 0.65, with lattice parameters expanded relative to elemental and rule-of mixtures values, suggesting the presence of self-interstitials. The as-deposited clusters were ferromagnetic at room temperature. Heat treatment at 600°C for 15 minutes followed by furnace cooling resulted in the size-dependent transformation of the clusters into additional, non-equilibrium structures that depended on cluster composition, while larger clusters followed bulk behavior. At about 65 atom % Fe, clusters transformed to a well-ordered, single fcc phase with a lattice parameter of 0.363 nm, whereas the phase diagram predicted two-phase equilibrium. The stabilization of a single fcc phase was explained by a thermodynamic analysis. This analysis suggests that the single phase stability in the Fe-Au nanoparticles arises from the fact that the introduction of a phase boundary is energetically opposed. Heat treatment of as-deposited particles results in L12 and L1 0ordered structures near 1:3, 3:1 and 1:1 (Fe:Au) stoichiometries respectively

  8. Interactions between soil structure and excess water formation on chernozem soils

    NASA Astrophysics Data System (ADS)

    Gál, N.; Farsang, A.

    2012-04-01

    The main natural resource of Hungary is soil therefore its protection is a fundamental obligation for the state and the farmers too. The frequency of the weather extremeties have increased due to the global climate change which takes effect also on the soil properties. The hungarian agriculture was stricken with drought in the 1990's, whereas excess water has caused damages in the previous decade. According to multi-variable correlation tests, pedological parameters influence on the formation of excess water besides hydrometeorological, geological or relief factors. But not only the soil parameters can take effect on the formation of excess water, but also excess water can modify the soil parameters - causing appearance of hydromorfical characteristics or physical degradation. In our research the interactions between soil structure, excess water and land use were investigated in the aspects of changes in the structure of the upper soil, on a cultivated study area (located on the South Hungarian Great Plain). Three excess water patches were appointed with analysis of multitemporal Landsat images in the study area and were connected a southwest-west-nordeast-east line, forming a 700 meter-long catena. In July, 2011 soil samples were collected along this catena at each 50 meters from the depth of 0-5 cm, 10-15 cm and 20-25 cm to compare the agronomical structure and aggregates stability of soils covered temporally by excess water and without it. Furthermore, penetration resistance and relative moisture of soil were determined at the deep of 60 cm in definite points of a 25x25 m grid on the 45 hectares study field using 3T System hand penetrometer in order to create a multilayer-map from the soil compaction datas. The results call the attention both to the physical soil degradation caused by excess water and to the risk of erosion due to inadequate tillage or cultivation.

  9. Flavonoids and tyrosine nitration: structure-activity relationship correlation with enthalpy of formation.

    PubMed

    Sadeghipour, Mitra; Terreux, Raphael; Phipps, Jenny

    2005-03-01

    The ability of 11 flavonoids, naturally occurring polyphenols, and their related structure-activity relationships (SAR's) for inhibiting peroxynitrite-induced nitration of tyrosine was investigated. The flavonoids under study could be classified into four groups having very distinct in vitro inhibition effects. We also calculated the heat of formation (DeltaH(f)) of the corresponding flavonoids radicals which supported this finding. The most effective flavonoids included: catechin, taxifolin, luteolin, quercetin, and myricetin which have a common structural feature of ortho-dihydroxyl moiety (3',4'-OH substitution). Naringenin, kaempferol, and morin were 50% less effective inhibitors than the former group of flavonoid while their activities were in the range of trolox (an alpha-tocopherol analogue). The common structural aspect of this group of flavonoids is 4'-OH substitution. Therefore, these two groups of flavonoids may have similar mechanisms for their inhibition activity. No inhibition activity was observed by galangin. Apigenin behaved as a pro-oxidant in our in vitro study. Naringin was as effective as the second group at 4 mM tyrosine concentration while did not illustrate any inhibitory effect at 1 mM concentration of tyrosine. Our study provides further evidence for the importance of the catechol B ring and to a lesser effect the importance of 4'-OH substitution. Moreover, we observed very little or no influence on activity of flavonoids by 3-OH substitution and/or a C2-C3 double bond conjugated with 4-keto group within the subgroup containing the catechol moiety. Theoretical calculation of DeltaDeltaH(f) for tyrosyl radical repair by flavonoids (TyO*+FlOH-->TyOH+FlO*) correlated well with our in vitro results (inhibition% = -10 (DeltaDeltaH(f)), R2=0.906). Furthermore, this correlation was independent of tyrosine concentration. This model can be used to accurately predict the inhibitory effect of flavonoids on nitrotyrosine formation.

  10. Complex formation between anisole and boron trifluoride: structural and binding properties.

    PubMed

    Lin, Tao; Zhang, Weijiang; Wang, Lichang

    2008-12-25

    The structures, energetics, and binding characteristics of complexes formed between anisole (C(6)H(5)OCH(3)) and boron trifluoride (BF(3)) were investigated using MP2 and B3LYP methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. Among the complexes with a 1:1 ratio of C(6)H(5)OCH(3) to BF(3), both B3LYP and MP2 methods predict the same structures and relative stability of the isomers; however, the B3LYP binding energies are smaller than the MP2 energies. Furthermore, the weaker the interaction, the greater the discrepancy in binding energy. The charge decomposition analysis (CDA) showed that there are two types of complexes: the Lewis acid-base adduct and the van der Waals complexes. The CDA results also illustrated that there is a significant donation from the oxygen lone pair electrons to the boron vacant orbital in the adduct. The van der Waals complexes were formed through the aromatic ring and BF(3) interaction or through the H and F interactions. The MP2 results showed that the formation of adduct at room temperature is thermodynamically favorable. Among the 1:2 C(6)H(5)OCH(3)-BF(3) complexes, the most stable structure consists of both the Lewis acid-base and van der Waals binding; i.e., one BF(3) binds with C(6)H(5)OCH(3) to form C(6)H(5)OCH(3) x BF(3) adduct, while the other BF(3) binds with this adduct through van der Waals interactions. The calculated binding energy of the 1:1 complex is close to the experimental heat of formation, which suggests that the 1:1 complexes are the most likely species in the C(6)H(5)OCH(3) and BF(3) mixture.

  11. Structural characterization of the fracture systems in the porcelanites: Comparing data from the Monterey Formation in California USA and the Sap Bon Formation in Central Thailand

    NASA Astrophysics Data System (ADS)

    Kanjanapayont, Pitsanupong; Aydin, Atilla; Wongseekaew, Kanitsorn; Maneelok, Wichanee

    2016-09-01

    The fractures in the porcelanites from the Monterey Formation in California USA and the Sap Bon Formation in Central Thailand were documented for a comparative study of their modes, distribution, and their relationship to other structures such as folds and bedding planes. Both formations consist in thinly bedded stiff units that are prone to folding, flexural slip, and cross-bedding brittle fracturing under compression. There are two assemblages in the porcelanites. The first assemblage includes commonly vertical high-angle opening mode fractures, left-lateral strike-slip faults, normal faults, and thrust faults. The second one is sub-horizontal fractures which are associated with folds, bedding slip, and thrusts faults in both Monterey and Sap Bon formations. The structural architectures of these rocks and the associated groups of structures are remarkably similar in terms of both opening and shearing modes and their relationships with the bedding due to their depositional architecture and the compressional tectonic regimes, in spite of the fact that the two locations are more than ten thousand kilometers apart and have very different ages of deformation.

  12. HOT X-RAY CORONAE AROUND MASSIVE SPIRAL GALAXIES: A UNIQUE PROBE OF STRUCTURE FORMATION MODELS

    SciTech Connect

    Bogdan, Akos; Forman, William R.; Vogelsberger, Mark; Sijacki, Debora; Mazzotta, Pasquale; Kraft, Ralph P.; Jones, Christine; David, Laurence P.; Bourdin, Herve; Gilfanov, Marat; Churazov, Eugene

    2013-08-01

    Luminous X-ray gas coronae in the dark matter halos of massive spiral galaxies are a fundamental prediction of structure formation models, yet only a few such coronae have been detected so far. In this paper, we study the hot X-ray coronae beyond the optical disks of two 'normal' massive spirals, NGC 1961 and NGC 6753. Based on XMM-Newton X-ray observations, hot gaseous emission is detected to {approx}60 kpc-well beyond their optical radii. The hot gas has a best-fit temperature of kT {approx} 0.6 keV and an abundance of {approx}0.1 Solar, and exhibits a fairly uniform distribution, suggesting that the quasi-static gas resides in hydrostatic equilibrium in the potential well of the galaxies. The bolometric luminosity of the gas in the (0.05-0.15)r{sub 200} region (r{sub 200} is the virial radius) is {approx}6 Multiplication-Sign 10{sup 40} erg s{sup -1} for both galaxies. The baryon mass fractions of NGC 1961 and NGC 6753 are f{sub b,NGC1961} {approx} 0.11 and f{sub b,NGC6753} {approx} 0.09, which values fall short of the cosmic baryon fraction. The hot coronae around NGC 1961 and NGC 6753 offer an excellent basis to probe structure formation simulations. To this end, the observations are confronted with the moving mesh code AREPO and the smoothed particle hydrodynamics code GADGET. Although neither model gives a perfect description, the observed luminosities, gas masses, and abundances favor the AREPO code. Moreover, the shape and the normalization of the observed density profiles are better reproduced by AREPO within {approx}0.5r{sub 200}. However, neither model incorporates efficient feedback from supermassive black holes or supernovae, which could alter the simulated properties of the X-ray coronae. With the further advance of numerical models, the present observations will be essential in constraining the feedback effects in structure formation simulations.

  13. Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica.

    PubMed

    Gasse, Barbara; Liu, Xi; Corre, Erwan; Sire, Jean-Yves

    2015-01-01

    Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of

  14. Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica.

    PubMed

    Gasse, Barbara; Liu, Xi; Corre, Erwan; Sire, Jean-Yves

    2015-01-01

    Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of

  15. Suture pattern formation in ammonites and the unknown rear mantle structure

    PubMed Central

    Inoue, Shinya; Kondo, Shigeru

    2016-01-01

    Ammonite shells have complex patterns of suture lines that vary across species. The lines are formed at the intersection of the outer shell wall and the septa. The wavy septa can form if the rear mantle of the ammonite, which functions as the template, has a complex shape. Previous hypotheses assumed that the rear mantle is like a flexible membrane that can be folded by some physical force. The elucidation of the mechanism of septa formation requires that the detailed shape of the septa should be known. We developed a new protocol of X-ray micro-computed tomography (CT) and obtained high-resolution three-dimensional (3D) images of the septa of the Upper Cretaceous ammonite Damesites cf. damesi. The obtained image suggested that the wavy and branched structures of the rear mantle grew autonomously. We found that some extant sea slugs have branched structures and showed similar shape and growth sequence as those in fossils, suggesting that the mantle of molluscs basically has the potential to form branched projections. Based on the characteristics of the obtained 3D structure, we explain how ammonites might have formed the complex suture patterns. PMID:27640361

  16. A novel structural effector from rust fungi is capable of fibril formation.

    PubMed

    Kemen, Eric; Kemen, Ariane; Ehlers, Andreas; Voegele, Ralf; Mendgen, Kurt

    2013-09-01

    It has been reported that filament-forming surface proteins such as hydrophobins are important virulence determinants in fungi and are secreted during pathogenesis. Such proteins have not yet been identified in obligate biotrophic pathogens such as rust fungi. Rust transferred protein 1 (RTP1p), a rust protein that is transferred into the host cytoplasm, accumulates around the haustorial complex. To investigate RTP1p structure and function, we used immunocytological, biochemical and computational approaches. We found that RTP1p accumulates in protuberances of the extra-haustorial matrix, a compartment that surrounds the haustorium and is separated from the plant cytoplasm by a modified host plasma membrane. Our analyses show that RTP1p is capable of forming filamentous structures in vitro and in vivo. We present evidence that filament formation is due to β-aggregation similar to what has been observed for amyloid-like proteins. Our findings reveal that RTP1p is a member of a new class of structural effectors. We hypothesize that RTP1p is transferred into the host to stabilize the host cell and protect the haustorium from degradation in later stages of the interaction. Thus, we provide evidence for transfer of an amyloid-like protein into the host cell, which has potential for the development of new resistance mechanisms against rust fungi.

  17. Spontaneous formation of hierarchically structured curly films of nickel carbonate hydrate through drying.

    PubMed

    Guo, Xiao-Hui; Yu, Shu-Hong; Lu, Yang; Yuan, Guang-Bi; Sedlák, Milos; Cölfen, Helmut

    2010-06-15

    Novel curly nickel carbonate hydrate film superstructures can be prepared for the first time via a facile drying process of the films formed on air/solution interface in the presence of double hydrophilic copolymer or polyelectrolyte additives. As-prepared curly film patches with average edge sizes of several hundred micrometers display adjustable curly features along different orientation. The coiling up degree of the film edges is strongly dependent on the polymer concentration in bulk solution. Most of these curly structures have a relatively smooth outer surface; however, the microstructures of the outer surface of curly films formed show porous network-like features. In addition, using different kinds of nickel salts can produce distinct curly film samples. A possible formation mechanism of the curly film structure has been proposed. The multiple interaction modes between nickel salt precursors and polymer can favor the self-organization of the film formed at the air/solution interface. This approach is expected to be extended for producing a variety of curly hierarchical structures.

  18. Structure of yeast Ape1 and its role in autophagic vesicle formation

    PubMed Central

    Su, Ming-Yuan; Peng, Wen-Hsin; Ho, Meng-Ru; Su, Shih-Chieh; Chang, Yuan-Chih; Chen, Guang-Chao; Chang, Chung-I

    2015-01-01

    In Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the form of a large complex into a Cvt vesicle using autophagic machinery, targeting it into the vacuole (the yeast lysosome) where it is proteolytically processed into its mature form, Ape1, by removal of an amino-terminal 45-amino acid propeptide. prApe1 is thought to serve as a scaffolding cargo critical for the assembly of the Cvt vesicle by presenting the propeptide to mediate higher-ordered complex formation and autophagic receptor recognition. Here we report the X-ray crystal structure of Ape1 at 2.5 Å resolution and reveal its dodecameric architecture consisting of dimeric and trimeric units, which associate to form a large tetrahedron. The propeptide of prApe1 exhibits concentration-dependent oligomerization and forms a stable tetramer. Structure-based mutagenesis demonstrates that disruption of the inter-subunit interface prevents dodecameric assembly and vacuolar targeting in vivo despite the presence of the propeptide. Furthermore, by examining the vacuolar import of propeptide-fused exogenous protein assemblies with different quaternary structures, we found that 3-dimensional spatial distribution of propeptides presented by a scaffolding cargo is essential for the assembly of the Cvt vesicle for vacuolar delivery. This study describes a molecular framework for understanding the mechanism of Cvt or autophagosomal biogenesis in selective macroautophagy. PMID:26208681

  19. Numerical modeling of the formation and structure of the Orientale impact basin

    NASA Astrophysics Data System (ADS)

    Potter, Ross W. K.; Kring, David A.; Collins, Gareth S.; Kiefer, Walter S.; McGovern, Patrick J.

    2013-05-01

    The Orientale impact basin is the youngest and best-preserved lunar multi-ring basin and has, thus, been the focus of studies investigating basin-forming processes and final structures. A consensus about how multi-ring basins form, however, remains elusive. Here we numerically model the Orientale basin-forming impact with the aim of resolving some of the uncertainties associated with this basin. By using two thermal profiles estimating lunar conditions at the time of Orientale's formation and constraining the numerical models with crustal structures inferred from gravity data, we provide estimates for Orientale's impact energy (2-9 × 1025 J), impactor size (50-80 km diameter), transient crater size (˜320-480 km), excavation depth (40-55 km), and impact melt volume (˜106 km3). We also analyze the distribution and deformation of target material and compare our model results and Orientale observations with the Chicxulub crater to investigate similarities between these two impact structures.

  20. A microscopic, non-equilibrium, statistical field theory for cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Bartelmann, Matthias; Fabis, Felix; Berg, Daniel; Kozlikin, Elena; Lilow, Robert; Viermann, Celia

    2016-04-01

    Building upon the recent pioneering work by Mazenko and by Das and Mazenko, we develop a microscopic, non-equilibrium, statistical field theory for initially correlated canonical ensembles of classical microscopic particles obeying Hamiltonian dynamics. Our primary target is cosmic structure formation, where initial Gaussian correlations in phase space are believed to be set by inflation. We give an exact expression for the generating functional of this theory and work out suitable approximations. We specify the initial correlations by a power spectrum and derive general expressions for the correlators of the density and the response field. We derive simple closed expressions for the lowest-order contributions to the nonlinear cosmological power spectrum, valid for arbitrary wave numbers. We further calculate the bispectrum expected in this theory within these approximations and the power spectrum of cosmic density fluctuations to first order in the gravitational interaction, using a recent improvement of the Zel’dovich approximation. We show that, with a modification motivated by the adhesion approximation, the nonlinear growth of the density power spectrum found in numerical simulations of cosmic structure evolution is reproduced well to redshift zero and for arbitrary wave numbers even within first-order perturbation theory. Our results present the first fully analytic calculation of the nonlinear power spectrum of cosmic structures.

  1. Suture pattern formation in ammonites and the unknown rear mantle structure.

    PubMed

    Inoue, Shinya; Kondo, Shigeru

    2016-01-01

    Ammonite shells have complex patterns of suture lines that vary across species. The lines are formed at the intersection of the outer shell wall and the septa. The wavy septa can form if the rear mantle of the ammonite, which functions as the template, has a complex shape. Previous hypotheses assumed that the rear mantle is like a flexible membrane that can be folded by some physical force. The elucidation of the mechanism of septa formation requires that the detailed shape of the septa should be known. We developed a new protocol of X-ray micro-computed tomography (CT) and obtained high-resolution three-dimensional (3D) images of the septa of the Upper Cretaceous ammonite Damesites cf. damesi. The obtained image suggested that the wavy and branched structures of the rear mantle grew autonomously. We found that some extant sea slugs have branched structures and showed similar shape and growth sequence as those in fossils, suggesting that the mantle of molluscs basically has the potential to form branched projections. Based on the characteristics of the obtained 3D structure, we explain how ammonites might have formed the complex suture patterns. PMID:27640361

  2. Molecular dynamics study of crater formation by core-shell structured cluster impact

    NASA Astrophysics Data System (ADS)

    Aoki, Takaaki; Seki, Toshio; Matsuo, Jiro

    2012-07-01

    Crater formation processes by the impacts of large clusters with binary atomic species were studied using molecular dynamics (MD) simulations. Argon and xenon atoms are artificially organized in core-shell cluster structures with various component ratios and irradiated on a Si(1 0 0) target surface. When the cluster has Xe1000 core covered with 1000 Ar atoms, and impacts at a total of 20 keV, the core Xe cluster penetrates into the deep area, and a crater with a conical shape is left on the target. On the other hand, in the case of a cluster with the opposite structure, Ar1000 core covered with 1000 Xe atoms, the cluster stops at a shallow area of the target. The incident cluster atoms are mixed and tend to spread in a lateral direction, which results in a square shaped crater with a shallower hole and wider opening. The MD simulations suggest that large cluster impacts cause different irradiation effects by changing the structure, even if the component ratio is the same.

  3. Radical Formation and Chemical Track Structure in Ion-Beam Irradiated DNA

    NASA Astrophysics Data System (ADS)

    Becker, David; Adhikary, Amitava; Khanduri, Deepti; Sevilla, Michael D.

    2009-12-01

    Ion-beam irradiation of hydrated DNA at 77 K results in formation of at least three base radicals and a variety of radicals on the sugar phosphate backbone that can be observed using Electron Spin Resonance (ESR) spectroscopy. From dose-response curves for these radicals, we have formulated a radiation-chemical model of the track structure for ion-beam irradiated DNA. The model for chemical behavior posits that the base radicals trapped at 77 K are formed almost entirely in the track penumbra. The lower yields observed in ion-beam irradiated samples results from the fact that only a portion of the energy deposited by the ion beam ends up in this γ-like region. The remainder of the energy is deposited in the core in which the proximity of ion-radical formation results in the fast recombination of oppositely charged radicals, so few survive in the core at 77 K. However, a second group of radicals, neutral sugar radicals, are not as susceptible to recombination as are ion radicals, and can survive after formation in the core; these are presumed to form predominantly in the core. They include the sugar radicals, C1'ṡC3'ṡC5'ṡ, formed from oxidative processes, and C3'ṡdephos and phosphorous radicals which are formed after immediate strand breaks. The later species are thought to result from reductive cleavage by low energy electrons (LEE.) The high energy density in the core results in excited state processes that produce additional sugar radicals. The spatial characteristics of the radicals, deduced from PELDOR experiments, indicates that multiply damaged cluster sites (MDS) are formed in the core; these would be biologically significant, if formed in cells.

  4. Understanding irregular shell formation of Nautilus in aquaria: chemical composition and structural analysis.

    PubMed

    Moini, Mehdi; O'Halloran, Aoife; Peters, Alan M; France, Christine A M; Vicenzi, Edward P; DeWitt, Tamsen G; Langan, Esther; Walsh, Tim; Speakman, Robert J

    2014-01-01

    Irregular shell formation and black lines on the outside of live chambered nautilus shells have been observed in all adult specimens at aquariums and zoos soon after the organisms enter aquaria. Black lines have also been observed in wild animals at sites of broken shell, but continued growth from that point returns to a normal, smooth structure. In contrast, rough irregular deposition of shell continues throughout residence in aquaria. The composition and reasons for deposition of the black material and mitigation of this irregular shell formation is the subject of the current study. A variety of analytical techniques were used, including stable isotope mass spectrometry (SI-MS), inductively coupled plasma mass spectrometry (ICP-MS), micro x-ray fluorescence (µXRF), X-ray diffraction (XRD), and scanning electron microscopy (SEM) based X-ray microanalysis. Results indicate that the black material contains excess amounts of copper, zinc, and bromine which are unrelated to the Nautilus diet. The combination of these elements and proteins plays an important role in shell formation, growth, and strengthening. Further study will be needed to compare the proteomics of the shell under aquaria versus natural wild environments. The question remains as to whether the occurrence of the black lines indicates normal healing followed by growth irregularities that are caused by stress from chemical or environmental conditions. In this paper we begin to address this question by examining elemental and isotopic differences of Nautilus diet and salt water. The atomic composition and light stable isotopic ratios of the Nautilus shell formed in aquaria verses wild conditions are presented.

  5. Terrestrial Planet Formation Constrained by the Structure of the Asteroid Belt

    NASA Astrophysics Data System (ADS)

    Morbidelli, Alessandro; Izidoro da Costa, Andre; Raymond, Sean; Winter, Othon

    2015-08-01

    Reproducing the large mass ratio between the Earth and Mars requires that the terrestrial planets formed from a narrow annulus, with a steep mass density gradient beyond 1 AU (Hansen, 2009). The Grand Tack scenario (Walsh et al., 2011) invokes a specific migration history of the giant planets of the Solar System to remove most of the mass initially beyond 1 AU and to leave the asteroid belt on an excited dynamical state. However, one could also invoke that the steep mass density gradient was achieved by the migration and pile-up of a large amount of small particles induced by gas-drag. This process has been proposed to explain the formation of close-in super Earths in extrasolar systems (e.g. Chatterjee and Tan, 2015). Here we show that the asteroid belt orbital excitation provides a crucial constraint against this scenario for the Solar System. We achieve this result by performing a series of numerical simulations of terrestrial planet formation and asteroid belt evolution, starting from disks of planetesimals and planetary embryos with various radial density gradients. Jupiter and Saturn are assumed on their current, non-migrating orbits. We find that disks with shallow density gradients allow the dynamical excitation of the asteroid belt by a self-stirring process, but lead inevitably to the formation of a Mars analog which is significantly more massive than the real planet. Instead, a disk with a surface density gradient proportional to 1/r^5 beyond 1 AU allows us to reproduce the Earth/Mars mass ratio, but leaves the asteroid belt on a dynamical state way too cold compared to the real belt. Therefore, we conclude that no disk profile can explain at the same time the structure of the terrestrial planet system and of the asteroid belt. Thus, the asteroid belt has to have been depleted and dynamically excited by an external agent as, for instance, in the Grand Tack scenario.

  6. Cosmological N-body Simulation of Galaxy and Large-Scale Structure Formation: The Gravity Frontier

    NASA Astrophysics Data System (ADS)

    Klypin, Anatoly

    2015-04-01

    One of the first N-body simulations done almost 50 years ago had only 200 self-gravitating particles. Even this first baby step made substantial impact on understanding how astronomical objects should form. Now powerful supercomputers and new algorithms allow astronomers produce N-body simulations that employ up to a trillion dark matter particles and produce vital theoretical predictions regarding formation, evolution, structure and statistics of objects ranging from dwarf galaxies to clusters and superclusters of galaxies. With only gravity involved in these theoretical models, one would naively expect that by now we should know everything we need about N-body dynamics of cosmological fluctuations. Not the case. It appears that the Universe was not cooperative and gave us divergencies in the initial conditions generated during the Inflation epoch and subsequent expansion of the Universe - the infinite phase-space density and divergent density fluctuations. Ever increasing observational demands on statistics and accuracy of theoretical predictions is another driving force for more realistic and larger N-body simulations. Large current and new planned observational projects such as BOSS, eBOSS, Euclid, LSST will bring information on spatial distribution, motion, and properties of millions of galaxies at different redshifts. Direct simulations of evolution of gas and formation of stars for millions of forming galaxies will not be available for years leaving astronomers with the only option - to develop methods to combine large N-body simulations with models of galaxy formation to produce accurate theoretical predictions. I will discuss the current status of the field and directions of its development.

  7. Understanding irregular shell formation of Nautilus in aquaria: chemical composition and structural analysis.

    PubMed

    Moini, Mehdi; O'Halloran, Aoife; Peters, Alan M; France, Christine A M; Vicenzi, Edward P; DeWitt, Tamsen G; Langan, Esther; Walsh, Tim; Speakman, Robert J

    2014-01-01

    Irregular shell formation and black lines on the outside of live chambered nautilus shells have been observed in all adult specimens at aquariums and zoos soon after the organisms enter aquaria. Black lines have also been observed in wild animals at sites of broken shell, but continued growth from that point returns to a normal, smooth structure. In contrast, rough irregular deposition of shell continues throughout residence in aquaria. The composition and reasons for deposition of the black material and mitigation of this irregular shell formation is the subject of the current study. A variety of analytical techniques were used, including stable isotope mass spectrometry (SI-MS), inductively coupled plasma mass spectrometry (ICP-MS), micro x-ray fluorescence (µXRF), X-ray diffraction (XRD), and scanning electron microscopy (SEM) based X-ray microanalysis. Results indicate that the black material contains excess amounts of copper, zinc, and bromine which are unrelated to the Nautilus diet. The combination of these elements and proteins plays an important role in shell formation, growth, and strengthening. Further study will be needed to compare the proteomics of the shell under aquaria versus natural wild environments. The question remains as to whether the occurrence of the black lines indicates normal healing followed by growth irregularities that are caused by stress from chemical or environmental conditions. In this paper we begin to address this question by examining elemental and isotopic differences of Nautilus diet and salt water. The atomic composition and light stable isotopic ratios of the Nautilus shell formed in aquaria verses wild conditions are presented. PMID:24797217

  8. DNA-Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes.

    PubMed

    Tretyakova, Natalia Y; Groehler, Arnold; Ji, Shaofei

    2015-06-16

    Noncovalent DNA-protein interactions are at the heart of normal cell function. In eukaryotic cells, genomic DNA is wrapped around histone octamers to allow for chromosomal packaging in the nucleus. Binding of regulatory protein factors to DNA directs replication, controls transcription, and mediates cellular responses to DNA damage. Because of their fundamental significance in all cellular processes involving DNA, dynamic DNA-protein interactions are required for cell survival, and their disruption is likely to have serious biological consequences. DNA-protein cross-links (DPCs) form when cellular proteins become covalently trapped on DNA strands upon exposure to various endogenous, environmental and chemotherapeutic agents. DPCs progressively accumulate in the brain and heart tissues as a result of endogenous exposure to reactive oxygen species and lipid peroxidation products, as well as normal cellular metabolism. A range of structurally diverse DPCs are found following treatment with chemotherapeutic drugs, transition metal ions, and metabolically activated carcinogens. Because of their considerable size and their helix-distorting nature, DPCs interfere with the progression of replication and transcription machineries and hence hamper the faithful expression of genetic information, potentially contributing to mutagenesis and carcinogenesis. Mass spectrometry-based studies have identified hundreds of proteins that can become cross-linked to nuclear DNA in the presence of reactive oxygen species, carcinogen metabolites, and antitumor drugs. While many of these proteins including histones, transcription factors, and repair proteins are known DNA binding partners, other gene products with no documented affinity for DNA also participate in DPC formation. Furthermore, multiple sites within DNA can be targeted for cross-linking including the N7 of guanine, the C-5 methyl group of thymine, and the exocyclic amino groups of guanine, cytosine, and adenine. This structural

  9. Does the tail wag the dog? How the structure of a glycosylphosphatidylinositol anchor affects prion formation.

    PubMed

    Bate, Clive; Nolan, William; Williams, Alun

    2016-03-01

    There is increasing interest in the role of the glycosylphosphatidylinositol (GPI) anchor attached to the cellular prion protein (PrP(C)). Since GPI anchors can alter protein targeting, trafficking and cell signaling, our recent study examined how the structure of the GPI anchor affected prion formation. PrP(C) containing a GPI anchor from which the sialic acid had been removed (desialylated PrP(C)) was not converted to PrP(Sc) in prion-infected neuronal cell lines and in scrapie-infected primary cortical neurons. In uninfected neurons desialylated PrP(C) was associated with greater concentrations of gangliosides and cholesterol than PrP(C). In addition, the targeting of desialylated PrP(C) to lipid rafts showed greater resistance to cholesterol depletion than PrP(C). The presence of desialylated PrP(C) caused the dissociation of cytoplasmic phospholipase A2 (cPLA2) from PrP-containing lipid rafts, reduced the activation of cPLA2 and inhibited PrP(Sc) production. We conclude that the sialic acid moiety of the GPI attached to PrP(C) modifies local membrane microenvironments that are important in PrP-mediated cell signaling and PrP(Sc) formation. PMID:26901126

  10. Southern Ocean frontal structure and sea-ice formation rates revealed by elephant seals

    PubMed Central

    Charrassin, J.-B.; Hindell, M.; Rintoul, S. R.; Roquet, F.; Sokolov, S.; Biuw, M.; Costa, D.; Boehme, L.; Lovell, P.; Coleman, R.; Timmermann, R.; Meijers, A.; Meredith, M.; Park, Y.-H.; Bailleul, F.; Goebel, M.; Tremblay, Y.; Bost, C.-A.; McMahon, C. R.; Field, I. C.; Fedak, M. A.; Guinet, C.

    2008-01-01

    Polar regions are particularly sensitive to climate change, with the potential for significant feedbacks between ocean circulation, sea ice, and the ocean carbon cycle. However, the difficulty in obtaining in situ data means that our ability to detect and interpret change is very limited, especially in the Southern Ocean, where the ocean beneath the sea ice remains almost entirely unobserved and the rate of sea-ice formation is poorly known. Here, we show that southern elephant seals (Mirounga leonina) equipped with oceanographic sensors can measure ocean structure and water mass changes in regions and seasons rarely observed with traditional oceanographic platforms. In particular, seals provided a 30-fold increase in hydrographic profiles from the sea-ice zone, allowing the major fronts to be mapped south of 60°S and sea-ice formation rates to be inferred from changes in upper ocean salinity. Sea-ice production rates peaked in early winter (April–May) during the rapid northward expansion of the pack ice and declined by a factor of 2 to 3 between May and August, in agreement with a three-dimensional coupled ocean–sea-ice model. By measuring the high-latitude ocean during winter, elephant seals fill a “blind spot” in our sampling coverage, enabling the establishment of a truly global ocean-observing system. PMID:18695241

  11. Identification of a Gene Essential for Sheathed Structure Formation in Sphaerotilus natans, a Filamentous Sheathed Bacterium

    PubMed Central

    Suzuki, Toshihiko; Kanagawa, Takahiro; Kamagata, Yoichi

    2002-01-01

    Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in substrate-rich media it grows as single rod-shaped cells, whereas in substrate-limited media it grows as filaments. To identify genes responsible for sheath formation, we carried out transposon Tn5 mutagenesis. Of the approximately 20,000 mutants obtained, 7 did not form sheathed structures. Sequencing of the Tn5-flanking regions showed that five of the seven Tn5 insertions converged at the same open reading frame, designated sthA. The deduced amino acids encoded by sthA were found to be homologous to glycosyltransferase, which is known to be involved in linking sugars to lipid carriers during bacterial exopolysaccharide biosynthesis. Disruption of the gene of the wild-type strain by inserting a kanamycin resistance gene cassette also resulted in sheathless growth under either type of nutrient condition. These findings indicate that sthA is a crucial component responsible for sheath formation. PMID:11772646

  12. Monodispersed bimetallic PdAg nanoparticles with twinned structures: formation and enhancement for the methanol oxidation.

    PubMed

    Yin, Zhen; Zhang, Yining; Chen, Kai; Li, Jing; Li, Wenjing; Tang, Pei; Zhao, Huabo; Zhu, Qingjun; Bao, Xinhe; Ma, Ding

    2014-01-01

    Monodispersed bimetallic PdAg nanoparticles can be fabricated through the emulsion-assisted ethylene glycol (EG) ternary system. Different compositions of bimetallic PdAg nanoparticles, Pd₈₀Ag₂₀, Pd₆₅Ag₃₅ and Pd₄₆Ag₅₄ can be obtained via adjusting the reaction parameters. For the formation process of the bimetallic PdAg nanoparticles, there have two-stage growth processes: firstly, nucleation and growth of the primary nanoclusters; secondly, formation of the secondary nanoparticles with the size-selection and relax process via the coalescence or aggregation of the primary nanoclusters. The as-prepared PdAg can be supported on the carbon black without any post-treatment, which exhibited high electro-oxidation activity towards methanol oxidation under alkaline media. More importantly, carbon-supported Pd₈₀Ag₂₀ nanoparticles reveal distinctly superior activities for the methanol oxidation, even if compared with commercial Pt/C electro-catalyst. It is concluded that the enhanced activity is dependant on the unique twinning structure with heterogeneous phase due to the dominating coalescence growth in EG ternary system. PMID:24608736

  13. Monodispersed bimetallic PdAg nanoparticles with twinned structures: Formation and enhancement for the methanol oxidation

    PubMed Central

    Yin, Zhen; Zhang, Yining; Chen, Kai; Li, Jing; Li, Wenjing; Tang, Pei; Zhao, Huabo; Zhu, Qingjun; Bao, Xinhe; Ma, Ding

    2014-01-01

    Monodispersed bimetallic PdAg nanoparticles can be fabricated through the emulsion-assisted ethylene glycol (EG) ternary system. Different compositions of bimetallic PdAg nanoparticles, Pd80Ag20, Pd65Ag35 and Pd46Ag54 can be obtained via adjusting the reaction parameters. For the formation process of the bimetallic PdAg nanoparticles, there have two-stage growth processes: firstly, nucleation and growth of the primary nanoclusters; secondly, formation of the secondary nanoparticles with the size-selection and relax process via the coalescence or aggregation of the primary nanoclusters. The as-prepared PdAg can be supported on the carbon black without any post-treatment, which exhibited high electro-oxidation activity towards methanol oxidation under alkaline media. More importantly, carbon-supported Pd80Ag20 nanoparticles reveal distinctly superior activities for the methanol oxidation, even if compared with commercial Pt/C electro-catalyst. It is concluded that the enhanced activity is dependant on the unique twinning structure with heterogeneous phase due to the dominating coalescence growth in EG ternary system. PMID:24608736

  14. Investigation of Pyrene Excimer formation in various manufacturing processes and ionic structures

    NASA Astrophysics Data System (ADS)

    Jang, Hyun-Sook; Nieh, Mu-Ping

    2013-03-01

    Electrospun pyrene (Py)/polystyrene/tetrabutylammonium hexafluorophosphate (TBAPF6) thin films can provide high-sensitivity and high-selectivity detection of nitro-aromatic explosives through fluorescence quenching of the Py excimers. However, we have found that the formation of Py excimers in Py/PS/TBAPF6 thin films depends greatly on the manufacturing processes. Our results indicate that high solvent vapor pressure promotes the Py excimer fluorescence, while high temperature (around or greater than Tg of the PS) has an opposite effect in absence of solvent - reducing the Py excimer fluorescence. Moreover, we have found that salts structure such as cation chain length, anion strength can significantly affect the formation of Py excimer both in solution and solid state, presumably due to self-aggregation of the salts and electrostatic interactions between ions and pyrene excimer. 13C-NMR and steady-state fluorescence result indicate that the salt induces peak shift to the downfield in the spectra and quenches the Py excimer intensity drastically. Ph.D. Candidate, Institute of Material Science, Polymer program

  15. The structure and formation mechanism of a sea fog event over the Yellow Sea

    NASA Astrophysics Data System (ADS)

    Guo, Jingtian; Li, Pengyuan; Fu, Gang; Zhang, Wei; Gao, Shanhong; Zhang, Suping

    2015-02-01

    In this paper, a heavy sea fog event occurring over the Yellow Sea on 11 April 2004 was investigated based upon observational and modeling analyses. From the observational analyses, this sea fog event is a typical advection cooling case. Sea surface temperature (SST) and specific humidity (SH) show strong gradients from south to north, in which warm water is located in the south and consequently, moisture is larger in the south than in the north due to evaporation processes. After fog formation, evaporation process provides more moisture into the air and further contributes to fog evolution. The sea fog event was reproduced by the Regional Atmospheric Modeling System (RAMS) reasonably. The roles of important physical processes such as radiation, turbulence as well as atmospheric stratification in sea fog's structure and its formation mechanisms were analyzed using the model results. The roles of long wave radiation cooling, turbulence as well as atmospheric stratification were analyzed based on the modeling results. It is found that the long wave radiative cooling at the fog top plays an important role in cooling down the fog layer through turbulence mixing. The fog top cooling can overpower warming from the surface. Sea fog develops upward with the aid of turbulence. The buoyancy term, i.e., the unstable layer, contributes to the generation of TKE in the fog region. However, the temperature inversion layer prevents fog from growing upward.

  16. Ionizing radiation decreases capillary-like structure formation by endothelial cells in vitro.

    PubMed

    Ahmad, Mansur; Khurana, Neerja R; Jaberi, Joby E

    2007-01-01

    For successful tissue engineering in surgical radiotherapy patients, irradiated endothelial cells (EC) must form new blood vessels to nourish and build connections with the engineered segment. Therefore, it is critical to understand neovasculogenesis by irradiated EC. The objective of this study was to determine the effects of ionizing radiation on endothelial cell proliferation and capillary-like structures (CLS) formation. Human Umbilical Vein Endothelial Cells (HUVEC) were irradiated with single or fractionated doses of radiation. Proliferation was determined by counting cells. CLS morphology was analyzed from photomicrographs. A single dose of 8 Gy radiation was highly lethal to HUVEC compared to lower dosage. A single dose had more of an inhibitory effect on cell proliferation compared to the same dose delivered in a fractionated manner. CLS formation began after cells reached confluency. To form a CLS, a single cell expanded, and a number of cells rearranged around its periphery in an oval fashion (mimicking a vessel wall). The central cell later disintegrated leaving a void, mimicking the lumen. Irradiated EC can form CLS, although they are fewer and smaller compared to those by sham cells. By disrupting the peripheral cells, >or=4 Gy doses significantly reduced the number of CLS. The disruptive affect was seen more with large CLS compared to small CLS. At different doses, the shapes of CLS were not significantly different. PMID:17028041

  17. Southern Ocean frontal structure and sea-ice formation rates revealed by elephant seals.

    PubMed

    Charrassin, J-B; Hindell, M; Rintoul, S R; Roquet, F; Sokolov, S; Biuw, M; Costa, D; Boehme, L; Lovell, P; Coleman, R; Timmermann, R; Meijers, A; Meredith, M; Park, Y-H; Bailleul, F; Goebel, M; Tremblay, Y; Bost, C-A; McMahon, C R; Field, I C; Fedak, M A; Guinet, C

    2008-08-19

    Polar regions are particularly sensitive to climate change, with the potential for significant feedbacks between ocean circulation, sea ice, and the ocean carbon cycle. However, the difficulty in obtaining in situ data means that our ability to detect and interpret change is very limited, especially in the Southern Ocean, where the ocean beneath the sea ice remains almost entirely unobserved and the rate of sea-ice formation is poorly known. Here, we show that southern elephant seals (Mirounga leonina) equipped with oceanographic sensors can measure ocean structure and water mass changes in regions and seasons rarely observed with traditional oceanographic platforms. In particular, seals provided a 30-fold increase in hydrographic profiles from the sea-ice zone, allowing the major fronts to be mapped south of 60 degrees S and sea-ice formation rates to be inferred from changes in upper ocean salinity. Sea-ice production rates peaked in early winter (April-May) during the rapid northward expansion of the pack ice and declined by a factor of 2 to 3 between May and August, in agreement with a three-dimensional coupled ocean-sea-ice model. By measuring the high-latitude ocean during winter, elephant seals fill a "blind spot" in our sampling coverage, enabling the establishment of a truly global ocean-observing system. PMID:18695241

  18. Combustion and structure formation in SHS processes under microgravity conditions: SHS plans for microgravity experiments

    NASA Technical Reports Server (NTRS)

    Merzhanov, A. G.

    1995-01-01

    This paper outlines ISMAN suggestions for the joint NASA-RSA project 'Combustion and Structure formation in SHS Processes under Microgravity Conditions'. The basic ideas of this work naturally follow from our almost 30-year experience in the field of SHS. As a matter of fact, we have already obtained some results in the following two directions closely related to the microgravity problem. One is the studies on SHS processes in the field of centrifugal forces. These studies aimed at the intensification of gravity-sensitive SHS processes in multicomponent highly caloric systems forming melts at high overloads (up to 2000 g). In other words, these studies had the objectives that are inverse to those in the microgravity studies. The second group of results directly relates to the microgravity problem and the project under consideration. These experiments played the important role in establishing links between SHS and microgravity.

  19. Influence of solidification accelerators on structure formation of anhydrite-containing binders

    NASA Astrophysics Data System (ADS)

    Anikanova, L.; Volkova, O.; Kudyakov, A.; Sarkisov, Y.; Tolstov, D.

    2016-01-01

    The article presents results of scientific analysis of chemical additives influence on acid fluoride binder. It was found that the influence of sulfate nature additives on the process of hydration and solidification of the binder is similar to influence of additives on indissoluble anhydrite. Additives with SO42- anion NO- are more efficient. The mentioned additives according to accelerating effect belong to the following succession: K2SO4 > Na2SO4 > FeSO4 > MgSO4. Facilitation of the process of hydration and solidification of the binder, increase in density and durability of the binder (32 MPa) is to the greatest extent achieved with the introduction of 2% sodium sulfate additive of the binder's mass into the composition of the binder along with the ultrasonic treatment of water solution. Directed crystal formation process with healing of porous structure by new growths presented as calcium sulfate dehydrate and hydroglauberite provides positive effect.

  20. Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division

    NASA Astrophysics Data System (ADS)

    Noguchi, Hiroshi

    2013-01-01

    Self-assembly dynamics in binary surfactant mixtures and structure changes of lipid vesicles induced by detergent solution are studied using coarse-grained molecular simulations. Disk-shaped micelles, the bicelles, are stabilized by detergents surrounding the rim of a bilayer disk of lipids. The self-assembled bicelles are considerably smaller than bicelles formed from vesicle rupture, and their size is determined by the concentrations of lipids and detergents and the interactions between the two species. The detergent-adsorption induces spontaneous curvature of the vesicle bilayer and results in vesicle division into two vesicles or vesicle rupture into worm-like micelles. The division occurs mainly via the inverse pathway of the modified stalk model. For large spontaneous curvature of the monolayers of the detergents, a pore is often opened, thereby leading to vesicle division or worm-like micelle formation.

  1. Formation of sprite streamers at subbreakdown conditions from ionospheric inhomogeneities resembling observed sprite halo structures

    NASA Astrophysics Data System (ADS)

    Kosar, Burcu C.; Liu, Ningyu; Rassoul, Hamid K.

    2013-12-01

    Modeling results of sprite streamer formation from large ionospheric inhomogeneities or patches (several tens to hundreds of meter wide) indicate that positive streamers can be initiated at subbreakdown conditions from the inhomogeneities with a density comparable to sprite halo densities. For spherical patches with a given radius, the minimum density required for streamer initiation decreases with increasing ambient field. For a given density, the minimum size of the inhomogeneity decreases with increasing ambient field. The modeling results on the associated optical emissions show that a luminous spherical-like cap appears around the lower tip of the ionization patch before streamer initiation, and the streamer is initiated from the bottom of this cap, which appears to be similar to streamer initiation from luminous structures in the lower ionosphere recorded by recent high-speed videos. Our study suggests that if the sprite halo front is unstable, inhomogeneities developing from it can initiate sprite streamers at subbreakdown conditions.

  2. Glass formation, properties and structure of soda-yttria-silica glasses

    NASA Technical Reports Server (NTRS)

    Angel, Paul W.; Hann, Raiford E.

    1992-01-01

    The glass formation region of the soda yttria silicate system was determined. The glasses within this region were measured to have a density of 2.4 to 3.1 g/cu cm, a refractive index of 1.50 to 1.60, a coefficient of thermal expansion of 7 x 10(exp -6)/C, softening temperatures between 500 and 780 C, and Vickers hardness values of 3.7 to 5.8 GPa. Aqueous chemical durability measurements were made on select glass compositions while infrared transmission spectra were used to study the glass structure and its effect on glass properties. A compositional region was identified which exhibited high thermal expansion, high softening temperatures, and good chemical durability.

  3. Glass formation, properties, and structure of soda-yttria-silicate glasses

    NASA Technical Reports Server (NTRS)

    Angel, Paul W.; Hann, Raiford E.

    1991-01-01

    The glass formation region of the soda yttria silicate system was determined. The glasses within this region were measured to have a density of 2.4 to 3.1 g/cu cm, a refractive index of 1.50 to 1.60, a coefficient of thermal expansion of 7 x 10(exp -6)/C, softening temperatures between 500 and 780 C, and Vickers hardness values of 3.7 to 5.8 GPa. Aqueous chemical durability measurements were made on select glass compositions while infrared transmission spectra were used to study the glass structure and its effect on glass properties. A compositional region was identified which exhibited high thermal expansion, high softening temperatures, and good chemical durability.

  4. Critical issues in the formation of quantum computer test structures by ion implantation

    SciTech Connect

    Schenkel, T.; Lo, C. C.; Weis, C. D.; Schuh, A.; Persaud, A.; Bokor, J.

    2009-04-06

    The formation of quantum computer test structures in silicon by ion implantation enables the characterization of spin readout mechanisms with ensembles of dopant atoms and the development of single atom devices. We briefly review recent results in the characterization of spin dependent transport and single ion doping and then discuss the diffusion and segregation behaviour of phosphorus, antimony and bismuth ions from low fluence, low energy implantations as characterized through depth profiling by secondary ion mass spectrometry (SIMS). Both phosphorus and bismuth are found to segregate to the SiO2/Si interface during activation anneals, while antimony diffusion is found to be minimal. An effect of the ion charge state on the range of antimony ions, 121Sb25+, in SiO2/Si is also discussed.

  5. Critical issues in the formation of quantum computer test structures by ion implantation

    NASA Astrophysics Data System (ADS)

    Schenkel, T.; Lo, C. C.; Weis, C. D.; Schuh, A.; Persaud, A.; Bokor, J.

    2009-08-01

    The formation of quantum computer test structures in silicon by ion implantation enables the characterization of spin readout mechanisms with ensembles of dopant atoms and the development of single atom devices. We briefly review recent results in the characterization of spin dependent transport and single ion doping and then discuss the diffusion and segregation behaviour of phosphorus, antimony and bismuth ions from low fluence, low energy implantations as characterized through depth profiling by secondary ion mass spectrometry (SIMS). Both phosphorus and bismuth are found to segregate to the SiO 2/Si interface during activation anneals, while antimony diffusion is found to be minimal. An effect of the ion charge state on the range of antimony ions, 121Sb 25+, in SiO 2/Si is also discussed.

  6. Formation of titanium carbonitride film by laser treatment: Structural and transport properties

    SciTech Connect

    Soni, Sheetal; Pandey, A.; Gupta, Ratnesh; Sinha, A. K.

    2015-06-24

    In-plane and Out-of-plane Grazing incidence X-ray diffraction is used to characterize the preferred orientation present in the titanium carbonitride films using ADXRD beamline at INDUS 2 synchrotron radiation source. GIXRD shows the formation of mixture of FCCTiC{sub x}N{sub (1-x)} films for different values of x along with the solid solution. From the in-plane and out-of-plane XRD measurements, we have observed that a specific texture along the c-axis of Ti has been formed during the laser treatment process. Due to the diffusion of C and N into Ti, the resistance of the specimen has been decreases with respect to the resistance of pure Ti sheet. The formed phases are stable and there is no structural relaxation has been observed during annealing process.

  7. Structure formation with a long-range scalar dark matter interaction

    SciTech Connect

    Nusser, Adi; Gubser, S.S.; Peebles, P.J.E.

    2005-04-15

    Numerical simulations show that a long-range scalar interaction in a single species of massive dark matter particles causes voids between the concentrations of large galaxies to be more nearly empty, suppresses accretion of intergalactic matter onto galaxies at low redshift, and produces an early generation of dense dark matter halos. These three effects, in moderation, seem to be improvements over the {lambda}CDM model predictions for cosmic structure formation. Because the scalar interaction in this model has negligible effect on laboratory physics and the classical cosmological tests, it offers an observationally attractive example of cosmology with complicated physics in the dark sector, notably a large violation of the weak equivalence principle.

  8. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments

    PubMed Central

    Gorgolewski, Krzysztof J.; Auer, Tibor; Calhoun, Vince D.; Craddock, R. Cameron; Das, Samir; Duff, Eugene P.; Flandin, Guillaume; Ghosh, Satrajit S.; Glatard, Tristan; Halchenko, Yaroslav O.; Handwerker, Daniel A.; Hanke, Michael; Keator, David; Li, Xiangrui; Michael, Zachary; Maumet, Camille; Nichols, B. Nolan; Nichols, Thomas E.; Pellman, John; Poline, Jean-Baptiste; Rokem, Ariel; Schaefer, Gunnar; Sochat, Vanessa; Triplett, William; Turner, Jessica A.; Varoquaux, Gaël; Poldrack, Russell A.

    2016-01-01

    The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations. PMID:27326542

  9. RR Lyrae stars as probes of the Milky Way structure and formation

    NASA Astrophysics Data System (ADS)

    Pietrukowicz, Pawel

    2016-08-01

    RR Lyrae stars being distance indicators and tracers of old population serve as excellent probes of the structure, formation, and evolution of our Galaxy. Thousands of them are being discovered in ongoing wide-field surveys. The OGLE project conducts the Galaxy Variability Survey with the aim to detect and analyze variable stars, in particular of RRab type, toward the Galactic bulge and disk, covering a total area of 3000 deg2. Observations in these directions also allow detecting background halo variables and unique studies of their properties and distribution at distances from the Galactic Center to even 40 kpc. In this contribution, we present the first results on the spatial distribution of the observed RRab stars, their metallicity distribution, the presence of multiple populations, and relations with the old bulge. We also show the most recent results from the analysis of RR Lyrae stars of the Sgr dwarf spheroidal galaxy, including its center, the globular cluster M54.

  10. Structure formation with a long-range scalar dark matter interaction

    NASA Astrophysics Data System (ADS)

    Nusser, Adi; Gubser, S. S.; Peebles, P. J.

    2005-04-01

    Numerical simulations show that a long-range scalar interaction in a single species of massive dark matter particles causes voids between the concentrations of large galaxies to be more nearly empty, suppresses accretion of intergalactic matter onto galaxies at low redshift, and produces an early generation of dense dark matter halos. These three effects, in moderation, seem to be improvements over the ΛCDM model predictions for cosmic structure formation. Because the scalar interaction in this model has negligible effect on laboratory physics and the classical cosmological tests, it offers an observationally attractive example of cosmology with complicated physics in the dark sector, notably a large violation of the weak equivalence principle.

  11. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.

    PubMed

    Gorgolewski, Krzysztof J; Auer, Tibor; Calhoun, Vince D; Craddock, R Cameron; Das, Samir; Duff, Eugene P; Flandin, Guillaume; Ghosh, Satrajit S; Glatard, Tristan; Halchenko, Yaroslav O; Handwerker, Daniel A; Hanke, Michael; Keator, David; Li, Xiangrui; Michael, Zachary; Maumet, Camille; Nichols, B Nolan; Nichols, Thomas E; Pellman, John; Poline, Jean-Baptiste; Rokem, Ariel; Schaefer, Gunnar; Sochat, Vanessa; Triplett, William; Turner, Jessica A; Varoquaux, Gaël; Poldrack, Russell A

    2016-01-01

    The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations. PMID:27326542

  12. InAs-based metal-oxide-semiconductor structure formation in low-energy Townsend discharge

    NASA Astrophysics Data System (ADS)

    Aksenov, M. S.; Kokhanovskii, A. Yu.; Polovodov, P. A.; Devyatova, S. F.; Golyashov, V. A.; Kozhukhov, A. S.; Prosvirin, I. P.; Khandarkhaeva, S. E.; Gutakovskii, A. K.; Valisheva, N. A.; Tereshchenko, O. E.

    2015-10-01

    We developed and applied a method of InAs passivation in the low-energy plasma of Townsend discharge. The controlled interface oxidation in the Ar:O2:CF4 gas mixture under visualization of gas discharge plasma allowed growing thin homogeneous films in the range of 5-15 nm thickness. Oxidation with the addition of CF4 in gas-discharge plasma led to the formation of In and As oxyfluorides with a wide insulating gap and isostructural interface with unpinned Fermi level behavior. The metal-oxide-semiconductor structure showed excellent capacitance-voltage characteristics: small frequency dispersion (<15 mV), density of interface states (Dit) in the gap below 5 × 1010 eV-1cm-2, and fixed charge (Qfix) below 5 × 1011 cm-2.

  13. Structure formation in immiscible two-species Bose-Einstein condensates in perturbed harmonic traps

    NASA Astrophysics Data System (ADS)

    Pattinson, Robert; Parker, Nick; Proukakis, Nick; Liu, I.-Kang; Gou, Shih-Chuan; Gardiner, Simon; McCarron, Daniel; Cho, Hung-Wen; Cornish, Simon; Billam, Tom

    2013-05-01

    We investigate the mean-field equilibrium solutions for a trapped two-species 87Rb-133Cs immiscible Bose-Einstein condensate, and show that the density profiles observed in a recent Bose-Einstein experiment (D. J. McCarron et al. Phys. Rev. A 84, 011603 (2011)), which include ball and shell formations and axially/radially separated states, can be reproduced when accounting for weak linear perturbations. We also demonstrate the importance of the coupled growth of the two condensates by a simple finite temperature model which reveals such structures to be generally metastable in the presence of dissipation, with our findings confirmed by the more accurate Stochastic Projected Gross-Pitaevskii equation.

  14. Semiconductor structural damage attendant to contact formation in III-V solar cells

    NASA Technical Reports Server (NTRS)

    Fatemi, Navid S.; Weizer, Victor G.

    1991-01-01

    In order to keep the resistive losses in solar cells to a minimum, it is often necessary for the ohmic contacts to be heat treated to lower the metal-semiconductor contact resistivity to acceptable values. Sintering of the contacts, however can result in extensive mechanical damage of the semiconductor surface under the metallization. An investigation of the detailed mechanisms involved in the process of contact formation during heat treatment may control the structural damage incurred by the semiconductor surface to acceptable levels, while achieving the desired values of contact resistivity for the ohmic contacts. The reaction kinetics of sintered gold contacts to InP were determined. It was found that the Au-InP interaction involves three consecutive stages marked by distinct color changes observed on the surface of the Au, and that each stage is governed by a different mechanism. A detailed description of these mechanisms and options to control them are presented.

  15. PROPOSED STANDARD TO GREATLY EXPAND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

    EPA Science Inventory



    PROPOSED ST ANDARD TO GREA TL Y EXP AND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

    The ability to assess the potential toxicity of environmental, pharmaceutical, or industrial chemicals based on chemical structure in...

  16. Formation, optical properties, and electronic structure of thin Yb silicide films on Si(111)

    NASA Astrophysics Data System (ADS)

    Galkin, N. G.; Maslov, A. M.; Polyarnyi, V. O.

    2005-06-01

    Continuous very thin (2.5-3.0 nm) and thin (16-18 nm) ytterbium suicide films with some pinhole density (3×107- 1×108 cm-2) have been formed on Si(111) by solid phase epitaxy (SPE) and reactive deposition epitaxy (RDE) growth methods on templates. The stoichiometric ytterbium suicide (YbSi2) formation has shown in SPE grown films by AES and EELS data. Very thin Yb suicide films grown by RDE method had the silicon enrichment in YbSi2 suicide composition. The analysis of LEED data and AFM imaging has shown that ytterbium suicide films had non-oriented blocks with the polycrystalline structure. The analysis of scanning region length dependencies of the root mean square roughness deviation (σR(L)) for grown suicide films has shown that the formation of ytterbium suicide in SPE and RDE growth methods is determined by the surface diffusion of Yb atoms during the three-dimensional growth process. Optical functions (n, k, α, ɛ1, ɛ2, Im ɛ1-1, neff, ɛeff) of ytterbium silicide films grown on Si(1 1 1) have been calculated from transmittance and reflectance spectra in the energy range of 0.1-6.2 eV. Two nearly discrete absorption bands have been observed in the electronic structure of Yb silicide films with different composition, which connected with interband transitions on divalent and trivalent Yb states. It was established that the reflection coefficient minimum in R-spectra at energies higher 4.2 eV corresponds to the state density minimum in Yb suicide between divalent and trivalent Yb states. It was shown from optical data that Yb silicide films have the semi-metallic properties with low state densities at energies less 0.4 eV and high state densities at 0.5-2.5 eV.

  17. Upscaling of permeability of anisotropic heterogeneous formations. 2. General structure and small perturbation analysis

    NASA Astrophysics Data System (ADS)

    Indelman, P.; Dagan, G.

    1993-04-01

    The general methodology developed in part 1 (Indelman and Dagan, this issue) of this study is applied to the detailed analysis of upscaled permeability. First, the structure of the dissipation function for the general conductivity, a tensor of stationary random components, is examined with the aid of dimensional analysis. It is shown that for arbitrary shapes of the numerical elements, the upscaled permeability has also this general structure, and the numbers of unknown parameters and equations match. This result suggests that the upscaling problem has an unique solution. In the particular case of scalar permeability of isotropic covariance of the actual formation, it is shown that a similar upscaled permeability is possible only for spherical (circular) numerical elements. Otherwise, the upscaled permeability has to be a tensor of anisotropic covariance. If the actual formation has a scalar permeability of axisymmetric covariance, upscaling preserves the last property only for axisymmetric partition elements, i.e., for a sphere, cylinder, and ellipsoid. Explicit expressions for the first moments of the upscaled permeability (mean, covariance) are derived at first order in the log permeability variance. The detailed computations for a scalar permeability of axisymmetric covariance and for axisymmetric numerical elements lead to simple results. The upscaled permeability expected values are components of an axisymmetric tensor, whereas the fluctuations are determined by a scalar random space function of anisotropic covariance. The general case of upscaling by a first-order approximation is examined in Appendix B. These results will be applied to a few particular cases in part 3 (Indelman, this issue).

  18. Effect of chemical structure and network formation on physical properties of di(cyanate ester) thermosets.

    PubMed

    Reams, Josiah T; Guenthner, Andrew J; Lamison, Kevin R; Vij, Vandana; Lubin, Lisa M; Mabry, Joseph M

    2012-02-01

    Key physical properties of three dicyanate ester monomers, bisphenol A dicyanate (BADCy), bisphenol E dicyanate (LECy), and the dicyanate of a silicon-containing analogue of bisphenol A (SiMCy) were investigated as a function of cyanurate conversion at conversions ranging from approximately 70% to greater than 90% in order to assess the range of applicability of both traditional and more unusual structure-property-process relationships known for cyanate ester resins. A more complete understanding of these relationships is essential for the continued development of cyanate ester resins and their composites for a wide variety of aerospace applications. The degree of cure in each system was determined by differential scanning calorimetry (DSC). The degree of conversion achieved at a given temperature was dependent on the structure of the repeat unit, with SiMCy displaying the highest relative ease of cure. The density at room temperature was found to decrease monotonically with increasing conversion for all monomer types studied. In contrast, the water uptake decreased with increasing cure for all three materials over most or all of the conversion range studied, but leveled off or began to increase with increasing conversion at conversions of approximately 90%. The T(g) decreased after exposure to hot water in resins with greater than 85% conversion, but unexpectedly increased in samples with lower conversions. An investigation of the effect of hot water exposure on network chemistry via infrared spectroscopy indicated that carbamate formation varied with both monomer chemistry and extent of cure, but was greatest for the BADCy polycyanurates. On the other hand, the unreacted cyanate ester band tended to disappear uniformly, suggesting that reactions other than carbamate formation (such as cyclotrimerization) may also take place during exposure to hot water, possibly giving rise to the observed unusual increases in T(g) upon exposure. PMID:22311550

  19. The instability theory of drumlin formation and its explanation of their varied composition and internal structure

    NASA Astrophysics Data System (ADS)

    Stokes, Chris R.; Fowler, Andrew C.; Clark, Chris D.; Hindmarsh, Richard C. A.; Spagnolo, Matteo

    2013-02-01

    Despite their importance in understanding glaciological processes and constraining large-scale flow patterns in palaeo-glaciology, there is little consensus as to how drumlins are formed. Attempts to solve the 'drumlin problem' often fail to address how they are created from an initially flat surface in the absence of obvious cores or obstacles. This is a key strength of the instability theory, which has been described in a suite of physically-based mathematical models and proposes that the coupled flow of ice and till causes spontaneous formation of relief in the till surface. Encouragingly, model predictions of bedform height and length are consistent with observations and, furthermore, the theory has been applied to a range of subglacial bedforms and not just drumlins. However, it has yet to confront the myriad observations relating to the composition and internal structure of drumlins and this could be seen as a major deficiency. This paper is a first attempt to assess whether the instability theory is compatible with the incredible diversity of sediments and structures found within drumlins. We summarise the underlying principles of the theory and then describe and attempt to explain the main types of drumlin composition (e.g. bedrock, till, glaciofluvial sediments, and combinations thereof). Contrary to a view which suggests that the presence of some sedimentary sequences (e.g. horizontally stratified cores) is inconsistent with the theory, we suggest that one would actually expect a diverse range of constituents depending on the inheritance of sediments that pre-date drumlin formation, the duration and variability of ice flow, and the balance between erosion and deposition (till continuity) at the ice-bed interface. We conclude that the instability theory is compatible with (and potentially strengthened by) what is known about drumlin composition and, as such, offers the most complete and promising solution to the drumlin problem to date.

  20. The Effects of Gravity on Combustion and Structure Formation During Synthesis of Advanced Materials

    NASA Technical Reports Server (NTRS)

    Varma, A.; Pelekh, A.; Mukasyan, A.

    1999-01-01

    Combustion in a variety of heterogeneous systems, leading to the synthesis of advanced materials, is characterized by high temperatures (2000-3500 K) and heating rates (up to 10(exp 6) K/s) at and ahead of the reaction front. These high temperatures generate liquids and gases which are subject to gravity-driven flow. The removal of such gravitational effects is likely to provide increased control of the reaction front, with a consequent improvement in control of the microstructure of the synthesized products. Thus, microgravity experiments can lead to major advances in the understanding of fundamental aspects of combustion and structure formation under the extreme conditions of the combustion synthesis wave. In addition, the specific features of microgravity environment allow one to produce unique materials, which cannot be obtained under terrestrial conditions. The general goals of the current research are: 1) to improve the understanding of fundamental phenomena taking place during combustion of heterogeneous systems, 2) to use low-gravity experiments for insight into the physics and chemistry of materials synthesis processes, and 3) based on the obtained knowledge, to optimize processing conditions for synthesis of advanced materials with desired microstructures and properties. This research follows logically from the results of investigations we have conducted in the framework of our previous grant on gravity influence on combustion synthesis (CS) of gasless systems. Prior work, by others and by us, has clearly demonstrated that gravity plays an important role during combustion synthesis of materials. The immediate tasks for the future are to quantitatively identify the nature of observed effects, and to create accurate local kinetic models of the processes, which can lead to a control of the microstructure and properties of the synthesized materials. In summary, this is the value of the proposed research. Based on our prior work, we focus on the fundamental

  1. Cryogenic Electron Microscopy Studies: Structure and Formation of Self-assembled Nanostructures in Solution

    NASA Astrophysics Data System (ADS)

    Lee, Han Seung

    Cryogenic electron microscopy (Cryo-EM) techniques are among the most powerful to characterize self-assembling soft materials (colloids, polymers, and microemulsions, etc.) at the nanometer scale, without any need for implicit models or assumptions about the structure. We can even visualize structure under dynamic conditions, capturing each stage of development. In this thesis, cryo-EM has been used to investigate the formation and structure of a variety of self-assembling soft materials. Visualization is complemented by small angle X-ray scattering (SAXS), dynamic light scattering, and conductivity measurements. In each case, cryo-EM provides new insights, not otherwise available, into the nanostructure development. Self-assembly phenomena at the molecular level are critical to the performance of tremendous number of applied systems ranging from personal care products to industrial products. To evaluate these self-assembled materials, multiple characterization techniques are required. We investigated aggregation behavior of cesium dodecyl sulfate (CsDS) ionic surfactant in aqueous solution. Coupled with the real space data from cryogenic transmission electron microscopy (Cryo-TEM) and the inverse space data from SAXS, the experimental result of CsDS in aqueous solution gave a new insight in CsDS micellar structures and their development as a function of concentration. Cryo-TEM showed the presence of the liquid-like hydrocarbon core in the CsDS micelles and relatively thick shell structures at a low CsDS concentration. The core-shell sphere structure micelle shifted to core-shell cylindrical micelle structure at high concentration. The morphology and structure of paclitaxel silicate (PTX) prodrug, encapsulated with amphiphilic poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) diblock copolymers were studied. The six different silicate PTX prodrug candidates were characterized with cryo-TEM. Direct imaging with cryo-TEM illustrated structure of prodrug

  2. Solvent-mediated gel formation, hierarchical structures, and rheological properties of organogels.

    PubMed

    Su, Ming-Ming; Yang, Hai-Kuan; Ren, Li-Jun; Zheng, Ping; Wang, Wei

    2015-01-28

    We report the formation of solvent-mediated gels as well as their hierarchical structures and rheological properties. The gelator used is a hybrid with a molecular structure of cholesterol-polyoxometalate-cholesterol, in which the cholesterol dissolves well in toluene and N,N-dimethylformamide (DMF), whereas the polyoxometalate cluster dissolves only in DMF. These solubility differences enable the gelator to form thermally reversible supramolecular organogels by mixing solvents of toluene and DMF when the volume fraction, ftol, of toluene is larger than 85.7 v/v%. We found a V-shaped correlation between the gelation times, tgel and ftol: tgel decreases from 1300 min to 2 min when ftol increases from 85.7 v/v% to 90.0 v/v%. It then increases from 2 min to 5800 min when ftol further increases from 90.0 v/v% to 100.0 v/v%. We observed ribbon-like self-assembled structures in the gels as well as a structural evolution from rigid and straight ribbons to twistable ones from ftol=85.7 v/v% to ftol=100.0 v/v%. These ribbons constitute two three-dimensional (3D) gel networks: one is constructed via physical connection of the rigid and straight ribbon, and the other is built up from ribbons splitting and intertwining. The latter has a better 3D gel network that offers improved rheological properties. Fundamentally, this solvent-mediated approach regulates the balance between solubility and insolubility of this gelator in the mixing solvents. It also provides a new method for the preparation of organogels. PMID:25482827

  3. Effect of Ternary Solutes on the Evolution of Structure and Gel Formation in Amphiphilic Copolymer Solutions

    NASA Astrophysics Data System (ADS)

    Meznarich, Norman Anthony Kang

    Aqueous solutions of polyoxyethylene-polyoxypropylene-polyoxyethylene (PEO-PPO-PEO) amphiphilic triblock copolymers (commercially known as Pluronic surfactants) undergo reversible and temperature-dependent micellization and arrangement into cubic ordered lattices known as "micelle gels". The macroscopic behavior of the ordering is a transition from a liquid to a gel. While the phase behavior and gel structure of pure Pluronic surfactant solutions have been well studied, less is known about the effects of added ternary solutes. In this dissertation, a comprehensive investigation into the effects of the added pharmaceutical methylparaben on solutions of F127 ranging from 10 to 30 wt% was conducted in order to better understand the behavior of F127 in multicomponent pharmaceutical formulations. The viscoelastic properties of F127 gel formation were studied using rheometry, where heating rates of 0.1, 1, and 10 degrees C/min were also used to probe the kinetics of the gel transition. In solutions containing methylparaben, F127 gelation occurred at up to 15 degrees C lower temperatures and was accelerated by a factor of three to four. Small angle x-ray scattering (SAXS) was used to characterize the structure of the ordered domains, and how they were affected by the presence of dissolved pharmaceuticals. It was found that ordered domain formation changed from heterogeneous nucleation and growth to possible homogeneous nucleation and growth. A roughly 2% reduction in the cubic lattice parameter was also observed for solutions containing methylparaben. Differential scanning calorimetry (DSC) experiments were performed on a series of different Pluronic surfactants in order to characterize the micellization behavior as a function of PPO center block length and PEO/PPO ratio. Added methylparaben suppressed the micellization endotherm, the degree of suppression depending linearly on the amount of added methylparaben, as well as the length of the PPO center block and PEO

  4. Formation of a protocluster: A virialized structure from gravoturbulent collapse. I. Simulation of cluster formation in a collapsing molecular cloud

    NASA Astrophysics Data System (ADS)

    Lee, Yueh-Ning; Hennebelle, Patrick

    2016-06-01

    Context. Stars are often observed to form in clusters and it is therefore important to understand how such a region of concentrated mass is assembled out of the diffuse medium. The properties of such a region eventually prescribe the important physical mechanisms and determine the characteristics of the stellar cluster. Aims: We study the formation of a gaseous protocluster inside a molecular cloud and associate its internal properties with those of the parent cloud by varying the level of the initial turbulence of the cloud with a view to better characterize the subsequent stellar cluster formation. Methods: We performed high resolution magnetohydrodynamic (MHD) simulations of gaseous protoclusters forming in molecular clouds collapsing under self-gravity. We determined ellipsoidal cluster regions via gas kinematics and sink particle distribution, permitting us to determine the mass, size, and aspect ratio of the cluster. We studied the cluster properties, such as kinetic and gravitational energy, and made links to the parent cloud. Results: The gaseous protocluster is formed out of global collapse of a molecular cloud and has non-negligible rotation owing to angular momentum conservation during the collapse of the object. Most of the star formation occurs in this region, which occupies only a small volume fraction of the whole cloud. This dense entity is a result of the interplay between turbulence and gravity. We identify such regions in simulations and compare the gas and sink particles to observed star-forming clumps and embedded clusters, respectively. The gaseous protocluster inferred from simulation results presents a mass-size relation that is compatible with observations. We stress that the stellar cluster radius, although clearly correlated with the gas cluster radius, depends sensitively on its definition. Energy analysis is performed to confirm that the gaseous protocluster is a product of gravoturbulent reprocessing and that the support of turbulent

  5. Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering

    NASA Astrophysics Data System (ADS)

    Sokolowski-Tinten, Klaus; Barty, Anton; Boutet, Sebastien; Shymanovich, Uladzimir; Chapman, Henry; Bogan, Mike; Marchesini, Stefano; Hau-Riege, Stefan; Stojanovic, Nikola; Bonse, Jörn; Rosandi, Yudi; Urbassek, Herbert M.; Tobey, Ra'anan; Ehrke, Henri; Cavalleri, Andrea; Düsterer, Stefan; Redlin, Harald; Frank, Matthias; Bajt, Sasa; Schulz, Joachim; Seibert, Marvin; Hajdu, Janos; Treusch, Rolf; Bostedt, Christoph; Hoener, M.; Möller, T.

    2010-10-01

    The structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.

  6. Formation of raiding parties for intergroup violence is mediated by social network structure

    PubMed Central

    Glowacki, Luke; Isakov, Alexander; Wrangham, Richard W.; McDermott, Rose; Fowler, James H.; Christakis, Nicholas A.

    2016-01-01

    Intergroup violence is common among humans worldwide. To assess how within-group social dynamics contribute to risky, between-group conflict, we conducted a 3-y longitudinal study of the formation of raiding parties among the Nyangatom, a group of East African nomadic pastoralists currently engaged in small-scale warfare. We also mapped the social network structure of potential male raiders. Here, we show that the initiation of raids depends on the presence of specific leaders who tend to participate in many raids, to have more friends, and to occupy more central positions in the network. However, despite the different structural position of raid leaders, raid participants are recruited from the whole population, not just from the direct friends of leaders. An individual’s decision to participate in a raid is strongly associated with the individual’s social network position in relation to other participants. Moreover, nonleaders have a larger total impact on raid participation than leaders, despite leaders’ greater connectivity. Thus, we find that leaders matter more for raid initiation than participant mobilization. Social networks may play a role in supporting risky collective action, amplify the emergence of raiding parties, and hence facilitate intergroup violence in small-scale societies. PMID:27790996

  7. The deep structure of lunar basins - Implications for basin formation and modification

    NASA Technical Reports Server (NTRS)

    Bratt, S. R.; Solomon, S. C.; Head, J. W.; Thurber, C. H.

    1985-01-01

    Models for the crustal structure in the vicinity of nine impact basins, from an inversion of gravity and topographic data from the lunar nearside are presented. The models display a low-density nonmare crustal layer and a mare basalt layer, both of variable thicknesses. Assuming that topography in mare areas is isostatically compensated before the emplacement of mare basalts and that compensation of mare basalt units may be neglected, a decomposition of the gravity anomaly into contributions from Moho relief and mare fill is permitted. Minimum values for mare basalt thicknesses are obtained but because mare basalts and mantle material are similar in density, the thicknesses of the nonmare crust are estimated. An important constraint is the crustal thickness inferred from the Apollo 12 and 14 landing sites from seismic observations. The crustal thickness model indicates that the crust is thinner beneath each of the major nearside basins than in surrounding areas. New bounds on the volume of material ejected from each basin are derived. The geological implications of structural differences among basins for the processes of basin formation and modification are evaluated as functions of time on the moon.

  8. The formation of cosmic structure in a texture-seeded cold dark matter cosmogony

    NASA Technical Reports Server (NTRS)

    Gooding, Andrew K.; Park, Changbom; Spergel, David N.; Turok, Neil; Gott, Richard, III

    1992-01-01

    The growth of density fluctuations induced by global texture in an Omega = 1 cold dark matter (CDM) cosmogony is calculated. The resulting power spectra are in good agreement with each other, with more power on large scales than in the standard inflation plus CDM model. Calculation of related statistics (two-point correlation functions, mass variances, cosmic Mach number) indicates that the texture plus CDM model compares more favorably than standard CDM with observations of large-scale structure. Texture produces coherent velocity fields on large scales, as observed. Excessive small-scale velocity dispersions, and voids less empty than those observed may be remedied by including baryonic physics. The topology of the cosmic structure agrees well with observation. The non-Gaussian texture induced density fluctuations lead to earlier nonlinear object formation than in Gaussian models and may also be more compatible with recent evidence that the galaxy density field is non-Gaussian on large scales. On smaller scales the density field is strongly non-Gaussian, but this appears to be primarily due to nonlinear gravitational clustering. The velocity field on smaller scales is surprisingly Gaussian.

  9. Structural characterization of toxic oligomers that are kinetically trapped during α-synuclein fibril formation.

    PubMed

    Chen, Serene W; Drakulic, Srdja; Deas, Emma; Ouberai, Myriam; Aprile, Francesco A; Arranz, Rocío; Ness, Samuel; Roodveldt, Cintia; Guilliams, Tim; De-Genst, Erwin J; Klenerman, David; Wood, Nicholas W; Knowles, Tuomas P J; Alfonso, Carlos; Rivas, Germán; Abramov, Andrey Y; Valpuesta, José María; Dobson, Christopher M; Cremades, Nunilo

    2015-04-21

    We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species.

  10. Thickness-controllable electrospun fibers promote tubular structure formation by endothelial progenitor cells

    PubMed Central

    Hong, Jong Kyu; Bang, Ju Yup; Xu, Guan; Lee, Jun-Hee; Kim, Yeon-Ju; Lee, Ho-Jun; Kim, Han Seong; Kwon, Sang-Mo

    2015-01-01

    Controlling the thickness of an electrospun nanofibrous scaffold by altering its pore size has been shown to regulate cell behaviors such as cell infiltration into a three-dimensional (3D) scaffold. This is of great importance when manufacturing tissue-engineering scaffolds using an electrospinning process. In this study, we report the development of a novel process whereby additional aluminum foil layers were applied to the accumulated electrospun fibers of an existing aluminum foil collector, effectively reducing the incidence of charge buildup. Using this process, we fabricated an electrospun scaffold with a large pore (pore size >40 μm) while simultaneously controlling the thickness. We demonstrate that the large pore size triggered rapid infiltration (160 μm in 4 hours of cell culture) of individual endothelial progenitor cells (EPCs) and rapid cell colonization after seeding EPC spheroids. We confirmed that the 3D, but not two-dimensional, scaffold structures regulated tubular structure formation by the EPCs. Thus, incorporation of stem cells into a highly porous 3D scaffold with tunable thickness has implications for the regeneration of vascularized thick tissues and cardiac patch development. PMID:25709441

  11. Spontaneous structural transition and crystal formation in minimal supramolecular polymer model

    PubMed Central

    Fichman, Galit; Guterman, Tom; Damron, Joshua; Adler-Abramovich, Lihi; Schmidt, Judith; Kesselman, Ellina; Shimon, Linda J. W.; Ramamoorthy, Ayyalusamy; Talmon, Yeshayahu; Gazit, Ehud

    2016-01-01

    The association of building blocks into supramolecular polymers allows the fabrication of diverse functional architectures at the nanoscale. The use of minimal assembly units to explore polymer dynamics and phase transitions significantly contributes to the application of polymer physicochemical paradigms in the field of supramolecular polymers. We present a minimal model that displays spontaneous coordinated structural transitions between micro- and nanostructures, hydrogels with nanoscale order, and single crystals. The simple amphiphilic 9-fluorenylmethoxycarbonyl-3,4-dihydroxyphenylalanine (Fmoc-DOPA) modified amino acid undergoes a noninduced transition from spherical assemblies into nanofibrils followed by sol-gel transition, nanotube formation via intermediate assembly, and crystallization within the gel. Notably, the transition kinetics is slow enough to allow both multistage and multiscale characterization of the supramolecular arrangement using electron microscopy, vibrational and circular dichroism spectroscopies, nuclear magnetic resonance, and x-ray crystallography. This minimalistic system is the first comprehensive model for a complete spontaneous structural transition between diverse states governed by distinct molecular interactions. PMID:26933679

  12. Structural characterization of toxic oligomers that are kinetically trapped during α-synuclein fibril formation

    PubMed Central

    Chen, Serene W.; Drakulic, Srdja; Deas, Emma; Ouberai, Myriam; Aprile, Francesco A.; Arranz, Rocío; Ness, Samuel; Roodveldt, Cintia; Guilliams, Tim; De-Genst, Erwin J.; Klenerman, David; Wood, Nicholas W.; Knowles, Tuomas P.J.; Alfonso, Carlos; Rivas, Germán; Abramov, Andrey Y.; Valpuesta, José María; Dobson, Christopher M.; Cremades, Nunilo

    2015-01-01

    We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species. PMID:25855634

  13. Spontaneous structural transition and crystal formation in minimal supramolecular polymer model.

    PubMed

    Fichman, Galit; Guterman, Tom; Damron, Joshua; Adler-Abramovich, Lihi; Schmidt, Judith; Kesselman, Ellina; Shimon, Linda J W; Ramamoorthy, Ayyalusamy; Talmon, Yeshayahu; Gazit, Ehud

    2016-02-01

    The association of building blocks into supramolecular polymers allows the fabrication of diverse functional architectures at the nanoscale. The use of minimal assembly units to explore polymer dynamics and phase transitions significantly contributes to the application of polymer physicochemical paradigms in the field of supramolecular polymers. We present a minimal model that displays spontaneous coordinated structural transitions between micro- and nanostructures, hydrogels with nanoscale order, and single crystals. The simple amphiphilic 9-fluorenylmethoxycarbonyl-3,4-dihydroxyphenylalanine (Fmoc-DOPA) modified amino acid undergoes a noninduced transition from spherical assemblies into nanofibrils followed by sol-gel transition, nanotube formation via intermediate assembly, and crystallization within the gel. Notably, the transition kinetics is slow enough to allow both multistage and multiscale characterization of the supramolecular arrangement using electron microscopy, vibrational and circular dichroism spectroscopies, nuclear magnetic resonance, and x-ray crystallography. This minimalistic system is the first comprehensive model for a complete spontaneous structural transition between diverse states governed by distinct molecular interactions. PMID:26933679

  14. Can non-Gaussian fluctuations for structure formation arise from inflation

    SciTech Connect

    Salopek, D.S.

    1991-02-01

    Non-Guassian fluctuation for structure formation may be generated during the inflationary epoch from the nonlinear interaction of two scalar fields with gravity. Semi-analytical calculations are given describing nonlinear long wavelength evolution in 3 + 1 dimensions. Long wavelength fields are governed by a single equation, the separated Hamilton-Jacobi equation (SHJE). I discuss complete analytic solutions of the SHJE for two scalar fields with a potential whose logarithm 1n V ({phi}{sub j}) is linear. More complicated potential surfaces may be approximated by continuously joining various linear 1n V({phi}{sub j}) potentials. Typically, non-Gaussian fluctuations arise when one passes over several sharp ridges in the potential surface. One can input this richer class of initial conditions into N-body codes to see the effects on the large scale structure in the Universe. The cleanest test of non-Gaussian fluctuations will hopefully occur in the near future from large angle microwave background anisotropy experiments. 13 refs., 3 figs.

  15. Structure and formation of H2Ti3O7 nanotubes in an alkali environment

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Chen, Q.; Peng, L.-M.

    2005-01-01

    The structure and growth of H2Ti3O7 -type nanotubes have been studied by first-principle calculations. It is shown that the asymmetry in the distribution of hydrogen on the two sides of the surface layer of a H2Ti3O7 crystal plate provides a sufficient driving force for the formation of the H2Ti3O7 nanotube. Hydrogen deficiency on one side of the surface layer of a H2Ti3O7 plate results in a surface tension that increases with increasing hydrogen deficiency and may eventually overcome the coupling from the layers beneath driving the surface layer to peel off from the crystal plate and roll into a tubular structure. While the radius of the resultant nanotube is determined mainly by the layer coupling energy, the thickness of the tube wall is determined by the residual charges on the peeled surface layer. Both the radius and the wall thickness may in principle be controlled via modifying the layer coupling strength and the net charges on the surface.

  16. Role of water on formation and structural features of Maya blue

    NASA Astrophysics Data System (ADS)

    Mondelli, C.; Sánchez del Río, M.; González, M. A.; Magazzú, A.; Cavallari, C.; Suárez, M.; García-Romero, E.; Romano, P.

    2012-02-01

    The Maya blue (MB) is an artificial pigment created between 500-800 A.D. and used in murals, pottery and sculptures by Mayas and other people in Mesoamerica. MB is resistant to age, acid, weathering, biodegradation and even modern chemical solvents, but the chemical reasons behind the resistance to chemical aggressions are still under debate. Water plays a fundamental role in the interactions between indigo and clay. The dynamics of the clay's zeolitic and structural water molecules during the formation of MB, usually stabilized by moderate heating, has been monitored by means of neutron inelastic scattering. Neutron incoherent scattering in these samples is only due to the hydrogen atoms, so the signal is very sensitive to the amount of released water, providing detailed information on the dehydration process. A simultaneous analysis of the coherent elastic scattering and the incoherent scattering allows observing and quantifying how the structure of the clay is affected by dehydration. Here we show that a quite resistant pigment can be obtained at room temperature simply by dehydrating a palygorskite-indigo mixture employing only vacuum, without any thermal treatment.

  17. Can non-Gaussian fluctuations for structure formation arise from inflation

    NASA Astrophysics Data System (ADS)

    Salopek, D. S.

    1991-02-01

    Non-Guassian fluctuation for structure formation may be generated during the inflationary epoch from the nonlinear interaction of two scalar fields with gravity. Semi-analytical calculations are given describing nonlinear long wavelength evolution in 3 + 1 dimensions. Long wavelength fields are governed by a single equation, the separated Hamilton-Jacobi equation (SHJE). Complete analytic solutions are discussed of the SHJE for two scalar fields with a potential whose logarithm 1n V (phi sub j) is linear. More complicated potential surfaces may be approximated by continuously joining various linear 1n V(phi sub j) potentials. Typically, non-Gaussian fluctuations arise when one passes over several sharp ridges in the potential surface. One can input this richer class of initial conditions into N-body codes to see the effects on the large scale structure in the Universe. The cleanest test of non-Gaussian fluctuations will hopefully occur in the near future from large angle microwave background anisotropy experiments.

  18. Nanoparticles based laser-induced surface structures formation on mesoporous silicon by picosecond laser beam interaction

    NASA Astrophysics Data System (ADS)

    Talbi, A.; Petit, A.; Melhem, A.; Stolz, A.; Boulmer-Leborgne, C.; Gautier, G.; Defforge, T.; Semmar, N.

    2016-06-01

    In this study, laser induced periodic surface structures were formed on mesoporous silicon by irradiation of Nd:YAG picosecond pulsed laser beam at 266 nm wavelength at 1 Hz repetition rate and with 42 ps pulse duration. The effects of laser processing parameters as laser beam fluence and laser pulse number on the formation of ripples were investigated. Scanning electron microscopy and atomic force microscopy were used to image the surface morphologies and the cross section of samples after laser irradiation. At relatively low fluence ∼20 mJ/cm2, ripples with period close to the laser beam wavelength (266 nm) and with an always controlled orientation (perpendicular to the polarization of ps laser beam) appeared after a large laser pulse number of 12,000. It has been found that an initial random distribution of SiOx nanoparticles is periodically structured with an increase of the laser pulse number. Finally, it is experimentally demonstrated that we formed a 100 nm liquid phase under the protusion zones including the pores in the picosecond regime.

  19. Properties and Formation of Erosional Pipe-Shaped Structures in Ignimbrites Around Valles Caldera, Jemez Mountains

    NASA Astrophysics Data System (ADS)

    Bailey, J.; Self, S.

    2011-12-01

    In three separate ignimbrite deposits of the Bandelier Tuff Formation around Valles Caldera (La Cueva, Otowi, and Tshirege Members, preferential weathering has exposed columnar or pipe-shaped structures. The features result from the compositional alteration of the ignimbrite creating a hardened resistance to erosion in elongated volumes of the non-welded deposits. These features are manifested with different widths and lengths, however, it is thought that their origins can be attributed to the similar alteration processes and conditions. This alteration was previously assumed to be vapor-phase alteration (Cas and Wright, 1988), but further analysis has shown the presence of zeolites suggesting the alteration was the result of saturation of the ignimbrite by meteoric water. The structures exist as groups (1 to 30 features) and here is a strong positive correlation between the diameter and spacing of pipes that could be representative of the capture area for water draining into the deposit. If the pipes started to form immediately after deposition of the ignimbrite, in a similar way to fumarolic pipes, they would likely be a more widespread phenomenon in the deposit. Rapidly occurring welding and vapor-phase alteration of the top of the ignimbrite may have stopped water reaching the interior of the deposit, except where valleys were rapidly incised. Each area where pipes occur must therefore experience localized conditions, which control formation at the time the valley is being formed. The suggestion is that landslides on oversteepened, friable valley walls exposed fresh, still hot, unaltered ignimbrite in which pipe structures could form if the material had cooled from its depositional temperature to within a suitable, specific range. An abundant supply of water from high rainfall and/or stream activity is also implied. The presence of the pipes gives an insight into the erosional evolution of ignimbrite-filled valleys over a period of almost 2 million years. One

  20. Structure of evolving Accretion Discs and their Implications to the Formation of Planetary Cores

    NASA Astrophysics Data System (ADS)

    Bitsch, Bertram; Morbidelli, A.; Crida, A.; Lega, E.

    2013-10-01

    Two features in a protoplanetary disc can have profound effects on planet formation. The first feature is "pressure bumps", i.e. local maxima in the gas surface density distribution that can arise e.g. at the inner edge of the dead zone. Pressure bumps stop the inward migration of small bodies undergoing gas drag (Brauer et al., 2008), promote the onset of the streaming instability (Johansen and Youdin, 2007), help the accretion of planetary embryos by the pebble-accretion process (Lambrechts and Johansen, 2012) and stop inward type-I migration by the planet-trap mechanism (Masset et al., 2006). The second feature is "scale height bumps", that originate from opacity transitions. The regions of the disc that are shadowed, where H/r decreases with r, allow planetary cores to migrate outwards due to entropy gradient effects (Paardekooper and Mellema (2006), Baruteau and Masset (2008)), until they reach the local minimum of the H/r profile (Bitsch et al. 2013). Thus, it is important to model the existence and the location of these structures in realistic protoplanetary discs. The structure of the disc is dependent on the mass-flux (accretion rate) through the disc, which determines the evolution of the density profile. This mass-flux changes in time, as the whole disc gets accreted onto the central star. We will show using 2D hydrodynamical models how the change of the accretion rate affects the disc structure and how this will change the sweet-spots for saving planetary cores from too rapid inward migration. We will focus here on "scale height bumps" in the disc that will change the alpha-viscosity and consequently the gas surface density (as the mass-flux is constant through the disc). Therefore the formation of pressure bumps is possible, whose prominence and effects on migration will be investigated in detail. This will give important indications of where and when in the disc the cores of giant planets and thus giant planets can form.

  1. Controlled formation of fluorescent metalloporphyrin-containing coordination polymer particles from seed structures by designed shape-transformation reactions.

    PubMed

    Sun, Yu; Li, Xiaopeng; Caravella, Alessio; Gao, Rongke

    2015-04-27

    Herein, nanorod structures and four-leaf clover structures of fluorescent zinc 5,10,15,20-tetra(4-pyridyl)-21H,23H-porphine (ZnTPyP)-containing coordination polymer particles (CPPs) were first synthesized by a bottom-up strategy assisted by surfactants and then employed as seed structures for further shape-transformation reactions. We have successfully designed the morphological transformation for different dimensions, achieving the controlled formation of octahedron structures at both the nanometer scale and micrometer scale from the seed structures. Our approach illustrates a new method to design and synthesize metalloporphyrin-containing CPPs in a systematic and controllable manner.

  2. 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.

  3. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  4. Shock tube study of the fuel structure effects on the chemical kinetic mechanisms responsible for soot formation, part 2

    NASA Technical Reports Server (NTRS)

    Frenklach, M.; Clary, D. W.; Ramachandra, M. K.

    1985-01-01

    Soot formation in oxidation of allene, 1,3-butadiene, vinylacetylene and chlorobenzene and in pyrolysis of ethylene, vinylacetylene, 1-butene, chlorobenzene, acetylen-hydrogen, benzene-acetylene, benzene-butadiene and chlorobenzene-acetylene argon-diluted mixtures was studied behind reflected shock waves. The results are rationalized within the framework of the conceptual models. It is shown that vinylacetylene is much less sooty than allene, which indicates that conjugation by itself is not a sufficient factor for determining the sooting tendency of a molecule. Structural reactivity in the context of the chemical kinetics is the dominant factor in soot formation. Detailed chemical kinetic modeling of soot formation in pyrolysis of acetylene is reported. The main mass growth was found to proceed through a single dominant route composed of conventional radical reactions. The practically irreversible formation reactions of the fused polycyclic aromatics and the overshoot by hydrogen atom over its equilibrium concentration are the g-driving kinetic forces for soot formation.

  5. Titanium embedded cage structure formation in Al(n)Ti+ clusters and their interaction with Ar.

    PubMed

    Torres, M B; Vega, A; Aguilera-Granja, F; Balbás, L C

    2014-05-01

    Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al(n)Ti(+) [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > nc determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al(n)Ti(+), experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic properties of singly titanium doped cationic clusters, Al(n)Ti(+) (n = 16-21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at nc = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (nc = 21) and their neutral counterparts (nc = 20). For the Al(n)Ti(+) · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al(n)Ti(+) clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For nc = 21, the smallest size of

  6. The topography of Ceres and implications for the formation of linear surface structures

    NASA Astrophysics Data System (ADS)

    Buczkowski, D.; Otto, K.; Ruesch, O.; Scully, J. E. C.; Williams, D. A.; Mest, S. C.; Schenk, P.; Jaumann, R.; Nathues, A.; Preusker, F.; Park, R. S.; Raymond, C. A.; Russell, C. T.

    2015-12-01

    NASA's Dawn spacecraft began orbiting the dwarf planet Ceres in April 2015. Framing Camera data from the Approach (1.3 km/px) and Survey (415 m/px) orbits include digital terrain models derived from processing stereo images. These models have supported various scientific studies of the surface. The eastern hemisphere of Ceres is topographically higher than the western hemisphere. Some of linear structures on Ceres (which include grooves, pit crater chains, fractures and troughs) appear to be radial to the large basins Urvara and Yalode, and most likely formed due to impact processes. However, set of regional linear structures (RLS) that do not have any obvious relationship to impact craters are found on the eastern hemisphere topographic high region. Many of the longer RLS are comprised of smaller structures that have linked together, suggestive of en echelon fractures. Polygonal craters, theorized to form when pervasive subsurface fracturing affects crater formation [1], are widespread on Ceres [2], and those proximal to the RLS have straight crater rims aligned with the grooves and troughs, suggesting that the RLS are fracture systems. A cross-section of one RLS is displayed in FC images of the Occator crater wall. Comparing these images to the digital terrain models show 1) that the structure dips ~60º and 2) there is downward motion on the hanging wall, implying normal faulting. The digital terrain models also reveal the presence of numerous positive relief features with sub-circular shapes. These dome-like features have been tentatively interpreted as volcanic/magmatic features [3]; other possibilities include salt domes. Analog models of domal uplift in areas of regional extension [4] predict patterns of linear structures similar to those observed in the RLS near Occator. Utilizing topography data provided by the Ceres digital terrain models, we assess the relationship between the RLS and nearby domes and topographic high regions to determine the mechanism

  7. Role of shear along horizontal plane in the formation of helicoidal structures

    NASA Astrophysics Data System (ADS)

    Koronovsky, N. V.; Gogonenkov, G. N.; Goncharov, M. A.; Timurziev, A. I.; Frolova, N. S.

    2009-09-01

    An unusual structural paragenesis, complicated by brachyanticlines, is revealed for the first time in the sedimentary cover of the West Siberian Plate by 3D seismic surveying. These are linear (in plan view) systems of en-echelon arranged low-amplitude normal faults related to wrench faults in the basement. On different sides off a wrench fault, the planes of normal faults dip in opposite directions, forming a helicoidal structure that resembles the blades of a propeller. In the section parallel to the wrench fault, the boundaries of the beds and normal fault planes dip in opposite directions as well. In the section across the strike of the normal faults converging toward the basement, the beds take the shape of an antiform with a crest sagged along the normal faults (flower structure). This structural assembly was formed as a result of interference of stress fields of horizontal shear in the vertical plane (induced by faulting in the basement) and in the horizontal plane (caused by gravity resistance of the cover). In this case, the displacements along the normal faults develop in both the vertical and, to a greater extent, horizontal directions, so that the faults in cover are actually characterized by normal-strike-slip kinematics. The regional N-S-trending compression of the West Siberian Plate is the main cause of shearing along the NW- and NE-trending faults in the basement, which make up a rhomb-shaped system in plan view. Petroliferous brachyanticlines, whose axes, notwithstanding tectonophysical laws, are oriented in the direction close to the maximum compression axis, are known in the large wrench fault zones of Western Siberia. Our experiments with equivalent materials showed that a local stress field arising at the ends of echeloned Riedel shears within a wrench fault zone may be a cause of the formation of such brachyanticlines. The progressive elongation of Riedel shears leads to the corresponding elongation of the brachyanticlines located between

  8. Titanium embedded cage structure formation in AlnTi+ clusters and their interaction with Ar

    NASA Astrophysics Data System (ADS)

    Torres, M. B.; Vega, A.; Aguilera-Granja, F.; Balbás, L. C.

    2014-05-01

    Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, AlnTi+ [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > nc determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally AlnTi+, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic properties of singly titanium doped cationic clusters, AlnTi+ (n = 16-21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at nc = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (nc = 21) and their neutral counterparts (nc = 20). For the {Al_nTi^+ {\\cdot} Ar} complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the AlnTi+ clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For nc = 21, the smallest size of

  9. Evolution of Fine-scale Penumbral Magnetic Structure and Formation of Penumbral Jets

    NASA Astrophysics Data System (ADS)

    Tiwari, S. K.; Moore, R. L.; Rempel, M.; Winebarger, A. R.

    2015-12-01

    Sunspot penumbra consists of spines (more vertical field) and penumbral filaments (interspines). Spines are outward extension of umbra. Penumbral filaments are recently found, both in observations and magnetohydrodynamic (MHD) simulations, to be magnetized stretched granule-like convective cells, with strong upflows near the head that continues along the central axis with weakening strength of the flow. Strong downflows are found at the tails of filaments and weak downflows along the sides of it. These lateral downflows often contain opposite polarity magnetic field to that of spines; most strongly near the heads of filaments. In spite of this advancement in understanding of small-scale structure of sunspot penumbra, how the filaments and spines evolve and interact remains uncertain. Penumbral jets, bright, transient features, seen in the chromosphere, are one of several dynamic events in sunspot penumbra. It has been proposed that these penumbral microjets result from component (acute angle) reconnection of the magnetic field in spines with that in interspines and could contribute to transition-region and coronal heating above sunspots. In a recent investigation, it was proposed that the jets form as a result of reconnection between the opposite polarity field at edges of filaments with spine field, and it was found that these jets do not significantly directly heat the corona above sunspots. We discuss how the proposed formation of penumbral jets is integral to the formation mechanism of penumbral filaments and spines, and may explain why penumbral jets are few and far between. We also point out that the generation of the penumbral jets could indirectly drive coronal heating via generation of MHD waves or braiding of the magnetic field.

  10. The Structural Properties and Star Formation History of Leo T from Deep LBT Photometry

    NASA Astrophysics Data System (ADS)

    de Jong, J. T. A.; Harris, J.; Coleman, M. G.; Martin, N. F.; Bell, E. F.; Rix, H.-W.; Hill, J. M.; Skillman, E. D.; Sand, D. J.; Olszewski, E. W.; Zaritsky, D.; Thompson, D.; Giallongo, E.; Ragazzoni, R.; DiPaola, A.; Farinato, J.; Testa, V.; Bechtold, J.

    2008-06-01

    We present deep, wide-field g and r photometry of the transition-type dwarf galaxy Leo T, obtained with the blue arm of the Large Binocular Telescope. The data confirm the presence of both very young (<1 Gyr) and much older (>5 Gyr) stars. We study the structural properties of the old and young stellar populations by preferentially selecting either population on the basis of their color and magnitude. The young population is significantly more concentrated than the old population, with half-light radii of 104 +/- 8 and 148 +/- 16 pc, respectively, and their centers are slightly offset. Approximately 10% of the total stellar mass is estimated to be represented by the young stellar population. Comparison of the color-magnitude diagram (CMD) with theoretical isochrones, as well as numerical CMD fitting, suggests that star formation began over 10 Gyr ago and continued in recent times until at least a few hundred Myr ago. The CMD-fitting results are indicative of two distinct star formation bursts, with a quiescent period around 3 Gyr ago, albeit at low significance. The results are consistent with no metallicity evolution and a value of [ Fe/H ] ~ - 1.5 over the entire age of the system. Finally, the data show little, if any, sign of tidal distortion of Leo T. Based on data acquired using the Large Binocular Telescope (LBT). The LBT is an international collaboration among institutions in the United States, Italy, and Germany. The LBT Corporation partners are the University of Arizona, on behalf of the Arizona university system; Istituto Nazionale di Astrofisica, Italy; LBT Beteiligungsgesellschaft, Germany, representing the Max Planck Society, the Astrophysical Institute Potsdam, and Heidelberg University; The Ohio State University; and The Research Corporation, on behalf of the University of Notre Dame, the University of Minnesota, and the University of Virginia.

  11. Terrestrial planet formation constrained by Mars and the structure of the asteroid belt

    NASA Astrophysics Data System (ADS)

    Izidoro, André; Raymond, Sean N.; Morbidelli, Alessandro; Winter, Othon C.

    2015-11-01

    Reproducing the large Earth/Mars mass ratio requires a strong mass depletion in solids within the protoplanetary disc between 1 and 3 au. The Grand Tack model invokes a specific migration history of the giant planets to remove most of the mass initially beyond 1 au and to dynamically excite the asteroid belt. However, one could also invoke a steep density gradient created by inward drift and pile-up of small particles induced by gas drag, as has been proposed to explain the formation of close-in super-Earths. Here we show that the asteroid belt's orbital excitation provides a crucial constraint against this scenario for the Solar system. We performed a series of simulations of terrestrial planet formation and asteroid belt evolution starting from discs of planetesimals and planetary embryos with various radial density gradients and including Jupiter and Saturn on nearly circular and coplanar orbits. Discs with shallow density gradients reproduce the dynamical excitation of the asteroid belt by gravitational self-stirring but form Mars analogues significantly more massive than the real planet. In contrast, a disc with a surface density gradient proportional to r-5.5 reproduces the Earth/Mars mass ratio but leaves the asteroid belt in a dynamical state that is far colder than the real belt. We conclude that no disc profile can simultaneously explain the structure of the terrestrial planets and asteroid belt. The asteroid belt must have been depleted and dynamically excited by a different mechanism such as, for instance, in the Grand Tack scenario.

  12. Structural rearrangements preceding dioxygen formation by the water oxidation complex of photosystem II

    PubMed Central

    Bao, Han; Burnap, Robert L.

    2015-01-01

    Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II. Recent studies implicate an oxo bridge atom, O5, of the Mn4CaO5 cluster, as the “slowly exchanging” substrate water molecule. The D1-V185N mutant is in close vicinity of O5 and known to extend the lag phase and retard the O2 release phase (slow phase) in this critical last S3+→S0 transition of water oxidation. The pH dependence, hydrogen/deuterium (H/D) isotope effect, and temperature dependence on the O2 release kinetics for this mutant were studied using time-resolved O2 polarography, and comparisons were made with WT and two mutants of the putative proton gate D1-D61. Both kinetic phases in V185N are independent of pH and buffer concentration and have weaker H/D kinetic isotope effects. Each phase is characterized by a parallel or even lower activation enthalpy but a less favorable activation entropy than the WT. The results indicate new rate-determining steps for both phases. It is concluded that the lag does not represent inhibition of proton release but rather, slowing of a previously unrecognized kinetic phase involving a structural rearrangement or tautomerism of the S3+ ground state as it approaches a configuration conducive to dioxygen formation. The parallel impacts on both the lag and O2 formation phases suggest a common origin for the defects surmised to be perturbations of the H-bond network and the water cluster adjacent to O5. PMID:26508637

  13. Structural rearrangements preceding dioxygen formation by the water oxidation complex of photosystem II.

    PubMed

    Bao, Han; Burnap, Robert L

    2015-11-10

    Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II. Recent studies implicate an oxo bridge atom, O5, of the Mn4CaO5 cluster, as the "slowly exchanging" substrate water molecule. The D1-V185N mutant is in close vicinity of O5 and known to extend the lag phase and retard the O2 release phase (slow phase) in this critical last [Formula: see text] transition of water oxidation. The pH dependence, hydrogen/deuterium (H/D) isotope effect, and temperature dependence on the O2 release kinetics for this mutant were studied using time-resolved O2 polarography, and comparisons were made with WT and two mutants of the putative proton gate D1-D61. Both kinetic phases in V185N are independent of pH and buffer concentration and have weaker H/D kinetic isotope effects. Each phase is characterized by a parallel or even lower activation enthalpy but a less favorable activation entropy than the WT. The results indicate new rate-determining steps for both phases. It is concluded that the lag does not represent inhibition of proton release but rather, slowing of a previously unrecognized kinetic phase involving a structural rearrangement or tautomerism of the S3 (+) ground state as it approaches a configuration conducive to dioxygen formation. The parallel impacts on both the lag and O2 formation phases suggest a common origin for the defects surmised to be perturbations of the H-bond network and the water cluster adjacent to O5.

  14. The formation and evolution of layered structures in porous media: effects of porosity and mechanical dispersion

    NASA Astrophysics Data System (ADS)

    Schoofs, Stan; Trompert, Ron A.; Hansen, Ulrich

    2000-03-01

    Horizontally layered structures can develop in porous or partially molten environments, such as hydrothermal systems, magmatic intrusions and the early Earth's mantle. The porosity φ of these natural environments is typically small. Since dissolved chemical elements unlike heat cannot diffuse through the solid rocks, heat and solute influence the interstitial fluid density in a different manner: heat advects slower than solute through the liquid by the factor φ, while diffusion of heat through the bulk porous medium is larger by the factor φ-1 times the ratio between the thermal and chemical diffusivities. By performing numerical experiments in which a rigid low-porosity medium is heated from below, we have studied the formation and evolution of layers in an initially stably stratified liquid. Growth of a convective layer through convective entrainment, the formation of a stable density interface on top of the layer and destabilization of the next layer are intimately linked. By monitoring the heat (solute) fluxes, it is observed that the transport of heat (solute) across the interface changes from convective entrainment towards a regime in which transfer is purely diffusive (dispersive). Because this transition occurs before the stage at which the lower layer arrives at the thermal equilibrium, we conclude that the layer growth stops when the density interface on top has grown sufficiently strong to keep the ascending plumes in the lower layer from convectively entraining more fluid from above. A simple balance between the most important forces, exerted on a fluid parcel in the lower layer, is proposed to determine this transition. This force balance also indicates whether a density interface keeps intact, migrates upwards or breaks down during the further evolution of the layered sequence. Finally, mechanical dispersion tends to increase transport of chemically dissolved elements across the density interface. Since this reduces the density difference between

  15. Structure and kinetics of formation of interphase layers of synthetic fatty acid aluminum soap at the water/oil interface

    SciTech Connect

    Chalykh, A.E.; Matveev, V.V.; Mityuk, D.Y.; Shal't, S.Y.; Tarasevich, B.N.

    1986-02-01

    The authors investigate the kinetics of formation of interphase layers (IL) at the interface between the phases: a 0.15% solution of aluminum soap of synthetic fatty acids (SFA) (fraction C/sub 17/-C/sub 21/) in n-decane/distilled water. The structure and the morphological properties of IL were investigated by transmission electron spectroscopy. The electron micrographs of the interphase layer of the soap at different stages of its formation show that the formation of a new phase starts with the appearance of small dispersed particles with spherical and fibrillar shapes. The results obtained supplement the authors' concepts about the mechanism of spontaneous microemulsification.

  16. Agrobacterium induced gall formation in bell pepper (Capsicum annuum L.) and formation of shoot-like structures expressing introduced genes.

    PubMed

    Liu, W; Parrott, W A; Hildebrand, D F; Collins, G B; Williams, E G

    1990-11-01

    The objective of this research was to define an in vitro regeneration and transformation system for bell pepper (Capsicum annuum L.) using six cultivars and one Guatemalan wild accession. The wild accession exhibited the best regeneration response. Only occasional elongation of shoot buds in 'Yolo Wonder L' was achieved by culture in the dark on a medium containing 10 mg/l BA and l mg/l IAA. Transformed shoot buds and leaf-like structures were obtained, showing beta- glucuronidase activity predominantly in the vascular and perivascular tissues, with no indication of contaminating Agrobacterium in the tissues. Attempts to regenerate whole transgenic plants from transformed shoot buds were unsuccessful. PMID:24227055

  17. In-situ Micro-structural Studies of Gas Hydrate Formation in Sedimentary Matrices

    NASA Astrophysics Data System (ADS)

    Kuhs, Werner F.; Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Schwarz, Jens-Oliver; Wolf, Martin; Enzmann, Frieder; Kersten, Michael; Haberthür, David

    2015-04-01

    The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in-situ with sub-micron resolution. Here, we report on synchrotron-based micro-tomographic studies by which the nucleation and growth processes of gas hydrate were observed in different sedimentary matrices (natural quartz, glass beds with different surface properties, with and without admixtures of kaolinite and montmorillonite) at varying water saturation. The nucleation sites can be easily identified and the growth pattern is clearly established. In under-saturated sediments the nucleation starts at the water-gas interface and proceeds from there to form predominantly isometric single crystals of 10-20μm size. Using a newly developed synchrotron-based method we have determined the crystallite size distributions (CSD) of the gas hydrate in the sedimentary matrix confirming in a quantitative and statistically relevant manner the impressions from the tomographic reconstructions. It is noteworthy that the CSDs from synthetic hydrates are distinctly smaller than those of natural gas hydrates [1], which suggest that coarsening processes take place in the sedimentary matrix after the initial hydrate formation. Understanding the processes of formation and coarsening may eventually permit the determination of the age of gas hydrates in sedimentary matrices [2], which are largely unknown at present. Furthermore, the full micro-structural picture and its evolution will enable quantitative digital rock physics modeling to reveal poroelastic properties and in this way to support the exploration and exploitation of gas hydrate resources in the future. [1] Klapp S.A., Hemes S., Klein H., Bohrmann G., McDonald I., Kuhs W.F. Grain size measurements of natural gas hydrates. Marine Geology 2010; 274(1-4):85-94. [2] Klapp S.A., Klein H, Kuhs W.F. First determination of gas hydrate

  18. Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

    PubMed

    Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

    2014-08-15

    The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor. PMID:25124437

  19. IUTAM Symposium on Vortex Dynamics: Formation, Structure and Function, 10-14 March 2013, Fukuoka, Japan

    NASA Astrophysics Data System (ADS)

    Fukumoto, Yasuhide

    2014-06-01

    This special issue of Fluid Dynamics Research contains the first of a two-part publication of the papers presented at the IUTAM Symposium on Vortex Dynamics: Formation, Structure and Function, held at the Centennial Hall, Kyushu University School of Medicine, Fukuoka, Japan, during the week of 10-14 March 2013. Vortices are ubiquitous structures in fluid mechanics spanning the range of scales from nanofluidics and microfluidics to geophysical and astrophysical flows. Vortices are the key to understanding many different phenomena. As a result, the subject of vortex dynamics continues to evolve and to constantly find new applications in biology, biotechnology, industrial and environmental problems. Vortices can be created by the separation of a flow from the surface of a body or at a density interface, and evolve into coherent structures. Once formed, a vortex acquires a function, depending on its individual structure. In this way, for example, insects gain lift and fish gain thrust. Surprisingly, despite the long history of vortex dynamics, only recently has knowledge about formation, structure and function of vortices been combined to yield new perspectives in the subject, thereby helping to solve outstanding problems brought about by modern advances in computer technology and improved experimental techniques. This symposium is a continuation, five years on, of the IUTAM Symposium '50 Years of Vortex Dynamics', Lyngby, Denmark that took place between 12-16 October 2008, organized by the late Professor Hassan Aref. Originally, Professor Aref was a member of the International Scientific Committee of this symposium and offered his enthusiasm and great expertise, to support its organization. To our shock, he suddenly passed away on 9 September 2011. Furthermore, Professor Slava Meleshko, a leading scientist of fluid and solid mechanics and an intimate friend of Professor Aref, was expected to make an eminent contribution to the symposium. Soon after this sad loss

  20. Kinetic description of the 3D electromagnetic structures formation in flows of expanding plasma coronas. Part 1: General

    NASA Astrophysics Data System (ADS)

    Gubchenko, V. M.

    2015-12-01

    In part I of the work, the physical effects responsible for the formation of low-speed flows in plasma coronas, coupled with formation of coronas magnetosphere-like structures, are described qualitatively. Coronal domain structures form if we neglect scales of spatial plasma dispersion: high-speed flows are accumulated in magnetic tubes of the open domains, while magnetic structures and low-speed flows are concentrated within boundaries of domains. The inductive electromagnetic process occurring in flows of the hot collisionless plasma is shown to underlie the formation of magnetosphere-like structures. Depending on the form of the velocity distribution function of particles (PDF), a hot flow differently reveals its electromagnetic properties, which are expressed by the induction of resistive and diamagnetic scales of spatial dispersion. These determine the magnetic structure scales and structure reconstruction. The inductive electromagnetic process located in lines of the plasma nontransparency and absorption, in which the structures of excited fields are spatially aperiodic and skinned to the magnetic field sources. The toroidal and dipole magnetic sources of different configurations are considered for describing the corona structures during the solar maximum and solar minimum.

  1. Mechanistic Studies of Combustion and Structure Formation During Synthesis of Advanced Materials

    NASA Technical Reports Server (NTRS)

    Varma, A.; Lau, C.; Mukasyan, A. S.

    2001-01-01

    Combustion in a variety of heterogeneous systems, leading to the synthesis of advanced materials, is characterized by high temperatures (2000-3500 K) and heating rates (up to 10(exp 6) K/s) at and ahead of the reaction front. These high temperatures generate liquids and gases which are subject to gravity-driven flow. The removal of such gravitational effects is likely to provide increased control of the reaction front, with a consequent improvement in control of the microstructure of the synthesized products. Thus, microgravity (mu-g) experiments lead to major advances in the understanding of fundamental aspects of combustion and structure formation under the extreme conditions of the combustion synthesis (CS) wave. In addition, the specific features of microgravity environment allow one to produce unique materials, which cannot be obtained under terrestrial conditions. The current research is a logic continuation of our previous work on investigations of the fundamental phenomena of combustion and structure formation that occur at the high temperatures achieved in a CS wave. Our research is being conducted in three main directions: 1) Microstructural Transformations during Combustion Synthesis of Metal-Ceramic Composites. The studies are devoted to the investigation of particle growth during CS of intermetallic-ceramic composites, synthesized from nickel, aluminum, titanium, and boron metal reactants. To determine the mechanisms of particle growth, the investigation varies the relative amount of components in the initial mixture to yield combustion wave products with different ratios of solid and liquid phases, under 1g and mu-g conditions; 2) Mechanisms of Heat Transfer during Reactions in Heterogeneous Media. Specifically, new phenomena of gasless combustion wave propagation in heterogeneous media with porosity higher than that achievable in normal gravity conditions, are being studied. Two types of mixtures are investigated: clad powders, where contact between

  2. Stringy models of modified gravity: space-time defects and structure formation

    SciTech Connect

    Mavromatos, Nick E.; Sakellariadou, Mairi; Yusaf, Muhammad Furqaan E-mail: mairi.sakellariadou@kcl.ac.uk

    2013-03-01

    Starting from microscopic models of space-time foam, based on brane universes propagating in bulk space-times populated by D0-brane defects (''D-particles''), we arrive at effective actions used by a low-energy observer on the brane world to describe his/her observations of the Universe. These actions include, apart from the metric tensor field, also scalar (dilaton) and vector fields, the latter describing the interactions of low-energy matter on the brane world with the recoiling point-like space-time defect (D-particle). The vector field is proportional to the recoil velocity of the D-particle and as such it satisfies a certain constraint. The vector breaks locally Lorentz invariance, which however is assumed to be conserved on average in a space-time foam situation, involving the interaction of matter with populations of D-particle defects. In this paper we clarify the role of fluctuations of the vector field on structure formation and galactic growth. In particular we demonstrate that, already at the end of the radiation era, the (constrained) vector field associated with the recoil of the defects provides the seeds for a growing mode in the evolution of the Universe. Such a growing mode survives during the matter dominated era, provided the variance of the D-particle recoil velocities on the brane is larger than a critical value. We note that in this model, as a result of specific properties of D-brane dynamics in the bulk, there is no issue of overclosing the brane Universe for large defect densities. Thus, in these models, the presence of defects may be associated with large-structure formation. Although our string inspired models do have (conventional, from a particle physics point of view) dark matter components, nevertheless it is interesting that the role of ''extra'' dark matter is also provided by the population of massive defects. This is consistent with the weakly interacting character of the D-particle defects, which predominantly interact only

  3. The features of ceramic materials structure formation when using hard-melting wastes of thermal power stations in charge stock

    NASA Astrophysics Data System (ADS)

    Skripnikova, Nelli; Yuriev, Ivan; Lutsenko, Alexander; Litvinova, Viktoriya

    2016-01-01

    The paper presents the analysis of aluminum silicate waste generated by thermal power station of the city of Seversk, Tomsk region, Russia. The chemical compositions of aluminum silicate waste are detected and the efficient mixture compositions with the addition of aluminum silicate waste are suggested herein. Ceramic brick structure formation is studied in this paper using X-ray phase and SEM analyses. It is identified that the formed vitreous phase facilitates such strengthening structural modifications as sintering out of pores and shrinkage of unmelted aluminum silicate particles with the following formation of a monolithic product.

  4. The influence of dynamical structural relaxation of point defect clusters on void formation in irradiated copper

    NASA Astrophysics Data System (ADS)

    Shimomura, Y.; Mukouda, I.; Sugio, K.

    1997-11-01

    In the neutron-irradiation experiment with a temperature controlled capsule at JMTR, residual-gas-free copper was irradiated at 200°C and 300°C together with as-received copper. The fluences were 5 × 10 18 n/cm 2 (the low fluence) to 1 × 10 20 n/cm 2 (the high fluence). TEM observation of the irradiated specimens showed that interstitial clusters form a colony at the low fluence which develops into a dislocation structure at the high fluence. Between the colonies only vacancy clusters in the form of voids and stacking fault tetrahedra (sft) were observed. There are no effects of residual gas atoms on the formation of voids at the low fluence although the effects become appreciable at the high fluence. The number of vacancies which are accumulated in a void is 350 times larger than that in a sft at the low fluence. The number density of voids decreased with increasing neutron fluence while the number density of sft increased. The voids form uniformly in copper irradiated to the low fluence while they were observed along dislocations at the high fluence. Computer simulations by molecular dynamics show that small interstitial clusters relax to a bundle of <110> crowdions and move long distances in response to small strain fields. Interstitial clusters move along a <110> direction and can switch to other <110> directions, and form groups of clusters. At high temperature, a dense colony of the clusters forms and develops into a dislocation structure. It is shown that small vacancy clusters relax to movable structures at high temperature. The structure consists of vacancies which are connected in a curved string shape. Along the vacancy strings, many relaxations of a tri-vacancy of Damask- Dienes-Weizer type (3v-sft) were observed. Such a relaxation to the 3v-sft type makes it difficult for a single vacancy evaporation. Small vacancy clusters move and coalesce into larger vacancy clusters. The linkage of the results of experiments and computer-simulations suggests

  5. Formation of dome and basin structures: Results from scaled experiments using non-linear rock analogues

    NASA Astrophysics Data System (ADS)

    Zulauf, J.; Zulauf, G.; Zanella, F.

    2016-09-01

    Dome and basin folds are structures with circular or slightly elongate outcrop patterns, which can form during single- and polyphase deformation in various tectonic settings. We used power-law viscous rock analogues to simulate single-phase dome-and-basin folding of rocks undergoing dislocation creep. The viscosity ratio between a single competent layer and incompetent matrix was 5, and the stress exponent of both materials was 7. The samples underwent layer-parallel shortening under bulk pure constriction. Increasing initial layer thickness resulted in a decrease in the number of domes and basins and an increase in amplitude, A, arc-length, L, wavelength, λ, and layer thickness, Hf. Samples deformed incrementally show progressive development of domes and basins until a strain of eY=Z = -30% is attained. During the dome-and-basin formation the layer thickened permanently, while A, L, and λ increased. A dominant wavelength was not attained. The normalized amplitude (A/λ) increased almost linearly reaching a maximum of 0.12 at eY=Z = -30%. During the last increment of shortening (eY=Z = -30 to -40%) the domes and basins did not further grow, but were overprinted by a second generation of non-cylindrical folds. Most of the geometrical parameters of the previously formed domes and basins behaved stable or decreased during this phase. The normalized arc-length (L/Hf) of domes and basins is significantly higher than that of 2D cylindrical folds. For this reason, the normalized arc length can probably be used to identify domes and basins in the field, even if these structures are not fully exposed in 3D.

  6. Evershed Flows as an Integral Part of Penumbral Formation and its Fine Structure

    NASA Astrophysics Data System (ADS)

    Ryutova, M.; Berger, T.; Lites, B.; Title, A.; Frank, Z.

    2008-05-01

    Observations of Evershed flows with the Solar Optical Telescope (SOT) on Hinode (Ichimito, Shine, Lites, et al. 2008, PASJ, 59, S593) showed that penumbral flows have small scale structures and much more complex properties than those of a simple outflow of material with unique direction and appearence. We address this problem and show that the flow properties are directly connected to the observed properties of penumbral filaments and are an integral part of penumbral development during sunspot formation. In our recent model (Ryutova, Berger, & Title, 2008, ApJ, 676, April), based on the observations that sunspot has a filamentary structure and consists of a dense conglomerate of non-collinear interlaced flux tubes, the penumbra is formed due to an on-going reconnection processes that leads to branching out of the peripheral flux tubes from the "trunk". As flux tubes have different parameters, branching occurs at different heights and with different inclinations, thus forming an "uncombed" penumbra. Each elemental act of reconnection generates an inevitable twist in the post-reconnection filaments that acquire a screw pinch configuration. This explains the remarkable dynamic stability of penumbral filaments and their observed properties, such as presence of dark cores, wrapping and spinning of filaments around each other, bright footpoints, etc. Here we show that propagation of twist along current carrying helical flux tubes is accompanied by plasma flows that may have diverse properties depending on the location of interacting flux tubes, their inclination and pitch. We apply the model to observations taken with the SOT instrument, which includes spectro-polarimetric data, and perform quantitative analysis.

  7. Computation Sheds Insight into Iron Porphyrin Carbenes' Electronic Structure, Formation, and N-H Insertion Reactivity.

    PubMed

    Sharon, Dina A; Mallick, Dibyendu; Wang, Binju; Shaik, Sason

    2016-08-01

    Iron porphyrin carbenes constitute a new frontier of species with considerable synthetic potential. Exquisitely engineered myoglobin and cytochrome P450 enzymes can generate these complexes and facilitate the transformations they mediate. The current work harnesses density functional theoretical methods to provide insight into the electronic structure, formation, and N-H insertion reactivity of an iron porphyrin carbene, [Fe(Por)(SCH3)(CHCO2Et)](-), a model of a complex believed to exist in an experimentally studied artificial metalloenzyme. The ground state electronic structure of the terminal form of this complex is an open-shell singlet, with two antiferromagnetically coupled electrons residing on the iron center and carbene ligand. As we shall reveal, the bonding properties of [Fe(Por)(SCH3)(CHCO2Et)](-) are remarkably analogous to those of ferric heme superoxide complexes. The carbene forms by dinitrogen loss from ethyl diazoacetate. This reaction occurs preferentially through an open-shell singlet transition state: iron donates electron density to weaken the C-N bond undergoing cleavage. Once formed, the iron porphyrin carbene accomplishes N-H insertion via nucleophilic attack. The resulting ylide then rearranges, using an internal carbonyl base, to form an enol that leads to the product. The findings rationalize experimentally observed reactivity trends reported in artificial metalloenzymes employing iron porphyrin carbenes. Furthermore, these results suggest a possible expansion of enzymatic substrate scope, to include aliphatic amines. Thus, this work, among the first several computational explorations of these species, contributes insights and predictions to the surging interest in iron porphyrin carbenes and their synthetic potential. PMID:27347808

  8. CARMA LARGE AREA STAR FORMATION SURVEY: STRUCTURE AND KINEMATICS OF DENSE GAS IN SERPENS MAIN

    SciTech Connect

    Lee, Katherine I.; Storm, Shaye; Mundy, Lee G.; Teuben, Peter; Pound, Marc W.; Salter, Demerese M.; Chen, Che-Yu; Fernández-López, Manuel; Looney, Leslie W.; Segura-Cox, Dominique; Rosolowsky, Erik; Arce, Héctor G.; Plunkett, Adele L.; Ostriker, Eve C.; Shirley, Yancy L.; Kwon, Woojin; Kauffmann, Jens; Tobin, John J.; Volgenau, N. H.; Tassis, Konstantinos; and others

    2014-12-20

    We present observations of N{sub 2}H{sup +} (J = 1 → 0), HCO{sup +} (J = 1 → 0), and HCN (J = 1 → 0) toward the Serpens Main molecular cloud from the CARMA Large Area Star Formation Survey (CLASSy). We mapped 150 arcmin{sup 2} of Serpens Main with an angular resolution of ∼7''. The gas emission is concentrated in two subclusters (the NW and SE subclusters). The SE subcluster has more prominent filamentary structures and more complicated kinematics compared to the NW subcluster. The majority of gas in the two subclusters has subsonic to sonic velocity dispersions. We applied a dendrogram technique with N{sub 2}H{sup +}(1-0) to study the gas structures; the SE subcluster has a higher degree of hierarchy than the NW subcluster. Combining the dendrogram and line fitting analyses reveals two distinct relations: a flat relation between nonthermal velocity dispersion and size, and a positive correlation between variation in velocity centroids and size. The two relations imply a characteristic depth of 0.15 pc for the cloud. Furthermore, we have identified six filaments in the SE subcluster. These filaments have lengths of ∼0.2 pc and widths of ∼0.03 pc, which is smaller than a characteristic width of 0.1 pc suggested by Herschel observations. The filaments can be classified into two types based on their properties. The first type, located in the northeast of the SE subcluster, has larger velocity gradients, smaller masses, and nearly critical mass-per-unit-length ratios. The other type, located in the southwest of the SE subcluster, has the opposite properties. Several YSOs are formed along two filaments which have supercritical mass per unit length ratios, while filaments with nearly critical mass-per-unit-length ratios are not associated with YSOs, suggesting that stars are formed on gravitationally unstable filaments.

  9. Computation Sheds Insight into Iron Porphyrin Carbenes' Electronic Structure, Formation, and N-H Insertion Reactivity.

    PubMed

    Sharon, Dina A; Mallick, Dibyendu; Wang, Binju; Shaik, Sason

    2016-08-01

    Iron porphyrin carbenes constitute a new frontier of species with considerable synthetic potential. Exquisitely engineered myoglobin and cytochrome P450 enzymes can generate these complexes and facilitate the transformations they mediate. The current work harnesses density functional theoretical methods to provide insight into the electronic structure, formation, and N-H insertion reactivity of an iron porphyrin carbene, [Fe(Por)(SCH3)(CHCO2Et)](-), a model of a complex believed to exist in an experimentally studied artificial metalloenzyme. The ground state electronic structure of the terminal form of this complex is an open-shell singlet, with two antiferromagnetically coupled electrons residing on the iron center and carbene ligand. As we shall reveal, the bonding properties of [Fe(Por)(SCH3)(CHCO2Et)](-) are remarkably analogous to those of ferric heme superoxide complexes. The carbene forms by dinitrogen loss from ethyl diazoacetate. This reaction occurs preferentially through an open-shell singlet transition state: iron donates electron density to weaken the C-N bond undergoing cleavage. Once formed, the iron porphyrin carbene accomplishes N-H insertion via nucleophilic attack. The resulting ylide then rearranges, using an internal carbonyl base, to form an enol that leads to the product. The findings rationalize experimentally observed reactivity trends reported in artificial metalloenzymes employing iron porphyrin carbenes. Furthermore, these results suggest a possible expansion of enzymatic substrate scope, to include aliphatic amines. Thus, this work, among the first several computational explorations of these species, contributes insights and predictions to the surging interest in iron porphyrin carbenes and their synthetic potential.

  10. Microtopography-Induced Lag Formation on Bedforms and Biogenic Structures in Aeolian Settings

    NASA Astrophysics Data System (ADS)

    Buynevich, I. V.

    2010-12-01

    In a variety of sand-dominated depositional settings, high-energy events typically culminate with the formation of a lag deposit, expressed as an increase in coarse fraction, accumulation of shell fragments, or a concentration of heavy minerals (density >2.9) beyond their background values. In aeolian settings, grain impact plays a greater role in sediment transport than under subaqueous conditions, but there is a similar segregation of minerals by size and density due to different threshold entrainment and fall velocities of sand grains. For fine-to-medium sand transition, near-surface wind velocities increase from 4.5 m/s for quartz to 6.5 m/s for magnetite, which has twice the density. Most heavy minerals occur in a finer fraction of the surface sediment layer, which further increases their entrainment threshold due to high pivot angles and sheltering by the lighter minerals. Prolonged periods of increased wind activity generate heavy-mineral-enriched horizons ranging in thickness from a few grain diameters to more than 10-20 cm, producing distinct marker horizons and placers of economic importance. However, even under relatively low wind regime, localized density lag may form due to minor variations in topography and bed roughness. This process was exemplified along Revere Beach (Massachusetts, USA), where a series of 15-cm-high steps were installed at the base of a low seawall to prevent the formation of aeolian ramp that facilitated frequent overtopping. During the following months, a clear trend was established where the heavy-mineral fraction (primarily almandine garnet) progressively increased in a landward direction, toward higher substrate elevations. In natural settings with even a small background fraction of heavy minerals (2-5%), microtopographic highs of less than 1 cm are sufficient for the formation of a density lag. In a backshore area of Assateague Island (Maryland, USA), a clear increase in heavy-mineral content (mostly magnetite) was observed

  11. Cosmic gamma-ray background from structure formation in the intergalactic medium

    PubMed

    Loeb; Waxman

    2000-05-11

    The Universe is filled with a diffuse background of gamma-ray radiation, the origin of which remains one of the unsolved puzzles of cosmology. Less than one-quarter of the gamma-ray flux can be attributed to unresolved discrete sources, such as active galactic nuclei; the remainder appears to constitute a truly diffuse background. Here we show that the shock waves induced by gravity in the gas of the intergalactic medium, during the formation of large-scale structures like filaments and sheets of galaxies, produce a population of highly relativistic electrons. These electrons scatter a small fraction of the cosmic microwave background photons in the local Universe up to gamma-ray energies, thereby providing the gamma-ray background. The predicted diffuse flux agrees with the observed background across more than four orders of magnitude in photon energy, and the model predicts that the gamma-ray background, though generated locally, is isotropic to better than five per cent on angular scales larger than a degree. Moreover, the agreement between the predicted and observed background fluxes implies a mean cosmological density of baryons that is consistent with Big Bang nucleosynthesis.

  12. A review of bioactive glasses: Their structure, properties, fabrication and apatite formation.

    PubMed

    Kaur, Gurbinder; Pandey, Om P; Singh, Kulvir; Homa, Dan; Scott, Brian; Pickrell, Gary

    2014-01-01

    Bioactive glass and glass-ceramics are used in bone repair applications and are being developed for tissue engineering applications. Bioactive glasses/Bioglass are very attractive materials for producing scaffolds devoted to bone regeneration due to their versatile properties, which can be properly designed depending on their composition. An important feature of bioactive glasses, which enables them to work for applications in bone tissue engineering, is their ability to enhance revascularization, osteoblast adhesion, enzyme activity and differentiation of mesenchymal stem cells as well as osteoprogenitor cells. An extensive amount of research work has been carried out to develop silicate, borate/borosilicate bioactive glasses and phosphate glasses. Along with this, some metallic glasses have also been investigated for biomedical and technological applications in tissue engineering. Many trace elements have also been incorporated in the glass network to obtain the desired properties, which have beneficial effects on bone remodeling and/or associated angiogenesis. The motivation of this review is to provide an overview of the general requirements, composition, structure-property relationship with hydroxyapatite formation and future perspectives of bioglasses.Attention has also been given to developments of metallic glasses and doped bioglasses along with the techniques used for their fabrication.

  13. Cyclodextrins in pharmaceutical formulations I: structure and physicochemical properties, formation of complexes, and types of complex.

    PubMed

    Jambhekar, Sunil S; Breen, Philip

    2016-02-01

    Cyclodextrins are cyclic oligosaccharides that have been recognized as pharmaceutical adjuvants for the past 20 years. The molecular structure of these glucose derivatives, which approximates a truncated cone, bucket, or torus, generates a hydrophilic exterior surface and a nonpolar interior cavity. Cyclodextrins can interact with appropriately sized drug molecules to yield an inclusion complex. These noncovalent inclusion complexes offer a variety of advantages over the noncomplexed form of a drug. Cyclodextrins are primarily used to enhance the aqueous solubility, physical chemical stability, and bioavailability of drugs. Their other applications include preventing drug-drug interactions, converting liquid drugs into microcrystalline powders, minimizing gastrointestinal and ocular irritation, and reducing or eliminating unpleasant taste and smell. Here, we discuss the physical chemical properties of various cyclodextrins, including the effects of substitutions on these properties. Additionally, we report on the regulatory status of their use, commercial products containing cyclodextrins, toxicological considerations, and the forces involved in complex formation. We also highlight the types of complex formed and discuss the methods used to determine the types of complex present. PMID:26686054

  14. UVMag: stellar formation, evolution, structure and environment with space UV and visible spectropolarimetry

    NASA Astrophysics Data System (ADS)

    Neiner, C.; Baade, D.; Fullerton, A.; Gry, C.; Hussain, G.; Lèbre, A.; Morin, J.; Petit, P.; Sundqvist, J. O.; ud-Doula, A.; Vidotto, A. A.; Wade, G. A.

    2014-11-01

    Important insights into the formation, structure, evolution and environment of all types of stars can be obtained through the measurement of their winds and possible magnetospheres. However, this has hardly been done up to now mainly because of the lack of UV instrumentation available for long periods of time. To reach this aim, we have designed UVMag, an M-size space mission equipped with a high-resolution spectropolarimeter working in the UV and visible spectral range. The UV domain is crucial in stellar physics as it is very rich in atomic and molecular lines and contains most of the flux of hot stars. Moreover, covering the UV and visible spectral domains at the same time will allow us to study the star and its environment simultaneously. Adding polarimetric power to the spectrograph will multiply tenfold the capabilities of extracting information on stellar magnetospheres, winds, disks, and magnetic fields. Examples of science objectives that can be reached with UVMag are presented for pre-main sequence, main sequence and evolved stars. They will cast new light onto stellar physics by addressing many exciting and important questions. UVMag is currently undergoing a Research & Technology study and will be proposed at the forthcoming ESA call for M-size missions. This spectropolarimeter could also be installed on a large UV and visible observatory (e.g. NASA's LUVOIR project) within a suite of instruments.

  15. Self-propelled worm-like filaments: spontaneous spiral formation, structure, and dynamics.

    PubMed

    Isele-Holder, Rolf E; Elgeti, Jens; Gompper, Gerhard

    2015-09-28

    Worm-like filaments that are propelled homogeneously along their tangent vector are studied by Brownian dynamics simulations. Systems in two dimensions are investigated, corresponding to filaments adsorbed to interfaces or surfaces. A large parameter space covering weak and strong propulsion, as well as flexible and stiff filaments is explored. For strongly propelled and flexible filaments, the free-swimming filaments spontaneously form stable spirals. The propulsion force has a strong impact on dynamic properties, such as the rotational and translational mean square displacement and the rate of conformational sampling. In particular, when the active self-propulsion dominates thermal diffusion, but is too weak for spiral formation, the rotational diffusion coefficient has an activity-induced contribution given by v(c)/ξ(P), where v(c) is the contour velocity and ξ(P) the persistence length. In contrast, structural properties are hardly affected by the activity of the system, as long as no spirals form. The model mimics common features of biological systems, such as microtubules and actin filaments on motility assays or slender bacteria, and artificially designed microswimmers. PMID:26256415

  16. Network inference of AP pattern formation system in D.melanogaster by structural equation modeling

    NASA Astrophysics Data System (ADS)

    Aburatani, S.; Toh, H.

    2014-03-01

    Within the field of systems biology, revealing the control systems functioning during embryogenesis is an important task. To clarify the mechanisms controlling sequential events, the relationships between various factors and the expression of specific genes should be determined. In this study, we applied a method based on Structural Equation Modeling (SEM), combined with factor analysis. SEM can include the latent variables within the constructed model and infer the relationships among the latent and observed variables, as a network model. We improved a method for the construction of initial models for the SEM calculation, and applied our approach to estimate the regulatory network for Antero-Posterior (AP) pattern formation in D. melanogaster embryogenesis. In this new approach, we combined cross-correlation and partial correlation to summarize the temporal information and to extract the direct interactions from the gene expression profiles. In the inferred model, 18 transcription factor genes were regulated by not only the expression of other genes, but also the estimated factors. Since each factor regulated the same type of genes, these factors were considered to be involved in maternal effects or spatial morphogen distributions. The interpretation of the inferred network model allowed us to reveal the regulatory mechanism for the patterning along the head to tail axis in D. melanogaster.

  17. Soot formation and temperature field structure in laminar propane-air diffusion flames at elevated pressures

    SciTech Connect

    Bento, Decio S.; Guelder, OEmer L.; Thomson, Kevin A.

    2006-06-15

    The effect of pressure on soot formation and the structure of the temperature field was studied in coflow propane-air laminar diffusion flames over the pressure range of 0.1 to 0.73 MPa in a high-pressure combustion chamber. The fuel flow rate was selected so that the soot was completely oxidized within the visible flame and the flame was stable at all pressures. Spectral soot emission was used to measure radially resolved soot volume fraction and soot temperature as a function of pressure. Additional soot volume fraction measurements were made at selected heights using line-of-sight light attenuation. Soot concentration values from these two techniques agreed to within 30% and both methods exhibited similar trends in the spatial distribution of soot concentration. Maximum line-of-sight soot concentration along the flame centerline scaled with pressure; the pressure exponent was about 1.4 for pressures between 0.2 and 0.73 MPa. Peak carbon conversion to soot, defined as the percentage of fuel carbon content converted to soot, also followed a power-law dependence on pressure, where the pressure exponent was near to unity for pressures between 0.2 and 0.73 MPa. Soot temperature measurements indicated that the overall temperatures decreased with increasing pressure; however, the temperature gradients increased with increasing pressure. (author)

  18. Membrane tubule formation by banana-shaped proteins with or without transient network structure

    PubMed Central

    Noguchi, Hiroshi

    2016-01-01

    In living cells, membrane morphology is regulated by various proteins. Many membrane reshaping proteins contain a Bin/Amphiphysin/Rvs (BAR) domain, which consists of a banana-shaped rod. The BAR domain bends the biomembrane along the rod axis and the features of this anisotropic bending have recently been studied. Here, we report on the role of the BAR protein rods in inducing membrane tubulation, using large-scale coarse-grained simulations. We reveal that a small spontaneous side curvature perpendicular to the rod can drastically alter the tubulation dynamics at high protein density, whereas no significant difference is obtained at low density. A percolated network is intermediately formed depending on the side curvature. This network suppresses tubule protrusion, leading to the slow formation of fewer tubules. Thus, the side curvature, which is generated by protein–protein and membrane–protein interactions, plays a significant role in tubulation dynamics. We also find that positive surface tensions and the vesicle membrane curvature can stabilize this network structure by suppressing the tubulation. PMID:26863901

  19. Studies of Structure Formation in Theories with a Repulsive Long-Range Gravitational Force

    NASA Astrophysics Data System (ADS)

    Lohiya, D.; Batra, A.; Mehra, S.; Mahajan, S.; Mukherjee, A.

    This paper reports on the emergence of structures in a class of alternative theories of gravity. These theories do not have any horizon, flatness, initial cosmological singularity and (possibly) quantization problems. The model is characterized by a dynamically induced gravitational constant with a wrong sign corresponding to repulsive gravitation on the large scale. A non-minimal coupling of a scalar field in the model can give rise to non-topological solitons in the theory. This results in domains (gravity balls) inside which an effective, canonical, attractive gravitational constant is induced. We consider simulations of the formation and evolution of such solutions. Starting with a single gravity ball, we consider its fragmentation into smaller (lower mass) balls - evolving by mutual repulsion. After several runs, we have been able to identify two parameters: the strength of the long-range gravitational constant and the size of the gravity balls, which can be used to generate appropriate two-point correlations of the distribution of these balls.

  20. The role of the dark matter distribution in the structure formation

    SciTech Connect

    Gómez, L. Gabriel; Rueda, Jorge A.

    2015-12-17

    We review the most important ingredients that compose the halo model of structure formation, emphasizing on the role played by the density profile of dark matter (DM). The theoretical predictions of the so-called warm DM (WDM) and cold DM (CDM) cosmologies at small scales are discussed in terms of recent numerical simulations and current observational data coming from rotation curves of galaxies. We elaborate on the recently introduced Ruffini-Argüelles-Rueda (RAR) DM profile, which is obtained from the configuration of equilibrium of a self-gravitating system of massive fermions, hereafter “inos”, and show that it can be a good candidate for WDM. A significant insight for this model might be inferred based on the analytical approach of the halo model, pointing out that there might have signals of quantum cores of galaxies on the non-linear matter power spectrum at small scales, which are however unfortunately inaccessible today with the current observational instruments. Upcoming surveys could test in the future the quantum features of galactic cores.

  1. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    NASA Astrophysics Data System (ADS)

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-01

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  2. Studying Star and Planet Formation with the Submillimeter Probe of the Evolution of Cosmic Structure

    NASA Technical Reports Server (NTRS)

    Rinehart, Stephen A.

    2005-01-01

    The Submillimeter Probe of the Evolution of Cosmic Structure (SPECS) is a far- infrared/submillimeter (40-640 micrometers) spaceborne interferometry concept, studied through the NASA Vision Missions program. SPECS is envisioned as a 1-km baseline Michelson interferometer with two 4- meter collecting mirrors. To maximize science return, SPECS will have three operational modes: a photometric imaging mode, an intermediate spectral resolution mode (R approximately equal to 1000-3000), and a high spectral resolution mode (R approximately equal to 3 x 10(exp 5)). The first two of these modes will provide information on all sources within a 1 arcminute field-of-view (FOV), while the the third will include sources in a small (approximately equal to 5 arcsec) FOV. With this design, SPECS will have angular resolution comparable to the Hubble Space Telescope (50 mas) and sensitivity more than two orders of magnitude better than Spitzer (5sigma in 10ks of approximately equal to 3 x 10(exp 7) Jy Hz). We present here some of the results of the recently-completed Vision Mission Study for SPECS, and discuss the application of this mission to future studies of star and planet formation.

  3. Membrane tubule formation by banana-shaped proteins with or without transient network structure

    NASA Astrophysics Data System (ADS)

    Noguchi, Hiroshi

    2016-02-01

    In living cells, membrane morphology is regulated by various proteins. Many membrane reshaping proteins contain a Bin/Amphiphysin/Rvs (BAR) domain, which consists of a banana-shaped rod. The BAR domain bends the biomembrane along the rod axis and the features of this anisotropic bending have recently been studied. Here, we report on the role of the BAR protein rods in inducing membrane tubulation, using large-scale coarse-grained simulations. We reveal that a small spontaneous side curvature perpendicular to the rod can drastically alter the tubulation dynamics at high protein density, whereas no significant difference is obtained at low density. A percolated network is intermediately formed depending on the side curvature. This network suppresses tubule protrusion, leading to the slow formation of fewer tubules. Thus, the side curvature, which is generated by protein–protein and membrane–protein interactions, plays a significant role in tubulation dynamics. We also find that positive surface tensions and the vesicle membrane curvature can stabilize this network structure by suppressing the tubulation.

  4. Indirect evidence for structural changes coupled with QB-. formation in photosystem II.

    PubMed

    Reifarth, F; Renger, G

    1998-05-29

    The thermal blockage of QA-. oxidation was analysed in PS II membrane fragments by monitoring flash-induced changes of the relative fluorescence quantum yield as a function of temperature. The results obtained reveal: (a) in dark-adapted samples the fraction of QA-. that is not reoxidised within a time domain of 10 s after the actinic flash increases with lowering the temperature (half-maximum effect at 250-260 K), (b) at low temperatures where QA-. generated in dark-adapted samples remains almost completely reduced, a significant extent of QA-. reoxidation arises when samples are used that were preilluminated at room temperature by one saturating flash followed by rapid freezing before performing the experiment, and (c) the extent of QA-. that is reoxidised at 258 K exhibits a characteristic binary oscillation as a function of the number of preillumination flashes given at room temperature. Based on these data it is inferred that QB and QB-. are located at different equilibrium positions in the QB site. As a consequence the formation of QB-. is coupled with significant structural changes that require sufficient flexibility of the protein matrix. This general feature corresponds with a recently proposed model for the acceptor side reactions of anoxygenic bacteria [Stowell, M.H.B., McPhillips, T.M., Rees, D.C., Soltis, S.M., Abresch, E. and Feher, G., Science 276 (1997) 812-816].

  5. Electronic structure changes during the surface-assisted formation of a graphene nanoribbon

    SciTech Connect

    Bronner, Christopher Tegeder, Petra; Utecht, Manuel; Saalfrank, Peter; Klamroth, Tillmann; Haase, Anton

    2014-01-14

    High conductivity and a tunability of the band gap make quasi-one-dimensional graphene nanoribbons (GNRs) highly interesting materials for the use in field effect transistors. Especially bottom-up fabricated GNRs possess well-defined edges which is important for the electronic structure and accordingly the band gap. In this study we investigate the formation of a sub-nanometer wide armchair GNR generated on a Au(111) surface. The on-surface synthesis is thermally activated and involves an intermediate non-aromatic polymer in which the molecular precursor forms polyanthrylene chains. Employing angle-resolved two-photon photoemission in combination with density functional theory calculations we find that the polymer exhibits two dispersing states which we attribute to the valence and the conduction band, respectively. While the band gap of the non-aromatic polymer obtained in this way is relatively large, namely 5.25 ± 0.06 eV, the gap of the corresponding aromatic GNR is strongly reduced which we attribute to the different degree of electron delocalization in the two systems.

  6. Membrane tubule formation by banana-shaped proteins with or without transient network structure

    NASA Astrophysics Data System (ADS)

    Noguchi, Hiroshi

    2016-02-01

    In living cells, membrane morphology is regulated by various proteins. Many membrane reshaping proteins contain a Bin/Amphiphysin/Rvs (BAR) domain, which consists of a banana-shaped rod. The BAR domain bends the biomembrane along the rod axis and the features of this anisotropic bending have recently been studied. Here, we report on the role of the BAR protein rods in inducing membrane tubulation, using large-scale coarse-grained simulations. We reveal that a small spontaneous side curvature perpendicular to the rod can drastically alter the tubulation dynamics at high protein density, whereas no significant difference is obtained at low density. A percolated network is intermediately formed depending on the side curvature. This network suppresses tubule protrusion, leading to the slow formation of fewer tubules. Thus, the side curvature, which is generated by protein-protein and membrane-protein interactions, plays a significant role in tubulation dynamics. We also find that positive surface tensions and the vesicle membrane curvature can stabilize this network structure by suppressing the tubulation.

  7. The role of the dark matter distribution in the structure formation

    NASA Astrophysics Data System (ADS)

    Gómez, L. Gabriel; Rueda, Jorge A.

    2015-12-01

    We review the most important ingredients that compose the halo model of structure formation, emphasizing on the role played by the density profile of dark matter (DM). The theoretical predictions of the so-called warm DM (WDM) and cold DM (CDM) cosmologies at small scales are discussed in terms of recent numerical simulations and current observational data coming from rotation curves of galaxies. We elaborate on the recently introduced Ruffini-Argüelles-Rueda (RAR) DM profile, which is obtained from the configuration of equilibrium of a self-gravitating system of massive fermions, hereafter "inos", and show that it can be a good candidate for WDM. A significant insight for this model might be inferred based on the analytical approach of the halo model, pointing out that there might have signals of quantum cores of galaxies on the non-linear matter power spectrum at small scales, which are however unfortunately inaccessible today with the current observational instruments. Upcoming surveys could test in the future the quantum features of galactic cores.

  8. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    SciTech Connect

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-15

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  9. Hierarchical structured tungsten oxide nanocrystals via hydrothermal route: microstructure, formation mechanism and humidity sensing

    NASA Astrophysics Data System (ADS)

    Pang, Hua-Feng; Li, Zhi-Jie; Xiang, Xia; Fu, Yong-Qing; Placido, Frank; Zu, Xiao-Tao

    2013-09-01

    Hierarchical structured tungsten oxide nanocrystals were synthesized via the hydrothermal route assisted by a capping agent of ammonium benzoate (AB). The products were characterized using scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. The experimental results show that the crystal microstructures could be changed from flower-shape to star-shape by changing the mole ratio of ammonium benzoate to sodium tungstate (AB/ST). The crystal phases were changed from orthorhombic WO3ṡ0.33H2O to hexagonal WO3 with the increase in the concentration of AB. Based on the results from Fourier transform infrared spectroscopy and time-dependent growth analysis, a self-assembly growth mechanism has been proposed for the formation of flower, spherical, and star-netted microstructures at different mole ratios of the AB/ST. The star-netted WO3 nanocrystals were applied as a sensitive layer for humidity sensing performed using a Love-mode ZnO/36∘ Y-cut LiTaO3 surface acoustic wave device, and a stable and sensitive response to the change of relative humidity was obtained.

  10. Formation and internal structure of superdense dark matter clumps and ultracompact minihaloes

    NASA Astrophysics Data System (ADS)

    Berezinsky, V. S.; Dokuchaev, V. I.; Eroshenko, Yu. N.

    2013-11-01

    We discuss the formation mechanisms and structure of the superdense dark matter clumps (SDMC) and ultracompact minihaloes (UCMH), outlining the differences between these types of DM objects. We define as SDMC the gravitationally bounded DM objects which have come into virial equilibrium at the radiation-dominated (RD) stage of the universe evolution. Such objects can be formed from the isocurvature (entropy) density perturbations or from the peaks in the spectrum of curvature (adiabatic) perturbation. The axion miniclusters (Kolb and Tkachev 1994) are the example of the former model. The system of central compact mass (e.g. in the form of SDMC or primordial black hole (PBH)) with the outer DM envelope formed in the process of secondary accretion we refer to as UCMH. Therefore, the SDMC can serve as the seed for the UCMH in some scenarios. Recently, the SDMC and UCMH were considered in the many works, and we try to systematize them here. We consider also the effect of asphericity of the initial density perturbation in the gravitational evolution, which decreases the SDMC amount and, as the result, suppresses the gamma-ray signal from DM annihilation.

  11. Underground structure of terrestrial mud volcanoes and abnormal water pressure formation in Niigata, Central JAPAN

    NASA Astrophysics Data System (ADS)

    Tanaka, K.; Shinya, T.; Miyata, Y.; Tokuyasu, S.

    2005-12-01

    Activity of mud volcano is thought to be caused by an abnormal water pressure generated in deep underground and make a serious problem for underground constructions such as railway tunnel, underground facility for radwaste and so on. It is important to investigate the underground structure of a mud volcano and the mechanism of abnormal water formation for site selection and safety assessment of such facilities. Serious trouble such as tunnel wall collapse due to the rock swelling has happened 180m deep under mud volcanoes. It took more than 10 years to excavate the section of 150 m long. 4 terrestrial mud volcanoes were found in the Tertiary sedimentary basin in Niigata, central Japan All the mud volcanoes are distributed along the rim of the topographic basin that is located at the NE-SW trending crest of mountainous area and distributed along the wing of anticline. Geological structure inside basin is heavily disturbed. The extinct mud volcano is exposed in the side-slope of newly constructed road and the internal vent structure of mud volcano can be observed. The vent is 30 m in diameter and is consisted of mud breccia and scaly network clay that is thought to be generated by hydro-fracturing and the following water-rock interaction between mudstone and groundwater. Groundwater erupted from mud volcano is highly saline with electric conductivity of 15 mS/cm and high 18 O/16 O isotope ratio of 1.2 parmillage. Also, the vitrinite reflectance is 1.5 to 1.9 % that is not expected in the sedimentary rocks exposed near ground surface. As a result, it is assumed that these erupted materials were introduced from the deep underground about 4000 m deep. CSA-MT geophysical exploration was carried out to survey the underground structure and obtained the profile of electrical resistivity from the surface to 800 m in depth. It is found that the disk-shaped low resistivity zone less than 1 m due to the high salinity content is identified in underground 600 m deep, 200 m thick

  12. Mechanism of ultrasonic energy-assisted formation of V-, Y-shaped nano-structures in conjugated polymers.

    PubMed

    Majumdar, D; Maiti, R P; Basu, S; Saha, S K

    2009-12-01

    Recently, hydrocarbon-nanostructures from organic solvent using ultrasonic energy were reported. However, their formation-dynamics remained unexplored. Here, we describe a new technique to synthesize controlled nanostructures (V-, Y-shape) from nanorods of conducting polyaniline applying ultrasonic energy. To characterize the conducting state (emaraldine) of these polyaniline nanorods, electrical measurements have been carried out from which it is seen that there is a crossover from metallic to semiconductor as temperature increases. The observed crossover has been explained by the core-shell structure of the nanorods with core resistivity much higher than the shell resistivity. The nonlinear current-voltage behavior is attributed to the formation of alternate ordered/disordered chain segments along the length of the nanorods. We also propose a model to explore the mechanism of formation of these V-, Y-shaped nanostructures. It is believed that bubble-formation occurs in liquid due to ultrasonic vibration; and asymmetry in the bubble is created when formed near the solid surface leading to jet formation. Liquid jets of collapsing bubble move with incredible velocity (400 km/h); collide with the nanorod to cause fragmentations followed by V-, Y-shaped structure formation when the imparted kinetic energy of jets is comparable with elastic energy of fragments.

  13. Study of silicon carbide formation by liquid silicon infiltration of porous carbon structures

    NASA Astrophysics Data System (ADS)

    Margiotta, Jesse C.

    Silicon carbide (SiC) materials are prime candidates for high temperature heat exchangers for next generation nuclear reactors due to their refractory nature and high thermal conductivity at elevated temperatures. This research has focused on demonstrating the potential of liquid silicon infiltration (LSI) for making SiC to achieve this goal. The major advantage of this method over other ceramic processing techniques is the enhanced capability of making fully dense, high purity SiC materials in complex net shapes. For successful formation of net shape SiC using LSI techniques, the carbon preform reactivity and pore structure must be controlled to allow the complete infiltration of the porous carbon structure followed by conversion of this carbon to SiC. We have established a procedure for achieving desirable carbon properties by using carbon precursors consisting of two readily available high purity organic materials, crystalline cellulose and phenolic resin. Phenolic resin yields a glassy carbon with low reactivity and porosity, and cellulose carbon is highly reactive and porous. By adjusting the ratio of these two materials in the precursor mixtures, the properties of the carbons produced can be controlled. We have identified the most favorable carbon precursor composition to be a cellulose:resin mass ratio of 6:4 for LSI formation of SiC. The optimum reaction conditions are a temperature of 1800°C, a pressure of 0.5 Torr of argon, and a time of 120 minutes. The fully dense net shape SiC material produced has a density of 2.96 g cm-3 (about 92% of pure SiC) and a SiC volume fraction of over 0.82. Kinetics of the LSI SiC formation process were studied by optical microscopy and quantitative digital image analysis. This study identified six reaction stages and provided important understanding of the process. Such knowledge can be used to further refine the LSI technique. Although the thermal conductivity of pure SiC at elevated temperatures is very high, thermal

  14. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.

    PubMed

    Cino, Elio A; Choy, Wing-Yiu; Karttunen, Mikko

    2012-08-14

    We have compared molecular dynamics (MD) simulations of a β-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 μs. The total simulation time was 37.2 μs. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 β-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like β-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, or GROMOS96 53a6 were used. The CHARMM27 simulations were able to form native hairpins in some of the elevated temperature simulations, while the OPLS-AA/L simulations did not yield native hairpin structures at any temperatures tested. Simulations that used charge-groups or peptide capping groups were not largely different from their uncapped counterparts with single atom charge-groups. On the other hand, phosphorylation of the threonine residue located at the β-turn significantly affected the hairpin formation. To our knowledge, this is the first study comparing such a large set of force fields with respect to β-hairpin folding. Such a comprehensive comparison will offer useful guidance to others conducting similar types of simulations.

  15. The Structure and Evolution of the Lagoon Nebula: Star Formation in the Sagittarius Arm

    NASA Astrophysics Data System (ADS)

    Tothill, N. F. H.

    1999-12-01

    The vast majority of star formation occurs in regions dominated by high-mass stars, such as the Orion complex. Through their hii regions, these massive stars profoundly affect the surrounding molecular gas, and quite probably trigger further star formation. This thesis presents the results of a submillimetre study of the interface between the Lagoon Nebula, M8, a large hii region in the southern hemisphere, and its associated molecular cloud. Continuum maps of M8 were obtained at wavelengths of 450 microns and 850 microns with SCUBA on the JCMT, and at 1.3 mm with the MPIfR 37-channel array at IRAM. A new subroutine was added to the data reduction facility for SCUBA (SURF); when skydip data are analysed to calculate the atmospheric opacity, this subroutine estimates the error in the fitted opacity. The performance of the subroutine is discussed, based on the M8 map data. The continuum maps are analysed by fitting gaussian profiles to the clumpy structure (on the 0.1 pc scale). Discrepancies between the fitted profiles at different wavelengths suggest that there are very considerable errors in this fitting process. There are a number of possible sources of contamination of the continuum emission, both non-thermal (free-free emission and molecular line emission) and thermal (greybody emission from hotter dust associated with the hii region and PDRs on the surfaces of the clumps). The likely magnitude of contamination from these sources is assessed: Line contamination is likely to be the largest, comprising between 10% and 50% of the detected continuum flux. The greybody emission from PDRs is likely to be in the range 10--20%. The other sources of contamination are unlikely to be larger than the calibration error (~10%). Partial maps of the Lagoon Nebula were obtained at the JCMT in the J = 3-2 transitions of various isotopomers of CO. These data are used to estimate the temperatures of the clumps, and to estimate their densities independently of the continuum

  16. Influence of the Photorhabdus luminescens phosphomannose isomerase gene, manA, on mannose utilization, exopolysaccharide structure, and biofilm formation.

    PubMed

    Amos, Matthew R; Sanchez-Contreras, Maria; Jackson, Robert W; Muñoz-Berbel, Xavier; Ciche, Todd A; Yang, Guowei; Cooper, Richard M; Waterfield, Nicholas R

    2011-02-01

    Extracellular polysaccharide (EPS) is produced by diverse bacterial pathogens and fulfills assorted roles, including providing a structural matrix for biofilm formation and more specific functions in virulence, such as protection against immune defenses. We report here the first investigation of some of the genes important for biofilm formation in Photorhabdus luminescens and demonstrate the key role of the phosphomannose isomerase gene, manA, in the structure of functional EPS. Phenotypic analyses of a manA-deficient mutant showed the importance of EPS in motility, insect virulence, and biofilm formation on abiotic surfaces as well as the requirement of this gene for the use of mannose as the sole carbon source. Conversely, this defect had no apparent impact on symbiosis with the heterorhabditid nematode vector. A more detailed analysis of biofilm formation revealed that the manA mutant was able to attach to surfaces with the same efficiency as that of the wild-type strain but could not develop the more extended biofilm matrix structures. A compositional analysis of P. luminescens EPS reveals how the manA mutation has a major effect on the formation of a complete, branched EPS. PMID:21148694

  17. Chemistry of Tertiary sediments in the surroundings of the Ries impact structure and moldavite formation revisited

    NASA Astrophysics Data System (ADS)

    Žák, Karel; Skála, Roman; Řanda, Zdeněk; Mizera, Jiří; Heissig, Kurt; Ackerman, Lukáš; Ďurišová, Jana; Jonášová, Šárka; Kameník, Jan; Magna, Tomáš

    2016-04-01

    Moldavites, tektites of the Central European strewn field, have been traditionally linked with the Ries impact structure in Germany. They are supposed to be derived mainly from the near-surface sediments of the Upper Freshwater Molasse of Miocene age that probably covered the target area before the impact. Comparison of the chemical composition of moldavites with that of inferred source materials requires recalculation of the composition of sediments to their water-, organic carbon- and carbon dioxide-free residuum. This recalculation reflects the fact that these compounds were lost almost completely from the target materials during their transformation to moldavites. Strong depletions in concentrations of many elements in moldavites relative to the source sediments (e.g., Mo, Cu, Ag, Sb, As, Fe) contrast with enrichments of several elements in moldavites (e.g., Cs, Ba, K, Rb). These discrepancies can be generally solved using two different approaches, either by involvement of a component of specific chemical composition, or by considering elemental fractionation during tektite formation. The proposed conceptual model of moldavite formation combines both approaches and is based on several steps: (i) the parent mixture (Upper Freshwater Molasse sediments as the dominant source) contained also a minor admixture of organic matter and soils; (ii) the most energetic part of the ejected matter was converted to vapor (plasma) and another part produced melt directly upon decompression; (iii) following further adiabatic decompression, the expanding vapor phase disintegrated the melt into small melt droplets and some elements were partially lost from the melt because of their volatility, or because of the volatility of their compounds, such as carbonyls of Fe and other transition metals (e.g., Ni, Co, Mo, Cr, and Cu); (iv) large positively charged ions such as Cs+, Ba2+, K+, Rb+ from the plasma portion were enriched in the late-stage condensation spherules or condensed

  18. Kinetics of Ferrite Recrystallization and Austenite Formation During Intercritical Annealing of the Cold-Rolled Ferrite/Martensite Duplex Structures

    NASA Astrophysics Data System (ADS)

    Mazaheri, Y.; Kermanpur, A.; Najafizadeh, A.; Kalashami, A. Ghatei

    2016-03-01

    Ultrafine-grained, dual-phase (UFG DP) steels were produced by a new route using an uncommon cold-rolling and subsequent intercritical annealing of ferrite/martensite duplex starting microstructures. The effects of processing parameters such as rolling reduction, intercritical annealing temperature, and time on the microstructural evaluations have been studied. UFG DP steels with an average grain size of about 1 to 2 μm were achieved by short intercritical annealing of the 80 pct cold-rolled duplex microstructures. The kinetics of ferrite recrystallization and austenite formation were studied based on the Johnson-Mehl-Avrami-Kolmogorov (JMAK) model. The proposed model for describing the isothermal austenite formation kinetics was applied successfully to the nonisothermal conditions. It was found that complete recrystallization of ferrite before the austenite formation led to the formation of a large extent randomly distributed austenite in the ferrite matrix and a chain-networked structure.

  19. Map showing structure contours on the top of the upper Jurassic Morrison Formation, Powder River basin, Wyoming and Montana

    USGS Publications Warehouse

    Crysdale, B.L.

    1991-01-01

    This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 2,429 of these wells that penetrate the Minnelusa Formation and equivalents.

  20. Biostratigraphy and structural setting of the Permian Coyote Butte Formation of central Oregon.

    USGS Publications Warehouse

    Wardlaw, B.R.; Nestell, M.K.; Dutro, J.T.

    1982-01-01

    Larger isolated outcrops of the limestones of the Coyote Butte Formation consistently contain younger over older faunas that range through most of the Leonardian Series of the Early Permian. The outcrops of the Coyote Butte Formation are interpreted as right- side up blocks probably introduced into the area as one massive exotic unit. The Coyote Butte Formation is very similar to the Lower Permain limestone near Quinn River Crossing, Nevada, and both are suggested to have a similar origin. The Coyote Butte Formation was probably introduced during a late-stage event to deforming Mesozoic oceanic sediments in Mesozoic time. -Authors

  1. Features of structures formation on the basis of chitosan derivatives by a prototype of 263 nm laser stereolithograph

    NASA Astrophysics Data System (ADS)

    Dudova, D. S.; Bardakova, K. N.; Akopova, T. A.; Timashev, P. S.; Minaev, N. V.

    2016-08-01

    We have developed technology of polysaccharides based matrices formation by laser stereolithography (SLA) method using UV range laser radiation. Experimental data on a laser parameters selection of single-layer structures polymerization for compositions based on unsaturated chitosan derivatives with different degree of substitution and with the addition of polyethylene glycol diacrylate is shown.

  2. Impact of molecular structure on secondary organic aerosol formation from aromatic hydrocarbon photooxidation under low-NOx conditions

    NASA Astrophysics Data System (ADS)

    Li, Lijie; Tang, Ping; Nakao, Shunsuke; Cocker, David R., III

    2016-08-01

    The molecular structure of volatile organic compounds determines their oxidation pathway, directly impacting secondary organic aerosol (SOA) formation. This study comprehensively investigates the impact of molecular structure on SOA formation from the photooxidation of 12 different eight- to nine-carbon aromatic hydrocarbons under low-NOx conditions. The effects of the alkyl substitute number, location, carbon chain length and branching structure on the photooxidation of aromatic hydrocarbons are demonstrated by analyzing SOA yield, chemical composition and physical properties. Aromatic hydrocarbons, categorized into five groups, show a yield order of ortho (o-xylene and o-ethyltoluene) > one substitute (ethylbenzene, propylbenzene and isopropylbenzene) > meta (m-xylene and m-ethyltoluene) > three substitute (trimethylbenzenes) > para (p-xylene and p-ethyltoluene). SOA yields of aromatic hydrocarbon photooxidation do not monotonically decrease when increasing alkyl substitute number. The ortho position promotes SOA formation while the para position suppresses aromatic oxidation and SOA formation. Observed SOA chemical composition and volatility confirm that higher yield is associated with further oxidation. SOA chemical composition also suggests that aromatic oxidation increases with increasing alkyl substitute chain length and branching structure. Further, carbon dilution conjecture developed by Li et al. (2016) is extended in this study to serve as a standard method to determine the extent of oxidation of an alkyl-substituted aromatic hydrocarbon.

  3. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms.

    PubMed

    Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo; Müsken, Mathias; Häussler, Susanne; Meyer-Hermann, Michael

    2016-01-01

    Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors. PMID:27611778

  4. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms

    PubMed Central

    Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo; Müsken, Mathias; Häussler, Susanne; Meyer-Hermann, Michael

    2016-01-01

    Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors. PMID:27611778

  5. Engineering Skills Formation in Britain: Cyclical and Structural Issues. Towards a National Skills Agenda. Skills Task Force Research Paper 7.

    ERIC Educational Resources Information Center

    Mason, Geoff

    Cyclical and structural issues in engineering skills formation in Great Britain were studied through a review of recent employment patterns, income patterns, employment projections, recent trends in education and training, and recent developments in technology and work organization. The review focused on the following issues: (1) the extent and…

  6. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms.

    PubMed

    Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo; Müsken, Mathias; Häussler, Susanne; Meyer-Hermann, Michael

    2016-09-09

    Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors.

  7. Structure formation in f(R) gravity: a distinguishing probe between the dark energy and modified gravity

    SciTech Connect

    Baghram, Shant; Rahvar, Sohrab E-mail: rahvar@sharif.edu

    2010-12-01

    In this work, we study the large scale structure formation in the modified gravity in the framework of Palatini formalism and compare the results with the equivalent smooth dark energy models as a tool to distinguish between these models. Through the inverse method, we reconstruct the dynamics of universe, modified gravity action and the structure formation indicators like the screened mass function and gravitational slip parameter. Consequently, we extract the matter density power spectrum for these two models in the linear regime and show that the modified gravity and dark energy models predictions are slightly different from each other at large scales. It is also shown that the growth index in the modified gravity unlike to the dark energy models is a scale dependent parameter. We also compare the results with those from the modified gravity in the metric formalism. The modification on the structure formation can also change the CMB spectrum at large scales however due to the cosmic variance it is hard to detect this signature. We show that a large number of SNIa data in the order of 2000 will enable us to reconstruct the modified gravity action with a suitable confidence level and test the cosmic acceleration models by the structure formation.

  8. Structural influences on preferential oxazolone versus diketopiperazine b(2+) ion formation for histidine analogue-containing peptides.

    PubMed

    Gucinski, Ashley C; Chamot-Rooke, Julia; Nicol, Edith; Somogyi, Árpád; Wysocki, Vicki H

    2012-05-01

    Studies of peptide fragment ion structures are important to aid in the accurate kinetic modeling and prediction of peptide fragmentation pathways for a given sequence. Peptide b(2)(+) ion structures have been of recent interest. While previously studied b(2)(+) ions that contain only aliphatic or simple aromatic residues are oxazolone structures, the HA b(2)(+) ion consists of both oxazolone and diketopiperazine structures. The structures of a series of histidine-analogue-containing Xxx-Ala b(2)(+) ions were studied by using action infrared multiphoton dissociation (IRMPD) spectroscopy, fragment ion hydrogen-deuterium exchange (HDX), and density functional theory (DFT) calculations to systematically probe the influence of different side chain structural elements on the resulting b(2)(+) ion structures formed. The b(2)(+) ions studied include His-Ala (HA), methylated histidine analogues, including π-methyl-HA and τ-methyl-HA, pyridylalanine (pa) analogues, including 2-(pa)A, 3-(pa)A, and 4-(pa)A, and linear analogues, including diaminobutanoic acid-Ala (DabA) and Lys-Ala (KA). The location and accessibility of the histidine π-nitrogen, or an amino nitrogen on an aliphatic side chain, were seen to be essential for diketopiperazine formation in addition to the more typical oxazolone structure formation, while blocking or removal of the τ-nitrogen did not change the b(2)(+) ion structures formed. Linear histidine analogues, DabA and KA, formed only diketopiperazine structures, suggesting that a steric interaction in the HisAla case may interfere with the complete trans-cis isomerization of the first amide bond that is necessary for diketopiperazine formation.

  9. Carbon clusters containing two metals atoms: Structures, growth mechanism, and fullerene formation

    SciTech Connect

    Shelimov, K.B.; Jarrold, M.F.

    1996-02-07

    Gas phase ion mobility measurments have been used to probe the structures and interconversion of La{sub 2}C{sub n}{sup +} (n = 1-100) isomers. The smallest La{sub 2}C{sub n}{sup +} clusters (n = 10) appear to be planar rings. However, planar mono and bicylic rings (the dominant isomers for C{sub n}{sup +} and LaC{sub n}{sup +}, n = 30, clusters) are not observed for the larger La{sub 2}C{sub n}{sup +} species. Instead, isomers which appear to be three-dimensional ring complexes dominate for unannealed La{sub 2}C{sub n}{sup +} (n + 17) clusters. The formation of these complexes is probably driven by electrostatic forces. For n = 30 the three-dimensional ring complexes isomerize into metallofullerenes (and metal-containing graphite sheets for n = 30-37). The estimated activation energies for these isomerization processes are about 1eV lower than those estimated for similar processes for planar C{sub n}{sup +} and LaC{sub n}{sup +} rings. Metallofullerenes with two non-endohedral metal atoms (for n = 28-29), one endohedral metal atom (for n = 31-100), and two endohedral metal atoms (for n > 64, only even n), are identified. Fullerene derivatives (presumably fullerene + ring complexes) are abundant in the unannealed isomer distributions for La{sub 2}C{sub n}{sup +} (n > 50) clusters, but readily isomerize into regular fullerenes upon collisional heating. 47 refs., 9 figs., 2 tabs.

  10. The structure and formation of metacercarial cysts in the trematode family Microphallidae travassos 1920.

    PubMed

    Galaktionov, K V; Malkova, I I; Irwin, S W; Saville, D H; Maguire, J G

    1997-03-01

    This study deals with the formation of the metacercarial cysts of four microphallid trematodes, Maritrema subdolum, M. arenaria, Levinseniella brachysoma and Microphallus claviformis. The first observable cyst was present around Maritrema arenaria 18 h p.i. (post-infection). The other species had not developed a cyst by day 8 p.i. but their cysts were apparent by day 16 p.i. These were bi-layered and that of M. subdolum was thicker than those of L. brachysoma and Microphallus claviformis of the same age. The structure of older cysts varied substantially between the four species. Microphallus claviformis and Maritrema subdolum cysts were fully formed at 30 days p.i. Like those of M. arenaria they were bi-layered, the outer layer (up to 3 microm thick) being electron-dense and the inner one (up to 7 microm thick) being less electron-dense. The cysts of fully formed L. brachysoma metacercariae were much more complex, composed of four layers, one of which was divisible into three sub-layers. It was concluded that the outer cyst layer was the product of secretory granules which were previously identified in cercarial tegument. The inner, thicker layer was derived from several sources. These included small tegument vesicles produced over the entire surface of the metacercariae, larger fragments of tegument released from the anterio-ventral region and material liberated from the metacercarial excretory bladder. This heterogeneous material accumulated in the cyst lumen for some time before becoming polymerized to form the thick inner layer or layers of the metacercarial cysts.

  11. Cosmological perturbations and structure formation in nonlocal infrared modifications of general relativity

    SciTech Connect

    Dirian, Yves; Foffa, Stefano; Kunz, Martin; Maggiore, Michele; Khosravi, Nima E-mail: Stefano.Foffa@unige.ch E-mail: Martin.Kunz@unige.ch

    2014-06-01

    We study the cosmological consequences of a recently proposed nonlocal modification of general relativity, obtained by adding a term m{sup 2}R □{sup −2}R to the Einstein-Hilbert action. The model has the same number of parameters as ΛCDM, with m replacing Ω{sub Λ}. At the background level, after fixing m so to reproduce the observed value of Ω{sub M}, we get a pure prediction for the equation of state of dark energy as a function of redshift, w{sub DE}(z), with w{sub DE}(0) in the range [−1.165,−1.135] as Ω{sub M} varies over the broad range Ω{sub M} element of [0.20,0.36]. We find that the cosmological perturbations are well-behaved, and the model fully fixes the dark energy perturbations as a function of redshift z and wavenumber k. The nonlocal model provides a good fit to supernova data and predicts deviations from General Relativity in structure formation and in weak lensing at the level of 3-4%, therefore consistent with existing data but readily detectable by future surveys. For the logarithmic growth factor we obtain γ ≅ 0.53, to be compared with γ ≅ 0.55 in ΛCDM. For the Newtonian potential on subhorizon scales our results are well fitted by Ψ(a;k) = [1+μ{sub s}a{sup s}]Ψ{sub GR}(a;k) with a scale-independent μ{sub s} ≅ 0.09 and s ≅ 2, while the anisotropic stress is negligibly small.

  12. Structure and organisation of SinR, the master regulator of biofilm formation in Bacillus subtilis.

    PubMed

    Colledge, Vicki L; Fogg, Mark J; Levdikov, Vladimir M; Leech, Andrew; Dodson, Eleanor J; Wilkinson, Anthony J

    2011-08-19

    sinR encodes a tetrameric repressor of genes required for biofilm formation in Bacillus subtilis. sinI, which is transcribed under Spo0A control, encodes a dimeric protein that binds to SinR to form a SinR-SinI heterodimer in which the DNA-binding functions of SinR are abrogated and repression of biofilm genes is relieved. The heterodimer-forming surface comprises residues conserved between SinR and SinI. Each forms a pair of α-helices that hook together to form an intermolecular four-helix bundle. Here, we are interested in the assembly of the SinR tetramer and its binding to DNA. Size-exclusion chromatography with multi-angle laser light scattering and crystallographic analysis reveal that a DNA-binding fragment of SinR (residues 1-69) is a monomer, while a SinI-binding fragment (residues 74-111) is a tetramer arranged as a dimer of dimers. The SinR(74-111) chain forms two α-helices with the organisation of the dimer similar to that observed in the SinR-SinI complex. The tetramer is formed through interactions of residues at the C-termini of the four chains. A model of the intact SinR tetramer in which the DNA binding domains surround the tetramerisation core was built. Fluorescence anisotropy and surface plasmon resonance experiments showed that SinR binds to an oligonucleotide duplex, 5'-TTTGTTCTCTAAAGAGAACTTA-3', containing a pair of SinR consensus sequences in inverted orientation with a K(d) of 300 nM. The implications of these data for promoter binding and the curious quaternary structural transitions of SinR upon binding to (i) SinI and (ii) the SinR-like protein SlrR, which "repurposes" SinR as a repressor of autolysin and motility genes, are discussed.

  13. Cosmology and astrophysics from relaxed galaxy clusters - V. Consistency with cold dark matter structure formation

    NASA Astrophysics Data System (ADS)

    Mantz, A. B.; Allen, S. W.; Morris, R. G.

    2016-10-01

    This is the fifth in a series of papers studying the astrophysics and cosmology of massive, dynamically relaxed galaxy clusters. Our sample comprises 40 clusters identified as being dynamically relaxed and hot in Papers I and II of this series. Here we use constraints on cluster mass profiles from X-ray data to test some of the basic predictions of cosmological structure formation in the cold dark matter (CDM) paradigm. We present constraints on the concentration-mass relation for massive clusters, finding a power-law mass dependence with a slope of κm = -0.16 ± 0.07, in agreement with CDM predictions. For this relaxed sample, the relation is consistent with a constant as a function of redshift (power-law slope with 1 + z of κζ = -0.17 ± 0.26), with an intrinsic scatter of σln c = 0.16 ± 0.03. We investigate the shape of cluster mass profiles over the radial range probed by the data (typically ˜50 kpc-1 Mpc), and test for departures from the simple Navarro-Frenk-White (NFW) form, for which the logarithmic slope of the density profile tends to -1 at small radii. Specifically, we consider as alternatives the generalized NFW (GNFW) and Einasto parametrizations. For the GNFW model, we find an average value of (minus) the logarithmic inner slope of β = 1.02 ± 0.08, with an intrinsic scatter of σβ = 0.22 ± 0.07, while in the Einasto case we constrain the average shape parameter to be α = 0.29 ± 0.04 with an intrinsic scatter of σα = 0.12 ± 0.04. Our results are thus consistent with the simple NFW model on average, but we clearly detect the presence of intrinsic, cluster-to-cluster scatter about the average.

  14. Terminal Alkene Formation by the Thioesterase of Curacin A Biosynthesis: Structure of a Decarboxylating Thioesterase

    SciTech Connect

    Gehret, Jennifer J.; Gu, Liangcai; Gerwick, William H.; Wipf, Peter; Sherman, David H.; Smith, Janet L.

    2011-11-07

    Curacin A is a polyketide synthase (PKS)-non-ribosomal peptide synthetase-derived natural product with potent anticancer properties generated by the marine cyanobacterium Lyngbya majuscula. Type I modular PKS assembly lines typically employ a thioesterase (TE) domain to off-load carboxylic acid or macrolactone products from an adjacent acyl carrier protein (ACP) domain. In a striking departure from this scheme the curacin A PKS employs tandem sulfotransferase and TE domains to form a terminal alkene moiety. Sulfotransferase sulfonation of {beta}-hydroxy-acyl-ACP is followed by TE hydrolysis, decarboxylation, and sulfate elimination (Gu, L., Wang, B., Kulkarni, A., Gehret, J. J., Lloyd, K. R., Gerwick, L., Gerwick, W. H., Wipf, P., Hakansson, K., Smith, J. L., and Sherman, D. H. (2009) J. Am. Chem. Soc. 131, 16033-16035). With low sequence identity to other PKS TEs (<15%), the curacin TE represents a new thioesterase subfamily. The 1.7-{angstrom} curacin TE crystal structure reveals how the familiar {alpha}/{beta}-hydrolase architecture is adapted to specificity for {beta}-sulfated substrates. A Ser-His-Glu catalytic triad is centered in an open active site cleft between the core domain and a lid subdomain. Unlike TEs from other PKSs, the lid is fixed in an open conformation on one side by dimer contacts of a protruding helix and on the other side by an arginine anchor from the lid into the core. Adjacent to the catalytic triad, another arginine residue is positioned to recognize the substrate {beta}-sulfate group. The essential features of the curacin TE are conserved in sequences of five other putative bacterial ACP-ST-TE tridomains. Formation of a sulfate leaving group as a biosynthetic strategy to facilitate acyl chain decarboxylation is of potential value as a route to hydrocarbon biofuels.

  15. CIRCUMSTELLAR STRUCTURE AROUND EVOLVED STARS IN THE CYGNUS-X STAR FORMATION REGION

    SciTech Connect

    Kraemer, Kathleen E.; Price, Stephan D.

    2010-06-15

    We present observations of newly discovered 24 {mu}m circumstellar structures detected with MIPS around three evolved stars in the Cygnus-X star-forming region. One of the objects, BD+43 3710, has a bipolar nebula, possibly due to an outflow or a torus of material. A second, HBHA 4202-22, a Wolf-Rayet candidate, shows a circular shell of 24 {mu}m emission suggestive of either a limb-brightened shell or disk seen face-on. No diffuse emission was detected around either of these two objects in the Spitzer 3.6-8 {mu}m IRAC bands. The third object is the luminous blue variable candidate G79.29+0.46. We resolved the previously known inner ring in all four IRAC bands. The 24 {mu}m emission from the inner ring extends {approx}1.'2 beyond the shorter wavelength emission, well beyond what can be attributed to the difference in resolutions between MIPS and IRAC. Additionally, we have discovered an outer ring of 24 {mu}m emission, possibly due to an earlier episode of mass loss. For the two shell stars, we present the results of radiative transfer models, constraining the stellar and dust shell parameters. The shells are composed of amorphous carbon grains, plus polycyclic aromatic hydrocarbons in the case of G79.29+0.46. Both G79.29+0.46 and HBHA 4202-22 lie behind the main Cygnus-X cloud. Although G79.29+0.46 simply may be on the far side of the cloud, HBHA 4202-22 is unrelated to the Cygnus-X star formation region.

  16. HIGH-RESOLUTION SIMULATION ON STRUCTURE FORMATION WITH EXTREMELY LIGHT BOSONIC DARK MATTER

    SciTech Connect

    Woo, T.-P.; Chiueh Tzihong E-mail: chiuehth@phys.ntu.edu.tw

    2009-05-20

    A bosonic dark matter model is examined in detail via high-resolution simulations. These bosons have particle mass of the order of 10{sup -22} eV and are noninteracting. If they do exist and can account for structure formation, these bosons must be condensed into the Bose-Einstein state and described by a coherent wave function. This matter, also known as fuzzy dark matter, is speculated to be able, first, to eliminate the subgalactic halos to solve the problem of overabundance of dwarf galaxies, and, second, to produce flat halo cores in galaxies suggested by some observations. We investigate this model with simulations up to 1024{sup 3} resolution in a 1 h {sup -1} Mpc box that maintains the background matter density {omega} {sub m} = 0.3 and {omega}{sub {lambda}} = 0.7. Our results show that the extremely light bosonic dark matter can indeed eliminate low-mass halos through the suppression of short-wavelength fluctuations, as predicted by the linear perturbation theory. But in contrast to expectation, our simulations yield singular cores in the collapsed halos, where the halo density profile is similar, but not identical, to the Navarro-Frenk-White profile. Such a profile arises regardless of whether the halo forms through accretion or merger. In addition, the virialized halos exhibit anisotropic turbulence inside a well-defined virial boundary. Much like the velocity dispersion of standard dark matter particles, turbulence is dominated by the random radial flow in most part of the halos and becomes isotropic toward the halo cores. Consequently, the three-dimensional collapsed halo mass distribution can deviate from spherical symmetry, as the cold dark matter halo does.

  17. The Star Formation History and Extended Structure of the Hercules Milky Way Satellite

    NASA Astrophysics Data System (ADS)

    Sand, David J.; Olszewski, Edward W.; Willman, Beth; Zaritsky, Dennis; Seth, Anil; Harris, Jason; Piatek, Slawomir; Saha, Abi

    2009-10-01

    We present imaging of the recently discovered Hercules Milky Way satellite and its surrounding regions to study its structure, star formation history and to thoroughly search for signs of disruption. We robustly determine the distance, luminosity, size, and morphology of Hercules utilizing a bootstrap approach to characterize our uncertainties. We derive a distance to Hercules via a comparison to empirical and theoretical isochrones, finding a best match with the isochrone of M92, which yields a distance of 133 ± 6 kpc. As previous studies have found, Hercules is very elongated, with epsilon = 0.67 ± 0.03 and a half-light radius of rh sime 230 pc. Using the color-magnitude-fitting package StarFISH, we determine that Hercules is old (>12 Gyr) and metal-poor ([Fe/H] ~ -2.0), with a spread in metallicity, in agreement with previous spectroscopic work. This result is robust with respect to slight variations in the distance to Hercules and mismatches between the observed Hercules color-magnitude diagram and theoretical isochrones. We infer a total absolute magnitude of MV = -6.2 ± 0.4. Our innovative search for external Hercules structure both in the plane of the sky and along the line of sight yields some evidence that Hercules is embedded in a larger stream of stars. A clear stellar extension is seen to the northwest with several additional candidate stellar overdensities along the position angle of Hercules out to ~35' (~1.3 kpc). While the association of any of the individual stellar overdensities with Hercules is difficult to determine, we do show that the summed color-magnitude diagram of all three is consistent with Hercules' stellar population. Finally, we estimate that any change in the distance to Hercules across its face is at most ~6 kpc, and the data are consistent with Hercules being at the same distance throughout. Based on data acquired using the Large Binocular Telescope (LBT). The LBT is an international collaboration among institutions in the US

  18. Elucidating the Effect of Biomolecule Structure on Calcium Carbonate Crystal Formation