Science.gov

Sample records for asymmetry-driven structure formation

  1. Asymmetry-driven structure formation in pair plasmas

    SciTech Connect

    Mahajan, S. M.; Shatashvili, N. L.; Berezhiani, V. I.

    2009-12-15

    The nonlinear propagation of electromagnetic waves in pair plasmas, in which the electrostatic potential plays a very important but subdominant role of a 'binding glue' is investigated. Several mechanisms for structure formation are investigated, in particular, the 'asymmetry' in the initial temperatures of the constituent species. It is shown that the temperature asymmetry leads to a (localizing) nonlinearity that is qualitatively different from the ones originating in ambient mass or density difference. The temperature-asymmetry-driven focusing-defocusing nonlinearity supports stable localized wave structures in 1-3 dimensions, which, for certain parameters, may have flat-top shapes.

  2. Geometric asymmetry driven Janus micromotors.

    PubMed

    Zhao, Guanjia; Pumera, Martin

    2014-10-07

    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.

  3. 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

  4. Cosmic structure formation

    NASA Technical Reports Server (NTRS)

    Bertschinger, Edumund

    1994-01-01

    This article reviews the prevailing paradigm for how galaxies and larger structures formed in the universe: gravitational instability. Basic observational facts are summarized to motivate the standard cosmological framework underlying most detailed investigations of structure formation. The observed univers approaches spatial uniformity on scales larger than about 10(exp 26) cm. On these scales gravitational dynamics is almost linear and therefore relatively easy to relate to observations of large-scale structure. On smaller scales cosmic structure is complicated not only by nonlinear gravitational clustering but also by nonlinear nongravitational gas dynamical processes. The complexity of these phenomena makes galaxy formation one of the grand challenge problems of the physical sciences. No fully satisfactory theory can presently account in detail for the observed cosmic structure. However, as this article summarizes, significant progress has been made during the last few years.

  5. Cosmic structure formation

    NASA Technical Reports Server (NTRS)

    Bertschinger, Edumund

    1994-01-01

    This article reviews the prevailing paradigm for how galaxies and larger structures formed in the universe: gravitational instability. Basic observational facts are summarized to motivate the standard cosmological framework underlying most detailed investigations of structure formation. The observed univers approaches spatial uniformity on scales larger than about 10(exp 26) cm. On these scales gravitational dynamics is almost linear and therefore relatively easy to relate to observations of large-scale structure. On smaller scales cosmic structure is complicated not only by nonlinear gravitational clustering but also by nonlinear nongravitational gas dynamical processes. The complexity of these phenomena makes galaxy formation one of the grand challenge problems of the physical sciences. No fully satisfactory theory can presently account in detail for the observed cosmic structure. However, as this article summarizes, significant progress has been made during the last few years.

  6. 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).

  7. Chiral asymmetry driven by unidirectional magnetic anisotropy in Spin-Orbitronic systems

    NASA Astrophysics Data System (ADS)

    Perna, Paolo; Ajejas, Fernando; Maccariello, Davide; Guerrero, Ruben; Camarero, Julio; Miranda, Rodolfo

    2016-10-01

    Spin-Orbit (SO) effects of a ferromagnetic (FM) layer can be artificially modified by interfacial exchange coupling with an anti-ferro magnet (AFM). Non-symmetric magnetization reversals as well as asymmetric transport behaviors are distinctive signatures of the symmetry-breaking induced by such interfacial coupling. We present a complete picture of the symmetry of the SO effects by studying the magneto-transport properties of single FM film and FM/AFM systems (exchanged-biased bilayer and spin-valve structures) with specific in-plane magnetic anisotropy. Single FM films with a well-defined (two-fold) uniaxial magnetic anisotropy display symmetric magnetization reversals and magneto-resistance responses for any value and direction of the applied magnetic field. On the contrary, in the exchange-biased structures, the exchange interaction at the interface between the FM and AFM layers is responsible of chiral asymmetries in magnetization reversal pathways as well as in the magneto-resistance behaviors. Such asymmetries are directly related to the additional unidirectional (one-fold) magnetic anisotropy imposed by the AFM. In particular, chiral reversals and MR responses are found around the magnetization hard-axis direction. This has been shown in FM/AFM bilayer and spin-valve (where the MR outputs are related to different transport phenomena, i.e. anisotropic magneto-resistance and giant magneto-resistance respectively), hence indicating that the chiral asymmetries are intrinsic of systems with unidirectional anisotropy.

  8. Structure and formation of microplasmin.

    PubMed Central

    Wu, H L; Shi, G Y; Wohl, R C; Bender, M L

    1987-01-01

    The structure of human microplasmin, prepared from plasmin in alkaline solution, has been studied. Microplasmin consists of two polypeptide chains connected by disulfide bonds. One polypeptide is the B chain of plasmin consisting of 230 amino acids, and the other peptide is the COOH-terminal portion of the A chain of plasmin consisting of 31 amino acid residues. Microplasmin has a molecular weight of 28,635, calculated from its primary sequence. It is slightly more positively charged than plasminogen and is a more hydrophobic molecule. The proposed scheme for the formation of microplasmin involves autolysis at specific peptide bonds and scrambling of especially sensitive disulfide bonds in alkaline solution. PMID:2962191

  9. 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

  10. Natural photonic crystals: formation, structure, function

    NASA Astrophysics Data System (ADS)

    Bartl, Michael H.; Dahlby, Michael R.; Barrows, Frank P.; Richens, Zachary J.; Terooatea, Tommy; Jorgensen, Matthew R.

    2012-03-01

    The structure and properties of natural photonic crystals are discussed using the colored scales of the beetle Lamprocyphus augustus as an example. While the exact mechanism behind the formation of these biopolymeric photonic structures has yet to be fully explored, similarities of these structures to intracellular cubic membrane architectures are introduced. Some crucial parameters behind the formation of cubic membranes are discussed. Using these insights, intracellular cubic membrane structures are transformed into an extracellular environment.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Evolution of atomic structure during nanoparticle formation

    DOE PAGES

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

    2014-04-14

    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 structuremore » 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.« less

  17. 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.

  18. 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.

  19. Structure formation control of foam concrete

    NASA Astrophysics Data System (ADS)

    Steshenko, Aleksei; Kudyakov, Aleksander; Konusheva, Viktoriya; Syrkin, Oleg

    2017-01-01

    The process of predetermined foam concrete structure formation is considered to be a crucial issue from the point of process control and it is currently understudied thus defining the need for additional research. One of the effective ways of structure formation control in naturally hardening foam concrete is reinforcement with dispersed fibers or introduction of plasticizers. The paper aims at studying the patterns of influence of microreinforcing and plasticizing additives on the structure and performance properties of foam concrete. Preparation of foam concrete mix has been conducted using one-step technology. The structure of modified foam concrete has been studied by means of electron microscopy. The cellular structure of foam concrete samples with the additives is homogeneous; the pores are uniformly distributed over the total volume. It has been revealed that introduction of the Neolas 5.2 plasticizer and microreinforcing fibers in the foam concrete mixture in the amount of 0.4 - 0.1 % by weight of cement leads to reduction of the average pore diameter in the range of 45.3 to 30.2 microns and the standard deviation of the pore average diameter from 23.6 to 9.2 in comparison with the sample without additive. Introduction of modifying additives has stimulated formation of a large number of closed pores. Thus porosity of conditionally closed pores has increased from 16.06 % to 34.48 %, which has lead to increase of frost resistance brand of foam concrete from F15 to F50 and to reduction of its water absorption by weight by 20 %.

  20. Continuum Theory of Dislocations: Cell Structure Formation

    NASA Astrophysics Data System (ADS)

    Limkumnerd, Surachate; Sethna, James P.

    2005-03-01

    Line-like topological defects inside metals are called dislocations. These dislocations in late stages of hardening form patterns called cell structures. We are developing a mesoscale theory for the formation of cell structures that systematically derives the order parameter fields and evolution laws from the conserved topological Burgers vector density or the Nye dislocation tensor. (In classical plasticity theories, describing scales large compared to these cells, one normally bypasses the complicated motions of the dislocations by supplying yield surface and plastic hardening function in order to determine the evolution of state variables.) Using Landau approach and a closure approximation, an evolution equation for the dislocation density tensor is obtained by employing simple symmetry arguments and the constraint that the elastic energy must decrease with time at fixed stress. The evolution laws lead to singularity formation at finite times, which we expect will be related to the formation of cell walls. Implementation of finite difference simulations using the upwind scheme and the results in one and higher dimensions will be discussed.

  1. Stochastic structure formation in random media

    NASA Astrophysics Data System (ADS)

    Klyatskin, V. I.

    2016-01-01

    Stochastic structure formation in random media is considered using examples of elementary dynamical systems related to the two-dimensional geophysical fluid dynamics (Gaussian random fields) and to stochastically excited dynamical systems described by partial differential equations (lognormal random fields). In the latter case, spatial structures (clusters) may form with a probability of one in almost every system realization due to rare events happening with vanishing probability. Problems involving stochastic parametric excitation occur in fluid dynamics, magnetohydrodynamics, plasma physics, astrophysics, and radiophysics. A more complicated stochastic problem dealing with anomalous structures on the sea surface (rogue waves) is also considered, where the random Gaussian generation of sea surface roughness is accompanied by parametric excitation.

  2. 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.

  3. STRUCTURE FORMATION IN THE SYMMETRON MODEL

    SciTech Connect

    Davis, Anne-Christine; Li Baojiu; Mota, David F.; Winther, Hans A.

    2012-03-20

    Scalar fields, strongly coupled to matter, can be present in nature and still be invisible to local experiments if they are subject to a screening mechanism. The symmetron is one such mechanism that relies on restoration of a spontaneously broken symmetry in regions of high density to shield the scalar fifth force. We have investigated structure formation in the symmetron model by using N-body simulations and find observable signatures in both the linear and nonlinear matter power spectrum and on the halo mass function. The mechanism for suppressing the scalar fifth force in high-density regions is also found to work very well.

  4. 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).

  5. 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.

  6. Structure Formation by Self Attracting Bacteria

    NASA Astrophysics Data System (ADS)

    Betterton, Meredith; Brenner, Michael

    1998-11-01

    Consider a box of material (initially of constant density) which both attracts itself and has some dispersive character. Eventually the material will clump into high density regions. The question addressed in this talk is: what are the number and sizes of the clumps that are formed? We address this in the context of chemotactic collapse of e. Coli. Experiments have given a detailed picture of the collapse process, showing that the bacteria initially form cylindrical structures which then destabilize into spherical clumps. On the other hand, linear stability analysis predicts that the system should form spherical aggregates directly. Our theory for the structure formation develops a generalization of an idea of Zeldovich (invented for a problem in cosmology). We present various calculations and numerical simulations to explain the patterns observed in experiments.

  7. Modulated structure formation in demixing paraffin blends

    NASA Astrophysics Data System (ADS)

    Gilbert, E. P.

    Small angle scattering (SANS and SAXS) and differential scanning calorimetry have been measured from C28:C36 normal paraffin mixtures of varying composition quenched from the melt. Satellite peaks are observed in the SAXS whose offset in Q, relative to Bragg diffraction peaks associated with the average structure, are composition dependent. The offset is close to the position of the most intense peak observed in SANS. Scattering from the quenched structures is consistent with a correlated displacement and substitutional disorder model yielding modulations that are incommensurate with the average lattice. DSC shows an additional endotherm in the mixtures that is not present in the pure components and is associated with this superstructure formation.

  8. 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.

  9. Dynamic Structures around Star Formation Regions

    NASA Astrophysics Data System (ADS)

    Choi, Minho

    1995-01-01

    Star formation is a dynamic and complex activity. In this thesis, we will study characteristic activities in star formation regions: protostellar collapse, bipolar outflow, and large scale rotation. In Chapter 1, we study a protostellar collapse in a low-mass star formation region. A dark cloud core, B335, is modeled as an inside-out collapse. The radiative transfer code uses the Monte Carlo method. Line profiles for several transitions of CS and rm H_2CO are computed and they agreed with the observations very well. In Chapter 2, we investigate kinematic structures in a high-mass star formation region. Monoceros R2 dense core region was observed with molecular lines. We suggest that the main part can be explained as a parsec scale toroid around the H scII region with its symmetry axis parallel to the CO outflow and the magnetic field. The Omega~ r^{-1} rotation profile indicates that rotation alone cannot support the dense core. We modeled the toroid with a 2-dimensional radiative transfer code. Our simple model can reproduce the intensities and profiles of observed CS transitions very well. In Chapter 3, extremely high velocity (EHV) wings are studied with CO lines. The results of our survey suggest that EHV wings are common around infrared sources of moderate to high luminosity in dense regions. Line ratios imply that the EHV gas is usually optically thin and warm. Characteristic velocities range from 20 to 40 km rm s^ {-1}, yielding timescales of 1600-4200 yr. Since most sources in this study are producing some ionizing photons, these short timescales suggest that neutral winds coexist with ionizing photons. We examined two possible sources for the extremely high velocity CO emission: a neutral stellar wind; and swept-up or entrained molecular gas. Neither can be ruled out. In Chapter 4, molecular outflows associated with GL 2591 and W28 A2 were studied with the (C scI) line. Upper limits are set on the (C scI) emission in the EHV line wings. These limits are

  10. Microbially-driven soil aggregate structure formation

    NASA Astrophysics Data System (ADS)

    Vasilyeva, Nadezda; Vladimirov, Artem; Matveev, Sergey; Smirnov, Alexander; Tyrtyshnikov, Eugene; Shein, Evgeny

    2017-04-01

    We propose a novel approach to mathematical modelling of soil aggregate structure formation. The model is self-consistent and describes physical process of soil particles aggregation/fragmentation as a result of organic matter micro-biochemical cycle. The model consists of two parts, first part describes biochemical cycle and is formulated as a system of chemical kinetic equations. The second part describes soil particles aggregation and fragmentation and is formulated as Smoluchowski equation, with coefficients dependent on the chemical composition, obtained by solving the first part of the model. The presented model allows observation of a complex aggregate structure development starting from a simple system of homogeneous mineral particles, organic matter solution and inoculant of microorganisms. With the help of numerical simulations we study fundamental mechanisms leading to multimodality of soil micro-aggregates size distributions and how it is affected by soil organic matter content. As an example, the model allows further consideration of soil physical occlusion effect on organic matter decomposition rates in soil aggregates.

  11. Silicene oxides: formation, structures and electronic properties

    PubMed Central

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

    2013-01-01

    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. PMID:24336409

  12. Formation of terahertz beams produced by artificial dielectric periodical structures

    NASA Astrophysics Data System (ADS)

    Khodzitsky, Mikhail K.; Vozianova, Anna V.; Gill, Viktoria V.; Chernyadiev, Alexander V.; Grebenchukov, Alexandr N.; Minin, Igor V.; Minin, Oleg V.

    2016-09-01

    This paper presents an investigation of terajets formation by dielectric periodic structure at terahertz frequencies in effective medium regime (photonic metamaterial). The dispersions of effective permittivity for three periodic structures formed by different types of plastics (ABS, PLA, Crystal) were analytically obtained for both regimes. Numerical simulation of this structure was performed by using COMSOL Multiphysics. The terajet formation was numerically shown.

  13. 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.

  14. Nonlinear structure formation in flat cosmological models

    NASA Technical Reports Server (NTRS)

    Martel, Hugo

    1995-01-01

    This paper describes the formation of nonlinear structure in flat (zero curvature) Friedmann cosmological models. We consider models with two components: the usual nonrelativistic component that evolves under gravity and eventually forms the large-scale structure of the universe, and a uniform dark matter component that does not clump under gravity, and whose energy density varies with the scale factor a(t) like a(t)(sup -n), where n is a free parameter. Each model is characterized by two parameters: the exponent n and the present density parameter Omega(sub 0) of the nonrelativistic component. The linear perturbation equations are derived and solved for these models, for the three different cases n = 3, n is greater than 3, and n is less than 3. The case n = 3 is relevant to model with massive neutrinos. The presence of the uniform component strongly reduces the growth of the perturbation compared with the Einstein-de Sitter model. We show that the Meszaros effect (suppression of growth at high redshift) holds not only for n = 4, radiation-dominated models, but for all models with n is greater than 3. This essentially rules out any such model. For the case n is less than 3, we numerically integrate the perturbation equations from the big bang to the present, for 620 different models with various values of Omega(sub 0) and n. Using these solutions, we show that the function f(Omega(sub 0), n) = (a/delta(sub +))d(delta)(sub +)/da, which enters in the relationship between the present density contrast delta(sub 0) and peculiar velocity field u(sub 0) is essentially independent of n. We derive approximate solutions for the second-order perturbation equations. These second-order solutions are tested against the exact solutions and the Zel'dovich approximation for spherically symmetric perturbations in the marginally nonlinear regime (the absolute value of delta is less than or approximately 1). The second-order and Zel'dovich solutions have comparable accuracy

  15. 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.

  16. 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.

  17. On the importance of cotranscriptional RNA structure formation

    PubMed Central

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

    2013-01-01

    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. PMID:24131802

  18. 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.

  19. Formation of tribological structures by laser ablation

    NASA Astrophysics Data System (ADS)

    Schilling, Niels; Paschke, Mike; Hendow, Sami T.; Klotzbach, Udo

    2012-03-01

    Many technical applications can benefit from the use of tribological structures in minimizing abrasive material wear and energy consumption without the integration of additional materials in a working assembly. Especially in lubricated friction systems, the tribological character can be significantly improved through the addition of oriented and repetitive microstructure. In this study, experimental tests are discussed for a small range of structure dimensions to verify the effect of optimizing the tribological contact performance. A nanosecond pulsed fiber laser is used to create various test structures with different sizes and form. The quality of the fabricated surface pattern, particularly form correctness, feathering and material modification effects of the ablated area is characterized and optimized. The influence of pulse duration, pulse energy and pulse delay using normal pulsing is presented and compared to various burst modes.

  20. 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.

  1. Structure and mechanism of a pentameric formate channel

    PubMed Central

    Waight, Andrew B.; Love, James; Wang, Da-Neng

    2013-01-01

    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 cell macrophages. We have determined the 2.13 Å structure of the formate channel FocA from Vibrio cholerae, which reveals a pentamer, with each monomer possessing its own substrate translocation pore. Surprisingly, 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 Å 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 substrate selectivity of the channel. PMID:20010838

  2. 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.

  3. G-triplex structure and formation propensity

    PubMed Central

    Cerofolini, Linda; Amato, Jussara; Giachetti, Andrea; Limongelli, Vittorio; Novellino, Ettore; Parrinello, Michele; Fragai, Marco; Randazzo, Antonio; Luchinat, Claudio

    2014-01-01

    The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3′ end TBA-truncated 11-mer oligonucleotide (11-mer-3′-t-TBA). Here we present the solution structure of 11-mer-3′-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3′-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3′-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3′ and the 5′ ends show that only the 11-mer-3′-t-TBA yields a relatively stable G-triplex. PMID:25378342

  4. Modelling of the new formation structures in the near space.

    PubMed

    Kulikova, N V; Pivnenko, E A

    1992-01-01

    Complex numerical model of young meteor stream formation taking into account reactive deceleration of cometary nucleus and its form change in the process of stream formation is discussed. The model made it possible to predict the existence of fine and superfine structures for young meteor streams, the characteristics of which agree with the observational data on the Draconid and Leonid meteor showers.

  5. Semiconductor structure and recess formation etch technique

    DOEpatents

    Lu, Bin; Sun, Min; Palacios, Tomas Apostol

    2017-02-14

    A semiconductor structure has a first layer that includes a first semiconductor material and a second layer that includes a second semiconductor material. The first semiconductor material is selectively etchable over the second semiconductor material using a first etching process. The first layer is disposed over the second layer. A recess is disposed at least in the first layer. Also described is a method of forming a semiconductor structure that includes a recess. The method includes etching a region in a first layer using a first etching process. The first layer includes a first semiconductor material. The first etching process stops at a second layer beneath the first layer. The second layer includes a second semiconductor material.

  6. 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

  7. Structure Formation in the Universe from Texture Induced Fluctuations

    NASA Astrophysics Data System (ADS)

    Durrer, Ruth; Zhou, Zhi-Hong

    1995-03-01

    We discuss structure formation with topological defects. First we present a partially new, local, and gauge invariant system of perturbation equations to treat microwave background and dark matter fluctuations induced by topological defects or any other type of seeds. We show that this system is well suited for numerical analysis of structure formation by applying it to the texture scenario. Our numerical results cover a larger dynamical range than previous investigations and are complementary to them since we use substantially different methods.

  8. 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.

  9. 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.

  10. Structure Formation with Generalized Dark Matter

    NASA Astrophysics Data System (ADS)

    Hu, Wayne

    1998-10-01

    The next generation of cosmic microwave background (CMB) experiments, galaxy surveys, and high-redshift observations can potentially determine the nature of the dark matter observationally. With this in mind, we introduce a phenomenological model for a generalized dark matter (GDM) component and discuss its effect on large-scale structure and CMB anisotropies. Specifying the gravitational influence of the otherwise noninteracting GDM requires not merely a model for its equation of state but one for its full stress tensor. From consideration of symmetries, conservation laws, and gauge invariance, we construct a simple but powerful three-component parameterization of these stresses that exposes the new phenomena produced by GDM. Limiting cases include: a particle component (e.g., weakly interacting massive particles, radiation, or massive neutrinos), a cosmological constant, and a scalar field component. Intermediate cases illustrate how the clustering properties of the dark matter can be specified independently of its equation of state. This freedom allows one to alter the amplitude and features in the matter-power spectrum relative to those of the CMB anisotropies while leaving the background cosmology fixed. Conversely, observational constraints on such phenomena can help determine the nature of the dark matter.

  11. Nonlinear structure formation in nonlocal gravity

    NASA Astrophysics Data System (ADS)

    Barreira, Alexandre; Li, Baojiu; Hellwing, Wojciech A.; Baugh, Carlton M.; Pascoli, Silvia

    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 ~ 1014 Msolar/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 gtrsim 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.

  12. Structure Formation Mechanisms during Solid Ti with Molten Al Interaction

    NASA Astrophysics Data System (ADS)

    Gurevich, L.; Pronichev, D.; Trunov, M.

    2016-02-01

    The study discuses advantages and disadvantages of previously proposed mechanisms of the formation of structure between solid Ti and molten Al and presents a new mechanism based on the reviewed and experimental data. The previously proposed mechanisms were classified into three groups: mechanisms of precipitation, mechanisms of destruction and mechanisms of chemical interaction between intermetallics and melt. The reviewed mechanisms did not explain the formation of heterogeneous interlayer with globular aluminide particles and thin layers of pure Al, while the present study reveals variation in the solid Ti/molten Al reaction kinetics during various phases of laminated metal-intermetallic composite formation. The proposed mechanism considers formed during composite fabrication thin oxide interlayers between Ti and Al evolution and its impact on the intermetallic compound formation and explains the initial slow rate of intermetallic interlayer formation and its subsequent acceleration when the oxide foils are ruptured.

  13. Circulating Microparticles Alter Formation, Structure, and Properties of Fibrin Clots

    PubMed Central

    Zubairova, Laily D.; Nabiullina, Roza M.; Nagaswami, Chandrasekaran; Zuev, Yuriy F.; Mustafin, Ilshat G.; Litvinov, Rustem I.; Weisel, John W.

    2015-01-01

    Despite the importance of circulating microparticles in haemostasis and thrombosis, there is limited evidence for potential causative effects of naturally produced cell-derived microparticles on fibrin clot formation and its properties. We studied the significance of blood microparticles for fibrin formation, structure, and susceptibility to fibrinolysis by removing them from platelet-free plasma using filtration. Clots made in platelet-free and microparticle-depleted plasma samples from the same healthy donors were analyzed in parallel. Microparticles accelerate fibrin polymerisation and support formation of more compact clots that resist internal and external fibrinolysis. These variations correlate with faster thrombin generation, suggesting thrombin-mediated kinetic effects of microparticles on fibrin formation, structure, and properties. In addition, clots formed in the presence of microparticles, unlike clots from the microparticle-depleted plasma, contain 0.1–0.5-μm size granular and CD61-positive material on fibres, suggesting that platelet-derived microparticles attach to fibrin. Therefore, the blood of healthy individuals contains functional microparticles at the levels that have a procoagulant potential. They affect the structure and stability of fibrin clots indirectly through acceleration of thrombin generation and through direct physical incorporation into the fibrin network. Both mechanisms underlie a potential role of microparticles in haemostasis and thrombosis as modulators of fibrin formation, structure, and resistance to fibrinolysis. PMID:26635081

  14. Coffee melanoidins: structures, mechanisms of formation and potential health impacts.

    PubMed

    Moreira, Ana S P; Nunes, Fernando M; Domingues, M Rosário; Coimbra, Manuel A

    2012-09-01

    During the roasting process, coffee bean components undergo structural changes leading to the formation of melanoidins, which are defined as high molecular weight nitrogenous and brown-colored compounds. As coffee brew is one of the main sources of melanoidins in the human diet, their health implications are of great interest. In fact, several biological activities, such as antioxidant, antimicrobial, anticariogenic, anti-inflammatory, antihypertensive, and antiglycative activities, have been attributed to coffee melanoidins. To understand the potential of coffee melanoidin health benefits, it is essential to know their chemical structures. The studies undertaken to date dealing with the structural characterization of coffee melanoidins have shown that polysaccharides, proteins, and chlorogenic acids are involved in coffee melanoidin formation. However, exact structures of coffee melanoidins and mechanisms involved in their formation are far to be elucidated. This paper systematizes the available information and provides a critical overview of the knowledge obtained so far about the structure of coffee melanoidins, mechanisms of their formation, and their potential health implications.

  15. 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.

  16. Formation and structure of amorphous carbon char from polymer materials

    NASA Astrophysics Data System (ADS)

    Lawson, John W.; Srivastava, Deepak

    2008-04-01

    Amorphous carbonaceous char produced from burning polymer solids has insulating properties that make it valuable in thermal protection and fire-retardant systems. A pyrolytic molecular dynamics simulation method is devised to study the transformation of the local microstructure from virgin polymer to a dense, disordered char. 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.

  17. Deamidation accelerates amyloid formation and alters amylin fiber structure

    PubMed Central

    Dunkelberger, Emily B.; Buchanan, Lauren E.; Marek, Peter; Cao, Ping; Raleigh, Daniel P.; Zanni, Martin T.

    2012-01-01

    Deamidation of asparagine and glutamine is the most common non-enzymatic, post-translational modification. Deamidation can influence the structure, stability, folding, and aggregation of proteins and has been proposed to play a role in amyloid formation. However there are no structural studies of the consequences of deamidation on amyloid fibers, in large part because of the difficulty of studying these materials using conventional methods. Here we examine the effects of deamidation on the kinetics of amyloid formation by amylin, the causative agent of type 2 diabetes. We find that deamidation accelerates amyloid formation and the deamidated material is able to seed amyloid formation by unmodified amylin. Using site-specific isotope labeling and two-dimensional infrared (2D IR) spectroscopy, we show that fibers formed by samples that contain deamidated polypeptide contain reduced amounts of β-sheet. Deamidation leads to disruption of the N-terminal β-sheet between Ala-8 and Ala-13, but β-sheet is still retained near Leu-16. The C-terminal sheet is disrupted near Leu-27. Analysis of potential sites of deamidation together with structural models of amylin fibers reveals that deamidation in the N-terminal β-sheet region may be the cause for the disruption of the fiber structure at both the N- and C-terminal β-sheet. Thus, deamidation is a post-translational modification that creates fibers which have an altered structure, but can still act as a template for amylin aggregation. Deamidation is very difficult to detect with standard methods used to follow amyloid formation, but isotope labeled IR spectroscopy provides a means for monitoring sample degradation and investigating the structural consequences of deamidation. PMID:22734583

  18. 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.

  19. 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.

  20. 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

  1. Formation of first structures in a ΛCDM Universe

    NASA Astrophysics Data System (ADS)

    Villalón, C.; Domínguez Romero, M.

    We developed simulations of the formation and evolution of the first structures using an AMR, grid-based code: Enzo. Our simulations are aimed to follow the complex physics of the joint evolution of super massive black holes and galaxies in the reionization epoch.

  2. The Gravitational Wave Symphony of Structure Formation: Overview

    NASA Astrophysics Data System (ADS)

    Lazio, T. Joseph W.; Burke-Spolaor, Sarah

    This Focus Meeting was designed to lie at the scientific intersection of structure formation and gravitational wave studies. In broad-strokes terms, binary supermassive black holes (BSMBHs) and cosmic strings may both play a central role in shaping the Universe as we know it.

  3. Formation of iron-rich shelled structures by microbial communities

    NASA Astrophysics Data System (ADS)

    Fernández-Remolar, David C.; Santamaría, Joan; Amils, Ricardo; Parro, Victor; Gómez-Ortíz, D.; Izawa, Matthew R. M.; Banerjee, Neil R.; Pérez Rodríguez, Raúl; Rodríguez, Nuria; López-Martínez, Nieves

    2015-01-01

    this paper, we describe the discovery and characterization of shelled structures that occur inside galleries of Pyrenees mines. The structures are formed by the mineralization of iron and zinc oxides, dominantly franklinite (ZnFe2O4) and poorly ordered goethite (α-FeO(OH)). Subsurface oxidation and hydration of polymetallic sulfide orebodies produce solutions rich in dissolved metal cations including Fe2+/3+ and Zn2+. The microbially precipitated shell-like structure grows by lateral or vertical stacking of thin laminae of iron oxide particles which are accreted mostly by fungal filaments. The resulting structures are composed of randomly oriented aggregates of needle-like, uniform-sized crystals, suggesting some biological control in the structure formation. Such structures are formed by the integration of two separated shells, following a complex process driven likely by different strategies of fungal microorganisms that produced the complex macrostructure.

  4. 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

  5. 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

  6. Formation of structure in small lead clusters under thermal effect

    NASA Astrophysics Data System (ADS)

    Baidyshev, V. S.; Gafner, Yu. Ya.

    2016-12-01

    The thermal effect on lead clusters with radii up to 5.5 nm has been investigated by the molecular dynamics method using a modified tight-binding potential TB-SMA. The melting of Pb nanoparticles of these sizes is strictly homogeneous, without the formation of a surface liquidlike layer. The primary fcc phase in the particles is retained upon heating in the overwhelming majority of model experiments. An analysis of the structure formation during crystallization has shown that structures with pentagonal symmetry are preferred for lead clusters in this case. It is noted that an increase in the nanoparticle size leads to the dominance of the dodecahedral structure over the icosahedral one.

  7. Structure formation with scalar field dark matter: the field approach

    SciTech Connect

    Magaña, Juan; Sánchez-Salcedo, F.J.; Matos, Tonatiuh; Suárez, Abril E-mail: tmatos@fis.cinvestav.mx E-mail: jsanchez@astro.unam.mx

    2012-10-01

    We study the formation of structure in the Universe assuming that dark matter can be described by a scalar field Φ-tilde with a potential V(Φ) = −m{sup 2}Φ-tilde {sup 2}/2+λΦ-tilde {sup 4}/4. We derive the evolution equations of the scalar field in the linear regime of perturbations. We investigate the symmetry breaking and possibly a phase transition of this scalar field in the early Universe. At low temperatures, the scalar perturbations have an oscillating growing mode and therefore, this kind of dark matter could lead to the formation of gravitational structures. In order to study the nonlinear regime, we use the spherical collapse model and show that, in the quadratic potential limit, this kind of dark matter can form virialized structures. The main difference with the traditional Cold Dark Matter paradigm is that the formation of structure in the scalar field model can occur at earlier times. Thus, if the dark matter behaves as a scalar field, large galaxies are expected to be formed already at high redshifts.

  8. Star formation and ISM morphology in tidally induced spiral structures

    NASA Astrophysics Data System (ADS)

    Pettitt, Alex R.; Tasker, Elizabeth J.; Wadsley, James W.; Keller, Ben W.; Benincasa, Samantha M.

    2017-07-01

    Tidal encounters are believed to be one of the key drivers of galactic spiral structure in the Universe. Such spirals are expected to produce different morphological and kinematic features compared to density wave and dynamic spiral arms. In this work, we present high-resolution simulations of a tidal encounter of a small mass companion with a disc galaxy. Included are the effects of gas cooling and heating, star formation and stellar feedback. The structure of the perturbed disc differs greatly from the isolated galaxy, showing clear spiral features that act as sites of new star formation, and displaying interarm spurs. The two arms of the galaxy, the bridge and tail, appear to behave differently; with different star formation histories and structure. Specific attention is focused on offsets between gas and stellar spiral features which can be directly compared to observations. We find that some offsets do exist between different media, with gaseous arms appearing mostly on the convex side of the stellar arms, though the exact locations appear highly time dependent. These results further highlight the differences between tidal spirals and other theories of arm structure.

  9. 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.

  10. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, Emily

    2008-01-01

    Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the era of structure formation in the early universe. Previous research in this field has been limited to calculating merger rates of MBHs using different models where many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span 5 to 6 orders of magnitude. We develop a semi-analytical, phenomenological model that includes plausible combinations of several physical parameters involved in the mergers. which we then turn around to determine how well LISA observations will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 structure formation era. We do this by generating synthetic LISA observable data (masses, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo (MCMC) method. This allows us to constrain the physical parameters of the mergers.

  11. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, Emily

    2008-01-01

    Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the era of structure formation in the early universe. Previous research in this field has been limited to calculating merger rates of MBHs using different models where many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span 5 to 6 orders of magnitude. We develop a semi-analytical, phenomenological model that includes plausible combinations of several physical parameters involved in the mergers. which we then turn around to determine how well LISA observations will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 structure formation era. We do this by generating synthetic LISA observable data (masses, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo (MCMC) method. This allows us to constrain the physical parameters of the mergers.

  12. Strain phase separation: Formation of ferroelastic domain structures

    NASA Astrophysics Data System (ADS)

    Xue, Fei; Li, Yongjun; Gu, Yijia; Zhang, Jinxing; Chen, Long-Qing

    2016-12-01

    Phase decomposition is a well-known process leading to the formation of two-phase mixtures. Here we show that a strain imposed on a ferroelastic crystal promotes the formation of mixed phases and domains, i.e., strain phase separation with local strains determined by a common tangent construction on the free energy versus strain curves. It is demonstrated that a domain structure can be understood using the concepts of domain/phase rule, lever rule, and coherent and incoherent strain phase separation, in a complete analogy to phase decomposition. The proposed strain phase separation model is validated using phase-field simulations and experimental observations of PbTi O3 and BiFe O3 thin films as examples. The proposed model provides a simple tool to guide and design domain structures of ferroelastic systems.

  13. Fourier imaging of non-linear structure formation

    NASA Astrophysics Data System (ADS)

    Brandbyge, Jacob; Hannestad, Steen

    2017-04-01

    We perform a Fourier space decomposition of the dynamics of non-linear cosmological structure formation in ΛCDM models. From N-body simulations involving only cold dark matter we calculate 3-dimensional non-linear density, velocity divergence and vorticity Fourier realizations, and use these to calculate the fully non-linear mode coupling integrals in the corresponding fluid equations. Our approach allows for a reconstruction of the amount of mode coupling between any two wavenumbers as a function of redshift. With our Fourier decomposition method we identify the transfer of power from larger to smaller scales, the stable clustering regime, the scale where vorticity becomes important, and the suppression of the non-linear divergence power spectrum as compared to linear theory. Our results can be used to improve and calibrate semi-analytical structure formation models.

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

    PubMed

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

    2015-08-03

    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.

  15. 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.

  16. Formation and structure of amorphous carbon char from polymer materials

    NASA Astrophysics Data System (ADS)

    Lawson, John; Srivastava, Deepak

    2008-03-01

    Amorphous carbonaceous char produced from burning polymer solids has insulating properties that makes it valuable for aerospace thermal protection systems as well as for fire retardants. A pyrolytic molecular dynamics simulation method is devised to study the transformation of the local microstructure from virgin polymer to a dense, disordered char. Release of polymer hydrogen is found to be critical to allow the system to collapse into a highly coordinated structure. Mechanisms of the char formation process and the morphology of the resulting structure are elucidated.

  17. Al-Ti-Zr master alloys: Structure formation

    NASA Astrophysics Data System (ADS)

    Popova, E. A.; Shubin, A. B.; Kotenkov, P. V.; Pastukhov, E. A.; Bodrova, L. E.; Fedorova, O. M.

    2012-05-01

    The effects of the composition of ternary Al-Ti-Zr master alloys, the overheating of their melts with respect to liquidus, and exposure to low-frequency vibrations on the structure formation in them are studied. It is shown that complex aluminide Al3(Zr x Ti1 - x ) with a metastable L12-type cubic lattice coinciding with the structure type of α Al primarily precipitates during the crystallization of Al-Ti-Zr melts under certain conditions. This fact makes such master alloys promising for modifying aluminum alloys.

  18. Structure formation of surfactant membranes under shear flow

    NASA Astrophysics Data System (ADS)

    Shiba, Hayato; Noguchi, Hiroshi; Gompper, Gerhard

    2013-07-01

    Shear-flow-induced structure formation in surfactant-water mixtures is investigated numerically using a meshless-membrane model in combination with a particle-based hydrodynamics simulation approach for the solvent. At low shear rates, uni-lamellar vesicles and planar lamellae structures are formed at small and large membrane volume fractions, respectively. At high shear rates, lamellar states exhibit an undulation instability, leading to rolled or cylindrical membrane shapes oriented in the flow direction. The spatial symmetry and structure factor of this rolled state agree with those of intermediate states during lamellar-to-onion transition measured by time-resolved scatting experiments. Structural evolution in time exhibits a moderate dependence on the initial condition.

  19. Crystal structure representations for machine learning models of formation energies

    SciTech Connect

    Faber, Felix; Lindmaa, Alexander; von Lilienfeld, O. Anatole; Armiento, Rickard

    2015-04-20

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

  20. Large-scale structure formation with global topological defects

    NASA Astrophysics Data System (ADS)

    Durrer, Ruth; Zhou, Zhi-Hong

    1996-05-01

    We investigate cosmological structure formation seeded by topological defects which may form during a phase transition in the early Universe. First, we derive a partially new, local, and gauge-invariant system of perturbation equations to treat microwave background and dark matter fluctuations induced by topological defects or any other type of seeds. We then show that this system is well suited for numerical analysis of structure formation by applying it to seeds induced by fluctuations of a global scalar field. Our numerical results cover a larger dynamical range than those covered by previous investigations and are complementary to them since we use substantially different methods. The resulting microwave background fluctuations are compatible with older simulations. We also obtain a scale-invariant spectrum of fluctuations although with somewhat higher amplitude. On the other hand, our dark matter results yield a smaller bias parameter compatible with b~2 on scales of 20h-1 Mpc in contrast with previous work which yielded larger bias factors. Our conclusions are thus more positive. According to the aspects analyzed in this work, global topological defect-induced fluctuations yield viable scenarios of structure formation and do better than standard CDM on large scales.

  1. 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.

  2. The structure of reionization in hierarchical galaxy formation models

    NASA Astrophysics Data System (ADS)

    Kim, Han-Seek; Wyithe, J. Stuart B.; Raskutti, Sudhir; Lacey, C. G.; Helly, J. C.

    2013-01-01

    Understanding the epoch of reionization and the properties of the first galaxies represents an important goal for modern cosmology. The structure of reionization and hence the observed power spectrum of redshifted 21-cm fluctuations are known to be sensitive to the astrophysical properties of the galaxies that drove reionization. Thus, detailed measurements of the 21-cm power spectrum and its evolution could lead to measurements of the properties of early galaxies that are otherwise inaccessible. In this paper, we make predictions for the ionized structure during reionization and the 21-cm power spectrum based on detailed models of galaxy formation. We combine the semi-analytic galform model implemented within the Millennium-II dark matter simulation, with a semi-numerical scheme to describe the resulting ionization structure. Semi-analytic models based on the Millennium-II Simulation follow the properties of galaxies within haloes of mass greater than ˜1.4 × 108 M⊙ at z > 6, corresponding to the faint sources thought to dominate reionization. Using these models we show that the details of supernovae (SNe) and radiative feedback affect the structure and distribution of ionized regions, and hence the slope and amplitude of the 21-cm power spectrum. These results indicate that forthcoming measurements of the 21-cm power spectrum could be used to uncover details of early galaxy formation. We find that the strength of SN feedback is the dominant effect governing the evolution of structure during reionization. In particular, we show SN feedback to be more important than radiative feedback, the presence of which we find does not influence either the total stellar mass or overall ionizing photon budget. Thus, if SN feedback is effective at suppressing star formation in high-redshift galaxies, we find that photoionization feedback does not lead to self-regulation of the reionization process as has been thought.

  3. 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.

  4. The Formation of Vortex Structures in a Screen Cylinder Wake

    NASA Astrophysics Data System (ADS)

    Azmi, Azlin Mohd; Lu, Yucen; Zhou, Tongming

    2017-09-01

    The formation of vortex structures in a screen cylinder wake was investigated in a wind tunnel at a Reynolds number of 7000. The screen cylinder was made of a stainless steel wire mesh with an open area ratio of 67%. The results showed that the screen cylinder wake could be classified into two distinct regions. The first region was characterised by the development of the shear layer vortices which resulted from Kelvin-Helmholtz instability. At about x/d = 2 0 (where d is the diameter of the cylinder) the shear layer vortices started to interact with each other across the centreline, and evolved downstream to form the alternately arranged ‘large-scale’ coherent structures. These structures were most pronounced at x/d = 40. The vortex formation region was therefore extended significantly downstream compared with that of the solid cylinder wake. The second region involved a gradual decay of the fully-formed large-scale structures, evidenced by the weak vorticity exchange across the wake centreline.

  5. 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

  6. Matrix vesicles: structure, composition, formation and function in calcification.

    PubMed

    Wuthier, Roy E; Lipscomb, Guy F

    2011-06-01

    Matrix vesicles (MVs) induce calcification during endochondral bone formation. Experimental methods for structural, compositional, and functional analysis of MVs are reviewed. MV proteins, enzymes, receptors, transporters, regulators, lipids and electrolytes are detailed. MV formation is considered from both structural and biochemical perspectives. Confocal imaging of Ca(2+) and H(+) were used to depict how living chondrocytes form MVs. Biochemical studies revealed that coordinated mitochondrial Ca(2+) and Pi metabolism produce MVs containing a nucleational complex (NC) of amorphous calcium phosphate, phosphatidylserine and annexin A5--all critical to the mechanism of mineral nucleation. Reconstitution of the NC and modeling with unilamellar vesicles reveal how the NC transforms into octacalcium phosphate, regulated by Mg(2+), Zn(2+) and annexin A5. Extravasation of intravesicular mineral is mediated by phospholipases and tissue-nonspecific alkaline phosphatase (TNAP). In the extravesicular matrix, hydroxyapatite crystal propagation is enhanced by cartilage collagens and TNAP, which destroys inhibitory PPi, and by metalloproteases that degrade proteoglycans. Other proteins also modulate mineral formation. Recent findings from single and multiple gene knockouts of TNAP, NPP1, ANK, PHOSPHO1, and Annexin A5 are reviewed.

  7. Electric field structures in thin films: formation and properties.

    PubMed

    Cassidy, Andrew; Plekan, Oksana; Balog, Richard; Dunger, Jack; Field, David; Jones, Nykola C

    2014-08-21

    A newly discovered class of molecular materials, so-called "spontelectrics", display spontaneous electric fields. Here we show that the novel properties of spontelectrics can be used to create composite spontelectrics, illustrating how electric fields in solid films may be structured on the nanoscale by combining layers of different spontelectric materials. This is demonstrated using the spontelectric materials nitrous oxide, toluene, isoprene, isopentane, and CF2Cl2. These yield a variety of tailored electric field structures, with individual layers harboring fields between 10(7) and 10(8) V/m. Fields may be of the same sign or of opposite sign, the latter enabling the creation of nanoscale potential wells. The formation of fields is followed using an established electron beam technique, employing the ASTRID synchrotron storage ring. The influence of temperature on heterolayer structures, displaying new Curie effects, and the nature of the interfacial region between different spontelectrics are also discussed.

  8. Comparative analysis of titanium oxide nanotubes ordered structure formation

    NASA Astrophysics Data System (ADS)

    Shchegoleva, S. A.; Titov, P. L.; Kondrikov, N. B.

    2017-09-01

    The comparative analysis of formation of highly-ordered nanotubes array of titanium oxide obtained by the method of anodizing in non-aqueous (No. 1) and semi-aqueous (No. 2) electrolytes is considered in this paper. Analysis of nanotubes formation current of both samples has shown that the fine structure of the current is observed: a series of small steps alternated by sharp swells. Attractor obtained from current implementation of sample No. 1 points at the existence of quasistochastic in terms of phase and strictly periodic mode of partial Levy flights. Attractor of sample No. 2 is more smoothed. Current realizations of both samples points at trigger mode of system behavior peculiar to auto-oscillating process.

  9. Structures and energetics for O2 formation in photosystem II.

    PubMed

    Siegbahn, Per E M

    2009-12-21

    Water oxidation, forming O(2) from water and sunlight, is a fundamental process for life on earth. In nature, the enzyme photosystem II (PSII) catalyzes this reaction. The oxygen evolving complex (OEC), the complex within PSII that catalyzes the actual formation of the O-O bond, contains four manganese atoms and one calcium atom connected by oxo bonds. Seven amino acid side chains in the structure, mostly carboxylates, are ligated to the metal atoms. In the study of many enzyme mechanisms, theoretical modeling using density functional theory has served as an indispensable tool. This Account summarizes theoretical research to elucidate the mechanism for water oxidation in photosynthesis, including the most recent findings. The development of successively larger models, ranging from 50 atoms in the active site up to the present model size of 170 atoms, has revealed the mechanism of O(2) formation with increasing detail. The X-ray crystal structures of PSII have provided a framework for optimizing the theoretical models. By constraint of the backbone atoms to be at the same positions as those in the X-ray structures, the theoretical structures are in good agreement with both the measured electron density and extended X-ray absorption fine structure (EXAFS) interpretations. By following the structural and energetic changes in those structures through the different steps in the catalytic process, we have modeled the oxidation of the catalytic complex, the binding of the two substrate water molecules, and the subsequent deprotonations of those substrate molecules. In these models, the OEC forms a basin into which the water molecules naturally fit. These findings demonstrate that the binding of the second water molecule causes a reconstruction, results that are consistent with earlier EXAFS measurements. Most importantly, this Account describes a low-barrier mechanism for formation of the O-O bond, involving an oxygen radical that reacts with a mu-oxo ligand of the OEC

  10. 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.

  11. Structures Formation In Slurry Flow In A Porous Medium

    NASA Astrophysics Data System (ADS)

    Kilchherr, R.; Koenders, M. A.

    A finely-grained, densely packed material is mixed with a Newtonian fluid and made to flow upwards through a porous medium. The slurry percolates through the medium and, because slurries are inherently non-Newtonian, structures formation takes place (see Koenders 1998). To visualise the effect, the fluid is chosen to be Rizella oil, while the porous medium is constituted of very heterogeneous Pyrex elements. The latter have virtually the same refractive index as the oil, which enables the study of the distribution of the solid fraction of the slurry, as this is the only non-transparent phase in the system. Pictures of the experiments are presented; using various forms of image processing, it is demonstrated that predominantly horizontal structures are formed in the flow process. The multiphase flow in the heterogeneous matrix has also been described theoretically using granular temperature theory (McTigue and Jenkins 1992) and the structures formation has been obtained in this way too. References Koenders M.A. 1998, Effects of microstructure and non-linearity in heterogeneous materials. J. Appl Phys 31, 1875-1882 McTigue D. and Jenkins J.T. 1992, Channel flow of a concentrated suspensions. In: Advances in Micromechanics of Granular Materials, Shen H.H. et al. (Eds.), pp 381 - 390, Elsevier, Oxford.

  12. Gap formation following climatic events in spatially structured plant communities

    PubMed Central

    Liao, Jinbao; De Boeck, Hans J.; Li, Zhenqing; Nijs, Ivan

    2015-01-01

    Gaps play a crucial role in maintaining species diversity, yet how community structure and composition influence gap formation is still poorly understood. We apply a spatially structured community model to predict how species diversity and intraspecific aggregation shape gap patterns emerging after climatic events, based on species-specific mortality responses. In multispecies communities, average gap size and gap-size diversity increased rapidly with increasing mean mortality once a mortality threshold was exceeded, greatly promoting gap recolonization opportunity. This result was observed at all levels of species richness. Increasing interspecific difference likewise enhanced these metrics, which may promote not only diversity maintenance but also community invasibility, since more diverse niches for both local and exotic species are provided. The richness effects on gap size and gap-size diversity were positive, but only expressed when species were sufficiently different. Surprisingly, while intraspecific clumping strongly promoted gap-size diversity, it hardly influenced average gap size. Species evenness generally reduced gap metrics induced by climatic events, so the typical assumption of maximum evenness in many experiments and models may underestimate community diversity and invasibility. Overall, understanding the factors driving gap formation in spatially structured assemblages can help predict community secondary succession after climatic events. PMID:26114803

  13. Formation of the Galactic Stellar Halo. I. Structure and Kinematics

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji; Chiba, Masashi

    2001-09-01

    We perform numerical simulations for the formation of the Galactic stellar halo, based on the currently favored cold dark matter theory of galaxy formation. Our numerical models, taking into account both dynamical and chemical evolution processes in a consistent manner, are aimed at explaining the observed structure and kinematics of the stellar halo in the context of hierarchical galaxy formation. The main results of the present simulations are summarized as follows: (1) Basic physical processes involved in the formation of the stellar halo, composed of metal-deficient stars with [Fe/H]<=-1.0, are described by both dissipative and dissipationless merging of subgalactic clumps and their resultant tidal disruption in the course of gravitational contraction of the Galaxy at high redshift (z>1). (2) The simulated halo has a density profile similar to the observed power-law form of ρ(r)~r-3.5 and also has a metallicity distribution similar to the observations. The halo shows virtually no radial gradient for stellar ages and only a small gradient for metallicities. (3) The dual nature of the halo, i.e., its inner flattened and outer spherical density distribution, is reproduced, at least qualitatively, by the present model. The outer spherical halo is formed via essentially dissipationless merging of small subgalactic clumps, whereas the inner flattened one is formed via three different mechanisms, i.e., dissipative merging between larger, more massive clumps, adiabatic contraction due to the growing Galactic disk, and gaseous accretion onto the equatorial plane. (4) For the simulated metal-poor stars with [Fe/H]<=-1.0, there is no strong correlation between metal abundances and orbital eccentricities, in good agreement with the recent observations. Moreover, the observed fraction of the low-eccentricity stars is reproduced correctly for [Fe/H]<=-1.6 and approximately for the intermediate-abundance range of -1.6<[Fe/H]<=-1.0. (5) The mean rotational velocity of the

  14. 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,…

  15. 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,…

  16. 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.

  17. Cosmological structure formation in Decaying Dark Matter models

    NASA Astrophysics Data System (ADS)

    Cheng, Dalong; Chu, M.-C.; Tang, Jiayu

    2015-07-01

    The standard cold dark matter (CDM) model predicts too many and too dense small structures. We consider an alternative model that the dark matter undergoes two-body decays with cosmological lifetime τ into only one type of massive daughters with non-relativistic recoil velocity Vk. This decaying dark matter model (DDM) can suppress the structure formation below its free-streaming scale at time scale comparable to τ. Comparing with warm dark matter (WDM), DDM can better reduce the small structures while being consistent with high redshfit observations. We study the cosmological structure formation in DDM by performing self-consistent N-body simulations and point out that cosmological simulations are necessary to understand the DDM structures especially on non-linear scales. We propose empirical fitting functions for the DDM suppression of the mass function and the concentration-mass relation, which depend on the decay parameters lifetime τ, recoil velocity Vk and redshift. The fitting functions lead to accurate reconstruction of the the non-linear power transfer function of DDM to CDM in the framework of halo model. Using these results, we set constraints on the DDM parameter space by demanding that DDM does not induce larger suppression than the Lyman-α constrained WDM models. We further generalize and constrain the DDM models to initial conditions with non-trivial mother fractions and show that the halo model predictions are still valid after considering a global decayed fraction. Finally, we point out that the DDM is unlikely to resolve the disagreement on cluster numbers between the Planck primary CMB prediction and the Sunyaev-Zeldovich (SZ) effect number count for τ ~ H0-1.

  18. Cosmological structure formation in Decaying Dark Matter models

    SciTech Connect

    Cheng, Dalong; Chu, M.-C.; Tang, Jiayu E-mail: mcchu@phy.cuhk.edu.hk

    2015-07-01

    The standard cold dark matter (CDM) model predicts too many and too dense small structures. We consider an alternative model that the dark matter undergoes two-body decays with cosmological lifetime τ into only one type of massive daughters with non-relativistic recoil velocity V{sub k}. This decaying dark matter model (DDM) can suppress the structure formation below its free-streaming scale at time scale comparable to τ. Comparing with warm dark matter (WDM), DDM can better reduce the small structures while being consistent with high redshfit observations. We study the cosmological structure formation in DDM by performing self-consistent N-body simulations and point out that cosmological simulations are necessary to understand the DDM structures especially on non-linear scales. We propose empirical fitting functions for the DDM suppression of the mass function and the concentration-mass relation, which depend on the decay parameters lifetime τ, recoil velocity V{sub k} and redshift. The fitting functions lead to accurate reconstruction of the the non-linear power transfer function of DDM to CDM in the framework of halo model. Using these results, we set constraints on the DDM parameter space by demanding that DDM does not induce larger suppression than the Lyman-α constrained WDM models. We further generalize and constrain the DDM models to initial conditions with non-trivial mother fractions and show that the halo model predictions are still valid after considering a global decayed fraction. Finally, we point out that the DDM is unlikely to resolve the disagreement on cluster numbers between the Planck primary CMB prediction and the Sunyaev-Zeldovich (SZ) effect number count for τ ∼ H{sub 0}{sup −1}.

  19. 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

  20. Formation and evolution of structure in loop cosmology.

    PubMed

    Bojowald, Martin; Kagan, Mikhail; Singh, Parampreet; Hernández, Hector H; Skirzewski, Aureliano

    2007-01-19

    Inhomogeneous cosmological perturbation equations are derived in loop quantum gravity, taking into account corrections, in particular, in gravitational parts. This provides a framework for calculating the evolution of modes in structure formation scenarios related to inflationary or bouncing models. Applications here are corrections to the Newton potential and to the evolution of large scale modes which imply nonconservation of curvature perturbations possibly noticeable in a running spectral index. These effects are sensitive to quantization procedures and test the characteristic behavior of correction terms derived from quantum gravity.

  1. Nonlinear structure formation with the environmentally dependent dilaton

    SciTech Connect

    Brax, Philippe; Davis, Anne-Christine; Shaw, Douglas J.; Li, Baojiu

    2011-05-15

    We have studied the nonlinear structure formation of the environmentally dependent dilaton model using N-body simulations. We find that the mechanism of suppressing the scalar fifth force in high-density regions works very well. Within the parameter space allowed by the solar-system tests, the dilaton model predicts small deviations of the matter power spectrum and the mass function from their {Lambda}CDM counterparts. The importance of taking full account of the nonlinearity of the model is also emphasized.

  2. Formation of three-dimensional Parylene C structures via thermoforming

    NASA Astrophysics Data System (ADS)

    Kim, B. J.; Chen, B.; Gupta, M.; Meng, E.

    2014-06-01

    The thermoplastic nature of Parylene C is leveraged to enable the formation of three-dimensional structures using a thermal forming (thermoforming) technique. Thermoforming involves the heating of Parylene films above its glass transition temperature while they are physically confined in the final desired conformation. Micro and macro scale three-dimensional structures composed of Parylene thin films were developed using the thermoforming process, and the resulting chemical and mechanical changes to the films were characterized. No large changes to the surface and bulk chemistries of the polymer were observed following the thermoforming process conducted in vacuum. Heat treated structures exhibited increased stiffness by a maximum of 37% depending on the treatment temperature, due to an increase in crystallinity of the Parylene polymer. This study revealed important property changes resulting from the process, namely (1) the development of high strains in thermoformed areas of small radii of curvature (30-90 µm) and (2) ˜1.5% bulk material shrinkage in thermoformed multilayered Parylene-Parylene and Parylene-metal-Parylene films. Thermoforming is a simple process whereby three-dimensional structures can be achieved from Parylene C-based thin film structures with tunable mechanical properties as a function of treatment temperature.

  3. Towards a computational modeling of structure formation in colloidal drying

    NASA Astrophysics Data System (ADS)

    Wagner, Alexander

    2014-03-01

    We present lattice Boltzmann models at different scales for the simulation of colloidal drying in the presence of polymers and structure formation in resulting phase-separation fronts. When a drop of colloid polymer mixture is exposed to an environment in which the solvent in which these particles are suspended evaporates an accumulation of non-volotile material at the rim of the drop is observed (coffee ring effect). When the solvent concentration is reduced bejond a certain threshold, the colloid polymer mixture undergoes phase separation. The structures formed by this phase-separation is observed to depend on the processing conditions. In this presentation we will briefly present the experimental observations and our numerical approach to address the observed phenomena.

  4. A Mechanism for E xB0 Structure Formation

    NASA Astrophysics Data System (ADS)

    Diamond, Patrick; Gurcan, Ozgur; Hahm, T. S.; Dif-Pradalier, Guilhem

    2012-10-01

    A novel mechanism for E xB0 staircase formation is proposed. Staircases are quasi-regular patterns of strong, localized shear layers and profile corrugations interspersed with regions of avalanching. The critical question is how do such quasi-regular patterns self-consistently form. We propose a simple model based on a.) symmetry constraints on the form of the flux, b.) the existence of a fluctuation amplitude dependent time delay between the profile perturbation and the flux. The time delay leads to the development of quasi-periodic jams or clusters in the transport flux. These in turn nucleate profile corrugations and a shear layer staircase. The implication for avalanche structure will be discussed. The aim of this work is a self-consistent treatment of the spatio-temporal structure of transport and flows.

  5. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  6. Formation and stability of secondary structures in globular proteins

    NASA Astrophysics Data System (ADS)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    We study two models for the formation and packing of helices and sheets in globular (compact) proteins. These models, based on weighted Hamiltonian paths on a regular lattice both exhibit a first order transition between a compact high temperature phase, with no extended secondary structures, and a quasi-frozen compact phase, with secondary structures invading the whole lattice. The quasi-frozen phase with very weak temperature dependence, is identified as the native phase of proteins, whereas the high-temperature phase may be relevant to the so-called molten globule state of proteins. Nous étudions deux modèles pour la formation et l'empilement d'hélices ou de feuillets dans la phase globulaire (compacte) des protéines. ces modèles, fondés sur des chemins hamiltoniens pondérés sur réseau, possèdent une transition de phase du premier ordre, entre (i) une phase haute température compacte, avec structures secondaires non étendues, et (ii) une phase compacte quasi-gelée, où les structures secondaires envahissent tout le réseau. La phase quasi-gelée, qui a une dépendance en température très faible, est identifiée à la phase native des protéines; la phase haute température est peut-être reliée à la phase native “globule fondu” (molten globule) des protéines.

  7. Structures of hydrocarbon hydrates during formation with and without inhibitors.

    PubMed

    Ohno, Hiroshi; Moudrakovski, Igor; Gordienko, Raimond; Ripmeester, John; Walker, Virginia K

    2012-02-09

    The formation of hydrates from a methane-ethane-propane mixture is more complex than with single gases. Using nuclear magnetic resonance (NMR) and high-pressure powder X-ray diffraction (PXRD), we have investigated the structural properties of natural gas hydrates crystallized in the presence of kinetic hydrate inhibitors (KHIs), two commercial inhibitors and two biological ice inhibitors, or antifreeze proteins (AFPs). NMR analyses indicated that hydrate cage occupancy was at near saturation for controls and most inhibitor types. Some exceptions were found in systems containing a new commercial KHI (HIW85281) and a recombinant plant AFP, suggesting that these two inhibitors could impact the kinetics of cavity formation. NMR analysis confirmed that the hydrate composition varies during crystal growth by kinetic effects. Strikingly, the coexistence of both structures I (sI) and II (sII) were observed in NMR spectra and PXRD profiles. It is suggested that sI phases may form more readily from liquid water. Real time PXRD monitoring showed that sI hydrates were less stable than sII crystals, and there was a conversion to the stable phase over time. Both commercial KHIs and AFPs had an impact on hydrate metastability, but transient sI PXRD intensity profiles indicated significantly different modes of interaction with the various inhibitors and the natural gas hydrate system.

  8. Novel casein hydrogels: formation, structure and controlled drug release.

    PubMed

    Song, Fei; Zhang, Li-Ming; Shi, Jun-Fei; Li, Nan-Nan

    2010-08-01

    To develop biocompatible, non-toxic materials for pharmaceutical and biomedical applications, the enzyme-assisted formation and structural characteristics of novel casein hydrogels were investigated by dynamic rheology and fractal analyses. As revealed by oscillatory time sweep and stress relaxation tests, the gelation time was shortened greatly and the hydrogel strength was enhanced obviously when a natural tissue enzyme, microbial transglutaminase (MTGase), was used. For aqueous system containing 10.0 wt% casein and 0.05 wt% MTGase, temperature dependence of the gelation time could be described by an Arrhenius plot with its apparent activation energy of 95.4 kJ/mol. In particular, the resultant casein hydrogel was found to show a "weak-link" behavior with fractal character. The use of the enzyme resulted in the increase of the fractal dimension and the formation of a more "tight" network structure. By means of this enzyme-assisted gelation, Vitamin B12 as the model drug could be incorporated into the casein hydrogel matrix under mild conditions and then show a prolonged release behavior. Copyright 2010 Elsevier B.V. All rights reserved.

  9. Banded Electron Structure Formation in the Inner Magnetosphere

    NASA Technical Reports Server (NTRS)

    Liemohn, M. W.; Khazanov, G. V.

    1997-01-01

    Banded electron structures in energy-time spectrograms have been observed in the inner magnetosphere concurrent with a sudden relaxation of geomagnetic activity. In this study, the formation of these banded structures is considered with a global, bounce-averaged model of electron transport, and it is concluded that this structure is a natural occurrence when plasma sheet electrons are captured on closed drift paths near the Earth. These bands do not appear unless there is capture of plasma sheet electrons; convection along open drift paths making open pass around the Earth do not have time to develop this feature. The separation of high-energy bands from the injection population due to the preferential advection of the gradient-curvature drift creates spikes in the energy distribution, which overlap to form a series of bands in the energy spectrograms. The lowest band is the bulk of the injected population in the sub-key energy range. Using the Kp history for an observed banded structure event, a cloud of plasma sheet electrons is captured and the development of their distribution function is examined and discussed.

  10. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26594372

  12. 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.

  13. 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.

  14. Laser induced formation of micro-rough structures

    NASA Astrophysics Data System (ADS)

    Singh, Rajiv K.; Fitz-Gerald, James M.

    1997-01-01

    Laser induced micro-rough structures (LIMS) are a by-product of laser ablation process and are created during multiple pulse irradiation on the surface of the material. Although LIMS have been found to be deleterious for the thin film deposition process, these surfaces have wide variety of applications in synthesis of adherent coatings in thermal expansion mismatched systems. Earlier models, based on interference effects of the laser beam, to explain the evolution of LIMS, are not consistent with the experimental results. Experiments were conducted on a wide variety of materials (e.g. SiC, alumina, YBaCuO superconductor, etc.) to understand the mechanisms for generation of the micro-rough structures. A novel model was developed to explain the characteristics of LIMS such as (i) feature orientation (ii) evolution of surface structures as a function of pulses, (iii) formation of LIMS within a energy window near ablation threshold and (iv) periodicity which is independent of the laser wavelength and incident angle.

  15. Structural basis of complement membrane attack complex formation

    PubMed Central

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

    2016-01-01

    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. PMID:26841837

  16. Structural basis of complement membrane attack complex formation.

    PubMed

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

    2016-02-04

    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.

  17. 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.

  18. Erbium-formate frameworks templated by diammonium cations: syntheses, structures, structural transition and magnetic properties.

    PubMed

    Li, Mengyuan; Liu, Bin; Wang, Bingwu; Wang, Zheming; Gao, Song; Kurmoo, Mohamedally

    2011-06-14

    Two structurally different Er-formate frameworks, one NaCl-like [dmenH(2)][Er(HCOO)(4)](2) (1) and the other pillared-layer type [tmenH(2)][Er(HCOO)(4)](2) (2), were obtained when templated by the corresponding protonated N,N'-dimethylethylenediamine (dmenH(2)) and N,N,N',N'-tetramethyl- ethylenediamine (tmenH(2)). The shape and size of the template cations dictate the different coordination geometries of erbium and consequently the framework topologies, though erbium adopts eight coordination in the two compounds. In the NaCl-like structure of 1, erbium is coordinated by eight anti-anti bridging formates in a square antiprism, while in the pillared-layer structure of 2, it is coordinated by six anti-anti bridging formates and one chelating formate in a pentagonal bipyramid. 2 exhibits a structural phase transition around -70 °C which is related to the disorder-order transition of the template cation. Both compounds behave as paramagnets between 2 and 300 K. However, they display field-dependent ac-susceptibilities with complicated field-induced magnetic relaxation processes, and the major slow ones probably results from spin-lattice relaxation.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Structural modification in the formation of starch – silver nanocomposites

    SciTech Connect

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

    2016-05-23

    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 (AgNO{sub 3}) 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 AgNO{sub 3}. Small angle neutron scattering (SANS) analysis showed that addition of silver nitrate modifies the starch to disc like structures and with increasing the AgNO{sub 3} concentration leads to the formation of fractals. This research could benefit battery technology where solid polymer membranes using starch is used.

  4. Redshift and structure formation in a spatially flat inhomogeneous universe

    NASA Astrophysics Data System (ADS)

    Moffat, J. W.; Tatarski, D. C.

    1992-05-01

    We study a spherically symmetric Tolman-Bondi cosmological model with globally flat spatial sections t=const. We consider the model valid for the description of the Universe after matter starts to dominate. The redshift and cosmological observations in the model are examined and a simple scenario of the changes in the structure formation when compared to the standard flat Friedmann-Robertson-Walker universe is proposed. This scenario is based on the fact that in our model different parts of the Universe spend unequal periods of time in the matter-dominated era. The correction to the cold-dark-matter spatial two-point correlation function is derived. Specific cases are examined corresponding to observationally based distributions of the density. We show that this not only leads to no contradictions, but significantly improves the fit of theoretically predicted correlation functions to observations.

  5. 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.

  6. Nano-sized Adsorbate Structure Formation in Anisotropic Multilayer System

    NASA Astrophysics Data System (ADS)

    Kharchenko, Vasyl O.; Kharchenko, Dmitrii O.; Yanovsky, Vladimir V.

    2017-05-01

    In this article, we study dynamics of adsorbate island formation in a model plasma-condensate system numerically. We derive the generalized reaction-diffusion model for adsorptive multilayer system by taking into account anisotropy in transfer of adatoms between neighbor layers induced by electric field. It will be found that with an increase in the electric field strength, a structural transformation from nano-holes inside adsorbate matrix toward separated nano-sized adsorbate islands on a substrate is realized. Dynamics of adsorbate island sizes and corresponding distributions are analyzed in detail. This study provides an insight into details of self-organization of adatoms into nano-sized adsorbate islands in anisotropic multilayer plasma-condensate systems.

  7. Simulating the Universe: Nonlinear Formation and Evolution of Cosmic Structure

    NASA Astrophysics Data System (ADS)

    Jeffrey David Emberson

    In this thesis, we harness the power of modern scientic computing to explore the formation and evolution of cosmological structure in a wide variety of astrophysical scenarios. We explore the nonlinear dynamics associated with the interplay between cold dark matter (CDM), baryons, ionizing radiation, and cosmic neutrinos, within regimes where analytic calculations necessarily fail. We begin by providing an overview of structure formation and its connections to the fields of study considered here: the epoch of reionization, galactic substructure evolution, and cosmic neutrinos. We then present a rigorous numerical convergence study of cosmological hydrodynamics simulations post-possessed with radiative transfer to study the impact of small-scale absorption systems within the intergalactic medium (IGM) during the onset of reionization. We present converged statistics of the IGM on smaller scales and earlier times than previously considered. Moreover, we provide strict resolution limits for hydrodynamic simulations to properly resolve the unheated IGM. Next we study the infall and dynamical evolution of CDM halos in a galactic host. We find the behaviour of low-mass subhalos is qualitatively different than previously described for high-mass subhalos. In particular, the evolution of low-mass subhalos, with masses less than 0.1 per cent that of the host, is mainly driven by their concentration. This presents an opportunity to use concentration as a predictive indicator of substructure evolution. We finish this thesis with an investigation of a recently proposed method for constraining individual neutrino mass from cosmological observations. Such a detection depends on the ability to reconstruct the CDM-neutrino relative velocity, which we show can be accomplished using linear transformations of an observed galaxy field. Based on this, we perform the world's largest cosmological N-body simulation and present preliminary results for the observational prospects of cosmic

  8. 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.

  9. 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

  10. Constraints on vacuum energy from structure formation and Nucleosynthesis

    NASA Astrophysics Data System (ADS)

    Adams, Fred C.; Alexander, Stephon; Grohs, Evan; Mersini-Houghton, Laura

    2017-03-01

    This paper derives an upper limit on the density ρΛ of dark energy based on the requirement that cosmological structure forms before being frozen out by the eventual acceleration of the universe. By allowing for variations in both the cosmological parameters and the strength of gravity, the resulting constraint is a generalization of previous limits. The specific parameters under consideration include the amplitude Q of the primordial density fluctuations, the Planck mass Mpl, the baryon-to-photon ratio η, and the density ratio ΩM/Ωb. In addition to structure formation, we use considerations from stellar structure and Big Bang Nucleosynthesis (BBN) to constrain these quantities. The resulting upper limit on the dimensionless density of dark energy becomes ρΛ/Mpl4 < 10-90, which is ~30 orders of magnitude larger than the value in our universe ρΛ/Mpl4 ~ 10-120. This new limit is much less restrictive than previous constraints because additional parameters are allowed to vary. With these generalizations, a much wider range of universes can develop cosmic structure and support observers. To constrain the constituent parameters, new BBN calculations are carried out in the regime where η and G = Mpl-2 are much larger than in our universe. If the BBN epoch were to process all of the protons into heavier elements, no hydrogen would be left behind to make water, and the universe would not be viable. However, our results show that some hydrogen is always left over, even under conditions of extremely large η and G, so that a wide range of alternate universes are potentially habitable.

  11. Jupiter’s Formation and Its Primordial Internal Structure

    NASA Astrophysics Data System (ADS)

    Lozovsky, Michael; Helled, Ravit; Rosenberg, Eric D.; Bodenheimer, Peter

    2017-02-01

    The composition of Jupiter and the primordial distribution of the heavy elements are determined by its formation history. As a result, in order to constrain the primordial internal structure of Jupiter, the growth of the core and the deposition and settling of accreted planetesimals must be followed in detail. In this paper we determine the distribution of the heavy elements in proto-Jupiter and determine the mass and composition of the core. We find that while the outer envelope of proto-Jupiter is typically convective and has a homogeneous composition, the innermost regions have compositional gradients. In addition, the existence of heavy elements in the envelope leads to much higher internal temperatures (several times 104 K) than in the case of a hydrogen–helium envelope. The derived core mass depends on the actual definition of the core: if the core is defined as the region in which the heavy-element mass fraction is above some limit (say, 0.5), then it can be much more massive (∼15 {M}\\oplus ) and more extended (10% of the planet’s radius) than in the case where the core is just the region with 100% heavy elements. In the former case Jupiter’s core also consists of hydrogen and helium. Our results should be taken into account when constructing internal structure models of Jupiter and when interpreting the upcoming data from the Juno (NASA) mission.

  12. Mucus glycoprotein structure, gel formation and gastrointestinal mucus function.

    PubMed

    Allen, A; Hutton, D A; Pearson, J P; Sellers, L A

    1984-01-01

    Gastrointestinal mucus occurs as a water-insoluble gel adherent to the mucosal surfaces and as a viscous, mobile solution in the lumen. The adherent gastroduodenal mucus gel is part of the mucosal defence against acid (with HCO3-), pepsin (diffusion barrier) and mechanical damage. Rheological studies show that gastrointestinal mucus is a weak, viscoelastic gel. The size and physical properties of the isolated component glycoproteins depend critically on the methods used to obtain them. A glycoprotein preparation of Mr approximately 2 X 10(6), which possesses the gel-forming properties of the native mucus, is considered to represent the secreted covalent entity in pig gastric and small intestinal mucus. These glycoproteins have a polymeric structure of subunits joined by disulphide bridges between non-glycosylated regions of their protein cores. Glycoprotein polymerization, essential for gel formation, is deficient in gastric mucus in peptic ulcer disease. In vivo, adherent mucus gel forms a thin but continuous cover of variable thickness (rat 5-500 microns) over the gastroduodenal mucosa. Luminal pepsin rapidly dissolves this mucus cover and its continuity is maintained by fresh mucus secretion. Bile, HCl, 2 M-NaCl and ethanol (less than 40%) do not destroy mucus gel structure. Prostaglandins and carbachol increase mucus thickness, affording better protection, but it is thought that continuity of the protective mucus cover is the critical factor in its protective functions.

  13. 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.

  14. Mitosis in Barbulanympha. I. Spindle structure, formation, and kinetochore engagement

    PubMed Central

    1978-01-01

    Successful culture of the obligatorily anaerobic symbionts residing in the hindgut of the wood-eating cockroach Cryptocercus punctulatus now permits continuous observation of mitosis in individual Barbulanympha cells. In Part I of this two-part paper, we report methods for culture of the protozoa, preparation of microscope slide cultures in which Barbulanympha survived and divided for up to 3 days, and an optical arrangement which permits observation and through-focus photographic recording of dividing cells, sequentially in differential interference contrast and rectified polarized light microscopy. We describe the following prophase events and structures: development of the astral rays and large extranuclear central spindle from the tips of the elongate-centrioles; the fine structure of spindle fibers and astral rays which were deduced in vivo from polarized light microscopy and seen as a particular array of microtubules in thin-section electron micrographs; formation of chromosomal spindle fibers by dynamic engagement of astral rays to the kinetochores embedded in the persistent nuclear envelope; and repetitive shortening of chromosomal spindle fibers which appear to hoist the nucleus to the spindle surface, cyclically jostle the kinetochores within the nuclear envelope, and churn the prophase chromosomes. The observations described here and in Part II have implications both for the evolution of mitosis and for understanding the mitotic process generally. PMID:681451

  15. The formation and structure of circumstellar and interstellar dust

    NASA Technical Reports Server (NTRS)

    Kroto, H. W.

    1990-01-01

    The intriguing abundance of long linear carbon chain molecules in some dark clouds and in circumstellar shells is still not well understood. Recent laboratory studies which have probed this problem indicate that when carbon vapor nucleates to form particles, linear chains and hollow cage molecules (fullerenes) also form at more-or-less the same time. The results have consequences for the formation, structures and spectroscopic properties of the molecular and dust components ejected from cool carbon-rich stars. A most interesting result of the experimental observations relates to the probability that a third character in addition to the chains and grains, the C(sub 60) molecule probably in the form of the ion C(sub 60)(sup +) in the less shielded regions, is present and perhaps responsible for some of the ubiquitously observed interstellar spectroscopic features such as the Diffuse Interstellar Features, the 2170A UV Absorption or perhaps some of the Unidentified Infrared Bands. Further study of small carbon particles which form in the gas phase has resulted in the discovery that they have quasi-icosahedral spiral shell structures. The role that such species may play in the interstellar medium as well as that played by C(sub 60) (or C sub 60 sup +) should soon be accessible to verification by a combination of laboratory experiment and astronomical spectroscopy.

  16. 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.

  17. High-resolution simulations of structure formation in the universe

    NASA Astrophysics Data System (ADS)

    Kravtsov, Andrey V.

    During the last decade, there has been ever increasing interest in the problem of galaxy formation in a cosmological context. Detailed studies of this phenomenon require three-dimensional numerical simulations of very high dynamic range. We have developed the Adaptive Refinement Tree (ART) numerical algorithm for high- resolution dissipationless and gasdynamical cosmological simulations. The algorithm follows particle trajectories and solves the equations of gasdynamics on both a cubic, uniform grid covering the entire computational volume and on finer meshes, introduced recursively in a fully adaptive manner in regions of interest. The refinement meshes are generated to effectively match an arbitrary geometry of the interesting regions, a property particularly important for cosmological simulations. In this thesis, I present a description of the method and its implementation, tests of the numerical code, and two applications which effectively demonstrate the high- resolution capabilities of the code. The first study concerns the abundances of galactic satellites in hierarchical models of structure formation. We find that the theoretical models predict much larger numbers of satellites around Milky Way-type galaxies than are actually observed. We then discuss several possible explanations for the differences in predicted and observed velocity functions, including the identification of some satellites with High-Velocity Clouds observed in the Local Group, and the existence of dark satellites which failed to accrete gas and form stars, due either to the expulsion of gas in the supernovae-driven winds or to gas heating by the intergalactic ionizing background. The second study concerns the problem of the galaxy clustering bias, the difference between the galaxy distribution and the overall distribution of matter, and its evolution with time. We use several statistics to study the bias evolution and find that in general, the bias is nonlinear and time- and scale

  18. Formation mechanisms, structure, solution behavior, and reactivity of aminodiborane.

    PubMed

    Li, Huizhen; Ma, Nana; Meng, Wenjuan; Gallucci, Judith; Qiu, Yongqing; Li, Shujun; Zhao, Qianyi; Zhang, Jie; Zhao, Ji-Cheng; Chen, Xuenian

    2015-09-30

    A facile synthesis of cyclic aminodiborane (NH2B2H5, ADB) from ammonia borane (NH3·BH3, AB) and THF·BH3 has made it possible to determine its important characteristics. Ammonia diborane (NH3BH2(μ-H)BH3, AaDB) and aminoborane (NH2BH2, AoB) were identified as key intermediates in the formation of ADB. Elimination of molecular hydrogen occurred from an ion pair, [H2B(NH3) (THF)](+)[BH4](-). Protic-hydridic hydrogen scrambling was proved on the basis of analysis of the molecular hydrogen products, ADB and other reagents through (2)H NMR and MS, and it was proposed that the scrambling occurred as the ion pair reversibly formed a BH5-like intermediate, [(THF)BH2NH2](η(2)-H2)BH3. Loss of molecular hydrogen from the ion pair led to the formation of AoB, most of which was trapped by BH3 to form ADB with a small amount oligomerizing to (NH2BH2)n. Theoretical calculations showed the thermodynamic feasibility of the proposed intermediates and the activation processes. The structure of the ADB·THF complex was found from X-ray single crystal analysis to be a three-dimensional array of zigzag chains of ADB and THF, maintained by hydrogen and dihydrogen bonding. Room temperature exchange of terminal and bridge hydrogens in ADB was observed in THF solution, while such exchange was not observed in diethyl ether or toluene. Both experimental and theoretical results confirm that the B-H-B bridge in ADB is stronger than that in diborane (B2H6, DB). The B-H-B bridge is opened when ADB and NaH react to form sodium aminodiboronate, Na[NH2(BH3)2]. The structure of the sodium salt as its 18-crown-6 ether adduct was determined by X-ray single crystal analysis.

  19. 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

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

    PubMed

    Zhang, Xijuan; Savalei, Victoria

    2016-06-01

    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, which replaces each response option in the Likert scale with a full sentence. We hypothesized that this format would result in a cleaner factor structure as compared with the Likert format. We tested this hypothesis on three popular psychological scales: the Rosenberg Self-Esteem scale, the Conscientiousness subscale of the Big Five Inventory, and the Beck Depression Inventory II. Scales in both formats showed comparable reliabilities. However, scales in the Expanded format had better (i.e., lower and more theoretically defensible) dimensionalities than scales in the Likert format, as assessed by both exploratory factor analyses and confirmatory factor analyses. We encourage further study and wider use of the Expanded format, particularly when a scale's dimensionality is of theoretical interest.

  1. Formation of surface nanodroplets facing a structured microchannel wall.

    PubMed

    Yu, Haitao; Maheshwari, Shantanu; Zhu, Jiuyang; Lohse, Detlef; Zhang, Xuehua

    2017-04-11

    Surface nanodroplets are important units for lab-on-a-chip devices, compartmentalised catalytic reactions, high-resolution near-field imaging, and many others. Solvent exchange is a simple solution-based bottom-up approach for producing surface nanodroplets by displacing a good solvent of the droplet liquid by a poor one in a narrow channel in the laminar regime. The droplet size is controlled by the solution composition and the flow conditions during the solvent exchange. In this paper, we investigated the effects of local microfluidic structures on the formation of surface nanodroplets. The microstructures consist of a microgap with a well-defined geometry, embedded on the opposite microchannel wall, facing the substrate where nucleation takes place. For a given channel height, the dimensionless control parameters were the Peclet number of the flow, the ratio between the gap height and the channel height, and the aspect ratio between the gap length and the channel height. We found and explained three prominent features in the surface nanodroplet distribution at the surface opposite to the microgap: (i) enhanced volume of the droplets; (ii) asymmetry as compared to the location of the gap in the spatial droplet distribution with increasing Pe; (iii) reduced exponent of the effective scaling law of the droplet size with Pe. The droplet size also varied with the aspect and height ratios of the microgap at a given Pe value. Our simulations of the profile of oversaturation in the channel reveal that the droplet size distribution may be attributed to the local flow patterns induced by the gap. Finally, in a tapered microchannel, a gradient of surface nanodroplet size was obtained. Our work shows the potential for controlling nanodroplet size and spatial organization on a homogeneous surface in a bottom-up approach by simple microfluidic structures.

  2. Cosmic structure formation: From first stars to large-scale filamentary structure

    NASA Astrophysics Data System (ADS)

    Cai, Zheng

    Theory of cosmic structure formation outlines how stars, galaxies, clusters of galaxies, and large-scale structures formed out of primordial density fluctuations. It presents us a picture of cosmic mass assembly, and places strong constraints on cosmological model. Both observations and theories suggest that structures formation follows a "bottom up" process, in which small, low-mass component form first, and gradually develop into larger, more massive systems. This dissertation focuses on three crucial stages of cosmic structure formation: first generation stars, quasar host galaxies and the large-scale galaxy overdensities. In Chapter 1, I present an overview of structure formation, acquainting readers with a general picture from first object in the Universe to large-scale structures at later epochs. In Chapter 2 and Chapter 3, I derive strong constraints to the star formation rates (SFRs) of very massive Population III (Pop III) stars in two high redshift galaxies at z = 7. By probing the He II emission lines for both galaxies, I conclude that the contributions of very massive Pop III stars to total the SFRs are less than 3%. In Chapter 4, I move to more massive systems, quasar host galaxies at z ˜ 3. Using damped Lyman alpha absorption systems as natural coronagraphs, I report that rest-frame far-UV emission of quasar host galaxy correlates strongly with quasar luminosity. This result suggests a co-evolution of supermassive black holes and their host galaxies. In Chapter 5, I develop a novel method for searching the most massive protoclusters at z = 2--3, by utilizing intergalactic Lyman alpha absorption. My investigations suggest that large intergalactic Lyman alpha absorption systems effectively trace the most overdense regions at large scale of ˜15 h -1 Mpc. In Chapter 6, I present our imaging observations of an extreme galaxy overdensity (protocluster) BOSS1441+4000, which is discovered using the techniques developed in Chapter 5. Furthermore, I report an

  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. Cosmological constraints on the radiation released during structure formation

    NASA Astrophysics Data System (ADS)

    Camarena, David; Marra, Valerio

    2016-11-01

    During the process of structure formation in the universe matter is converted into radiation through a variety of processes such as light from stars, infrared radiation from cosmic dust, and gravitational waves from binary black holes/neutron stars and supernova explosions. The production of this astrophysical radiation background (ARB) could affect the expansion rate of the universe and the growth of perturbations. Here, we aim at understanding to which level one can constraint the ARB using future cosmological observations. We model the energy transfer from matter to radiation through an effective interaction between matter and astrophysical radiation. Using future supernova data from large synoptic survey telescope and growth-rate data from Euclid we find that the ARB density parameter is constrained, at the 95% confidence level, to be Ω_{ar_0}<0.008. Estimates of the energy density produced by well-known astrophysical processes give roughly Ω_{ar_0}˜ 10^{-5}. Therefore, we conclude that cosmological observations will only be able to constrain exotic or not-well understood sources of radiation.

  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. 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.

  7. 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.

  8. 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.

  9. Structure Formation in Semi-Dilute Polymer Solution during Electrospinning

    NASA Astrophysics Data System (ADS)

    Zussman, Eyal; Paley, Yakov; Arinstein, Arkadii; Shuster, Kim

    2012-02-01

    In our recent work it was shown that longitudinal stretching of electrospun highly entangled semi-dilute polymer solution caused by jet hydrodynamic forces, transforms the topological network to an almost fully-stretched state within less than 1 mm from the jet start (PRE, 2011). Further evolution of the polymer network is related to a disentanglement of polymer chains and transformation of the topological network structure. As was sown by Malkin et al., (Rheol. Acta, 2011) high deformation rate of a topological polymer network, results in reptations of macromolecules caused by uncompensated local forces, whereas Brownian motion effect is negligible. Based on this conclusion, we examine the disentanglement process, using a mechanical pulley-block system assembled from multiple pulleys suspended by elastic springs, and taut string connecting two blocks. Each pulley corresponds to a topological knot; the taut string corresponds to a reptated chain; the springs correspond to surrounded polymer chains; and the blocks correspond to local deformation force. It turned out that the system is sensitive to system parameters. The pulleys can approach each other and the string stops to move. Such a behavior corresponds to formation of bundle of knots of entangled chains. In other conditions, the string continuously moves while the pulleys did not approach each other which corresponds to disentanglement of polymer chains. These experiments clarify the disentanglement kinetics in rapid-deformed polymer system.

  10. Cosmology and Structure Formation with Scalar Field Dark Matter

    NASA Astrophysics Data System (ADS)

    Rindler-Daller, Tanja; Li, Bohua; Shapiro, Paul R.

    2013-04-01

    The exploration of the nature of the cosmological dark matter is an ongoing hot topic in modern cosmology and particle physics. Suggested candidates include ultra-light particles which are described by a real or complex scalar field. Previous literature has revealed the richness of this candidate in terms of its power to explain astrophysical and cosmological observations, from the background cosmological evolution to galactic rotation curves. However, a lot of research remains to be done to find out which parts of the parameter space of this kind of dark matter is able to explain observations on all scales consistently. In this talk, we will present our current and ongoing work on the study of complex scalar field dark matter (SFDM). We find that this SFDM underwent three distinctive states in the early Universe, a scalar-field dominated, a radiation-dominated and a matter-dominated phase. The timing and longevity of each phase places important first constraints on the parameters of the model. For this SFDM model, we revisit classical problems of structure formation theory, like the tophat collapse, the problem of virial shocks, and the cosmological infall problem for an isolated halo, in order to find viable model parameters which match the constraints from cosmology.

  11. Dynamic phase separation: from coarsening to turbulence via structure formation.

    PubMed

    Golovin, A A; Pismen, L M

    2004-09-01

    We investigate some new two-dimensional evolution models belonging to the class of convective Cahn-Hilliard models: (i) a local model with a scalar order parameter, (ii) a nonlocal model with a scalar order parameter, and (iii) a model with a vector order parameter. These models are applicable to phase-separating system where concentration gradients cause hydrodynamic motion due to buoyancy or Marangoni effect. The numerical study of the models shows transition from coarsening, typical of Cahn-Hilliard systems, to spatiotemporally irregular behavior (turbulence), typical of the Kuramoto-Sivashinsky equation, which is obtained in the limit of very strong driving. The transition occurs not in a straightforward way, but through the formation of spatial patterns that emerge for intermediate values of the driving intensity. As in driven one-dimensional models studied before, the mere presence of the driving force, however small, breaks the symmetry between the two separating phases, as well as increases the coarsening rate. With increasing driving, coarsening stops. The dynamics is generally irregular at strong driving, but exhibits specific structural features.

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

    SciTech Connect

    Führer, Florian; Rigopoulos, Gerasimos E-mail: gerasimos.rigopoulos@ncl.ac.uk

    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.

  13. Foam and cluster structure formation by latex particles at the air/water interface

    NASA Astrophysics Data System (ADS)

    Ruiz-Garcia, Jaime; Gámez-Corrales, Rogelio; Ivlev, Boris I.

    1997-02-01

    We report the formation of two-dimensional foam and cluster structures by spherical polystyrene particles trapped at the air/water interface. The colloidal foam is a transient structure that evolves to the formation of clusters, but clusters can also be formed after deposition of the sample. We also observed the formation of small aggregates, whose formation along with the cluster stabilization can be explained in terms of a balance between electrostatic repulsive and van der Waals attractive interactions.

  14. Cosmological Consequences of Gravitation: Structure Formation and Gravitational Waves

    NASA Astrophysics Data System (ADS)

    Book, Laura G.

    This thesis contains work on four topics which fit into two broad areas of research: the quest to understand structure formation and through it the properties of the dark matter, and the search for primordial gravitational radiation. The first project details the effect of an accretion shock on the colors of satellites in galaxy clusters. A new model of ram pressure stripping including an accretion shock with variable radius is developed and implemented in the Galform semi-analytic model of galaxy formation. A comparison of this model with previous models and with observations indicates that current data is unable to discriminate between models, though future observations will be able to place stronger constraints on the role of ram pressure stripping in and around clusters. Next, an analysis of the angular momentum evolution of dark matter particles in high-resolution N-body simulations of dark matter halos is presented. We find that individual particle angular momentum is not conserved, and also that the angular momentum of radial shells varies over the age of the Universe by up to factors of a few. These results have serious implications for the validity of current analytical models that assume angular momentum conservation. Two methods for detecting the primordial gravitational wave (GW) background are then presented. Such a background, if detected, could greatly impact our understanding of the early universe. The first proposed method uses the apparent angular velocities of astrophysical objects induced by GWs, which may be detectable with upcoming astrometric missions such as the GAIA satellite. This work improves upon previous order-of-magnitude estimates, and presents a full calculation of the expected signal from a stochastic background of GWs. The second method uses bipolar spherical harmonics decomposition, a formalism to characterize departures from statistical isotropy and Gaussianity, to quantify the expected lensing of the cosmic microwave background

  15. 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.

  16. Innovative design of composite structures: Use of curvilinear fiber format to improve structural efficiency

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

    To increase the effectiveness and efficiency of fiber-reinforced materials, the use of fibers in a curvilinear rather than the traditional straightline format is explored. The capacity of a laminated square plate with a central circular hole loaded in tension is investigated. The orientation of the fibers is chosen so that the fibers in a particular layer are aligned with the principle stress directions in that layer. Finite elements and an iteration scheme are used to find the fiber orientation. A noninteracting maximum strain criterion is used to predict load capacity. The load capacities of several plates with different curvilinear fibers format are compared with the capacities of more conventional straightline format designs. It is found that the most practical curvilinear design sandwiches a group of fibers in a curvilinear format between a pair of +/-45 degree layers. This design has a 60% greater load capacity than a conventional quasi-isotropic design with the same number of layers. The +/-45 degree layers are necessary to prevent matrix cracking in the curvilinear layers due to stresses perpendicular to the fibers in those layers. Greater efficiencies are achievable with composite structures than now realized.

  17. 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.

  18. 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.

  19. 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.

  20. Structural determinants for the formation of sulfhemeprotein complexes

    PubMed Central

    Román-Morales, Elddie; Pietri, Ruth; Ramos-Santana, Brenda; Vinogradov, Serge N.; Lewis-Ballester, Ariel; López-Garriga, Juan

    2010-01-01

    Several hemoglobins were explored by UV-Vis and resonance Raman spectroscopy to define sulfheme complex formation. Evaluation of these proteins upon the reaction with H2O2 or O2 in the presence of H2S suggest: (a) the formation of the sulfheme derivate requires a HisE7 residue in the heme distal site with an adequate orientation to form an active ternary complex; (b) that the ternary complex intermediate involves the HisE7, the peroxo or ferryl species, and the H2S molecule. This moiety precedes and triggers the sulfheme formation. PMID:20732304

  1. The Bok globule BHR 160: structure and star formation

    NASA Astrophysics Data System (ADS)

    Haikala, L. K.; Reipurth, B.

    2017-01-01

    Context. BHR 160 is a virtually unstudied cometary globule within the Sco OB4 association in Scorpius at a distance of 1600 pc. It is part of a system of cometary clouds which face the luminous O star HD 155806. BHR 160 is special because it has an intense bright rim. Aims: We attempt to derive physical parameters for BHR 160 and to understand its structure and the origin of its peculiar bright rim. Methods: BHR 160 was mapped in the , and C18O(2-1) and (1-0) and CS (3-2) and (2-1) lines. These data, augmented with stellar photometry derived from the ESO VVV survey, were used to derive the mass and distribution of molecular material in BHR 160 and its surroundings. Archival mid-infrared data from the WISE satellite was used to find IR excess stars in the globule and its neighbourhood. Results: An elongated 1' by 0.´6 core lies adjacent to the globule bright rim. emission covers the whole globule, but the , C18Oand CS emission is more concentrated to the core. The line profiles indicate the presence of outflowing material near the core, but the spatial resolution of the mm data is not sufficient for a detailed spatial analysis. The BHR 160 mass estimated from the C18Omapping is100 ± 50 M⊙ (d/1.6 kpc)2 where d is the distance to the globule. Approximately 70% of the mass lies in the dense core. The total mass of molecular gas in the direction of BHR 160 is 210 ± 80 (d/1.6 kpc)2 M⊙ when estimated from the more extended VVV near-infrared photometry. We argue that the bright rim of BHR 160 is produced by a close-by early B-type star, HD 319648, that was likely recently born in the globule. This star is likely to have triggered the formation of a source, IRS 1, that is embedded within the core of the globule and detected only in Ks and by WISE and IRAS. Based on observations made with ESO Telescopes at the La Silla or Paranal Observatories.Reduced molecular line spectra (The SEST spectra as FITS files) are only available at the CDS via anonymous ftp to http

  2. The Relation Between Item Format and the Structure of the Eysenck Personality Inventory

    ERIC Educational Resources Information Center

    Velicer, Wayne F.; Stevenson, John F.

    1978-01-01

    A Likert seven-choice response format for personality inventories allows finer distinctions by subjects than the traditional two-choice format. The Eysenck Personality Inventory was employed in the present study to test the hypothesis that use of the expanded format would result in a clearer and more accurate indication of test structure.…

  3. 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.

  4. Influence of spatial effects on coherent structures formation in a supersonic flow near a plate

    NASA Astrophysics Data System (ADS)

    Lipatov, I. I.; Tugazakov, R. Ya.

    2017-06-01

    Formation of coherent structures in supersonic flow near flat plate with a reflecting strong shock wave is studied. Also, a problem of harmonic wave influencing the flow near plate has been investigated. Similar mechanisms of coherent structures formation in both unsteady problems are found due to secondary instability arising in a flow.

  5. Memory formation: from network structure to neural dynamics.

    PubMed

    Feldt, Sarah; Wang, Jane X; Hetrick, Vaughn L; Berke, Joshua D; Zochowski, Michal

    2010-05-13

    Understanding the neural correlates of brain function is an extremely challenging task, since any cognitive process is distributed over a complex and evolving network of neurons that comprise the brain. In order to quantify observed changes in neuronal dynamics during hippocampal memory formation, we present metrics designed to detect directional interactions and the formation of functional neuronal ensembles. We apply these metrics to both experimental and model-derived data in an attempt to link anatomical network changes with observed changes in neuronal dynamics during hippocampal memory formation processes. We show that the developed model provides a consistent explanation of the anatomical network modifications that underlie the activity changes observed in the experimental data.

  6. 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.

  7. 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…

  8. 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.

  9. The effect of surface adsorption on tertiary structure formation in helical polymers.

    PubMed

    Williams, Matthew J; Bachmann, Michael

    2017-07-14

    The formation of tertiary structures made up of helical polymer segments is influenced by the introduction of an attractive substrate onto which the polymer can adsorb. We perform replica-exchange Monte Carlo simulations to study the formation of helical structures in the vicinity of an attractive generic substrate by means of a coarse-grained hybrid model and compare the structural phase space for both adsorbed and free helical polymers. We introduce suitable structural order parameters to understand the features of distinct structural phases. Hyperphase diagrams, parameterized by the torsional energy scale and temperature, enable the investigation of structural properties of entire classes of helical polymers.

  10. The effect of surface adsorption on tertiary structure formation in helical polymers

    NASA Astrophysics Data System (ADS)

    Williams, Matthew J.; Bachmann, Michael

    2017-07-01

    The formation of tertiary structures made up of helical polymer segments is influenced by the introduction of an attractive substrate onto which the polymer can adsorb. We perform replica-exchange Monte Carlo simulations to study the formation of helical structures in the vicinity of an attractive generic substrate by means of a coarse-grained hybrid model and compare the structural phase space for both adsorbed and free helical polymers. We introduce suitable structural order parameters to understand the features of distinct structural phases. Hyperphase diagrams, parameterized by the torsional energy scale and temperature, enable the investigation of structural properties of entire classes of helical polymers.

  11. 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.

  12. 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

  13. FORMATION AND STRUCTURE OF THE SPORE OF BACILLUS COAGULANS

    PubMed Central

    Ohye, D. F.; Murrell, W. G.

    1962-01-01

    Spore formation in Bacillus coagulans has been studied by electron microscopy using an epoxy resin (Araldite) embedding technique. The developmental stages from the origin of the initial spore septum to the mature spore were investigated. The two forespore membranes developed from the double layer of cytoplasmic membrane. The cortex was progressively deposited between these two membranes. The inner membrane finally became the spore protoplasmic membrane, and the outer membrane part of the inner spore coat or the outer spore coat itself. In the mature spore the completed integuments around the spore protoplasm consisted of the cortex, a laminated inner coat, and a dense outer coat. No exosporium was observed. The method of formation of the cortex and the spore coats is discussed. PMID:14481435

  14. 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

  15. Formation of periodic structures on glass with laser irradiation

    NASA Astrophysics Data System (ADS)

    Peng, Ying Zi; An, Cheng Wu; Wu, Dong Jiang; Hong, Ming Hui; Lu, Yong Feng; Chong, Tow Chong

    2003-07-01

    Regular and tidy periodic structures hae been directly induced on glasses using a CW CO2 laser beam with linear polarization. It is experimentally shown that precise periodic structures with the period of several microns can be formed by means of well-set laser parameters. The orientation of the periodic structures formed is the same as that of the laser polarization no matter what the scanning direction is. The occurrence of periodic structures is very sensitive to laser power level and scanning velocity. To obtain appropriate periodic patterns, a combined condition of laser energy and scanning velocity must be satisfied. The period, width and height of the structures are dependent on processing parameters. An interesting phenomenon is that the period decreases with increasing scanning velocity. Permanent relieves with periods, widths and heights varied with the laser parameters are also studied.

  16. Effect of poisson ratio on cellular structure formation.

    PubMed

    Bischofs, I B; Schwarz, U S

    2005-08-05

    Mechanically active cells in soft media act as force dipoles. The resulting elastic interactions are long ranged and favor the formation of strings. We show analytically that due to screening, the effective interaction between strings decays exponentially, with a decay length determined only by geometry. Both for disordered and ordered arrangements of cells, we predict novel phase transitions from paraelastic to ferroelastic and antiferroelastic phases as a function of the Poisson ratio.

  17. Network Formation: Neighborhood Structures, Establishment Costs, and Distributed Learning

    DTIC Science & Technology

    2012-09-19

    element equal to 1; and (iii) λ ≥ 0 is a parameter used to model possible perturbations in the decision making process, also called mutations [33...vol. 106, no. 2, pp. 265–295, 2002. [19] N. Olaizola and F. Valenciano, “One-way flow network formation under constraints,” University of the Basque ...57–84, 1993. [34] L. Breiman, Probability. Philadelphia: SIAM, 1992. [35] M. Kandori, G. Mailath, and R. Rob, “Learning, mutation , and long-run

  18. Granuloma formation by muramyl dipeptide associated with branched fatty acids, a structure probably essential for tubercle formation by Mycobacterium tuberculosis.

    PubMed Central

    Emori, K; Nagao, S; Shigematsu, N; Kotani, S; Tsujimoto, M; Shiba, T; Kusumoto, S; Tanaka, A

    1985-01-01

    Muramyl dipeptide, which does not induce epithelioid granuloma when injected alone dissolved in phosphate-buffered saline, could induce extensive granulomas in guinea pigs when chemically conjugated with branched, but not linear, fatty acids. Peptidoglycan fragments of Staphylococcus epidermidis could evoke epithelioid granulomas when incorporated in a water-in-oil emulsion. These findings suggest the importance of a lipid bound to muramyl dipeptide for granuloma formation. In view of the fact that mycobacteria uniquely contain large amounts of branched fatty acids, it was proposed that the complex of muramyl dipeptide and branched fatty acids, mostly mycolic acids, is a structure in tubercle bacilli responsible for tubercle formation. Images PMID:3924828

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Axion-like particle dark matter in the linear regime of structure formation

    NASA Astrophysics Data System (ADS)

    Yang, Qiaoli; di, Haoran

    2017-04-01

    If axion-like particles (ALPs) constitute a major part of dark matter (DM), due to their bosonic nature and a relatively small mass, they could behave differently from the pointlike dark matter particles on the formation of the cosmic structures. When studying the structure formation, it is often useful to consider DM as a special fluid with a given density and a given velocity. ALP fluid obeys the same continuity equation compared to the pointlike collisionless DM, but has a different first-order velocity equation. In the linear regime of structure formation, the resulted observational differences are negligible for the QCD axions but can be interesting for very light ALPs.

  7. Formation of core-shell structure in high entropy alloy coating by laser cladding

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Wu, Wanfei; He, Yizhu; Li, Mingxi; Guo, Sheng

    2016-02-01

    The formation of core-shell structure is an interesting phenomenon occurring during the solidification process, due to the liquid phase separation. The formation of core-shell structure in high-entropy alloys, a new class of advanced metallic materials, has not been reported previously, and thus constitutes an intriguing scientific question. Here, we firstly report the formation of core-shell structure in one laser cladded high-entropy alloy, where we show the nanosized-Y2O3 powder addition, serves as the catalyst for the liquid phase separation.

  8. Formation and Structure of Graphene Waves on Fe(110)

    NASA Astrophysics Data System (ADS)

    Vinogradov, N. A.; Zakharov, A. A.; Kocevski, V.; Rusz, J.; Simonov, K. A.; Eriksson, O.; Mikkelsen, A.; Lundgren, E.; Vinogradov, A. S.; Mårtensson, N.; Preobrajenski, A. B.

    2012-07-01

    A very rich Fe-C phase diagram makes the formation of graphene on iron surfaces a challenging task. Here we demonstrate that the growth of graphene on epitaxial iron films can be realized by chemical vapor deposition at relatively low temperatures, and that the formation of carbides can be avoided in excess of the carbon-containing precursors. The resulting graphene monolayer creates a novel periodically corrugated pattern on Fe(110). Using low-energy electron microscopy and scanning tunneling microscopy, we show that it is modulated in one dimension forming long waves with a period of ˜4nm parallel to the [001] direction of the substrate, with an additional height modulation along the wave crests. The observed topography of the graphene/Fe superstructure is well reproduced by density functional theory calculations, and found to result from a unique combination of the lattice mismatch and strong interfacial interaction, as probed by core-level photoemission and x-ray absorption spectroscopy.

  9. Formation and structure of graphene waves on Fe(110).

    PubMed

    Vinogradov, N A; Zakharov, A A; Kocevski, V; Rusz, J; Simonov, K A; Eriksson, O; Mikkelsen, A; Lundgren, E; Vinogradov, A S; Mårtensson, N; Preobrajenski, A B

    2012-07-13

    A very rich Fe-C phase diagram makes the formation of graphene on iron surfaces a challenging task. Here we demonstrate that the growth of graphene on epitaxial iron films can be realized by chemical vapor deposition at relatively low temperatures, and that the formation of carbides can be avoided in excess of the carbon-containing precursors. The resulting graphene monolayer creates a novel periodically corrugated pattern on Fe(110). Using low-energy electron microscopy and scanning tunneling microscopy, we show that it is modulated in one dimension forming long waves with a period of ∼4  nm parallel to the [001] direction of the substrate, with an additional height modulation along the wave crests. The observed topography of the graphene/Fe superstructure is well reproduced by density functional theory calculations, and found to result from a unique combination of the lattice mismatch and strong interfacial interaction, as probed by core-level photoemission and x-ray absorption spectroscopy.

  10. The Spatial Distribution of Star Formation in Galaxies: Observing the Emergence of Galactic Structure

    NASA Astrophysics Data System (ADS)

    Nelson, Erica June

    A high resolution measurement of the distribution of star formation within galaxies is key to understanding the emergence of galactic structure. The aim of this thesis is to understand how the structure of galaxies is built by developing a new method to spatially resolve their star formation. Using Ha maps for 2676 galaxies, this thesis shows where star formation is distributed in galaxies during the epoch 0.7 < z < 1.5 when a third of the total star formation in the history of the universe occurred. Across the star formation rate - stellar mass plane (the "main sequence"), star formation is `spatially coherent': in galaxies with higher than average star formation rates, Ha is enhanced throughout the disk; similarly, in galaxies with low star formation rates Ha is depressed throughout the disk. This places constraints both on the mechanisms for enhancing and quenching star formation as well as on how the structure of galaxies is built. The disk scale length of star formation in galaxies is larger than that of the stars, a direct demonstration that the disks of galaxies grow inside-out. While most star formation in most galaxies occurs in disks, not all of it does. With the first spatially resolved measurement of the Balmer decrement at z > 1, it can be seen that galaxies with M* > 1010M ⊙ have significant dust attenuation toward their centers. This means that we are witnessing the build-up of the dense stellar cores of massive galaxies through dust-obscured in-situ star formation. The most massive galaxies are thought to have formed their dense stellar cores at even earlier cosmic epochs. This thesis presents the first confirmed example of a massive galaxy core in the process of formation at z = 2.3. It has one of the highest velocity dispersions ever measured for a normal star forming galaxy and also appears to be building through very dense, dust-enshrouded star formation.

  11. Exploring Galaxy Formation and Evolution via Structural Decomposition

    NASA Astrophysics Data System (ADS)

    Kelvin, Lee; Driver, Simon; Robotham, Aaron; Hill, David; Cameron, Ewan

    2010-06-01

    The Galaxy And Mass Assembly (GAMA) structural decomposition pipeline (GAMA-SIGMA Structural Investigation of Galaxies via Model Analysis) will provide multi-component information for a sample of ~12,000 galaxies across 9 bands ranging from near-UV to near-IR. This will allow the relationship between structural properties and broadband, optical-to-near-IR, spectral energy distributions of bulge, bar, and disk components to be explored, revealing clues as to the history of baryonic mass assembly within a hierarchical clustering framework. Data is initially taken from the SDSS & UKIDSS-LAS surveys to test the robustness of our automated decomposition pipeline. This will eventually be replaced with the forthcoming higher-resolution VST & VISTA surveys data, expanding the sample to ~30,000 galaxies.

  12. 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.

  13. 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.

  14. Structural Basis for TSC-1 TSC-2 Complex Formation

    DTIC Science & Technology

    2008-03-01

    Cancer 4, 665-676. 3. Irminger-Finger, I., Leung, W. C., Li, J., Dubois- Dauphin , M., Harb, J., Feki, A., Jefford, C. E., Soriano, J. V., Jaconi, M...Brookhaven National Laboratory, Long Island , NY. The structure of the FE65 WW–Mn10 complex was solved by MAD methods, using SeMet-substituted FE65 WW

  15. 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.

    2017-01-01

    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 per cent) in the central cluster volume at all epochs. The dissipation via compressive modes is found to be more important (˜30 per cent of the total) only at large radii (≥0.5rvir) 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. Secondly, in the cluster interior vortex, stretching is dominant, although the other terms also contribute substantially.

  16. Structure and Formation of Elliptical and Spheroidal Galaxies

    NASA Astrophysics Data System (ADS)

    Kormendy, John; Fisher, David B.; Cornell, Mark E.; Bender, Ralf

    2009-05-01

    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 Sérsic log I vprop r 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 MVT <= -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 <= MVT <= -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 Sérsic 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 Sérsic-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 Sérsic indices n > 4 uncorrelated

  17. 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

  18. Formation of limit-periodic structures by quadrupole particles confined to a triangular lattice

    NASA Astrophysics Data System (ADS)

    Rutkowski, David M.; Marcoux, Catherine; Socolar, Joshua E. S.; Hall, Carol K.

    2017-01-01

    We have performed Monte Carlo (MC) simulations on two-dimensional systems of quadrupole particles confined to a triangular lattice in order to determine the conditions that permit the formation of a limit-periodic phase. We have found that limit-periodic structures form only when the rotations of the particles are confined to a set of six orientations aligned with the lattice directions. Related structures including striped and unidirectional rattler phases form when π /π 6 rotations or continuous rotations are allowed. Order parameters signaling the formation of the limit-periodic structure and related structures are measured as a function of temperature. Our findings on the formation of the limit-periodic structure elucidate features relevant to the experimental creation of such a structure, which is expected to have interesting vibrational and electromagnetic modes.

  19. Macroscopically structured polymer formation governed by spatial patterns in the Belousov Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Kalishyn, Yevhen Yu.; Khavrus, Vyacheslav O.; Strizhak, Peter E.; Seipel, Michael; Münster, Arno F.

    2002-09-01

    We report the formation of macroscopically structured cross-linked polyacrylamide hydrogel in the Belousov-Zhabotinsky (BZ) system (oxidation of malonic acid by bromate catalyzed by ferroin). Here, acrylamide, the cross-linker bis-acrylamide, and polymerization initiator are added into the BZ system. We show that the formation of waves and ripples in the polymer is governed by spatial structures emerging in the BZ system. Without any spatial structures in the BZ system only the formation of a spatially uniform polymer is observed. Without cross-linker, a spatially uniform polymer was observed as well. Structured polymer formation is caused by the interaction of chemical reactions in the BZ system and the polymerization process including gelation and cross-linking of the monomer units.

  20. 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.

  1. Experimental formation of brittle structural assemblages in oblique divergence

    NASA Astrophysics Data System (ADS)

    Smith, J. V.; Durney, D. W.

    1992-12-01

    A series of experiments is reported in which brittle minor structures are initiated in narrow deformation zones in clay under conditions of kinematically controlled oblique divergent displacement. Nineteen settings of boundary displacement angle were used from pure wrench to pure divergence under conditions favouring either faults (dry experiments) or extension fractures (wet experiments). Pure wrench produced the well known assemblage of Riedel strike-slip faults whereas experiments in pure divergence produced conjugate arrays of normal faults and extension fractures with a dihedral angle of 30° bisected by the direction of the zone, as has been described in rift zones. Experiments with boundary displacements at intermediate settings show a continuum of structural orientations and dihedral angles between these two extremes. A boundary between assemblages dominated by strike-slip faults and extensional faults was found at a displacement angle of 45° from the deformation zone. These results are interpreted kinematically in terms of: (1) principal axes of infinitesimal incremental strain; (2) material dilatancy control on shear structure dihedral angles; and (3) whether the vertical strain in divergent wrench settings is a thickening (strike-slip assemblage) or a thinning (normal fault assemblage).

  2. Formation of lanthanum beryllate real structure under different crystallization conditions

    SciTech Connect

    Tsvetkov, E.G. . E-mail: tsvetkov@uiggm.nsc.ru; Rylov, G.M.; Matrosov, V.N.

    2006-02-02

    The aim of this paper is to characterize the major structural defects of lanthanum beryllate single crystals grown by the Czochralski method, including those doped with rare-earth elements, and to reveal their relationship to specific properties of the crystal structure of La{sub 2}Be{sub 2}O{sub 5} and with their crystallization conditions. As a basic method for research, we used transmission X-ray topography. It was established that the defect state of La{sub 2}Be{sub 2}O{sub 5} crystals prepared by this method can be caused by different types of dislocations and their ordered assemblies, solid-phase inclusions of crucible metal and eutectically co-crystallizing phases, as well as by face growth sectors with elevated content of dopant. We show a possibility for growing single crystals of doped lanthanum beryllate having a minimum quantity of structural defects that could be suitable for manufacture of high quality laser rods.

  3. 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.

  4. Formation of Deformation Band Structures Normal to the Shear Plane

    NASA Astrophysics Data System (ADS)

    Balasko, C. M.; Schultz, R. A.

    2001-12-01

    Recent fieldwork has shown that many of the geometric relationships previously observed in cataclastic deformation bands are based on a two dimensional view of a three dimensional structure. When the bands are viewed in the shear direction lenses and inosculating bands are seen, as first noted by Aydin [1978] and later by many others. When viewed normal to the shear direction "ladder structures" (linked mode II echelon stepovers or duplexes) and conjugate structures are seen [Davis, 1999]. Davis [1999] grouped these two geometries as different classes of deformation bands and many have interpreted the duplexes as strain localization in Riedel shear zones. Here we demonstrate an alternative explanation. When viewed normal to the shear direction, deformation bands display either mutually crosscutting ("conjugate") sets or contractional stepovers ("duplexes") between interacting mode-II bands. Our field observations reveal that the principal difference between the two is the relative distance separating the parallel echelon bands. Bands that are sufficiently close interact mechanically to promote linking bands within the stepovers. These linking bands are younger than the bounding echelon bands. Because the orientations of bands within the stepovers are the same as that of "conjugate" bands that are more widely spaced, we infer that the magnitude of stress within the stepovers was increased somewhat over background values, but that stress rotations within the stepovers were negligible. To accomplish this, the echelon deformation bands must be strong relative to the host rock and accommodate only small offsets, leading to only minor perturbations of the local stress state in their vicinity. Ladder structure, "radiator rock" [Davis, 1999], and linked echelon stepovers demonstrate a progression from distributed to more localized strain of the sandstone, with the scale dependent on the size and offset magnitude of individual bands. Occurrence of linked echelon stepovers

  5. Fuel Structure and Pressure Effects on the Formation of Soot Particles in Diffusion Flames

    DTIC Science & Technology

    1990-05-01

    higher values of the pressure power dependence appear to be related to fuel structure effects , the direct nature of which remains to be understood...61102F 2308 A2 11. TITLE (Include Security Classification) "Fuel Structure and Pressure Effects on the Formation of Soot Particlesin Diffusion Flames...block number) Studies emphasizing the effects of fuel concentration and operating pressure on the formation of soot particles have been conducted in a

  6. Formation of Structure and Properties of Carbide-Free Bainite in Steel 30KhGSA

    NASA Astrophysics Data System (ADS)

    Panov, D. O.; Simonov, Yu. N.; Leont'ev, P. A.; Kaletin, A. Yu.; Georgiev, M. N.

    2016-05-01

    The process of formation of carbide-free bainite, its structure and properties in steel 30KhGSA are studied. The results of a dilatometric analysis are used to determine the temperature and time boundaries of formation of upper and lower carbide-free bainite. The methods of scanning and transmission electron microscopy are used to determine the special features of the structure of bainite as a function of the temperature of isothermal treatment.

  7. 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.

  8. 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).

  9. Dynamics versus structure: breaking the density degeneracy in star formation

    NASA Astrophysics Data System (ADS)

    Parker, Richard J.

    2014-12-01

    The initial density of individual star-forming regions (and by extension the birth environment of planetary systems) is difficult to constrain due to the `density degeneracy problem': an initially dense region expands faster than a more quiescent region due to two-body relaxation and so two regions with the same observed present-day density may have had very different initial densities. We constrain the initial densities of seven nearby star-forming regions by folding in information on their spatial structure from the {Q}-parameter and comparing the structure and present-day density to the results of N-body simulations. This in turn places strong constraints on the possible effects of dynamical interactions and radiation fields from massive stars on multiple systems and protoplanetary discs. We apply our method to constrain the initial binary population in each of these seven regions and show that the populations in only three - the Orion Nebula Cluster, ρ Oph, and Corona Australis - are consistent with having evolved from the Kroupa universal initial period distribution and a binary fraction of unity.

  10. 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.

  11. 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.

  12. Geochemistry and structure of the Hawley Formation: Northwestern Massachusetts

    SciTech Connect

    Kim, J.; Jacobi, R. . Dept. of Geology)

    1993-03-01

    The Hawley Formation in northwestern Massachusetts is composed of mafic and felsic, (trondhjemitic) igneous units and black sulfidic schists and quartzites. The dominant lithology is a thinly foliated hbd-plag.-chi-qtz.-Fe carbonate schist with or without hornblende fasicules. Locally, this schist has alternating folia of chl/hbd and plag. and probably has a volcaniclastic protolith. Distinct pillows and tuffs are observed locally. In general, these schists have flat REE patterns at 10X chondrite and plot as IABs on discrimination diagrams. In the eastern part of the Hawley, some amphibolites show concave upward REE patterns, plot in the IAT or boninite field on discrimination diagrams, and appear to have boninitic affinities. The felsic lithologies are trondhjemitic and are intrusive into the IAT/boninite amphibolites. The intrusive nature is based on the presence of mafic xenoliths and intruded rafts of country rock in the trondhjemite as well as the occurrence of thin tabular trondhjemite bodies in sharp contact with the surrounding amphibolite. The trondhjemite varies from coarse-grained weakly foliated qtz-plag.-biotite gneiss with probable relict igneous zoned plagioclases to finer-grained well foliated qtz-plag.-garnet-hbd gneiss. REE patterns for the trondhjemites are weakly U-shaped with moderate to pronounced negative Eu anomalies. The trondhjemites, surrounding amphibolites, and black sulfidic schists and quartzites of the eastern part of the Hawley are intruded by massive, granular, medium grained, plagioclase phenocryst amphibolites with chilled margins. These intrusive sills predate or are coeval with the dominant foliation in the Hawley. Both sills and country rock contain a contact-parallel foliation as well as a later foliation at a low angle to the earlier foliation. The sill amphibolites are high TiO2 high Zr varieties that plot as MORBs to WPBs on discrimination diagrams and exhibit slightly LREE enriched MORB-like to T-MORB REE patterns.

  13. 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.

  14. Comparison between structurally connected propellant formation flying and electromagnetic formation flying spacecraft configurations for Gen-X mission

    NASA Astrophysics Data System (ADS)

    Ahsun, Umair; Rodgers, Lennon; Miller, David W.

    2005-08-01

    Gen-X is a next generation concept x-ray telescope that would be approximately 1000-times more sensitive than current x-ray telescopes such as Chandra. Since Gen-X will require focal lengths greater than 50 meters, formation flying the detector module behind the primary mirror is a feasible option. This study investigates the viability of a novel approach referred to as Electromagnetic Formation Flight (EMFF). EMFF uses High Temperature Superconducting (HTS) coils to generate force and torque between the primary and detector modules. EMFF subsystems such as coils, thermal control and power are sized as a function of different system parameters such as slew rate, focal length and detector mass. To investigate the viability of EMFF, a comparison is made between three different techniques for keeping the detector at the focal length distance behind the primary mirror assembly. The first architecture uses a deployable truss to create a Structurally Connected X-ray telescope (SCX), the second uses propellant-based formation flying (PFF) and the third uses Electromagnetic Formation Flying (EMFF).

  15. 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.

  16. Change of surface structure upon foam film formation.

    PubMed

    Ridings, Christiaan; Andersson, Gunther G

    2015-03-16

    The charge distribution and coverage with surfactant molecules at foam film surfaces plays an important role in determining foam film structure and stability. This work uses the concentration depth profiling technique neutral impact collision ion scattering spectroscopy to experimentally observe the charge distribution in a foam film for the first time. The charge distribution at the surface of a foam film and the surface of the corresponding bulk liquid were measured for a cationic surfactant solution and the surface excess as well as the electric potential were determined. Describing the internal pressure of foam films by using the electrochemical potential is introduced as a new concept. The foam film can be seen to have a more negative surface charge compared to the bulk liquid surface due to re-arranging of the surfactant molecules. It is discussed how the change in surface excess and electric potential change the electrochemical potential and the stability of the foam film.

  17. Structure formation upon barocryodeformation of a steel of austenitic class

    NASA Astrophysics Data System (ADS)

    Antoshina, I. A.; Khaymovich, P. A.; Chernyaeva, E. V.; Shulgin, N. A.

    2016-10-01

    Data are given concerning the opportunity of applying barocryodeformation (plastic deformation under the conditions of severe uniform compression at cryogenic temperatures) to produce ultrafine-disperse martensitic structure in Kh18N10T steel (≤0.08 C, 18 Cr, 10 Ni, <0.7 Ti, ≤2 Mn, ≤0.8 Si (wt %)), which ensures an increase in the physicomechanical characteristics of material that are unattainable when using other types of treatment. Experiments are described that make it possible to explain the high (in spite of the presence of large forces of uniform compression) rate of completion of the martensitic transition upon the deformation of the steel under such conditions.

  18. Structural characterization of casein micelles: shape changes during film formation

    NASA Astrophysics Data System (ADS)

    Gebhardt, R.; Vendrely, C.; Kulozik, U.

    2011-11-01

    The objective of this study was to determine the effect of size-fractionation by centrifugation on the film structure of casein micelles. Fractionated casein micelles in solution were asymmetrically distributed with a small distribution width as measured by dynamic light scattering. Films prepared from the size-fractionated samples showed a smooth surface in optical microscopy images and a homogeneous microstructure in atomic force micrographs. The nano- and microstructure of casein films was probed by micro-beam grazing incidence small angle x-ray scattering (μGISAXS). Compared to the solution measurements, the sizes determined in the film were larger and broadly distributed. The measured GISAXS patterns clearly deviate from those simulated for a sphere and suggest a deformation of the casein micelles in the film.

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

    PubMed Central

    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

    2015-01-01

    Summary 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. PMID:26687357

  20. Structure and decomposition of the silver formate Ag(HCO2)

    NASA Astrophysics Data System (ADS)

    Puzan, Anna N.; Baumer, Vyacheslav N.; Mateychenko, Pavel V.

    2017-02-01

    Crystal structure of the silver formate Ag(HCO2) has been determined (orthorhombic, sp.gr. Pccn, a=7.1199(5), b=10.3737(4), c=6.4701(3)Å, V=477.88(4) Å3, Z=8). The structure contains isolated formate ions and the pairs Ag22+ which form the layers in (001) planes (the shortest Ag-Ag distances is 2.919 in the pair and 3.421 and 3.716 Å between the nearest Ag atoms of adjacent pairs). Silver formate is unstable compound which decompose spontaneously vs time. Decomposition was studied using Rietveld analysis of the powder diffraction patterns. It was concluded that the diffusion of Ag atoms leads to the formation of plate-like metal particles as nuclei in the (100) planes which settle parallel to (001) planes of the silver formate matrix.

  1. Structural characteristics of green tea catechins for formation of protein carbonyl in human serum albumin.

    PubMed

    Ishii, Takeshi; Mori, Taiki; Ichikawa, Tatsuya; Kaku, Maiko; Kusaka, Koji; Uekusa, Yoshinori; Akagawa, Mitsugu; Aihara, Yoshiyuki; Furuta, Takumi; Wakimoto, Toshiyuki; Kan, Toshiyuki; Nakayama, Tsutomu

    2010-07-15

    Catechins are polyphenolic antioxidants found in green tea leaves. Recent studies have reported that various polyphenolic compounds, including catechins, cause protein carbonyl formation in proteins via their pro-oxidant actions. In this study, we evaluate the formation of protein carbonyl in human serum albumin (HSA) by tea catechins and investigate the relationship between catechin chemical structure and its pro-oxidant property. To assess the formation of protein carbonyl in HSA, HSA was incubated with four individual catechins under physiological conditions to generate biotin-LC-hydrazide labeled protein carbonyls. Comparison of catechins using Western blotting revealed that the formation of protein carbonyl in HSA was higher for pyrogallol-type catechins than the corresponding catechol-type catechins. In addition, the formation of protein carbonyl was also found to be higher for the catechins having a galloyl group than the corresponding catechins lacking a galloyl group. The importance of the pyrogallol structural motif in the B-ring and the galloyl group was confirmed using methylated catechins and phenolic acids. These results indicate that the most important structural element contributing to the formation of protein carbonyl in HSA by tea catechins is the pyrogallol structural motif in the B-ring, followed by the galloyl group. The oxidation stability and binding affinity of tea catechins with proteins are responsible for the formation of protein carbonyl, and consequently the difference in these properties of each catechin may contribute to the magnitude of their biological activities.

  2. 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.

  3. Pattern guided structure formation in polymer films of asymmetric blends

    NASA Astrophysics Data System (ADS)

    Raczkowska, J.; Bernasik, A.; Budkowski, A.; Cyganik, P.; Rysz, J.; Raptis, I.; Czuba, P.

    2006-03-01

    Two off-critical blends of poly(2-vinylpyridine) and polystyrene, 2:3 and 3:2 (w:w) PVP:PS, were spin-cast (with varied domain scale R) onto periodically ( λ = 4 μm) patterned substrate. The pattern consisted of two alternating symmetric stripes: Au attracting PVP and neutral self-assembled monolayer. The resulting droplet-type morphologies were recorded with Scanning Force Microscopy and examined with integral geometry approach. PVP-rich islands of the 2:3 PVP:PS films form, for a wide R/ λ range, strongly anisotropic morphologies. They show up, for R/ λ ˜ 0.5, a weak λ/2-substructure of smaller PVP droplets in addition to the domains periodic with λ. The 3:2 blend exhibits morphologies with dominant λ-structure of PVP ribbons, which encircle PS droplets. For R/ λ ˜ 0.5, smaller PS domains are also present but no λ/2-substructure is formed. The | χE|-values of droplet surface density are reduced, as compared to homogeneous substrate, for the 3:2 blend (with | χE| → 0 for R ˜ λ). This effect is absent for the 2:3 mixture.

  4. 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. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Sunspot magnetic structure and interspot radio source formation

    NASA Astrophysics Data System (ADS)

    Solov'ev, A. A.

    2015-12-01

    The magnetic structure of a typical sunspot is represented as a set of three interacting magnetic fluxes. The first one, F1, escapes upward from the sunspot umbra and closes through the corona on the sunspot of opposite polarity. The second, F2, forms the sunspot penumbra. It includes Evershed flows emerging from the sunspot, the heavy photospheric plasma of which cannot be pulled up to the corona. For this reason, the F2 flux at the outer edge of the penumbra should close on the photosphere adjacent to the sunspot, i.e., here the F2 field changes sign. The third flux, F3, is the external magnetic field flux and has the same polarity as F1. Thus, magnetic fields of different signs occur near the outer boundary of the sunspot penumbra. Magnetic reconnections will inevitably take place there. Smalland multiscale current sheets in which particles are accelerated are formed. The latter fill short and low magnetic loops that connect sunspots of different polarity in the bipolar group and form interspot radio sources at the tops of these loops.

  6. 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.

  7. 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.

  8. 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.

  9. Family Structure History: Links to Relationship Formation Behaviors in Young Adulthood

    ERIC Educational Resources Information Center

    Ryan, Suzanne; Franzetta, Kerry; Schelar, Erin; Manlove, Jennifer

    2009-01-01

    Using data from three waves of the National Longitudinal Study of Adolescent Health (N = 4,667), we examined the intergenerational link between parental family structure history and relationship formation in young adulthood. We investigated (a) whether parental family structure history is associated with young adults' own relationship formation…

  10. Family Structure History: Links to Relationship Formation Behaviors in Young Adulthood

    ERIC Educational Resources Information Center

    Ryan, Suzanne; Franzetta, Kerry; Schelar, Erin; Manlove, Jennifer

    2009-01-01

    Using data from three waves of the National Longitudinal Study of Adolescent Health (N = 4,667), we examined the intergenerational link between parental family structure history and relationship formation in young adulthood. We investigated (a) whether parental family structure history is associated with young adults' own relationship formation…

  11. Peculiarities of the structure formation of nanoscale coatings from the vacuum arc discharge plasma

    NASA Astrophysics Data System (ADS)

    Kostrin, D. K.; Pikus, M. I.; Smirnov, E. A.; Lisenkov, A. A.

    2017-01-01

    In this paper features of the structure formation of nanoscale coatings (TiN)–(AlN)– (Ti–Al–N) in the vacuum arc discharge plasma are considered. The composition and structure of the formed nanoscale coatings are studied. The main factors influencing the quality of the formed coatings are shown.

  12. 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.

  13. 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.

  14. Cell surface attachment structures contribute to biofilm formation and xylem colonization by Erwinia amylovora.

    PubMed

    Koczan, Jessica M; Lenneman, Bryan R; McGrath, Molly J; Sundin, George W

    2011-10-01

    Biofilm formation plays a critical role in the pathogenesis of Erwinia amylovora and the systemic invasion of plant hosts. The functional role of the exopolysaccharides amylovoran and levan in pathogenesis and biofilm formation has been evaluated. However, the role of biofilm formation, independent of exopolysaccharide production, in pathogenesis and movement within plants has not been studied previously. Evaluation of the role of attachment in E. amylovora biofilm formation and virulence was examined through the analysis of deletion mutants lacking genes encoding structures postulated to function in attachment to surfaces or in cellular aggregation. The genes and gene clusters studied were selected based on in silico analyses. Microscopic analyses and quantitative assays demonstrated that attachment structures such as fimbriae and pili are involved in the attachment of E. amylovora to surfaces and are necessary for the production of mature biofilms. A time course assay indicated that type I fimbriae function earlier in attachment, while type IV pilus structures appear to function later in attachment. Our results indicate that multiple attachment structures are needed for mature biofilm formation and full virulence and that biofilm formation facilitates entry and is necessary for the buildup of large populations of E. amylovora cells in xylem tissue.

  15. 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.

  16. Effect of mesa structure formation on the electrical properties of zinc oxide thin film transistors.

    PubMed

    Singh, Shaivalini; Chakrabarti, P

    2014-05-01

    ZnO based bottom-gate thin film transistor (TFT) with SiO2 as insulating layer has been fabricated with two different structures. The effect of formation of mesa structure on the electrical characteristics of the TFTs has been studied. The formation of mesa structure of ZnO channel region can definitely result in better control over channel region and enhance value of channel mobility of ZnO TFT. As a result, by fabricating a mesa structured TFT, a better value of mobility and on-state current are achieved at low voltages. A typical saturation current of 1.85 x 10(-7) A under a gate bias of 50 V is obtained for non mesa structure TFT while for mesa structured TFT saturation current of 5 x 10(-5) A can be obtained at comparatively very low gate bias of 6.4 V.

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

    PubMed Central

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

    2016-01-01

    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

  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 roles of tertiary amine structure, background organic matter and chloramine species on NDMA formation.

    PubMed

    Selbes, Meric; Kim, Daekyun; Ates, Nuray; Karanfil, Tanju

    2013-02-01

    N-nitrosodimethylamine (NDMA), a probable human carcinogen, is a disinfection by-product that has been detected in chloraminated and chlorinated drinking waters and wastewaters. Formation mechanisms and precursors of NDMA are still not well understood. The main objectives of this study were to systematically investigate (i) the effect of tertiary amine structure, (ii) the effect of background natural organic matter (NOM), and (iii) the roles of mono vs. dichloramine species on the NDMA formation. Dimethylamine (DMA) and 20 different tertiary aliphatic and aromatic amines were carefully examined based on their functional groups attached to the basic DMA structure. The wide range (0.02-83.9%) of observed NDMA yields indicated the importance of the structure of tertiary amines, and both stability and electron distribution of the leaving group of tertiary amines on NDMA formation. DMA associated with branched alkyl groups or benzyl like structures having only one carbon between the ring and DMA structure consistently gave higher NDMA yields. Compounds with electron withdrawing groups (EWG) reacted preferentially with monochloramine, whereas compounds with electron donating group (EDG) showed tendency to react with dichloramine to form NDMA. When the selected amines were present in NOM solutions, NDMA formation increased for compounds with EWG while decreased for compounds with EDG. This impact was attributed to the competitions between NOM and amines for chloramine species. The results provided additional information to the commonly accepted mechanism for NDMA formation including chloramine species reacting with tertiary amines and the role of the leaving group on overall NDMA conversion.

  1. 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.

  2. Formation of the structures from dusty clusters in neon dc discharge under cooling

    NASA Astrophysics Data System (ADS)

    Polyakov, D. N.; Shumova, V. V.; Vasilyak, L. M.

    2016-11-01

    The formation of structures consisted of dusty clusters in plasma at the discharge tube cooling to a temperature of liquid nitrogen was discovered. The dependence of the reduced electric field in the positive column of a discharge on gas temperature was experimentally measured. Depending on the pressure of neon were observed the different structural transitions in the regions of growing current-voltage characteristics at low discharge currents ≤ 1 mA. It was found that the regions of existence of structured clusters and the regions of structural transitions were characterized by the higher values of the reduced electric field than the regions of destruction of ordered structures.

  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. Multilayered and digitally structured presentation formats of trustworthy recommendations: a combined survey and randomised trial

    PubMed Central

    Vandvik, Per Olav; Alonso-Coello, Pablo; Akl, Elie A; Thornton, Judith; Rigau, David; Adams, Katie; O'Connor, Paul; Guyatt, Gordon; Kristiansen, Annette

    2017-01-01

    Objectives To investigate practicing physicians' preferences, perceived usefulness and understanding of a new multilayered guideline presentation format—compared to a standard format—as well as conceptual understanding of trustworthy guideline concepts. Design Participants attended a standardised lecture in which they were presented with a clinical scenario and randomised to view a guideline recommendation in a multilayered format or standard format after which they answered multiple-choice questions using clickers. Both groups were also presented and asked about guideline concepts. Setting Mandatory educational lectures in 7 non-academic and academic hospitals, and 2 settings involving primary care in Lebanon, Norway, Spain and the UK. Participants 181 practicing physicians in internal medicine (156) and general practice (25). Interventions A new digitally structured, multilayered guideline presentation format and a standard narrative presentation format currently in widespread use. Primary and secondary outcome measures Our primary outcome was preference for presentation format. Understanding, perceived usefulness and perception of absolute effects were secondary outcomes. Results 72% (95% CI 65 to 79) of participants preferred the multilayered format and 16% (95% CI 10 to 22) preferred the standard format. A majority agreed that recommendations (multilayered 86% vs standard 91%, p value=0.31) and evidence summaries (79% vs 77%, p value=0.76) were useful in the context of the clinical scenario. 72% of participants randomised to the multilayered format vs 58% for standard formats reported correct understanding of the recommendations (p value=0.06). Most participants elected an appropriate clinical action after viewing the recommendations (98% vs 92%, p value=0.10). 82% of the participants considered absolute effect estimates in evidence summaries helpful or crucial. Conclusions Clinicians clearly preferred a novel multilayered presentation format to the

  5. A virtual structure approach to formation control of unicycle mobile robots using mutual coupling

    NASA Astrophysics Data System (ADS)

    Sadowska, Anna; van den Broek, Thijs; Huijberts, Henri; van de Wouw, Nathan; Kostić, Dragan; Nijmeijer, Henk

    2011-11-01

    In this article, the formation control problem for unicycle mobile robots is studied. A distributed virtual structure control strategy with mutual coupling between the robots is proposed. The rationale behind the introduction of the coupling terms is the fact that these introduce additional robustness of the formation with respect to perturbations as compared to typical leader-follower approaches. The applicability of the proposed approach is shown in simulations and experiments with a group of wirelessly controlled mobile robots.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Structural Analysis of G-Quadruplex Formation at the Human MEST Promoter

    PubMed Central

    Kennedy, Martin A.

    2017-01-01

    The promoter region of the imprinted gene MEST contains several motifs capable of forming G-quadruplex (G4) structures, which appear to contribute to consistent allelic dropout during polymerase chain reaction (PCR) analysis of this region. Here, we extend our previous analysis of MEST G4 structures by applying fluorescent footprinting techniques to assess non B-DNA structure and topology in dsDNA from the full MEST promoter region, under conditions that mimic PCR. We demonstrate that the buffer used for PCR provides an extremely favourable milieu for G4 formation, and that cytosine methylation helps maintain G4 structures during PCR. Additionally, we demonstrate G4 formation at motifs not previously identified through bioinformatic analysis of the MEST promoter, and provide nucleotide level resolution for topological reconstruction of these structures. These observations increase our understanding of the mechanisms through which methylation and G4 contribute towards allelic drop-out during PCR. PMID:28052120

  11. Star formation, structure, and formation mechanism of cometary globules: near-infrared observations of CG 1 and CG 2

    NASA Astrophysics Data System (ADS)

    Mäkelä, M. M.; Haikala, L. K.

    2013-02-01

    Context. Cometary globule (CG) 1 and CG 2 are "classic" cometary globules in the Gum Nebula. They have compact heads and long dusty tails that point away from the centre of the Gum Nebula. Aims: We study the structure of CG 1 and CG 2 and the star formation in them to find clues to the CG formation mechanism. The two possible CG formation mechanisms, radiation-driven implosion (RDI) and a supernova blast wave, produce a characteristic mass distribution where the major part of the mass is situated in either the head (RDI) or the tail (supernova blast). Methods: CG 1 and CG 2 were imaged in the near infrared (NIR) JsHKs bands. NIR photometry was used to locate NIR excess objects and to create visual extinction maps of the CGs. The AV maps allow us to analyse the large-scale structure of CG 1 and CG 2. Archival images from the WISE and Spitzer satellites and HIRES-processed IRAS images were used to study the globule's small-scale structure. Fits were made to the spectral energy distribution plots of the NIR-excess stars to estimate their age and mass. Results: In addition to the previously known CG 1 IRS 1 we discovered three new NIR-excess objects in IR imaging, two in CG 1 and one in CG 2. CG 2 IRS 1 is the first detection of star formation in CG 2. The objects are young low-mass stars. CG 1 IRS 1 is probably a class I protostar in the head of CG 1. CG 1 IRS 1 drives a bipolar outflow, which is very weak in CO, but the cavity walls are seen in reflected light in our NIR and in the Spitzer 3.6 and 4.5 μm images. Strong emission from excited polycyclic aromatic hydrocarbon particles and very small grains were detected in the CG 1 tail. The total mass of CG 1 in the observed area is 41.9 M⊙ of which 16.8 M⊙ lies in the head. For CG 2 these values are 31.0 M⊙ total and 19.1 M⊙ in the head. The observed mass distribution does not offer a firm conclusion for the formation mechanism of the two CGs: CG 1 is in too evolved a state, and in CG 2 part of the globule

  12. Controlling branching structure formation of the salivary gland by the degree of chitosan deacetylation.

    PubMed

    Hsiao, Ya-Chuan; Chen, Chun-Nan; Chen, You-Tzung; Yang, Tsung-Lin

    2013-09-01

    The salivary gland is characterized by ramified epithelial branches, a specific tissue structure responsible for saliva production and regulation. To regenerate the salivary gland function, it is important to establish the tissue structure. Chitosan is a deacetylated derivative of chitin with wide biomedical applications. Because of its deacetylated nature, chitosan has different properties when prepared with different degrees of deacetylation (DDA). However, the impact of chitosan DDA on the effect of regulating tissue structure formation remains unexplored. In this study, the embryonic murine submandibular gland (SMG) was used as a model to investigate the role of chitosan DDA in regulating tissue structure formation of the salivary gland. When chitin substrates with different DDA were used, the branching numbers of cultured SMG explants changed. Similar effects were observed in the culture with chitosan prepared using different degrees of acetylation. The mRNA expressions of type I and type III collagen were elevated in SMG explants with enhanced branching morphogenesis, as was the protein level. In addition to the amounts of collagen, type I and type III collagen fibers were spatially present in the epithelial-mesenchymal junction of developing branches in the culture with chitosan of a specific range of DDA. The branch-promoting effect of chitosan DDA was abolished when SMG explants were treated with collagenase, both early in the stage of branch initiation and with the establishment of the branching structure. The branch-promoting effect of chitosan DDA disappeared when antisense oligonucleotides were applied to specifically block type III collagen. This study demonstrates for the first time that DDA of chitosan affects tissue structure formation. The different proportions of side-chain components of chitin derivatives regulate structural formation of cultured SMG, indicating that DDA is an important parameter using chitosan as a biomaterial for tissue

  13. 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.

  14. 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.

  15. Formation of abnormal structures and their effects on the ductility of eutectoid steel

    NASA Astrophysics Data System (ADS)

    An, Kang-Suk; Jeong, Shin Woong; Bea, Hyeong Jun; Nam, Won Jong

    2016-11-01

    The formation of abnormal structures and their effects on reduction of area (RA) were investigated in eutectoid steels transformed at different temperatures ranging from 560 °C-650 °C. The occurrence of abnormal structures, such as upper bainite, degenerate pearlite, free ferrite, and grain boundary cementite, was confirmed. The volume fraction of upper bainite and degenerate pearlite decreased on increasing the transformation temperature, while the amount of free ferrite increased. As the transformation temperature increased, RA increased, reached a maximum, and then decreased, while the tensile strength continuously decreased. The crack formations during the tensile test could be classified into three types: tearing, shear cracking, and void formation/ coalescence. The decrease of the ductility at low transformation temperatures was attributed to the increased amount of upper bainite and degenerate pearlite, since the formation of cracks occurred by tearing interfaces or by void formation at abnormal structures during the tensile test. Meanwhile, the decrease in RA at high transformation temperatures was attributed to the occurrence of shear cracking rather than the presence of abnormal structures.

  16. Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

    PubMed

    White, Neil A; Hoogstraten, Charles G

    2017-09-01

    The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Formation of self-assembled micro- and nano-domain structures in uniaxial ferroelectrics

    NASA Astrophysics Data System (ADS)

    Shur, V. Ya; Shur, A. G.; Akhmatkhanov, A. R.

    2017-04-01

    We present the experimental study of appearance of domain wall shape instabilities and self-assembled domain structures in uniaxial ferroelectrics lithium niobate and lithium tantalate covered by artificial dielectric layer. The domain structure evolution has been considered as a manifestation of nucleation processes similar to the first order phase transformation. The necessary conditions for formation of self-assembled domain structures including the highly non-equilibrium switching conditions and stability of concave angles were proposed. The formation of the self-assembled domain shape instabilities under application of the uniform external electric field during switching (domain growth) and backswitching (domain shrinkage) has been studied experimentally with these conditions fulfilled. The formation of the bumps at the vortexes of hexagon domain for diameter above 3 - 5 μm with subsequent oriented growth was obtained in stoichiometric lithium tantalate. The formation of quasi-regular fish-bone domain structure has been revealed during spontaneous backswitching in Mg doped lithium niobate. The resulted structure consisted of the narrow residual domains with width from 200 to 500 nm appeared as a result of finger growth to the center of hexagon domain. The obtained decreasing of the number of the residual domains during growth has been attributed to strong electrostatic interaction of domain walls.

  18. Formation and atomic structure of boron nitride nanotubes with a cup-stacked structure

    NASA Astrophysics Data System (ADS)

    Oku, Takeo; Koi, Naruhiro; Suganuma, Katsuaki; Belosludov, Rodion V.; Kawazoe, Yoshiyuki

    2007-08-01

    Boron nitride (BN) nanotubes were synthesized by annealing Fe 4N/B powder at 1000 ∘C for 1 h in a nitrogen gas atmosphere, and large amounts of BN nanotubes with a cup-stacked structure were obtained after a purification process. The atomic structures of the cup-stacked BN nanotubes were investigated by high-resolution electron microscopy as well as molecular mechanics calculations, and compared with double walled BN nanotubes. The present results indicate that the cup-stacked structure with a cone angle of 20 ∘ is more stable than the structure with an angle of 38 ∘ and ordinary nanotube structures.

  19. 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.

  20. HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation.

    PubMed

    Park, Jihye; Lammers, Fabienne; Herr, Winship; Song, Ji-Joon

    2012-10-23

    Host-cell factor 1 (HCF-1) is an unusual transcriptional regulator that undergoes a process of proteolytic maturation to generate N- (HCF-1(N)) and C- (HCF-1(C)) terminal subunits noncovalently associated via self-association sequence elements. Here, we present the crystal structure of the self-association sequence 1 (SAS1) including the adjacent C-terminal HCF-1 nuclear localization signal (NLS). SAS1 elements from each of the HCF-1(N) and HCF-1(C) subunits form an interdigitated fibronectin type 3 (Fn3) tandem repeat structure. We show that the C-terminal NLS recruited by the interdigitated SAS1 structure is required for effective formation of a transcriptional regulatory complex: the herpes simplex virus VP16-induced complex. Thus, HCF-1(N)-HCF-1(C) association via an integrated Fn3 structure permits an NLS to facilitate formation of a transcriptional regulatory complex.

  1. Evaluation of the NCPDP Structured and Codified Sig Format for e-prescriptions.

    PubMed

    Liu, Hangsheng; Burkhart, Q; Bell, Douglas S

    2011-01-01

    To evaluate the ability of the structure and code sets specified in the National Council for Prescription Drug Programs Structured and Codified Sig Format to represent ambulatory electronic prescriptions. We parsed the Sig strings from a sample of 20,161 de-identified ambulatory e-prescriptions into variables representing the fields of the Structured and Codified Sig Format. A stratified random sample of these representations was then reviewed by a group of experts. For codified Sig fields, we attempted to map the actual words used by prescribers to the equivalent terms in the designated terminology. Proportion of prescriptions that the Format could fully represent; proportion of terms used that could be mapped to the designated terminology. The fields defined in the Format could fully represent 95% of Sigs (95% CI 93% to 97%), but ambiguities were identified, particularly in representing multiple-step instructions. The terms used by prescribers could be codified for only 60% of dose delivery methods, 84% of dose forms, 82% of vehicles, 95% of routes, 70% of sites, 33% of administration timings, and 93% of indications. The findings are based on a retrospective sample of ambulatory prescriptions derived mostly from primary care physicians. The fields defined in the Format could represent most of the patient instructions in a large prescription sample, but prior to its mandatory adoption, further work is needed to ensure that potential ambiguities are addressed and that a complete set of terms is available for the codified fields.

  2. Evaluation of the NCPDP Structured and Codified Sig Format for e-prescriptions

    PubMed Central

    Burkhart, Q; Bell, Douglas S

    2011-01-01

    Objective To evaluate the ability of the structure and code sets specified in the National Council for Prescription Drug Programs Structured and Codified Sig Format to represent ambulatory electronic prescriptions. Design We parsed the Sig strings from a sample of 20 161 de-identified ambulatory e-prescriptions into variables representing the fields of the Structured and Codified Sig Format. A stratified random sample of these representations was then reviewed by a group of experts. For codified Sig fields, we attempted to map the actual words used by prescribers to the equivalent terms in the designated terminology. Measurements Proportion of prescriptions that the Format could fully represent; proportion of terms used that could be mapped to the designated terminology. Results The fields defined in the Format could fully represent 95% of Sigs (95% CI 93% to 97%), but ambiguities were identified, particularly in representing multiple-step instructions. The terms used by prescribers could be codified for only 60% of dose delivery methods, 84% of dose forms, 82% of vehicles, 95% of routes, 70% of sites, 33% of administration timings, and 93% of indications. Limitations The findings are based on a retrospective sample of ambulatory prescriptions derived mostly from primary care physicians. Conclusion The fields defined in the Format could represent most of the patient instructions in a large prescription sample, but prior to its mandatory adoption, further work is needed to ensure that potential ambiguities are addressed and that a complete set of terms is available for the codified fields. PMID:21613642

  3. Optical formation of stable waveguiding structures from a photopolymerisable composition with a nonpolymerisable component

    SciTech Connect

    Mensov, Sergei N; Polushtaitsev, Yu V

    2012-06-30

    We report formation of stable dielectric waveguiding structures from a photopolymerisable composition containing a nonpolymerisable component by optical radiation. A computer simulation has shown that the use of nonpolymerisable additives not only retains the self-trapping modes of incident radiation but also provides matching conditions for the synthesised waveguiding structure with standard optical fibres at telecommunication wavelengths. The efficiency of these nonlinear wave processes for connecting single-mode fibres SMF-28 is experimentally confirmed.

  4. The Structural Formation and Physical Behaviour of Cross-Linked Epoxy Resins

    DTIC Science & Technology

    1981-04-01

    and by dicyandiamide or by catalytic polymerization are discussed and compared with those obtained by amine or anhydride curing. The highest...system. (e) Dicyandiamide cross-linking Structure formation reactions with dicyandiamide follow a complex pattern. Not only is one concerned with the...investigation4s one must consider cleavage of the dicyandiamide with the production of 2-aminooxazoline derivatives, in accordance with Fig 5. The structural

  5. Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42.

    PubMed

    Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Nussinov, Ruth

    2008-06-05

    We report all-atom molecular dynamics simulations of annular beta-amyloid (17-42) structures, single- and double-layered, in solution. We assess the structural stability and association force of Abeta annular oligomers associated through different interfaces, with a mutated sequence (M35A), and with the oxidation state (M35O). Simulation results show that single-layered annular models display inherent structural instability: one is broken down into linear-like oligomers, and the other collapses. On the other hand, a double-layered annular structure where the two layers interact through their C-termini to form an NC-CN interface (where N and C are the N and C termini, respectively) exhibits high structural stability over the simulation time due to strong hydrophobic interactions and geometrical constraints induced by the closed circular shape. The observed dimensions and molecular weight of the oligomers from atomic force microscopy (AFM) experiments are found to correspond well to our stable double-layered model with the NC-CN interface. Comparison with K3 annular structures derived from the beta 2-microglobulin suggests that the driving force for amyloid formation is sequence specific, strongly dependent on side-chain packing arrangements, structural morphologies, sequence composition, and residue positions. Combined with our previous simulations of linear-like Abeta, K3 peptide, and sup35-derived GNNQQNY peptide, the annular structures provide useful insight into oligomeric structures and driving forces that are critical in amyloid fibril formation.

  6. Effect of fuel molecular structure on soot formation in gas turbine engines

    NASA Technical Reports Server (NTRS)

    Naegeli, D. W.; Moses, C. A.

    1980-01-01

    A high-pressure research combustor operating over a wide range of burner inlet conditions was used to determine the effects of fuel molecular structure on soot formation. Six test fuels with equal hydrogen content (12.8 percent) were blended to stress different molecular components and final boiling points. The fuels containing high concentrations (20 percent) of poly-cyclic aromatics and partially saturated polycyclic structures such as tetralin, produced more soot than would be expected from a hydrogen content correlation for typical petroleum based fuels. However, fuels containing naphthenes, such as decalin, agreed with the hydrogen content correlation. The contribution of polycylic aromatics to soot formation was equivalent to a reduction in fuel hydrogen content of about 1%. The fuel sensitivity to soot formation due to the polycyclic aromatic contribution decreased as burner inlet pressure and fuel/air ratio increased.

  7. Effect of fuel molecular structure on soot formation in gas turbine engines

    NASA Technical Reports Server (NTRS)

    Naegeli, D. W.; Moses, C. A.

    1980-01-01

    A high-pressure research combustor operating over a wide range of burner inlet conditions was used to determine the effects of fuel molecular structure on soot formation. Six test fuels with equal hydrogen content (12.8 percent) were blended to stress different molecular components and final boiling points. The fuels containing high concentrations (20 percent) of poly-cyclic aromatics and partially saturated polycyclic structures such as tetralin, produced more soot than would be expected from a hydrogen content correlation for typical petroleum based fuels. However, fuels containing naphthenes, such as decalin, agreed with the hydrogen content correlation. The contribution of polycylic aromatics to soot formation was equivalent to a reduction in fuel hydrogen content of about 1%. The fuel sensitivity to soot formation due to the polycyclic aromatic contribution decreased as burner inlet pressure and fuel/air ratio increased.

  8. Structure Formation of Spinning Polymer Fibers Studied by Monte Carlo Simulations

    NASA Astrophysics Data System (ADS)

    Hu, Wenbing; Liu, Qi

    2014-03-01

    We performed dynamic Monte Carlo simulations of lattice polymer solutions to investigate the solidification process in a fluid filament after extruded from a spinneret into a coagulation bath. We observed skin-core structure formation under the interplay of phase separation and polymer crystallization. We found that a radial temperature gradient dominates the formation of a highly oriented solid skin, while a radial influx of non-solvent dominates the formation of a concentrated core. The processing parameters can adjust and even eliminate the skin-core structure in the fibers. Our molecular-level observations facilitate a better understanding of the fiber processing for the industry to make high quality fibers. The financial support of National Natural Science Foundation of China (Grant No. 20825415 and 21274061) and the National Basic Research Program of China (Grant No. 2011CB606100) is appreciated.

  9. A standard format for reporting atomic positions in measured or calculated surface structures: The CIF file

    NASA Astrophysics Data System (ADS)

    Marks, Laurence D.

    2010-06-01

    In his editorial in this issue, the editor-in-chief emphasizes the editorial policy that any paper which involves a crystallographic structure (whether experimentally measured or theoretically calculated) must also include a complete listing of all the atomic positions within the crystal structure, either as supporting information or directly within the paper itself. He also strongly recommends that the complete crystallographic data set be included as supporting information. At the request of the editor-in-chief, I outline here the reasons why this is scientifically desirable. Furthermore, I propose here that the Surface Science community adopt the same standard format for reporting these as is already widely used in bulk crystallography publications, namely the inclusion of a Crystallographic Information Format file (or CIF file) as supporting information. Finally, I describe the details of this specific file format, with illustrative examples.

  10. 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.

  11. Formation and characterization of supramolecular structures of β-lactoglobulin and lactoferrin proteins.

    PubMed

    Saraiva, Camila Santiago; Dos Reis Coimbra, Jane Sélia; de Carvalho Teixeira, Alvaro Vianna Novaes; de Oliveira, Eduardo Basílio; Teófílo, Reinaldo Francisco; da Costa, Angélica Ribeiro; de Almeida Alves Barbosa, Éverton

    2017-10-01

    Combination of β-lactoglobulin (β-Lg) and lactoferrin (Lf), biomacromolecules derived from bovine whey, was used in the formation of supramolecular structures by thermal gelation technique to adjust the pH. Furthermore, the influence of the molar ratio, temperature, pH, and heating time in the formation of supramolecular structures were also studied. The characterization of the protein supramolecular structures was performed using dynamic light scattering, zeta potential measurements, molecular spectrofluorimetry, and circular dichroism spectroscopy. The thermal behavior of the pure proteins was investigated by differential scanning calorimetry. The protein denaturation temperatures were of around 85°C for the β-Lg and around 52°C and 85°C (a small portion) for the Lf. The protein molar ratio of 2:1 Lf/β-Lg was used to form the structures, whose characterization showed that the best conditions of supramolecular structure formation occurred at pH6.5 and at temperatures of 62.5°C. In those conditions, more stable systems with reduced hydrophobic surface and average sizes between 30 and 100nm were generated. The correlation between pH and temperature suggests that the method of preparation of the supramolecular structure affects its size during storage. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Large-scale magnetic structure formation in three-dimensional magnetohydrodynamic turbulence

    SciTech Connect

    Malapaka, Shiva Kumar; Müller, Wolf-Christian

    2013-11-20

    The inverse cascade of magnetic helicity in three-dimensional magnetohydrodynamic (3D-MHD) turbulence is believed to be one of the processes responsible for large-scale magnetic structure formation in astrophysical systems. In this work, we present an exhaustive set of high-resolution direct numerical simulations of both forced and decaying 3D-MHD turbulence, to understand this structure formation process. It is first shown that an inverse cascade of magnetic helicity in small-scale driven turbulence does not necessarily generate coherent large-scale magnetic structures. The observed large-scale magnetic field, in this case, is severely perturbed by magnetic fluctuations generated by the small-scale forcing. In the decaying case, coherent large-scale structures form similarly to those observed astronomically. Based on the numerical results, the formation of large-scale magnetic structures in some astrophysical systems is suggested to be the consequence of an initial forcing that imparts the necessary turbulent energy into the system, which, after the forcing shuts off, decays to form the large-scale structures. This idea is supported by representative examples, e.g., clusters of galaxies.

  13. 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.

  14. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

    PubMed Central

    Pavelka, Antonín; Valasatava, Yana; Prlić, Andreas

    2017-01-01

    Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis. PMID:28574982

  15. Formation and Properties of Laser-Induced Periodic Surface Structures on Different Glasses.

    PubMed

    Gräf, Stephan; Kunz, Clemens; Müller, Frank A

    2017-08-10

    The formation and properties of laser-induced periodic surface structures (LIPSS) was investigated on different technically relevant glasses including fused silica, borosilicate glass, and soda-lime-silicate glass under irradiation of fs-laser pulses characterized by a pulse duration τ = 300 fs and a laser wavelength λ = 1025 nm. For this purpose, LIPSS were fabricated in an air environment at normal incidence with different laser peak fluence, pulse number, and repetition frequency. The generated structures were characterized by using optical microscopy, scanning electron microscopy, focused ion beam preparation and Fast-Fourier transformation. The results reveal the formation of LIPSS on all investigated glasses. LIPSS formation on soda-lime-silicate glass is determined by remarkable melt-formation as an intra-pulse effect. Differences between the different glasses concerning the appearing structures, their spatial period and their morphology were discussed based on the non-linear absorption behavior and the temperature-dependent viscosity. The findings facilitate the fabrication of tailored LIPSS-based surface structures on different technically relevant glasses that could be of particular interest for various applications.

  16. 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

  17. Alternative DNA structure formation in the mutagenic human c-MYC promoter.

    PubMed

    Del Mundo, Imee Marie A; Zewail-Foote, Maha; Kerwin, Sean M; Vasquez, Karen M

    2017-05-05

    Mutation 'hotspot' regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood. To address this issue, we investigated the folding preferences of oligonucleotides from a chromosomal breakpoint hotspot in the human c-MYC oncogene containing both potential G4-forming and H-DNA-forming elements. We characterized the structures formed in the presence of G4-DNA-stabilizing K+ ions or H-DNA-stabilizing Mg2+ ions using multiple techniques. We found that under conditions favorable for H-DNA formation, a stable intramolecular triplex DNA structure predominated; whereas, under K+-rich, G4-DNA-forming conditions, a plurality of unfolded and folded species were present. Thus, within a limited region containing sequences with the potential to adopt multiple structures, only one structure predominates under a given condition. The predominance of H-DNA implicates this structure in the instability associated with the human c-MYC oncogene. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Formation of met-cars and face-centered cubic structures. Thermodynamically or kinetically controlled

    SciTech Connect

    Wei, S.; Guo, B.C.; Deng, H.T.; Kerns, K.; Purnell, J.; Buzza, S.A.; Castleman, A.W. Jr. )

    1994-05-18

    On the basis of a series of experimental studies from our laboratory, it is well established that metallocarbohedrenes, or Met-Cars for short, are a stable class of cluster materials. To account for their exceptional stability, we initially proposed a pentagonal dodecahedron structure. This cage-like structure is consistent with all the experimental findings. In general, there are two possible structures that can be developed in these metal-carbon systems, i.e., Met-Cars and cubes. Since only one structural pattern is generally observed for one particular cluster system, it has been suggested that their thermodynamical stabilities might be responsible for the selective formation of specific structures, e.g., Met-Cars or fcc structures. Herein, we present new experimental results on the system of Nb[sub m]C[sub n] under various conditions. It is shown that the experimental conditions are extremely critical for the formation of either Met-Cars or cubic structures, as predicted by Reddy and Khanma. Moreover, the new data show that the cubic structures do not develop on top of Met-Cars, but rather, they grow independently. The experiments were performed by using both time-of-flight and quadrupole mass spectrometer techniques coupled with a laser vaporization source. 23 refs., 1 fig.

  19. 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.

  20. Alternative DNA structure formation in the mutagenic human c-MYC promoter

    PubMed Central

    del Mundo, Imee Marie A.; Zewail-Foote, Maha; Kerwin, Sean M.

    2017-01-01

    Abstract Mutation ‘hotspot’ regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood. To address this issue, we investigated the folding preferences of oligonucleotides from a chromosomal breakpoint hotspot in the human c-MYC oncogene containing both potential G4-forming and H-DNA-forming elements. We characterized the structures formed in the presence of G4-DNA-stabilizing K+ ions or H-DNA-stabilizing Mg2+ ions using multiple techniques. We found that under conditions favorable for H-DNA formation, a stable intramolecular triplex DNA structure predominated; whereas, under K+-rich, G4-DNA-forming conditions, a plurality of unfolded and folded species were present. Thus, within a limited region containing sequences with the potential to adopt multiple structures, only one structure predominates under a given condition. The predominance of H-DNA implicates this structure in the instability associated with the human c-MYC oncogene. PMID:28334873

  1. How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy

    PubMed Central

    2015-01-01

    There is an enormous amount of interest in the structures and formation mechanisms of amyloid fibers. In this Perspective, we review the most common structural motifs of amyloid fibers and discuss how infrared spectroscopy and isotope labeling can be used to identify their structures and aggregation kinetics. We present three specific strategies, site-specific labeling to obtain residue-by-residue structural information, isotope dilution of uniformly labeled proteins for identifying structural folds and protein mixtures, and expressed protein ligation for studying the domain structures of large proteins. For each of these methods, vibrational couplings are the source of the identifying features in the infrared spectrum. Examples are provided using the proteins hIAPP, Aβ, polyglutamine, and γD-crystallin. We focus on FTIR spectroscopy but also describe new observables made possible by 2D IR spectroscopy. PMID:24932380

  2. 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.

  3. 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

  4. The formation mechanism of the periodic nanograting structure by the Weibel instability

    NASA Astrophysics Data System (ADS)

    Gouda, A. M.; Sakagami, H.; Ogata, T.; Hashida, M.; Sakabe, S.

    2016-04-01

    The two-dimensional particle in cell code has been used to demonstrated the formation mechanism for the periodic nanograting structure using 500-fs pulses of an ultra-fast laser with wavelength 800 nm, incidence angle 0°, linearly-polarized, and intensity 1018 W/cm2 µm2 in hydrogen plasma. The periodic nanograting structure has been clearly self-organized at the boundary between the preformed plasma and the dense plasma at t = 250 fs. By time evolution of the magnetic field and the current density in the dense plasma, it has been found that the Weibel instability plays a significant role to form the periodic nanograting structure.

  5. 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)

  6. Formation of Ni(OH)2 hybrid structures on Carbon Cloth

    NASA Astrophysics Data System (ADS)

    Dahonog, L. A.; Ocon, J. D.; Balela, M. D. L.

    2017-05-01

    Nickel hydroxide [Ni(OH)2] structures were successfully grown on carbon cloth via hydrothermal treatment followed by annealing. The Ni(OH)2 structures grown on carbon cloth were characterized using X-Ray Diffraction (XRD) and Scanning Electron Microscope (SEM) analysis. XRD analysis revealed the formation of α and β phases of Ni(OH)2. Microflowers and interconnected grass-like particles were observed on the surface of the carbon cloth. The as-prepared sample could be a promising material for the fabrication of high energy storage devices because of its unique structures.

  7. Organogel formation rationalized by Hansen solubility parameters: influence of gelator structure.

    PubMed

    Bonnet, Julien; Suissa, Gad; Raynal, Matthieu; Bouteiller, Laurent

    2015-03-21

    Some organic compounds form gels in liquids by forming a network of anisotropic fibres. Based on extensive solubility tests of four gelators of similar structures, and on Hansen solubility parameter formalism, we have probed the quantitative effect of a structural variation of the gelator structure on its gel formation ability. Increasing the length of an alkyl group of the gelator obviously reduces its polarity, which leads to a gradual shift of its solubility sphere towards lower δp and δh values. At the same time, its gelation sphere is shifted - to a much stronger extent - towards larger δp and δh values.

  8. 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.

  9. Using chemical shifts to determine structural changes in proteins upon complex formation.

    PubMed

    Cavalli, Andrea; Montalvao, Rinaldo W; Vendruscolo, Michele

    2011-08-04

    Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the determination of the structures of protein complexes is that the changes in the chemical shifts upon binding tend to be rather limited and indeed often smaller than the standard errors made in the predictions of chemical shifts corresponding to given structures. We present a procedure that, despite this problem, enables one to use of chemical shifts to determine accurately the conformational changes that take place upon complex formation.

  10. 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.

  11. A Novel Structured Format for Engaging Pharmacy Students in Bioethics Discussions.

    PubMed

    Horton, Evan R; Morin, Anna; Pervanas, Helen C; Mukherjee, S Mimi; Belliveau, Paul

    2014-11-15

    To describe an active, structured ethics/professionalism discussion format developed for an elective course titled Ethics and Professionalism in Pharmacy. The format uses the acronym ETHICS (Evaluate, Teach, Hear, Interview, Concede, Self-reflect). Before class, students evaluated (Evaluate) literature pertaining to ethics/professionalism topics. Class consisted of faculty-led ethics/professionalism lecture (Teach), student-driven, case discussion, and online self-reflection. Guided by Hear, Interview, and Concede, groups addressed cases from stakeholder perspectives (patient, pharmacist, etc.) considering ethical rules and principles. At the end of class, students answered self-reflection questions. Precourse and postcourse surveys evaluated the impact on students' perceptions of ethical and professional tenets. The format allowed students to actively engage in ethics/professionalism discussions, transforming class into an interactive, structured, student-centered session with self-reflection. The format allowed application of concepts to controversial situations. Although the format was created for a pharmacy elective, it is adaptable to any teaching situation.

  12. A Novel Structured Format for Engaging Pharmacy Students in Bioethics Discussions

    PubMed Central

    Morin, Anna; Pervanas, Helen C.; Mukherjee, S. Mimi; Belliveau, Paul

    2014-01-01

    Objective: To describe an active, structured ethics/professionalism discussion format developed for an elective course titled Ethics and Professionalism in Pharmacy. Design: The format uses the acronym ETHICS (Evaluate, Teach, Hear, Interview, Concede, Self-reflect). Before class, students evaluated (Evaluate) literature pertaining to ethics/professionalism topics. Class consisted of faculty-led ethics/professionalism lecture (Teach), student-driven, case discussion, and online self-reflection. Guided by Hear, Interview, and Concede, groups addressed cases from stakeholder perspectives (patient, pharmacist, etc.) considering ethical rules and principles. At the end of class, students answered self-reflection questions. Precourse and postcourse surveys evaluated the impact on students’ perceptions of ethical and professional tenets. Assessment: The format allowed students to actively engage in ethics/professionalism discussions, transforming class into an interactive, structured, student-centered session with self-reflection. Conclusion: The format allowed application of concepts to controversial situations. Although the format was created for a pharmacy elective, it is adaptable to any teaching situation. PMID:26056409

  13. Early Structure Formation from Primordial Density Fluctuations with a Blue, Tilted Power Spectrum

    NASA Astrophysics Data System (ADS)

    Hirano, Shingo; Zhu, Nick; Yoshida, Naoki; Spergel, David; Yorke, Harold W.

    2015-11-01

    While observations of large-scale structure and the cosmic microwave background (CMB) provide strong constraints on the amplitude of the primordial power spectrum (PPS) on scales larger than 10 Mpc, the amplitude of the power spectrum on sub-galactic length scales is much more poorly constrained. We study early structure formation in a cosmological model with a blue-tilted PPS. We assume that the standard scale-invariant PPS is modified at small length scales as P(k)∼ {k}{m{{s}}} with ms > 1. We run a series of cosmological hydrodynamic simulations to examine the dependence of the formation epoch and the characteristic mass of primordial stars on the tilt of the PPS. In models with ms > 1, star-forming gas clouds are formed at z > 100 when the formation of hydrogen molecules is inefficient because the intense CMB radiation destroys chemical intermediates. Without efficient coolant, the gas clouds gravitationally contract while retaining a high temperature. The protostars formed in such “hot” clouds grow very rapidly through accretion to become extremely massive stars that may leave massive black holes with a few hundred solar masses at z > 100. The shape of the PPS critically affects the properties and the formation epoch of the first generation of stars. Future experiments on CMB polarization and spectrum distortion may provide important information on the nature of the first stars and their formation epoch, and hence on the shape of the small-scale power spectrum.

  14. 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.

  15. Observation of metastable self-organised structure during porous silicon formation

    NASA Astrophysics Data System (ADS)

    Skorupska, K.; Jakubowicz, J.; Jungblut, H.; Lewerenz, H. J.

    2004-07-01

    The initial processes leading from an atomically flat Si surface to porous silicon formation are not well known and detailed surface analytical investigations on the dissolution steps are still lacking. By performing electrochemical experiments in dilute ammonium fluoride solutions at moderate pH values, we are able to investigate the process of dissolution from first pit formation to the formation of transitory mesa-type terraces on atomically flat n-Si(111) by atomic force microscopy. Mesa-type structures with flat extended terraces surrounded by strongly corrugated areas are observed after different conditioning procedures. The mesas exhibit terrace edges aligned with respect to preferred surface orientations, which results in pentagonal, hexagonal or higher composed structures. The findings can be interpreted in terms of the formation of sidewalls exhibiting only a limited number of crystal orientations: {111}, {110} and {113}. Because these faces can be electrochemically H terminated in a 1×1 manner, we suggest that their stability accounts for the variety of observed structures.

  16. 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

  17. 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.

  18. 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.

  19. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

    PubMed

    Sloma, Michael F; Mathews, David H

    2016-12-01

    RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  20. 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.

  1. 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.

  2. An Objective Structured Clinical Examination to Improve Formative Assessment for Senior Pediatrics Residents

    PubMed Central

    Mangold, Karen A.; Jeffers, Justin M.; Burns, Rebekah A.; Trainor, Jennifer L.; Unti, Sharon M.; Eppich, Walter; Adler, Mark D.

    2015-01-01

    Background Residency programs are developing new methods to assess resident competence and to improve the quality of formative assessment and feedback to trainees. Simulation is a valuable tool for giving formative feedback to residents. Objective To develop an objective structured clinical examination (OSCE) to improve formative assessment of senior pediatrics residents. Methods We developed a multistation examination using various simulation formats to assess the skills of senior pediatrics residents in communication and acute resuscitation. We measured several logistical factors (staffing and program costs) to determine the feasibility of such a program. Results Thirty-one residents participated in the assessment program over a 3-month period. Residents received formative feedback comparing their performance to both a standard task checklist and to peers' performance. The program required 16 faculty members per session, and had a cost of $624 per resident. Conclusions A concentrated assessment program using simulation can be a valuable tool to assess residents' skills in communication and acute resuscitation and provide directed formative feedback. However, such a program requires considerable financial and staffing resources. PMID:26457159

  3. 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.

  4. Gum formation tendencies of olefinic structures in gasoline and synergistic effect of sulphur compounds

    SciTech Connect

    Nagpal, J.M.; Joshi, G.C.; Aswal, D.S.

    1995-04-01

    The high octane gasoline pool contains varying amounts of cracked naphthas as an important ingredient in formulating high octane lead free gasoline. The cracked naphthas are largely from Fluidized Catalytic Cracking (FCC) units and to lesser extend from thermal cracking units. While the role of olefinic unsaturation in gum formation during storage of gasoline has been extensively studied, there is little published work on contribution of individual olefin types in storage stability and gum formation tendency of gasoline containing these compound types. In the present work we report our results on storage stability and gum formation tendency of different olefin types present in cracked naphthas through model compound matrix. It is found that cyclic olefins and cyclic diolefins are the most prolific gum formers. We have also studied the role of sulfur compounds present in the gasolines on gum formation tendency of olefins. While thiols enhance gum formation from all olefinic types, sulfides and disulfides interact depending on the structure of olefins. These can have either an accelerating, or inhibiting effect on gum formation.

  5. 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

  6. 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.

  7. 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.

  8. Formation of undulated lamellar structure from ABC block terpolymer blends with different chain lengths

    NASA Astrophysics Data System (ADS)

    Matsushita, Yushu; Suzuki, Jiro; Izumi, Yuuki; Matsuoka, Kohei; Takahashi, Shuji; Aoyama, Yoshitaka; Mihira, Tomohiro; Takano, Atsushi

    2010-11-01

    The effect of molecular weight distribution of ABC linear terpolymers on the formation of periodic structures was investigated. Three poly(isoprene-b-styrene-b-2-vinylpridine) triblockterpolymers with molecular weights of 26k, 96k, and 150k were blended variously. Three-phase, four-layer lamellar structures were observed when polydispersity index (PDI) was low, but it has been found that simple lamellar structure with flat surface transforms into an undulated lamellar one, where two interfaces, i.e., I/S and S/P, are both undulated, and they are synchronizing each other if PDI exceeds the critical value. This new structure could be formed due to the periodic and "weak" localization of three chains along the domain interfaces, which produces periodic surfaces with nonconstant mean curvatures. With further increase of PDI, the blend macroscopically phase-separated into different microphase-separated structures.

  9. Development of structure in natural silk spinning and poly(vinyl alcohol) hydrogel formation

    NASA Astrophysics Data System (ADS)

    Willcox, Patricia Jeanene

    This research involves the characterization of structure and structure formation in aqueous systems. Particularly, these studies investigate the effect of various processing variables on the structure formation that occurs upon conversion from aqueous solution to fiber or hydrogel. The two processes studied include natural silk fiber spinning and physical gelation of poly(vinyl alcohol), PVOH, in water. The techniques employed combine cryogenic technology for sample preparation and direct observation by transmission electron microscopy with electron diffraction, atomic force microscopy, optical rheometry, X-ray scattering and optical microscopy. In order to explore the full range of structure formation in natural silk spinning, studies are conducted in vivo and in vitro. In vivo structural investigations are accomplished through the cryogenic quenching and subsequent microtoming of live silk-spinning animals, Nephila clavipes (spider) and Bombyx mori (silkworm). Observations made using transmission electron microscopy, electron diffraction and atomic force microscopy indicate a cholesteric liquid crystalline mesophase of aqueous silk fibroin in both species. The mechanism of structure formation in solution is studied in vitro using optical rheometry on aqueous solutions made from regenerated Bombyx mori cocoon silk. Concentrated solutions exhibit birefringence under flow, with a wormlike conformation of the silk molecules in concentrated salt solution. Changes in salt concentration and pH of the aqueous silk solutions result in differing degrees of alignment and aggregation. These results suggest that structural control in the natural silk spinning process is accomplished by chemical manipulation of the electrostatic interactions and hydrogen bonding between chains. Application of cryogenic methods in transmission electron microscopy also provides a unique look at hydration-dependent structures in gels of poly(vinyl alcohol) produced by freeze-thaw processing

  10. Dissipation of MeV ion energy in solids, structure formation and phase changes

    NASA Astrophysics Data System (ADS)

    Sen, P.; Aggarwal, G.; Tiwari, U.

    1998-12-01

    Instabilities arise out of dynamic events and can lead to nonequilibrium (self-organization) processes. Ion irradiation is by nature a nonequilibrium process and hence formation of structures, metastable or otherwise is to be expected. Recently, it has been theoretically predicted that metals under ion irradiation can lead to dissipative structure formation arising out of radiation damage and their subsequent annealing. The possibility of direct observation of such structures in metals under irradiation is however reduced due to nonavailability of a large concentration of defects (mainly point defects) at any point of time. In this experimental presentation we show that this can be overcome through the involvement of microstructural imperfections which rearrange during irradiation. Employing microstructurally impure specimens of Fe and Ni, it is shown that heavy ions dissipate their electronic energy to modify atomic arrangements at the microstructure. The increased concentration of defects (atomic rearrangements), amenable to statistical decay is shown to produce effects in the 4-probe resistivity measurements which we assign to dissipative structure formation.

  11. The formation, function and regulation of amyloids: insights from structural biology.

    PubMed

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. © 2016 The Association for the Publication of the Journal of Internal Medicine.

  12. Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

    SciTech Connect

    Hudry, Damien; Abeykoon, A. M. M.; Dooryhee, E.; Nykypanchuk, D.; Dickerson, J. H.

    2016-11-23

    Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF4:Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF4:Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF4:Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group P$\\bar{6}$ is the one that best describes the crystal structure of NaGdF4:Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide

  13. Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

    DOE PAGES

    Hudry, Damien; Abeykoon, A. M. M.; Dooryhee, E.; ...

    2016-11-23

    Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF4:Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF4:Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF4:Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group Pmore » $$\\bar{6}$$ is the one that best describes the crystal structure of NaGdF4:Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide-doped nanostructures.« less

  14. Evaluation of Reliability in Structured Viva Voce As a Formative Assessment of Dental Students.

    PubMed

    Ganji, Kiran Kumar

    2017-05-01

    An oral assessment is a direct way to assess students' learning outcomes by questioning them. The format of oral examinations (viva voce) is not uniform. Unlike interviews, which usually have structured question lists, oral assessments usually do not have a question structure. Structured viva voce overcomes the weaknesses of traditional viva voce The aim of this study was to assess the reliability of structured viva voce as a formative assessment of dental students. A sample of 65 third-year and 70 fourth-year dental students at one dental school in India were subjected to structured viva voce examinations with questions derived from the subject of periodontics. Each examinee answered five questions (two open and three closed) asked by trained unbiased examiners. The structured viva voce examinations were conducted on the seventh and 14th days after the last lecture of a one-month lecture series. Scores were tabulated into three domains of Bloom's taxonomy: knowledge, comprehension, and application. Regarding knowledge, the mean scores were 1.24±0.59 (seventh day) and 1.66±0.64 (14th day), and the difference was statistically significant (p<0.05). Regarding comprehension, the mean scores were 0.92±0.57 (seventh day) and 1.44±0.65 (14th day), and the difference was statistically significant (p<0.05). Regarding application, the mean scores were 0.56±0.50 (seventh day) and 1.0±0.43 (14th day) in Domain II, and the difference was statistically significant (p<0.05). The results suggest that structured viva voce was a reliable method for the formative assessment of these dental students.

  15. Structural features and formation of lower Cretaceous AV1 layer in the Soviet oil field (Tomsk Oblast)

    NASA Astrophysics Data System (ADS)

    Zhamsaranova, A. B.; Osipova, E. N.; Gaydukova, T. A.; Aksenova, N. V.

    2016-09-01

    The analysis of the collected geological and geophysical information on AV1 layer known as Ryabchik formation is carried out. The facial conditions of this formation which define structural features of «Ryabchik» sandstones formations are considered. Maps characterizing permeability and porosity of reservoir are plotted. Areal tracking technique of sand streaks is given.

  16. 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.

  17. 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.

  18. Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

    NASA Astrophysics Data System (ADS)

    Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

    2015-04-01

    The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

  19. Domanik deposits in Volga-Ural basin: Structure and formation conditions

    NASA Astrophysics Data System (ADS)

    Zavialova, Anna; Chupahina, Vitaliya; Stupakova, Antonina; Suslova, Anna

    2017-04-01

    The high-carbon Domanic deposits within a Mukhano-Erohovsky trough in Volga-Ural Basin was analyzed from materials of the well cores in the region. Detailed macroscopic description of the cores was provided based on samples and thin sections. In this way, the composition, structure, conditions of sedimentation of high-carbon formation, reservoir properties of rocks, and their distributions in the sections were identified. It was concluded that the Volga-Ural basin is a pre-Ural foreland basin where Domanic siliceous carbonate shale formation formed during the peak of Late Devonian transgression. Domanic rich organic formation of Upper Devonian - Lower Carboniferous age is represented by clay-siliceous-carbonate and clean calcareous and siliceous rocks. These rocks formed in a calm sea basin with environments of shallow shelf, intrashelf depressions and their slopes. The most organic-rich deposits were accumulated in the central parts of the depression uncompensated by sediments.

  20. 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.

  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. 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.

  3. β-Hairpin-Mediated Formation of Structurally Distinct Multimers of Neurotoxic Prion Peptides

    PubMed Central

    Gill, Andrew C.

    2014-01-01

    Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new

  4. Grand Design and Flocculent Spiral Structure in Computer Simulations with Star Formation and Gas Heating

    NASA Astrophysics Data System (ADS)

    Elmegreen, B. G.; Thomasson, M.

    1993-05-01

    An algorithm for star formation and gas heating is included in numerical simulations of galaxy disks. With a high disk mass and an inner Q-barrier, the simulations spontaneously generate and then maintain for several revolutions a long-lived two-arm spiral wave mode that resembles a grand design galaxy. Eventually a multiple arm pattern appears because of a growing m = 3 component; multiple arm patterns also form right away if there is no Q barrier. When the stellar Q-value exceeds ~2.5 because of a low disk mass or a large velocity dispersion, stellar spirals do not form at all; if the relative gas mass is also small in this case (about 10 % of the total galaxy mass or less), then the spiral structure is purely flocculent, i.e., composed of numerous short arms in only the gas and star formation component. The star formation algorithm is made as realistic as possible, with young stars forming in virialized cloud complexes, moving kinematically as tracer particles, and heating their environments at the observed average rate. The results illustrate the importance for spiral structure of the stellar Q and the star formation thermostat in the interstellar gas.

  5. Indole affects the formation of multicellular aggregate structures in Pantoea agglomerans YS19.

    PubMed

    Yu, Xuemei; Jiang, Jing; Liang, Chen; Zhang, Xiao; Wang, Jieru; Shen, Delong; Feng, Yongjun

    2016-01-01

    Pantoea agglomerans YS19 is an endophytic diazotrophic bacterium isolated from rice. As well as having the ability to form a biofilm, as do most bacteria, it is characterized by the formation of a unique multicellular aggregate structure called symplasmata. Indole is traditionally known as a metabolite of the amino acid tryptophan, which, however, has recently been shown to participate in various regulations of bacterial physiological processes, including stress resistance, quorum sensing and biofilm formation. Here, an indole signal was found to promote symplasmata formation, yet inhibit biofilm formation, indicating different regulatory pathways of indole in the construction of the two structures. However, symplasmata showed almost an equivalent stress-resistant capability, as compared with biofilms, for YS19 to confront acids, heavy metals (Cu(2+)), and UV treatments. Moreover, indole was tested to show a promoting effect on exopolysaccharides (EPS) production and an inhibition effect on the expression of an outer membrane protein OmpW. These results provide evidence for understanding the regulatory mechanisms of indole on such multicellular aggregates.

  6. 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.

  7. 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.

  8. Gaining Thermodynamic Insight From Distinct Glass Formation Kinetics of Structurally Similar Organic Compounds.

    PubMed

    Kalra, Arjun; Luner, Paul; Taylor, Lynne S; Byrn, Stephen R; Li, Tonglei

    2017-06-23

    Thermodynamic and kinetic aspects of crystallization of 12 structurally similar organic compounds were investigated from the supercooled liquid state by calorimetric and rheologic measurements. Based on their crystallization behaviors, these compounds were divided into 3 categories: stable glass formers, poor glass formers, and good glass formers with poor stability on reheating. Correlation was sought between thermodynamic quantities and glass formation based on nucleation and crystal growth theories. Larger values of enthalpy of fusion and melting point were found to correlate with poor glass-forming ability. Conversely, lower entropy of fusion was found to correlate with glass formation. Examination of kinetic aspects of glass formation revealed 2 important facets of good glass formers, that is, rapid increase in viscosity on supercooling and high melting point viscosity compared with non-glass formers. A broader relationship was sought between entropy of fusion and glass formation by including several glass formers from literature. Our analysis indicated that good glass formers tend to have an entropy of fusion closer to 0.3 J cm(-3) K(-1). The structural similarity of the compounds in this study provides insights regarding the nature of intermolecular interactions responsible for the observed effect on entropy of fusion, viscosity, and crystallization kinetics. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  9. 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.

  10. 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.

  11. 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.

  12. Do I Know You? How Individual Recognition Affects Group Formation and Structure

    PubMed Central

    2017-01-01

    Groups in nature can be formed by interactions between individuals, or by external pressures like predation. It is reasonable to assume that groups formed by internal and external conditions have different dynamics and structures. We propose a computational model to investigate the effects of individual recognition on the formation and structure of animal groups. Our model is composed of agents that can recognize each other and remember previous interactions, without any external pressures, in order to isolate the effects of individual recognition. We show that individual recognition affects the number and size of groups, and the modularity of the social networks. This model can be used as a null model to investigate the effects of external factors on group formation and persistence. PMID:28125708

  13. 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.

  14. Venus banded terrain - Tectonic models for band formation and their relationship to lithospheric thermal structure

    NASA Technical Reports Server (NTRS)

    Solomon, S. C.; Head, J. W.

    1984-01-01

    Two classes of tectonic models for the formation of band structure on Venus mountain ranges are quantitatively evaluated: folding models and extensional models. The characteristics of banded terrain on Ishtar Terra are reviewed, particularly the evidence for a tectonic origin and such important details of band geometry as the spacing between adjacent bands. The tectonic models are tested against these observed features, and it it shown that both classes of models are possible explanations of banded terrain as long as the outer elastic-brittle layer of the Venus crust is at most a few kilometers thick. A general assessment is given of hypotheses for the origin of banded terrain and of the relationship between mechanical models for band formation and the thermal structure of the Venus lithosphere.

  15. Structural Relaxation of 3-Dimensionally Confined Polymer Glasses: Isobaric versus Isochoric Glass Formation

    NASA Astrophysics Data System (ADS)

    Guo, Yunlong; Zhang, Chuan; Priestley, Rodney

    2011-03-01

    We have measured the glassy-state structural relaxation of aqueous suspended polystyrene (PS) nanoparticles and the corresponding silica-capped PS nanoparticles via modulated differential scanning calorimetry. Suspended and capped-PS nanoparticles undergo glass formation and subsequent physical aging under isobaric and isochoric conditions, respectively. To account for glass transition temperature (Tg) changes with confinement, physical aging measurements were performed at a constant value of Tg minus Ta, where Ta is the aging temperature. With deceasing diameter, aqueous suspended PS nanoparticles exhibited enhanced physical aging rates in comparison to bulk PS. At all values of Tg minus Ta investigated, capped-PS nanoparticles aged at reduced rates compared to the corresponding aqueous suspended PS nanoparticles. Due to differences in paths to glass formation, suspended and capped-PS nanoparticles aged to different apparent equilibrium states. We captured the physical aging behavior of all nanoparticles via the Tool, Narayanaswamy, and Moynihan (TNM) model of structural relaxation.

  16. Particle-in-Cell simulations of filamentary structures formation in DBD-tissue interaction

    NASA Astrophysics Data System (ADS)

    Likhanskii, Alexandre; Messmer, Peter

    2011-10-01

    Recent studies demonstrated high potential of the dielectric barrier discharge (DBD) plasmas for medical applications, such as sterilization or tissue regeneration. Despite intensive experimental studies have been conducted, the mechanism of plasma-tissue interaction still remains unclear. One of the open questions for the plasma-medical applications is the mechanism of filamentary structures formation in plasma and their interaction with tissues. Since formation of filaments is a purely kinetic effect, this issue needs to be addressed using kinetic, Particle-In-Cell simulation approach. We will present results of such numerical study. We performed 2D simulations of multiple streamers generation in atmospheric air using Tech-X's 2D/3D hybrid simulation tool VORPAL. We will demonstrate the resolution of the filamentary structure and will report the plasma properties. We will also address the plasma-induced effects on the tissue.

  17. Rim structure formation and high burnup fuel behavior of large-grained UO 2 fuels

    NASA Astrophysics Data System (ADS)

    Une, K.; Hirai, M.; Nogita, K.; Hosokawa, T.; Suzawa, Y.; Shimizu, S.; Etoh, Y.

    2000-01-01

    Irradiation-induced fuel microstructural evolution of the sub-divided grain structure, or rim structure, of large-grained UO 2 pellets has been examined through detailed PIEs. Besides standard grain size pellets with a grain size range of 9-12 μm, two types of undoped and alumino-silicate doped large-grained pellets with a range of 37-63 μm were irradiated in the Halden heavy water reactor up to a cross-sectional pellet average burnup of 86 GWd/t. The effect of grain size on the rim structure formation was quantitatively evaluated in terms of the average Xe depression in the pellet outside region measured by EPMA, based on its lower sensitivity for Xe enclosed in the coarsened rim bubbles. The Xe depression in the high burnup pellets above 60 GWd/t was proportional to d-0.5- d-1.0 ( d: grain size), and the two types of large-grained pellets showed remarkable resistance to the rim structure formation. A high density of dislocations preferentially decorated the as-fabricated grain boundaries and the sub-divided grain structure was localized there. These observations were consistent with our proposed formation mechanism of rim structure, in which tangled dislocation networks are organized into the nuclei for recrystallized or sub-divided grains. In addition to higher resistance to the microstructure change, the large-grained pellets showed a smaller swelling rate at higher burnups and a lower fission gas release during base irradiation.

  18. Colorimetric method for identifying plant essential oil components that affect biofilm formation and structure.

    PubMed

    Niu, C; Gilbert, E S

    2004-12-01

    The specific biofilm formation (SBF) assay, a technique based on crystal violet staining, was developed to locate plant essential oils and their components that affect biofilm formation. SBF analysis determined that cinnamon, cassia, and citronella oils differentially affected growth-normalized biofilm formation by Escherichia coli. Examination of the corresponding essential oil principal components by the SBF assay revealed that cinnamaldehyde decreased biofilm formation compared to biofilms grown in Luria-Bertani broth, eugenol did not result in a change, and citronellol increased the SBF. To evaluate these results, two microscopy-based assays were employed. First, confocal laser scanning microscopy (CLSM) was used to examine E. coli biofilms cultivated in flow cells, which were quantitatively analyzed by COMSTAT, an image analysis program. The overall trend for five parameters that characterize biofilm development corroborated the findings of the SBF assay. Second, the results of an assay measuring growth-normalized adhesion by direct microscopy concurred with the results of the SBF assay and CLSM imaging. Viability staining indicated that there was reduced toxicity of the essential oil components to cells in biofilms compared to the toxicity to planktonic cells but revealed morphological damage to E. coli after cinnamaldehyde exposure. Cinnamaldehyde also inhibited the swimming motility of E. coli. SBF analysis of three Pseudomonas species exposed to cinnamaldehyde, eugenol, or citronellol revealed diverse responses. The SBF assay could be useful as an initial step for finding plant essential oils and their components that affect biofilm formation and structure.

  19. Establishment of a Uniform Format for Data Reporting of Structural Material Properties for Reliability Analysis

    DTIC Science & Technology

    1994-06-30

    uniaxial yield strength of HY80 steels . The following is a description of a potential flow pattern of the database data retrieval program. i) The...Emphasis is placed on strength and toughness properties of marine steels and their welds. The format developed and reported in the SSC report 352 was...Parent M aterial ................................... 58 5.1.1 A Hierarchy for Pooling Tensile Data of Marine Structural Steels (Appendix B

  20. Structural organization and dynamics of exopolysaccharide matrix and microcolonies formation by Streptococcus mutans in biofilms.

    PubMed

    Xiao, J; Koo, H

    2010-06-01

    To investigate the structural organization and dynamics of exopolysaccharides (EPS) matrix and microcolonies formation by Streptococcus mutans during the biofilm development process. Biofilms of Strep. mutans were formed on saliva-coated hydroxyapatite (sHA) discs in the presence of glucose or sucrose (alone or mixed with starch). At specific time points, biofilms were subjected to confocal fluorescence imaging and computational analysis. EPS matrix was steadily formed on sHA surface in the presence of sucrose during the first 8 h followed by a threefold biomass increase between 8 and 30 h of biofilm development. The initial formation and further development of three-dimensional microcolony structure occurred concomitantly with EPS matrix synthesis. Tridimensional renderings showed EPS closely associated with microcolonies throughout the biofilm development process forming four distinct domains (i) between sHA surface and microcolonies, (ii) within, (iii) covering and (iv) filling the spaces between microcolonies. The combination of starch and sucrose resulted in rapid formation of elevated amounts of EPS matrix and faster assembly of microcolonies by Strep. mutans, which altered their structural organization and susceptibility of the biofilm to acid killing (vs sucrose-grown biofilms; P < 0.05). Our data indicate that EPS modulate the development, sequence of assembly and spatial distribution of microcolonies by Strep. mutans. Simultaneous visualization and analysis of EPS matrix and microcolonies provide a more precise examination of the structural organization of biofilms than labelling bacteria alone, which could be a useful approach to elucidate the exact mechanisms by which Strep. mutans influences oral biofilm formation and possibly identify novel targets for effective antibiofilm therapies.

  1. [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.

  2. Structure and Morphology of RESOLVE Galaxies in Relation to Environment, Gas, and Star Formation

    NASA Astrophysics Data System (ADS)

    Kannappan, Sheila; Hood, Callie; Snyder, Elaine M.; Eckert, Kathleen D.; Stark, David; RESOLVE Team

    2017-01-01

    We examine the structure and morphology of galaxies in the RESOLVE (REsolved Spectroscopy Of a Local VolumE) survey, a census of >1500 galaxies with baryonic mass >~10^9 Msun spanning multiple environments across >50,000 cubic Mpc of the nearby cosmic web. We investigate the statistical distribution of basic structural parameters as well as tidal streams and compact cores identified by image decomposition. Our results offer clues to the drivers of diversity in star formation and gas properties, particularly the unexpected phenomenon of red, gas depleted dwarf galaxies that are not satellites. RESOLVE was supported by NSF award AST-0955368.

  3. Conformal Ni-silicide formation over three-dimensional device structures

    SciTech Connect

    Zhu Zhiwei; Zhang Shili; Gao Xindong; Kubart, Tomas; Zhang Zhibin; Wu Dongping

    2012-07-30

    This letter reports on conformal formation of ultrathin Ni-silicide films over a three-dimension structure relevant to the most advanced tri-gate transistor architecture. This is achieved by combining ionization of the sputtered Ni atoms with application of an appropriate bias to the Si substrate during the sputter-deposition of Ni films. In comparison, use of ordinary DC sputtering for Ni deposition results in thinner or less uniform silicide films on the vertical sidewalls than on the top surface of the three-dimensional structure. The roughened Si sidewall surface is ascribed to be responsible for a deteriorated thermal stability of the resultant silicide films.

  4. 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.

  5. A model of social network formation under the impact of structural balance

    NASA Astrophysics Data System (ADS)

    Li, Pei; Cheng, Jiajun; Chen, Yingwen; Wang, Hui

    2016-03-01

    Social networks have attracted remarkable attention from both academic and industrial societies and it is of great importance to understand the formation of social networks. However, most existing research cannot be applied directly to investigate social networks, where relationships are heterogeneous and structural balance is a common phenomenon. In this paper, we take both positive and negative relationships into consideration and propose a model to characterize the process of social network formation under the impact of structural balance. In this model, a new node first establishes a link with an existing node and then tries to connect to each of the newly connected node’s neighbors. If a new link is established, the type of this link is determined by structural balance. Then we analyze the degree distribution of the generated network theoretically, and estimate the fractions of positive and negative links. All analysis results are verified by simulations. These results are of importance to understand the formation of social networks, and the model can be easily extended to consider more realistic situations.

  6. Formation of new high density glycogen-microtubule structures is induced by cardiac steroids.

    PubMed

    Fridman, Eleonora; Lichtstein, David; Rosen, Haim

    2012-02-24

    Cardiac steroids (CS), an important class of naturally occurring compounds, are synthesized in plants and animals. The only established receptor for CS is the ubiquitous Na(+),K(+)-ATPase, a major plasma membrane transporter. The binding of CS to Na(+),K(+)-ATPase causes the inhibition of Na(+) and K(+) transport and elicits cell-specific activation of several intracellular signaling mechanisms. It is well documented that the interaction of CS with Na(+),K(+)-ATPase is responsible for numerous changes in basic cellular physiological properties, such as electrical plasma membrane potential, cell volume, intracellular [Ca(2+)] and pH, endocytosed membrane traffic, and the transport of other solutes. In the present study we show that CS induces the formation of dark structures adjacent to the nucleus in human NT2 and ACHN cells. These structures, which are not surrounded by membranes, are clusters of glycogen and a distorted microtubule network. Formation of these clusters results from a relocation of glycogen and microtubules in the cells, two processes that are independent of one another. The molecular mechanisms underlying the formation of the clusters are mediated by the Na(+),K(+)-ATPase, ERK1/2 signaling pathway, and an additional unknown factor. Similar glycogen clusters are induced by hypoxia, suggesting that the CS-induced structural change, described in this study, may be part of a new type of cellular stress response.

  7. Controlled synthesis and formation mechanism of monodispersive lanthanum vanadate nanowires with monoclinic structure

    SciTech Connect

    Tian, Li; Sun, Qiliang; Xu, Xijun; Li, Yaolin; Long, Yunfei; Zhu, Guangshan

    2013-04-15

    Monodisperse LaVO{sub 4} nanowires with relatively high aspect ratio larger than 50 have been prepared by a one-step solvothermal synthesis. This method provides a simple, inexpensive, controllable and reproducible process to produce LaVO{sub 4} nanowires with an average diameter of 15 nm and a high aspect ratio. The as-synthesized products have been characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and fast Fourier transform spectroscopy (FFT), indicative of a well-crystalline monoclinic structure and ascendant nanowire-morphology. The formation mechanism is suggested that oriented attachment plays a vital role in the growth of LaVO{sub 4} nanowires, which recommends a favorable route to fabricate similar morphological and structural nanometer materials. - Graphical abstract: The formation of LaVO{sub 4} nanowires is attributed to oriented attachment, a combination of nanocrystallites through their suitable surface planes, that is, with the same crystallographic orientations of [−120]. Highlights: ► Monodisperse LaVO{sub 4} nanowires with high aspect ratio have been prepared solvothermally without any templates. ► The morphology and structure of LaVO{sub 4} nanowires were characterized by XRD, SEM, TEM techniques. ► The formation mechanism of LaVO{sub 4} nanowires is suggested that oriented attachment plays a vital role.

  8. Gold Cluster Formation on C60 Surfaces: Au-Cluster Beads and Self-Organized Structures

    NASA Astrophysics Data System (ADS)

    Reinke, Petra; Liu, Hui

    2007-03-01

    Petra Reinke, Hui Liu, Department of Materials Science and Engineering, University of Virginia The investigation of C60-Au interaction is central to the advancement of solar cell and nanotechnology applications of C60. C60 grows in a quasi-layer-by-layer mode on a pristine graphite surface and form a special surface structure (coexistence of round and fractal islands). The deposition of Au leads to the formation of a complex array of different surface structures, while the basic island structure of the C60 is preserved. The Au-clusters nucleate preferentially at the graphite-first fullerene layer islands edge forming beadlike structures. A roughness analysis of the fullerene surface indicates the presence of Au atoms embedded in the fullerene surface, situated in the troughs in between the large molecules. The analysis of the spatial and size distributions of Au clusters provides the basis for the development of a qualitative model which describes the relevant surface processes in the Au-fullerene system. The simultaneous deposition of Au and C60 leads to the formation of organized structures, in which Au clusters are embedded in a ring of fullerene molecules with a constant width.

  9. On the similarity in the formation mechanism of the fracture structure of a rock massif

    NASA Astrophysics Data System (ADS)

    Bagdasar'yan, A. G.; Sytenkov, V. N.; Fedyanina, L. T.; Shemetov, P. A.

    2011-04-01

    Local segments of the Earth's crust reside at the mechanical nonequilibrium and continuously obtain and dissipate mechanical energy. The energy exchange between the structural elements of a geophysical medium determines its state, especially if the medium is fragmented into blocks. The stationary state of a rock differs from its static equilibrium by the fact that the mechanical energy is conserved because the energy input is equal to the energy dissipation. From this point of view, the cracks, the faults, and the block structure are not simply the manifestations of rock destruction, but rather the mode of existence of a medium with large irreversible deformations. Then, the fracture structure, whose formation is actually a response of a rock to large irreversible deformation, becomes, in terms of physics, the characteristic of the state of a geophysical medium; for example, it allows one to assess the parameters of the deformation processes during the period of formation of the fracture structure. The present paper addresses the identification of the features of the fracture structure in geological objects of different scales.

  10. Chemical separation of primordial Li+ during structure formation caused by nanogauss magnetic field

    NASA Astrophysics Data System (ADS)

    Kusakabe, Motohiko; Kawasaki, Masahiro

    2015-01-01

    During the structure formation, charged and neutral chemical species may have separated from each other at the gravitational contraction in primordial magnetic field (PMF). A gradient in the PMF in a direction perpendicular to the field direction leads to the Lorentz force on the charged species. Resultantly, an ambipolar diffusion occurs, and charged species can move differently from neutral species, which collapses gravitationally during the structure formation. We assume a gravitational contraction of neutral matter in a spherically symmetric structure, and calculate fluid motions of charged and neutral species. It is shown that the charged fluid, i.e. proton, electron, and 7Li+, can significantly decouple from the neutral fluid depending on the field amplitude. The charged species can, therefore, escape from the gravitational collapse. We take the structure mass, the epoch of the gravitational collapse, and the comoving Lorenz force as parameters. We then identify a parameter region for an effective chemical separation. This type of chemical separation can reduce the abundance ratio of Li/H in early structures because of inefficient contraction of 7Li+ ion. Therefore, it may explain Li abundances of Galactic metal-poor stars which are smaller than the prediction in standard big bang nucleosynthesis model. Amplitudes of the PMFs are controlled by a magnetohydrodynamic turbulence. The upper limit on the field amplitude derived from the turbulence effect is close to the value required for the chemical separation.

  11. 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.

  12. 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

  13. Selforganized Structure Formation in Organized Microstructuring by Laser-Jet Etching

    NASA Astrophysics Data System (ADS)

    Rabbow, T. J.; Plath, P. J.; Mora, A.; Haase, M.

    Laser-jet induced wet etching of stainless steel in 5M H3PO4 has been investigated. By this method, it is possible to cut and microstructure metals and alloys that form passive layers in strong etchants. Due to the laser heating of the metal and the adjacent layers of the etchant, the passive layer is removed and an active dissolution of the base metal together with the formation of hydrogen is observed. The reactions are limited by the transport of fresh acid and the removal of dissolved metal. A jet of etchant reduces the transport limitations. For definite ranges of the laser power, the feed velocity and the etchant jet velocity, a regime of periodic structure formation of the kerf, often called ripples, has been found. The ripple length depends on all three parameters. The ripple formation can be brought into correlation with a periodic change of the intensity of the reflected light as well as oscillations of the potential workpiece. It could be shown that the periodic structure formation is connected to a spreading of an etching front from the laser activated area, that temporarily moves ahead to the laser. This leads to modulations of the interface for the laser absorption, which results, for example, in oscillations of the intensity of the reflected light. This means the laser induced etching reaction attracts a feedback based on the conditions of absorption for the laser. For those parameters of feed velocity, laser power and etchant jet velocity, without ripple formation the laser induced etching front is of a constant distance to the laser which results in steady conditions at the interface for the absorption of the laser.

  14. 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.

  15. Selected Data for Wells and Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation in the Black Hills Area, South Dakota

    DTIC Science & Technology

    1999-01-01

    Selected Data for Wells and Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison...Test Holes Used in Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation...Structure-Contour Maps of the Inyan Kara Group, Minnekahta Limestone, Minnelusa Formation, Madison Limestone, and Deadwood Formation in the Black Hills Area

  16. Role of structure imperfection in the formation of the magnetotransport properties of rare-earth manganites with a perovskite structure

    NASA Astrophysics Data System (ADS)

    Pashchenko, A. V.; Pashchenko, V. P.; Prokopenko, V. K.; Turchenko, V. A.; Revenko, Yu. F.; Mazur, A. S.; Sycheva, V. Ya.; Liedienov, N. A.; Pitsyuga, V. G.; Levchenko, G. G.

    2017-01-01

    The structure, the structure imperfection, and the magnetoresistance, magnetotransport, and microstructure properties of rare-earth perovskite La0.3Ln0.3Sr0.3Mn1.1O3-δ manganites are studied by X-ray diffraction, thermogravimetry, electrical resistivity measurement, magnetic, 55Mn NMR, magnetoresistance measurement, and scanning electron microscopy. It is found that the structure imperfection increases, and the symmetry of a rhombohedrally distorted R3̅ c perovskite structure changes into its pseudocubic type during isovalent substitution for Ln = La3+, Pr3+, Nd3+, Sm3+, or Eu3+ when the ionic radius of an A cation decreases. Defect molar formulas are determined for a real perovskite structure, which contains anion and cation vacancies. The decrease in the temperatures of the metal-semiconductor ( T ms) and ferromagnet-paramagnet ( T C) phase transitions and the increase in electrical resistivity ρ and activation energy E a with increasing serial number of Ln are caused by an increase in the concentration of vacancy point defects, which weaken the double exchange 3 d 4(Mn3+)-2 p 6(O2-)-3 d 3(Mn4+)- V ( a)-3 d 4(Mn3+). The crystal structure of the compositions with Ln = La contains nanostructured planar clusters, which induce an anomalous magnetic hysteresis at T = 77 K. Broad and asymmetric 55Mn NMR spectra support the high-frequency electronic double exchange Mn3+(3 d 4) ↔ O2-(2 p 6) ↔ Mn4+(3 d 3) and indicate a heterogeneous surrounding of manganese by other ions and vacancies. A correlation is revealed between the tunneling magnetoresistance effect and the crystallite size. A composition-structure imperfection-property experimental phase diagram is plotted. This diagram supports the conclusion about a strong influence of structure imperfection on the formation of the magnetic, magnetotransport, and magnetoresistance properties of rare-earth perovskite manganites.

  17. Including crystal structure attributes in machine learning models of formation energies via Voronoi tessellations

    NASA Astrophysics Data System (ADS)

    Ward, Logan; Liu, Ruoqian; Krishna, Amar; Hegde, Vinay I.; Agrawal, Ankit; Choudhary, Alok; Wolverton, Chris

    2017-07-01

    While high-throughput density functional theory (DFT) has become a prevalent tool for materials discovery, it is limited by the relatively large computational cost. In this paper, we explore using DFT data from high-throughput calculations to create faster, surrogate models with machine learning (ML) that can be used to guide new searches. Our method works by using decision tree models to map DFT-calculated formation enthalpies to a set of attributes consisting of two distinct types: (i) composition-dependent attributes of elemental properties (as have been used in previous ML models of DFT formation energies), combined with (ii) attributes derived from the Voronoi tessellation of the compound's crystal structure. The ML models created using this method have half the cross-validation error and similar training and evaluation speeds to models created with the Coulomb matrix and partial radial distribution function methods. For a dataset of 435 000 formation energies taken from the Open Quantum Materials Database (OQMD), our model achieves a mean absolute error of 80 meV/atom in cross validation, which is lower than the approximate error between DFT-computed and experimentally measured formation enthalpies and below 15% of the mean absolute deviation of the training set. We also demonstrate that our method can accurately estimate the formation energy of materials outside of the training set and be used to identify materials with especially large formation enthalpies. We propose that our models can be used to accelerate the discovery of new materials by identifying the most promising materials to study with DFT at little additional computational cost.

  18. 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.

  19. Theory of structure formation in snowfields motivated by penitentes, suncups, and dirt cones.

    PubMed

    Betterton, M D

    2001-05-01

    Penitentes and suncups are structures formed as snow melts, typically high in the mountains. When the snow is dirty, dirt cones and other structures can form instead. Building on previous field observations and experiments, this paper presents a theory of ablation morphologies, and the role of surface dirt in determining the structures formed. The glaciological literature indicates that sunlight, heating from air, and dirt all play a role in the formation of structure on an ablating snow surface. The present paper formulates a minimal model for the formation of ablation morphologies as a function of measurable parameters and considers the linear stability of this model. The dependence of ablation morphologies on weather conditions and initial dirt thickness is studied, focusing on the initial growth of perturbations away from a flat surface. We derive a single-parameter expression for the melting rate as a function of dirt thickness, which agrees well with a set of measurements by Driedger. An interesting result is the prediction of a dirt-induced traveling instability for a range of parameters.

  20. Structural analysis of SgvP involved in carbon-sulfur bond formation during griseoviridin biosynthesis.

    PubMed

    Li, Qin; Chen, Yan; Zhang, Guiqin; Zhang, Huaidong

    2017-05-01

    Griseoviridin (GV) is a broad-spectrum antibiotic with antibacterial and antifungal activity. In the GV biosynthetic pathway, SgvP catalyzes formation of the carbon-sulfur bond in GV. Herein, we report the recombinant expression and characterization of SgvP from Streptomyces griseoviridis NRRL2427. We also present the 2.6 Å crystal structure of SgvP, which is the first structure of a cytochrome P450 involved in carbon-sulfur bond formation in GV. Structural analysis indicates that Pro237 in the I-helix of SgvP may play a critical role in dioxygen binding and proton transfer during the catalytic cycle. Of the three channels we observed in SgvP, channel 3 may be essential for substrate ingress and egress from the active site, while channels 1 and 2 may be the solvent and water pathway, respectively. Coordinate and structure factor were deposited in the Protein Data Bank database under the accession number 4MM0. © 2017 Federation of European Biochemical Societies.

  1. Investigation on the Effects of the Formation of a Silver "Flower-Like Structure" on Graphene

    NASA Astrophysics Data System (ADS)

    Zakaria, Rozalina; Yusoff, Siti Fatimah Az Zahra; Law, Kok Chung; Lim, Chin Seong; Ahmad, Harith

    2017-01-01

    In this report, we experimentally investigate the formation of "flower-like silver structures" on graphene. Using an electrochemical deposition technique with deposition times of 2.5 and 5 min, agglomerations of silver nanoparticles (AgNPs) were deposited on the graphene surfaces, causing the formation of "flower-like structures" on the graphene substrate. Localized surface plasmon resonance (LSPR) was observed in the interaction between the structures and the graphene substrate. The morphology of the samples was observed using a field-emission scanning electron microscope (FESEM) and Raman spectroscopy. Thereafter, the potential of the flower-like Ag microstructures on graphene for use in Raman spectroscopic applications was examined. The signal showed a highest intensity value after a deposition time of 5 min, as portrayed by the intense local electromagnetic fields. For a better understanding, the CST Microwave Studio software, based on the finite element method (FEM), was applied to simulate the absorption characteristics of the structures on the graphene substrate. The absorption peak was redshifted due to the increment of the nanoparticle size.

  2. Heparin-binding growth factor 1 induces the formation of organoid neovascular structures in vivo.

    PubMed Central

    Thompson, J A; Haudenschild, C C; Anderson, K D; DiPietro, J M; Anderson, W F; Maciag, T

    1989-01-01

    One of the promises of modern molecular biology has been the opportunity to use genetically modified human cells in a patient to permanently restore inborn errors of metabolism. Although it has been possible to introduce genes into mammalian cells and to control their expression, it has proven difficult to introduce mammalian cells as carriers of the modified genetic information into hosts. The successful implantation of selective cells cannot be achieved without adequate vascular support, an essential step toward integration and reconstitution of a new biological function. Although a partial solution to this problem has been found by inducing specific site-directed neovessel formation using heparin-binding growth factor 1 (HBGF-1) adsorbed to a collagen matrix, these implants function for only a short period (weeks). We now report the formation of organoid neovascular structures using polytetrafluoroethylene fibers coated with collagen and HBGF-1 implanted in the peritoneal cavity of the rat. The organoid structures contained readily visible vascular lumina and nonvascular structures that resemble nerve tissue. It was also possible to demonstrate that the vascular system on the implant is continuous with the vascular tree of the host. This feature was used to demonstrate that the organoid structures are capable of sustaining the biological function of implanted normal rat hepatocytes over long periods of time (months) in the homozygous Gunn rat, thereby facilitating future applications involving the delivery of new genetic information. Images PMID:2479012

  3. Monitoring Single-Stranded DNA Secondary Structure Formation by Determining the Topological State of DNA Catenanes

    PubMed Central

    Liang, Xingguo; Kuhn, Heiko; Frank-Kamenetskii, Maxim D.

    2006-01-01

    Single-stranded DNA (ssDNA) has essential biological functions during DNA replication, recombination, repair, and transcription. The structure of ssDNA must be better understood to elucidate its functions. However, the available data are too limited to give a clear picture of ssDNA due to the extremely capricious structural features of ssDNA. In this study, by forming DNA catenanes and determining their topology (the linking number, Lk) through the electrophoretic analysis, we demonstrate that the studies of catenanes formed from two ssDNA molecules can yield valuable new information about the ssDNA secondary structure. We construct catenanes out of two short (60/70 nt) ssDNA molecules by enzymatic cyclization of linear oligodeoxynucleotides. The secondary structure formed between the two DNA circles determines the topology (the Lk value) of the constructed DNA catenane. Thus, formation of the secondary structure is experimentally monitored by observing the changes of linking number with sequences and conditions. We found that the secondary structure of ssDNA is much easier to form than expected: the two strands in an internal loop in the folded ssDNA structure prefer to braid around each other rather than stay separately forming a loop, and a duplex containing only mismatched basepairs can form under physiological conditions. PMID:16461397

  4. 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

  5. Self-Templated Formation of Hollow Structures for Electrochemical Energy Applications.

    PubMed

    Yu, Le; Wu, Hao Bin; Lou, Xiong Wen David

    2017-02-21

    The rational design and synthesis of hollow structured functional materials are of great significance as both fundamental challenges in materials science and practical solutions for efficient energy utilization in modern society. The unique structural features of hollow functional materials bring outstanding electrochemical properties for both energy storage and electrocatalysis. However, conventional templating methods are normally less efficient in constructing hollow structures with desirable compositions and architectures. In the past decade, many novel synthetic approaches directly converting templates into hollow structures have been developed. Collectively termed as the "self-templated" strategy, it makes use of various physical/chemical processes to transform solid templates into hollow structures of target materials. Of particular note is the outstanding capability to construct complex hollow architectures of a wide variety of inorganic or hybrid functional materials, thus providing effective solutions for various electrochemical energy applications. In this Account, we present the recent progress in self-templated formation of hollow structures especially with complex architectures, and their remarkable performance in electrochemical energy-related technologies. These advanced self-templated methods are summarized as three categories. "Selective etching" creates hollow structures from solid templates of same materials by removing some of the internal parts, forming multishelled or unusual hollow architectures. "Outward diffusion" utilizes the relocation of mass in templates from inner region to outer region driven by various mechanisms, to construct hollow structures with multiple or hierarchical shells. "Heterogeneous contraction" typically applies to thermally decomposable templates and generates various hollow structures under nonequilibrium heating conditions. We further demonstrate some remarkable electrochemical properties of such hollow structures

  6. 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

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

    PubMed Central

    Mei, Xiaohu; Atkinson, David

    2015-01-01

    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 intermediate 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. PMID:26048453

  8. 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.

  9. 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.

  10. Formation mechanism for hexagonal-structured self-assemblies of nanocrystalline titania templated by cetyltrimethylammonium bromide.

    PubMed

    Sakai, Toshio; Yano, Hanae; Ohno, Mitsuru; Shibata, Hirobumi; Torigoe, Kanjiro; Utsumi, Shigenori; Sakamoto, Kazutami; Koshikawa, Naokiyo; Adachi, Satoshi; Sakai, Hideki; Abe, Masahiko

    2008-01-01

    Hexagonal-structured self-assemblies of nanocrystalline (anatase) titania templated by cetyltrimethylammonium bromide (C(16)H(33)N(CH(3))(3)Br; CTAB) (Hex-ncTiO(2)/CTAB Nanoskeleton) were formed after mixing of aqueous solutions containing CTAB spherical micelles and titanium oxysulfate acid hydrate (TiOSO(4).xH(2)SO(4).xH(2)O) as a titania precursor in the absence of any other additives. Formation mechanism of the Hex-ncTiO(2)/CTAB Nanoskeleton was examined in terms of the reaction temperature, titania precursor/CTAB mixing ratio, surfactant type, electrostatic interaction, micelle formation and molecular component. We found that crystal growth of crystalline (anatase) titania (polymorphic crystallization) was promoted with higher temperature and lower titania precursor content in aqueous solutions. In addition, we revealed that the crystalline (anatase) titania was formed in polycation, poly(allylamine hydrochloride ([CH(2)CH(CH(2)NH(2))HCl](n); PAH), and formamide (HCONH(2)) solutions. On the other hand, no titania formation was observed in anionic systems such as sodium dodecyl sulfate (CH(3)(CH(2))(11)OSO(3)Na; SDS) and poly(sodium 4-styrenesulfonate ([C(8)H(7)SO(3)Na](n); PSSS). This indicates that hydrolysis reaction of the titania precursor is initiated by not only cations but also nitrogen atoms in molecules and polymers. Hexagonally structure was formed in only cationic surfactant micellar solutions but not in polycation solutions and formamide.

  11. Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima: Structural Insights into Complex Formation

    SciTech Connect

    Morar, Mariya; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-10-02

    In the fourth step of the purine biosynthetic pathway, formyl glycinamide ribonucleotide (FGAR) amidotransferase, also known as PurL, catalyzes the conversion of FGAR, ATP, and glutamine to formyl glycinamidine ribonucleotide (FGAM), ADP, P{sub i}, and glutamate. Two forms of PurL have been characterized, large and small. Large PurL, present in most Gram-negative bacteria and eukaryotes, consists of a single polypeptide chain and contains three major domains: the N-terminal domain, the FGAM synthetase domain, and the glutaminase domain, with a putative ammonia channel located between the active sites of the latter two. Small PurL, present in Gram-positive bacteria and archaea, is structurally homologous to the FGAM synthetase domain of large PurL, and forms a complex with two additional gene products, PurQ and PurS. The structure of the PurS dimer is homologous with the N-terminal domain of large PurL, while PurQ, whose structure has not been reported, contains the glutaminase activity. In Bacillus subtilis, the formation of the PurLQS complex is dependent on glutamine and ADP and has been demonstrated by size-exclusion chromatography. In this work, a structure of the PurLQS complex from Thermotoga maritima is described revealing a 2:1:1 stoichiometry of PurS:Q:L, respectively. The conformational changes observed in TmPurL upon complex formation elucidate the mechanism of metabolite-mediated recruitment of PurQ and PurS. The flexibility of the PurS dimer is proposed to play a role in the activation of the complex and the formation of the ammonia channel. A potential path for the ammonia channel is identified.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Structure and hydrogel formation studies on homologs of a lactoglobulin-derived peptide.

    PubMed

    Guy, Marie-Michèle; Voyer, Normand

    2012-04-01

    In order to study the impact of the amino acid sequence on the morphology of peptide-based nanostructures and their hydrogel formation, we designed a series of analogs of a milk-derived octapeptide (OP), mainly using strategic amino acid substitutions. Electronic transmission microscopy (TEM) and circular dichroism (CD) spectropolarimetry were used to analyze the nanostructures formed, and to characterize some structural features of the modified peptides. Further, the potential to form hydrogels was investigated for all of the analogous peptides. We learned that those able to undergo secondary structure transition to β-sheet conformation form strong gels. The results reported highlight some key structural properties that explain the self-assembly propensity of Peptide OP. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

    PubMed Central

    Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

    2015-01-01

    The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

  18. Slip as the basic mechanism for formation of deformation relief structural elements

    NASA Astrophysics Data System (ADS)

    Lychagin, D. V.; Alfyorova, E. A.

    2017-07-01

    The experimental results of investigation of the nickel single crystal surface morphology after compression deformation are presented. The quasi-periodic character of the deformation profile, common for shear deformation of different types of relief structural elements, is found. It is demonstrated that the morphological manifestation of these structural elements is determined by local shear systems along octahedral planes. The regularities of the deformation structure in these regions defining the material extrusion and intrusion regions and the specific features of disorientation accumulation are established. If reorientation of local regions takes part in the relief element formation, along with octahedral slip, much stronger growth of the surface area is observed. The possibility of application of two-dimensional and three-dimensional surface roughness parameters for description of deformation relief is considered.

  19. 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).

  20. 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.

  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. 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

  3. Structure formation in a colliding flow: The Herschel view of the Draco nebula

    NASA Astrophysics Data System (ADS)

    Miville-Deschênes, M.-A.; Salomé, Q.; Martin, P. G.; Joncas, G.; Blagrave, K.; Dassas, K.; Abergel, A.; Beelen, A.; Boulanger, F.; Lagache, G.; Lockman, F. J.; Marshall, D. J.

    2017-03-01

    Context. The Draco nebula is a high Galactic latitude interstellar cloud observed at velocities corresponding to the intermediate velocity cloud regime. This nebula shows unusually strong CO emission and remarkably high-contrast small-scale structures for such a diffuse high Galactic latitude cloud. The 21 cm emission of the Draco nebula reveals that it is likely to have been formed by the collision of a cloud entering the disk of the Milky Way. Such physical conditions are ideal to study the formation of cold and dense gas in colliding flows of diffuse and warm gas. Aims: The objective of this study is to better understand the process of structure formation in a colliding flow and to describe the effects of matter entering the disk on the interstellar medium. Methods: We conducted Herschel-SPIRE observations of the Draco nebula. The clumpfind algorithm was used to identify and characterize the small-scale structures of the cloud. Results: The high-resolution SPIRE map reveals the fragmented structure of the interface between the infalling cloud and the Galactic layer. This front is characterized by a Rayleigh-Taylor (RT) instability structure. From the determination of the typical length of the periodic structure (2.2 pc) we estimated the gas kinematic viscosity. This allowed us to estimate the dissipation scale of the warm neutral medium (0.1 pc), which was found to be compatible with that expected if ambipolar diffusion were the main mechanism of turbulent energy dissipation. The statistical properties of the small-scale structures identified with clumpfind are found to be typical of that seen in molecular clouds and hydrodynamical turbulence in general. The density of the gas has a log-normal distribution with an average value of 103 cm-3. The typical size of the structures is 0.1-0.2 pc, but this estimate is limited by the resolution of the observations. The mass of these structures ranges from 0.2 to 20 M⊙ and the distribution of the more massive structures

  4. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.

    PubMed

    Simonović, Miljan; Steitz, Thomas A

    2009-01-01

    The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.

  5. 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.

  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. Perfringolysin O structure and mechanism of pore formation as a paradigm for cholesterol-dependent cytolysins.

    PubMed

    Johnson, Benjamin B; Heuck, Alejandro P

    2014-01-01

    Cholesterol-dependent cytolysins (CDCs) constitute a family of pore forming toxins secreted by Gram-positive bacteria. These toxins form transmembrane pores by inserting a large β-barrel into cholesterol-containing membrane bilayers. Binding of water-soluble CDCs to the membrane triggers the formation of oligomers containing 35-50 monomers. The coordinated insertion of more than seventy β-hairpins into the membrane requires multiple structural conformational changes. Perfringolysin O (PFO), secreted by Clostridium perfringens, has become the prototype for the CDCs. In this chapter, we will describe current knowledge on the mechanism of PFO cytolysis, with special focus on cholesterol recognition, oligomerization, and the conformational changes involved in pore formation.

  8. Blister formation in Mo/Si multilayered structures induced by hydrogen ions

    NASA Astrophysics Data System (ADS)

    van den Bos, R. A. J. M.; Lee, C. J.; Benschop, J. P. H.; Bijkerk, F.

    2017-07-01

    We report on blister formation in nanometer thick Mo/Si multilayer structures due to exposure to hydrogen ion fluxes. The influence of hydrogen flux and ion energy for blister formation have been measured and compared to a blister model. The blister number density increases significantly around 100 eV when increasing the ion energy from 50 to 200 eV. This stepwise behavior could be explained by the fact that for energies  >100 eV hydrogen ions could directly penetrate to the depth where delamination takes place. From the blister model also the blisters internal pressure and surface energy was calculated to be around 100-800 MPa and γ =1.87~\\text{J}~{{\\text{m}}-2} respectively.

  9. Contribution of cotranslational folding to the rate of formation of native protein structure.

    PubMed Central

    Fedorov, A N; Baldwin, T O

    1995-01-01

    To compare the process of protein folding in the cell with refolding following denaturation in vitro, we have investigated and compared the kinetics of renaturation of a full-length protein upon dilution from concentrated urea with the rate of folding in the course of biosynthesis. Formation of enzymatically active bacterial luciferase, an alpha beta heterodimer, occurred 2 min after completion of beta-subunit synthesis in an Escherichia coli cell-free system. Renaturation of urea-denatured beta subunit, either in the presence of the cell-free protein synthesis system or in buffer solutions, proceeded more slowly. Cellular components present in the cell-free protein synthesis system slightly accelerated the rate of refolding of urea-unfolded beta subunit. The results indicate that the luciferase beta subunit begins the folding process cotranslationally and that cotranslational folding contributes to the rapid formation of the native structure in the cell. Images Fig. 1 PMID:7862665

  10. Atg5 regulates formation of MyD88 condensed structures and MyD88-dependent signal transduction.

    PubMed

    Inomata, Megumi; Into, Takeshi; Niida, Shumpei; Murakami, Yukitaka

    2013-08-09

    MyD88 is known as an essential adaptor protein for Toll-like receptors (TLRs). Previous studies have shown that transfected MyD88 forms condensed structures in the cytoplasm. However, upon TLR stimulation, there is little formation of endogenous MyD88 condensed structures. Thus, the formation of MyD88 condensed structures is tightly suppressed, but the mechanism and significance of this suppression are currently unknown. Here we show that Atg5, a key regulatory protein of autophagy, inhibits the formation of MyD88 condensed structures. We found that endogenous MyD88 had already formed condensed structures in Atg5-deficient cells and that the formation of condensed structures was further enhanced by TLR stimulation. This suppressive effect of Atg5 may not be associated with autophagic processes because MyD88 itself was not degraded and because TLR stimulation did not induce LC3 punctate formation and LC3 conversion. Immunoprecipitation analysis revealed that Atg5 could interact with MyD88. Furthermore, Atg5 deficiency increased formation of the MyD88-TRAF6 signaling complex induced by TLR stimulation, and it enhanced activation of NF-κB signaling but not MAPKs and Akt. These findings indicate that Atg5 regulates the formation of MyD88 condensed structures through association with MyD88 and eventually exerts a modulatory effect on MyD88-dependent signaling.

  11. 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

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

    PubMed

    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 degrees 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 degrees 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.

  13. Structure formation in grade 20 steel during equal-channel angular pressing and subsequent heating

    NASA Astrophysics Data System (ADS)

    Dobatkin, S. V.; Odesskii, P. D.; Raab, G. I.; Tyutin, M. R.; Rybalchenko, O. V.

    2016-11-01

    The structure formation and the mechanical properties of quenched and tempered grade 20 steel after equal-channel angular pressing (ECAP) at various true strains and 400°C are studied. Electron microscopy analysis after ECAP shows a partially submicrocrystalline and partially subgrain structure with a structural element size of 340-375 nm. The structural element size depends on the region in which the elements are formed (polyhedral ferrite, needle-shaped ferrite, tempered martensite, and pearlite). Heating of the steel after ECAP at 400 and 450°C increases the fraction of high-angle boundaries and the structural ferrite element size to 360-450 nm. The fragmentation and spheroidization of cementite lamellae of pearlite and subgrain coalescence in the regions of needle-shaped ferrite and tempered martensite take place at a high ECAP true strain and heating temperature. Structural refinement ensures considerable strengthening, namely, UTS 742-871 MPa at EL 11-15.3%. The strength slightly increases, whereas the plasticity slightly decreases when the true strain increases during ECAP. After ECAP and heating, the strength and plastic properties of the grade 20 steel remain almost the same.

  14. The geology of Svalbard: structural, stratigraphic and geomorphic response to the formation of two passive margins

    NASA Astrophysics Data System (ADS)

    Osmundsen, P. T.; Braathen, A.; Maher, H.

    2012-04-01

    Svalbard is located at the junction of the North Atlantic and Arctic margins, preserves an onshore structural and stratigraphic record that spans from the Devonian to the Cenozoic and records several phases of extension characterized by different tectonic transport vectors. Contractional events such as the Devonian, so-called 'Svalbardian' fold phase and the formation of an Early Cenozoic fold and thrust belt have locally modified the evidence for extension and basin formation. However, several generations of extensional structures and associated, tectonically controlled basins are displayed in world-class exposures at different locations in the archipelago. At present, we focus on the following onshore features related to extension and margin formation: 1. Late-post orogenic extension: An extensional detachment and metamorphic core complex was recently identified by us in northwestern Spitsbergen, involving re-interpretation of tectonic contacts interpreted previously as thrusts. The undulating extensional detachment appears to have controlled 'Old Red' basin formation from the Early into the Late Devonian. The core complex evolved into a N-S trending anticline with flanks that eventually became the locus of strike-slip and normal faulting. Some of these faults were demonstrably reactivated, and we propose that the Devonian structural template became important in controlling the location of later rift structures that developed from the Carboniferous onwards. 2. Carboniferous rifting: Normal faulting controlled sedimentation in Carboniferous basins including an up to 2 km deep, coastal/marine half-graben with mixed siliclastic, carbonate and evaporite fill exposed in Central Spitsbergen. The Billefjorden Fault zone (BFZ) reactivates an older, N-S trending Devonian reverse fault, and coarse siliclastic debris was transported into the basin along relay ramps that developed between the normally reactivated strands of the BFZ. Monoclinal folds, interpreted previously

  15. The evolution of the Onaping Formation at the Sudbury impact structure

    NASA Astrophysics Data System (ADS)

    Grieve, Richard A. F.; Ames, Doreen E.; Morgan, Joanna V.; Artemieva, Natalia

    2010-05-01

    The 1.4-1.6km thick Onaping Formation consists of a complex series of breccias and ``melt bodies'' lying above the Sudbury Igneous Complex (SIC) at the Sudbury impact structure. Based on the presence of shocked lithic clasts and various ``glassy'' phases, the Onaping has been described as a ``suevitic'' breccia, with an origin, at least in part, as fallback material. Recent mapping and a redefined stratigraphy have emphasized similarities and differences in its various vitric phases, both as clast types and discrete intrusive bodies. The nature of the Onaping and that of other ``suevitic'' breccias overlying impact melt sheets is reviewed. The relative thickness, internal stratigraphic and lithological character, and the relative chronology of depositional units indicate multiple processes were involved over some time in the formation of the Onaping. The Sudbury structure formed in a foreland basin and water played an essential role in the evolution of the Onaping, as indicated by a major hydrothermal system generated during its formation. Taken together, observations and interpretations of the Onaping suggest a working hypothesis for the origin of the Onaping that includes not only impact but also the interaction of sea water with the impact melt, resulting in repeated explosive interactions involving proto-SIC materials and mixing with pre-existing lithologies. This is complicated by additional brecciation events due to the intrusion of proto-SIC materials into the evolving and thickening Onaping. Fragmentation mechanisms changed as the system evolved and involved vesiculation in the formation of the upper two-thirds of the Onaping.

  16. The Effects of Subsurface Bioremediation on Soil Structure, Colloid Formation, and Contaminant Transport

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Liang, X.; Zhuang, J.; Radosevich, M.

    2016-12-01

    Anaerobic bioremediation is widely applied to create anaerobic subsurface conditions designed to stimulate microorganisms that degrade organic contaminants and immobilize toxic metals in situ. Anaerobic conditions that accompany such techniques also promotes microbially mediated Fe(III)-oxide mineral reduction. The reduction of Fe(III) could potentially cause soil structure breakdown, formation of clay colloids, and alternation of soil surface chemical properties. These processes could then affect bioremediation and the migration of contaminants. Column experiments were conducted to investigate the impact of anaerobic bioreduction on soil structure, hydraulic properties, colloid formation, and transport of three tracers (bromide, DFBA, and silica shelled silver nanoparticles). Columns packed with inoculated water stable soil aggregates were placed in anaerobic glovebox, and artificial groundwater media was pumped into the columns to simulate anaerobic bioreduction process for four weeks. Decent amount of soluble Fe(II) accompanied by colloids were detected in the effluent from bioreduction columns a week after initiation of bioreduction treatment, which demonstrated bioreduction of Fe(III) and formation of colloids. Transport experiments were performed in the columns before and after bioreduction process to assess the changes of hydraulic and surface chemical properties through bioreduction treatment. Earlier breakthrough of bromide and DFBA after treatment indicated alterations in flow paths (formation of preferential flow paths). Less dispersion of bromide and DFBA, and less tailing of DFBA after treatment implied breakdown of soil aggregates. Dramatically enhanced transport and early breakthrough of silica shelled silver nanoparticles after treatment supported the above conclusion of alterations in flow paths, and indicated changes of soil surface chemical properties.

  17. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Regulating temporospatial dynamics of morphogen for structure formation of the lacrimal gland by chitosan biomaterials.

    PubMed

    Hsiao, Ya-Chuan; Yang, Tsung-Lin

    2017-01-01

    The lacrimal gland is an important organ responsible for regulating tear synthesis and secretion. The major work of lacrimal gland (LG) is to lubricate the ocular surface and maintain the health of eyes. Functional deterioration of the lacrimal gland happens because of aging, diseases, or therapeutic complications, but without effective treatments till now. The LG originates from the epithelium of ocular surface and develops by branching morphogenesis. To regenerate functional LGs, it is required to explore the way of recapitulating and facilitating the organ to establish the intricate and ramified structure. In this study, we proposed an approach using chitosan biomaterials to create a biomimetic environment beneficial to the branching structure formation of developing LG. The morphogenetic effect of chitosan was specific and optimized to promote LG branching. With chitosan, increase in temporal expression and local concentration of endogenous HGF-related molecules creates an environment around the emerging tip of LG epithelia. By efficiently enhancing downstream signaling of HGF pathways, the cellular activities and behaviors were activated to contribute to LG branching morphogenesis. The morphogenetic effect of chitosan was abolished by either ligand or receptor deprivation, or inhibition of downstream signaling transduction. Our results elucidated the underlying mechanism accounting for chitosan morphogenetic effects on LG, and also proposed promising approaches with chitosan to assist tissue structure formation of the LG. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. 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.

  20. Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation

    PubMed Central

    Araiso, Yuhei; Palioura, Sotiria; Ishitani, Ryuichiro; Sherrer, R. Lynn; O’Donoghue, Patrick; Yuan, Jing; Oshikane, Hiroyuki; Domae, Naoshi; DeFranco, Julian; Söll, Dieter; Nureki, Osamu

    2008-01-01

    The micronutrient selenium is present in proteins as selenocysteine (Sec). In eukaryotes and archaea, Sec is formed in a tRNA-dependent conversion of O-phosphoserine (Sep) by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS). Here, we present the crystal structure of Methanococcus maripaludis SepSecS complexed with PLP at 2.5 Å resolution. SepSecS, a member of the Fold Type I PLP enzyme family, forms an (α2)2 homotetramer through its N-terminal extension. The active site lies on the dimer interface with each monomer contributing essential residues. In contrast to other Fold Type I PLP enzymes, Asn247 in SepSecS replaces the conserved Asp in binding the pyridinium nitrogen of PLP. A structural comparison with Escherichia coli selenocysteine lyase allowed construction of a model of Sep binding to the SepSecS catalytic site. Mutations of three conserved active site arginines (Arg72, Arg94, Arg307), protruding from the neighboring subunit, led to loss of in vivo and in vitro activity. The lack of active site cysteines demonstrates that a perselenide is not involved in SepSecS-catalyzed Sec formation; instead, the conserved arginines may facilitate the selenation reaction. Structural phylogeny shows that SepSecS evolved early in the history of PLP enzymes, and indicates that tRNA-dependent Sec formation is a primordial process. PMID:18158303

  1. Training order and structural location of meaningful stimuli: effects on equivalence class formation.

    PubMed

    Nartey, Richard K; Arntzen, Erik; Fields, Lanny

    2015-12-01

    In the present study, equivalence class formation was influenced by the temporal point of inclusion of a meaningful stimulus when baseline relations were serially or sequentially trained, and much less so by the location of the meaningful stimulus in the nodal structure of the class. In Experiment 1, participants attempted to form three 3-node, 5-member classes (A→B→C→D→E) under the simultaneous protocol. After serially training the baseline relations AB, BC, CD, and DE, in that order, the emergence of all emergent relations was tested concurrently. In the A-as-PIC condition, A was meaningful stimulus and B to E were meaningless stimulus, and 60 % of the participants formed classes. In addition, classes were formed by 40 %, 70 %, 40 %, and 20 % of the participants in the B-as-PIC, C-as-PIC, D-as-PIC, and E-as-PIC groups, respectively. Thus, the likelihood of class formation could have been influenced by the location of a meaningful stimulus in the class structure and/or by its order of introduction during training. In Experiment 2, we controlled for any effect of order of introduction by the concurrent training of all of the baseline relations. Regardless of the location of the meaningful stimulus, 0-20 % of participants formed classes. Thus, the temporal order of introducing a meaningful stimulus was the primary modulator of the class-enhancing property of meaningful stimuli, and not the location of the meaningful stimulus in the class structure.

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

    PubMed

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

    2013-09-03

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

  3. Structural and facies characterization of the Niobrara Formation in Goshen and Laramie counties, Wyoming

    NASA Astrophysics Data System (ADS)

    Kernan, Nicholas Devereux

    The Niobrara Formation is a fine-grained marine rock deposited in the Western Interior Seaway during the Late Cretaceous. It is composed of fossil-rich interlayered shale, marls, and chalks. Recent interest in the Niobrara has grown due to the advent of lateral drilling and multi-stage hydraulic fracturing. This technology allows operators to economically extract hydrocarbons from chalkier Niobrara facies. Yet two aspects of the Niobrara Formation have remained enigmatic. The first is the occurrence of abundant, randomly oriented, layer-bound, normal faults. The second is the large degree of vertical heterogeneity. This research aimed to increase understanding in both these aspects of the Niobrara Formation. Randomly oriented normal faults have been observed in Niobrara outcrops for nearly a hundred years. Recent high resolution 3D seismic in the Denver Basin has allowed investigators to interpret these faults as part of a polygonal fault system (PFS). PFS are layer bound extensional structures that typically occur in fine-grained marine sediments. Though their genesis and development is still poorly understood, their almost exclusive occurrence in fine-grained rocks indicates their origin is linked to lithology. Interpretation of a 3D seismic cube in Southeast Wyoming found a tier of polygonal faulting within the Greenhorn-Carlile formations and another tier of polygonal faulting within the Niobrara and Pierre formations. This research also found that underlying structural highs influence fault growth and geometries within both these tiers. Core data and thin sections best describe vertical heterogeneity in fine-grained rocks. This investigation interpreted core data and thin sections in a well in Southeast Wyoming and identified 10 different facies. Most of these facies fall within a carbonate/clay spectrum with clay-rich facies deposited during periods of lower sea level and carbonate-rich facies deposited during periods of higher sea level. Because the average

  4. Formation of large-scale structures in ablative Kelvin-Helmholtz instability

    NASA Astrophysics Data System (ADS)

    Wang, L. F.; Ye, W. H.; Don, Wai-Sun; Sheng, Z. M.; Li, Y. J.; He, X. T.

    2010-12-01

    In this research, we studied numerically nonlinear evolutions of the Kelvin-Helmholtz instability (KHI) with and without thermal conduction, aka, the ablative KHI (AKHI) and the classical KHI (CKHI). The second order thermal conduction term with a variable thermal conductivity coefficient is added to the energy equation in the Euler equations in the AKHI to investigate the effect of thermal conduction on the evolution of large and small scale structures within the shear layer which separate the fluids with different velocities. The inviscid hyperbolic flux of Euler equation is computed via the classical fifth order weighted essentially nonoscillatory finite difference scheme and the temperature is solved by an implicit fourth order finite difference scheme with variable coefficients in the second order parabolic term to avoid severe time step restriction imposed by the stability of the numerical scheme. As opposed to the CKHI, fine scale structures such as the vortical structures are suppressed from forming in the AKHI due to the dissipative nature of the second order thermal conduction term. With a single-mode sinusoidal interface perturbation, the results of simulations show that the growth of higher harmonics is effectively suppressed and the flow is stabilized by the thermal conduction. With a two-mode sinusoidal interface perturbation, the vortex pairing is strengthened by the thermal conduction which would allow the formation of large-scale structures and enhance the mixing of materials. In summary, our numerical studies show that thermal conduction can have strong influence on the nonlinear evolutions of the KHI. Thus, it should be included in applications where thermal conduction plays an important role, such as the formation of large-scale structures in the high energy density physics and astrophysics.

  5. Formation of large-scale structures in ablative Kelvin-Helmholtz instability

    SciTech Connect

    Wang, L. F.; Ye, W. H.; He, X. T.; Don, Wai-Sun; Sheng, Z. M.; Li, Y. J.

    2010-12-15

    In this research, we studied numerically nonlinear evolutions of the Kelvin-Helmholtz instability (KHI) with and without thermal conduction, aka, the ablative KHI (AKHI) and the classical KHI (CKHI). The second order thermal conduction term with a variable thermal conductivity coefficient is added to the energy equation in the Euler equations in the AKHI to investigate the effect of thermal conduction on the evolution of large and small scale structures within the shear layer which separate the fluids with different velocities. The inviscid hyperbolic flux of Euler equation is computed via the classical fifth order weighted essentially nonoscillatory finite difference scheme and the temperature is solved by an implicit fourth order finite difference scheme with variable coefficients in the second order parabolic term to avoid severe time step restriction imposed by the stability of the numerical scheme. As opposed to the CKHI, fine scale structures such as the vortical structures are suppressed from forming in the AKHI due to the dissipative nature of the second order thermal conduction term. With a single-mode sinusoidal interface perturbation, the results of simulations show that the growth of higher harmonics is effectively suppressed and the flow is stabilized by the thermal conduction. With a two-mode sinusoidal interface perturbation, the vortex pairing is strengthened by the thermal conduction which would allow the formation of large-scale structures and enhance the mixing of materials. In summary, our numerical studies show that thermal conduction can have strong influence on the nonlinear evolutions of the KHI. Thus, it should be included in applications where thermal conduction plays an important role, such as the formation of large-scale structures in the high energy density physics and astrophysics.

  6. Influence of electrified surface of cementitious materials on structure formation of hardened cement paste

    NASA Astrophysics Data System (ADS)

    Alekseev, A.; Gusakov, A.

    2015-01-01

    To provide high strength and durability of concrete it is necessary to study the influence of physical and chemical and mechanical principles of dispersed cementitious systems. The experimental bench was developed to study the influence of electrified surface of cementitious materials on structure formation of hardened cement paste. The test bench allows accelerating the processes of dissolution of cementing materials in water due to influence of electric discharge on their surface. Cement activation with high-voltage corona discharge when AC current is applied allows increasing the ultimate compressive strength of hardened cement paste by 46% at the age of one day and by 20% at the age of 28 days.

  7. 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.

  8. Creative Curriculum: The Experience of Writing and Teaching Formative Objective Structured Clinical Examinations (FOSCEs).

    PubMed

    Harrod, Tom P; Gomes, Alexandra W

    2017-01-01

    The launch of the revised medical school curriculum in fall 2014 provided new opportunities for librarians to collaborate with clinical faculty. As a result of past informatics instruction embedded in the first-year curriculum, librarians were invited to expand this content as part of a new Formative Objective Structured Clinical Examination (FOSCE) initiative. This article describes the stages of this project from writing and teaching the FOSCE informatics cases to improvements which were made after the first year. A description of the overall curriculum and information about lessons learned in each of these stages is included.

  9. 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.

  10. Ultrafine-grained structure formation in Ti-6Al-4V alloy via warm swaging

    NASA Astrophysics Data System (ADS)

    Klimova, M.; Boeva, M.; Zherebtsov, S.; Salishchev, G.

    2014-08-01

    The influence of warm swaging on the structure and properties of Ti-6Al-4V alloy was studied. Warm swaging of the alloy in the interval 680-500°C with the total strain of ɛ=2.66 was found to be resulted in the formation of a homogeneous globular microstructure with a grain size of 0.4 μm in both longitudinal and transversal sections. Room temperature tensile strength and tensile elongation of the swaged alloy was 1315MPa and 10.5%, respectively. Ultrafine-grained Ti-6Al-4V alloy produced by swaging exhibited good workability at 600-700 °C.

  11. 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.

  12. Simulation of Domain Formation in p-Si/SiGe Quantum Cascade Structures

    NASA Astrophysics Data System (ADS)

    Ikonic, Z.; Harrison, P.; Kelsall, R. W.

    Domain formation in p-doped Si/SiGe quantum cascades is considered using a carrier scattering transport framework. The hole flow along the cascade is described via scattering between quantized states belonging to neighbouring periods, caused by phonons, alloy disorder, and carrier-carrier interactions. The generation of either periodic or of nonperiodic domains is studied in uniformly or modulationally doped cascades, and criteria for their appearance are found. The domains in modulationally doped cascades have a relatively smaller effect on the energy structure than in uniformly doped ones.

  13. Hollow structure formation of intense ion beams with sharp edge in background plasmas

    SciTech Connect

    Hu, Zhang-Hu; Wang, You-Nian

    2016-02-15

    The transport of intense ion beams with sharp radial beam edge in plasmas has been studied with two-dimensional electromagnetic particle simulations. The initial solid beam evolves into a hollow beam due to the nonlinear sharp transverse force peak in the regions of beam edge. The magnitude and nonlinearity of this peak are enhanced as the ion beam travels further into the plasma, due to the self-consistent interactions between the beam ions and the plasma electrons. This structure formation is shown to be independent on the beam radius.

  14. Formation and dynamics of large-scale magnetic structures in the ionosphere of Venus

    NASA Technical Reports Server (NTRS)

    Cloutier, P. A.

    1984-01-01

    The formation and dynamics of large-scale magnetic structures in the ionosphere of Venus are examined. It is shown that such structures must be the result of steady state convection of interplanetary field lines into the ionosphere by the small amount of solar wind plasma (less than or approximately equal to 1-5 percent) absorbed by the planetary atmosphere below the ionopause, rather than isolated remnants of large fields persisting for long periods without connection to the solar wind induced current and convection pattern. In particular, it is demonstrated that the magnetic diffusion of such structures would result in their dissipation with time scales of 1-10 min, if they were not steady state structures in convective and diffusive equilibriuim. It is shown that the equations governing the diffusion of these magnetic structures are similar to those governing diffusion of a gas out of an enclosed chamber with a porous wall, and a simple analog is illustrated. The application of these results to magnetic fields of astrophysical plasmas is discussed.

  15. 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.

  16. Formation of nanoporous structure in silicon substrate using two-stage annealing process

    NASA Astrophysics Data System (ADS)

    Denisenko, Yuri I.; Rudakov, Valery I.

    2016-12-01

    The experimental results relating to exciting the defect-impurity subsystem of a (001)-oriented Si substrate containing ion-synthesized buried Si:P:O layer and transformation of the material into a porous medium are represented. After coimplantation with P+ and O2+ ions, the substrates are subjected to the annealing in non-isothermal reactor at two average temperatures (900 and 1100°C, 5 min) and two opposite directions of an axial temperature gradient grad T. The temperature difference between reversed sides of the substrate is estimated of the order of 1.5 and 3 °C, respectively. After further thermal evolution in conventional furnace (1150 °C, 4 hours) and cleaving, the formation of two types of a porous structure in the specimens is exposed. The first type of this structure is the developed porous structure, where initially spheroid-like empty voids have grown up in size and changed their shape to form octahedron construction. The second type of this structure is a regular array of hollow tubes oriented along screw components of misfit dislocations. In the both cases, the porous structures always are initiated on the substrates, whose implanted sides have been faced to the cold pedestal during annealing in non-isothermal reactor.

  17. 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

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

    PubMed

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-03-17

    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.

  19. Exoelectrogenic biofilm as a template for sustainable formation of a catalytic mesoporous structure.

    PubMed

    Yates, Matthew D; Cusick, Roland D; Ivanov, Ivan; Logan, Bruce E

    2014-11-01

    Mesoporous structures can increase catalytic activity by maximizing the ratio of surface area to volume, but current synthesis techniques utilize expensive polymers and toxic chemicals. A Geobacter sulfurreducens biofilm was used as a sustainable template to form mesoporous Pd structures while eliminating the need for synthetic chemicals. The bulk of the biofilm material was removed by thermal treatments after nanoparticle formation, producing a catalytic Pd mesoporous (pore size 9.7 ± 0.1 nm) structure attached to the graphite electrode with a 1.5-2 µm thick backbone composed of nanoparticles (∼200 nm). A control electrode electrochemically plated with Pd in the absence of a biofilm exhibited a variable planar Pd base (∼0.5-3 µm thick) with sporadic Pd extrusions (∼2 µm across, 1-5 µm tall) from the surface. The biotemplated mesoporous structure produced 15-20% higher stable current densities during H2 oxidation tests than the electrochemically plated control electrode, even though 30% less Pd was present in the biotemplated catalyst. These results indicate that electroactive biofilms can be used as a sustainable base material to produce nanoporous structures without the need for synthetic polymers. Biotechnol. Bioeng. 2014;111: 2349-2354. © 2014 Wiley Periodicals, Inc.

  20. The Role of Microbial Iron Reduction in the Formation of Proterozoic Molar Tooth Structures

    NASA Astrophysics Data System (ADS)

    Hodgskiss, M. S. W.; Kunzmann, M.; Halverson, G. P.; Poirier, A.

    2016-12-01

    Molar tooth structures are poorly understood early diagenetic, microspar-filled voids in clay-rich carbonate sediments. They are a common structure in sedimentary successions dating from 2600-720 Ma, but do not occur in rocks older or younger. Despite being volumetrically significant in carbonate rocks of this age, their formation and disappearance are poorly understood. Here, we present iron isotope data, supported by carbon and oxygen isotopes, major and minor element concentrations, and total organic carbon and pyrite contents for samples from ten regions spanning 1870-635 Ma. The iron isotopic composition of molar tooth structures is almost always lighter (modal depletion of 2‰) than the carbonate or siliciclastic components in the host sediment, whereas carbon isotopes are indistinguishable. We interpret the isotopically light iron in molar tooth structures to have been produced by microbial iron reduction utilising Fe-oxyhydroxides and smectites. The microbial conversion of smectite to illite results in a volume reduction of clay minerals ( 30%), while locally increasing pore water alkalinity. Therefore, this biogeochemical process is a viable mechanism to produce voids and subsequently precipitate carbonate minerals. The disappearance of molar tooth structures is likely linked to a combination of a decrease in smectite abundance, a decline in the marine DIC reservoir, and increase in the concentration of O2 in shallow seawater in the mid-Neoproterozoic.

  1. 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.

  2. Strong Electro‐Optic Effect and Spontaneous Domain Formation in Self‐Assembled Peptide Structures

    PubMed Central

    Lafargue, Clément; Handelman, Amir; Shimon, Linda J. W.; Rosenman, Gil; Zyss, Joseph

    2017-01-01

    Short peptides made from repeating units of phenylalanine self‐assemble into a remarkable variety of micro‐ and nanostructures including tubes, tapes, spheres, and fibrils. These bio‐organic structures are found to possess striking mechanical, electrical, and optical properties, which are rarely seen in organic materials, and are therefore shown useful for diverse applications including regenerative medicine, targeted drug delivery, and biocompatible fluorescent probes. Consequently, finding new optical properties in these materials can significantly advance their practical use, for example, by allowing new ways to visualize, manipulate, and utilize them in new, in vivo, sensing applications. Here, by leveraging a unique electro‐optic phase microscopy technique, combined with traditional structural analysis, it is measured in di‐ and triphenylalanine peptide structures a surprisingly large electro‐optic response of the same order as the best performing inorganic crystals. In addition, spontaneous domain formation is observed in triphenylalanine tapes, and the origin of their electro‐optic activity is unveiled to be related to a porous triclinic structure, with extensive antiparallel beta‐sheet arrangement. The strong electro‐optic response of these porous peptide structures with the capability of hosting guest molecules opens the door to create new biocompatible, environmental friendly functional materials for electro‐optic applications, including biomedical imaging, sensing, and optical manipulation. PMID:28932664

  3. Strong Electro-Optic Effect and Spontaneous Domain Formation in Self-Assembled Peptide Structures.

    PubMed

    Gilboa, Barak; Lafargue, Clément; Handelman, Amir; Shimon, Linda J W; Rosenman, Gil; Zyss, Joseph; Ellenbogen, Tal

    2017-09-01

    Short peptides made from repeating units of phenylalanine self-assemble into a remarkable variety of micro- and nanostructures including tubes, tapes, spheres, and fibrils. These bio-organic structures are found to possess striking mechanical, electrical, and optical properties, which are rarely seen in organic materials, and are therefore shown useful for diverse applications including regenerative medicine, targeted drug delivery, and biocompatible fluorescent probes. Consequently, finding new optical properties in these materials can significantly advance their practical use, for example, by allowing new ways to visualize, manipulate, and utilize them in new, in vivo, sensing applications. Here, by leveraging a unique electro-optic phase microscopy technique, combined with traditional structural analysis, it is measured in di- and triphenylalanine peptide structures a surprisingly large electro-optic response of the same order as the best performing inorganic crystals. In addition, spontaneous domain formation is observed in triphenylalanine tapes, and the origin of their electro-optic activity is unveiled to be related to a porous triclinic structure, with extensive antiparallel beta-sheet arrangement. The strong electro-optic response of these porous peptide structures with the capability of hosting guest molecules opens the door to create new biocompatible, environmental friendly functional materials for electro-optic applications, including biomedical imaging, sensing, and optical manipulation.

  4. 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.

  5. Formation of Periodic Structures (2D-PhCs) by Scanning Electron Lithography

    NASA Astrophysics Data System (ADS)

    Utkin, Dmitriy; Shklyev, Alexander; Tsarev, Andrey; Latyshev, Alexander; Nasimov, Dmitriy

    The formation of the periodic structures based on Si-materials by electron beam lithography technique has been studied. We have investigated lithography processes such as designing, exposition, development, etching end others. The developed technique allows forming close-packed arrays of elements and holes in the nanometre range. This can be used to produce two-dimensional photonic crystals (2D PhCs) with emitting micro cavities (missing holes) with lateral size parameters within an accuracy of about 2% in the Si (100) substrate and in silicon-on-insulator structures. Such accuracy is expected to be sufficient for obtaining the cavities-coupling radiation interference from large areas of 2D PhCs.

  6. 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.

    2016-12-01

    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.

  7. 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.

  8. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    PubMed Central

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-01-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures—formed by a single sequence—may be a key feature in preventing bacterial resistance and could explain why sequence–function relationships in AMPs remain elusive. PMID:27874004

  9. 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.

  10. A composite study on the structure and formation of ozone miniholes and minihighs over central Europe

    NASA Astrophysics Data System (ADS)

    Koch, G.; Wernli, H.; Schwierz, C.; Staehelin, J.; Peter, T.

    2005-06-01

    Two different mechanisms have been proposed to be important for the formation of extreme total ozone events in mid-latitudes, so-called miniholes: (A) far-range meridional transport of air masses from regions with different climatological ozone mixing ratios, and (B) (local) adiabatic vertical displacement of isentropes. Here, the relative importance of these two mechanisms is studied using two different ozone profile reconstruction techniques for all miniholes and minihighs (events with anomalously high ozone) during the time period 1980-1989 over Switzerland. Composites for the two types of events of their vertical potential vorticity (PV) reveal a vertical dipole structure of PV anomalies in the lower and middle stratosphere. They, in agreement with the profile reconstructions, highlight the importance of fast far-range transport (mechanism A). Dynamically consistent with this PV structure is a relatively weak vertical displacement of isentropes between the PV dipole, that provides an additional but less important contribution (mechanism B).

  11. Tergal and pleural structures contribute to the formation of ectopic prothoracic wings in cockroaches.

    PubMed

    Elias-Neto, Moysés; Belles, Xavier

    2016-08-01

    Wings were a fundamental morphological innovation for the adaptive radiation of insects, the most diversified group among all animals. Pterygote insects have two pairs of wings, the mesothoracic (T2) forewings and the metathoracic (T3) hindwings, whereas the prothorax (T1) is wingless. Using RNA interference approaches, we have found that the gene Sex combs reduced (Scr) determines the wingless identity of T1 in the cockroach Blattella germanica. Interference of Scr triggers the formation of ectopic wing structures in T1, which are formed from the expansion of the latero-posterior region of the pronotum, along with a contribution of the epimeron, a pleurite of T1. These data support the theory of a dual origin for insect wings, from pronotal (tergal origin theory) and pleural (pleural origin theory) structures and genes.

  12. 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

  13. Tergal and pleural structures contribute to the formation of ectopic prothoracic wings in cockroaches

    PubMed Central

    Elias-Neto, Moysés

    2016-01-01

    Wings were a fundamental morphological innovation for the adaptive radiation of insects, the most diversified group among all animals. Pterygote insects have two pairs of wings, the mesothoracic (T2) forewings and the metathoracic (T3) hindwings, whereas the prothorax (T1) is wingless. Using RNA interference approaches, we have found that the gene Sex combs reduced (Scr) determines the wingless identity of T1 in the cockroach Blattella germanica. Interference of Scr triggers the formation of ectopic wing structures in T1, which are formed from the expansion of the latero-posterior region of the pronotum, along with a contribution of the epimeron, a pleurite of T1. These data support the theory of a dual origin for insect wings, from pronotal (tergal origin theory) and pleural (pleural origin theory) structures and genes. PMID:27853616

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

    DOE PAGES

    Im, Mi-Young; Lee, Ki-Suk; Vogel, Andreas; ...

    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. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.

    PubMed

    Ermler, U; Grabarse, W; Shima, S; Goubeaud, M; Thauer, R K

    1997-11-21

    Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.

  16. Structure Formation in a Variable Dark Energy Model and Observational Constraints

    NASA Astrophysics Data System (ADS)

    Arbabi-Bidgoli, S.; Movahed, M. S.

    The interpretation of a vast number of cosmological observations in the framework of FRW models suggests that the major part of the energy density of the universe is in form of dark energy with still unknown physical nature. In some models for dark energy, which are motivated by particle physics theory, the equation of state and the contribution of dark energy to the energy density of the universe can be variable. Here we study structure formation in a parameterized dark energy model, and compare its predictions with recent observational data, from the Supernova Ia gold sample and the parameters of large scale structure determined by the 2-degree Field Galaxy Redshift Survey (2dFGRS), and put some constraints on the free parameters of this model.

  17. 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.

  18. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    NASA Astrophysics Data System (ADS)

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-11-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

  19. 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.

  20. Substrate-dependent electronic structure and film formation of MAPbI3 perovskites

    PubMed Central

    Olthof, Selina; Meerholz, Klaus

    2017-01-01

    We present investigations on the interface formation between the hybrid perovskite MAPbI3 and various substrates, covering a wide range of work functions. The perovskite films are incrementally evaporated in situ while the electronic structure is evaluated using photoelectron spectroscopy. Our results show that there is an induction period in the growth of the perovskite during which volatile compounds are formed, catalyzed by the substrate. The duration of the induction period depends strongly on the nature of the substrate material, and it can take up to 20–30 nm of formal precursor deposition before the surface is passivated and the perovskite film starts forming. The stoichiometry of the 2–3 nm thin passivation layer deviates from the expected perovskite stoichiometry, being rich in decomposition products of the organic cation. During the regular growth of the perovskite, our measurements show a deviation from the commonly assumed flat band condition, i.e., dipole formation and band bending dominate the interface. Overall, the nature of the substrate not only changes the energetic alignment of the perovskite, it can introduce gap states and influence the film formation and morphology. The possible impact on device performance is discussed. PMID:28084313

  1. 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.

  2. Zeolite Nanoparticles Inhibit Aβ-Fibrinogen Interaction and Formation of a Consequent Abnormal Structural Clot.

    PubMed

    Derakhshankhah, Hossein; Hajipour, Mohammad Javad; Barzegari, Ebrahim; Lotfabadi, Alireza; Ferdousi, Maryam; Saboury, Ali Akbar; Ng, Eng Poh; Raoufi, Mohammad; Awala, Hussein; Mintova, Svetlana; Dinarvand, Rassoul; Mahmoudi, Morteza

    2016-11-16

    EMT-type zeolite nanoparticles (EMT NPs) with particle size of 10-20 nm and external surface area of 200 m(2)/g have shown high selective affinity toward plasma protein (fibrinogen). Besides, the EMT NPs have demonstrated no adverse effect on blood coagulation hemostasis. Therefore, it was envisioned that the EMT NPs could inhibit possible β-amyloid (Aβ)-fibrinogen interactions that result in the formation of structurally abnormal clots, which are resistant to lysis, in cerebral vessels of patients with Alzheimer disease (AD). To evaluate this hypothesis, the clot formation and degradation of Aβ-fibrinogen in the presence and absence of the EMT zeolite NPs were assessed. The results clearly showed that the delay in clot dissolution was significantly reduced in the presence of zeolite NPs. By formation of protein corona, the EMT NPs showed a negligible reduction in their inhibitory strength. Docking of small molecules (Aβ-fibrinogen) introduced a novel potential inhibitory candidate. The zeolite NPs showed similar inhibitory effects on binding of fibrinogen to both Aβ(25-35) and/or Aβ(1-42). This indicates that the inhibitory strength of these NPs is independent of Aβ sequence, and it is suggested that the zeolite NPs adsorb fibrinogen and specifically obstruct their Aβ binding sites. Therefore, the zeolite NPs can be the safe and effective inhibitors in preventing Aβ-fibrinogen interaction and consequent cognitive damage.

  3. Substrate-dependent electronic structure and film formation of MAPbI3 perovskites

    NASA Astrophysics Data System (ADS)

    Olthof, Selina; Meerholz, Klaus

    2017-01-01

    We present investigations on the interface formation between the hybrid perovskite MAPbI3 and various substrates, covering a wide range of work functions. The perovskite films are incrementally evaporated in situ while the electronic structure is evaluated using photoelectron spectroscopy. Our results show that there is an induction period in the growth of the perovskite during which volatile compounds are formed, catalyzed by the substrate. The duration of the induction period depends strongly on the nature of the substrate material, and it can take up to 20–30 nm of formal precursor deposition before the surface is passivated and the perovskite film starts forming. The stoichiometry of the 2–3 nm thin passivation layer deviates from the expected perovskite stoichiometry, being rich in decomposition products of the organic cation. During the regular growth of the perovskite, our measurements show a deviation from the commonly assumed flat band condition, i.e., dipole formation and band bending dominate the interface. Overall, the nature of the substrate not only changes the energetic alignment of the perovskite, it can introduce gap states and influence the film formation and morphology. The possible impact on device performance is discussed.

  4. Mimas And Enceladus: Formation And Interior Structure From Astromteric Reduction Of Cassini Images

    NASA Astrophysics Data System (ADS)

    Tajeddine, Radwan; Lainey, V.; Rambaux, N.; Cooper, N. J.; Charnoz, S.; Murray, C. D.

    2012-10-01

    The origin and evolution of the Saturnian satellites is still debated. While the canonical formation model creates many main moons in Saturn's subnebulae, a new model suggests a possible formation at the outer edge of a past massive ring (Charnoz et al. 2011). Furthermore, many interior structure models were suggested for Enceladus in order to explain the geysers observed in its South polar region. For instance, Nimmo and Pappalardo (2006) suggest the existence of a low density anomaly in the ice crust, and Collins and Goodman (2007) explain these geysers by an internal local "sea" with higher density than the ice crust. It is also noteworthy that in the model of Charnoz et al. (2011), the core of the satellites is not necessarily symmetric, due to the accretion of icy material onto large silicate chunks (> 10 - 100 Km). All these previous models may result in a shift between the center of mass and the center of figure of the satellites. We used the astrometry of Cassini ISS NAC images of Mimas and Enceladus to attempt to quantify such a shift considering, on one hand, the satellite's observed position as the center of figure and, on the other hand, its predicted position from the orbital ephemeris as the center of mass. In studying such a shift, we may add new constraints to the existing models and possibly discriminate between the various interior and formation models of the Saturnian system.

  5. A critical role for dendritic cells in the formation of lymphatic vessels within tertiary lymphoid structures.

    PubMed

    Muniz, Luciana R; Pacer, Michelle E; Lira, Sergio A; Furtado, Glaucia C

    2011-07-15

    Ectopic, or tertiary, lymphoid aggregates often form in chronically inflamed areas. Lymphatic vessels, as well as high endothelial venules, form within these lymphoid aggregates, but the mechanisms underlying their development are poorly understood. Overexpression of the chemokine CCL21 in the thyroid of transgenic mice leads to formation of lymphoid aggregates containing topologically segregated T and B lymphocytes, dendritic cells (DCs), and specialized vasculature, including Lyve-1(+)/Prox-1(+) lymphatic vessels. In this article, we show that adoptive transfer of mature CD4(+) T cells into animals expressing CCL21 in a RAG-deficient background promotes the influx of host NK cells and DCs into the thyroid and the formation of new lymphatic vessels within 10 d. This process is dependent on the expression of lymphotoxin ligands by host cells, but not by the transferred CD4(+) T cells. Ablation of host DCs, but not NK cells, reduces the formation of new lymphatic vessels in the thyroid. Taken together, these data suggest a critical role for CD11c(+) DCs in the induction of lymphangiogenesis in tertiary lymphoid structures.

  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. Structural changes of Salinibacter sensory rhodopsin I upon formation of the K and M photointermediates.

    PubMed

    Suzuki, Daisuke; Sudo, Yuki; Furutani, Yuji; Takahashi, Hazuki; Homma, Michio; Kandori, Hideki

    2008-12-02

    Sensory rhodopsin I (SRI) is one of the most interesting photosensory receptors in nature because of its ability to mediate opposite signals depending on light color by photochromic one-photon and two-photon reactions. Recently, we characterized SRI from eubacterium Salinibacter ruber (SrSRI). This protein allows more detailed information about the structure and structural changes of SRI during its action to be obtained. In this paper, Fourier transform infrared (FTIR) spectroscopy is applied to SrSRI, and the spectral changes upon formation of the K and M intermediates are compared with those of other archaeal rhodopsins, SRI from Halobacterium salinarum (HsSRI), sensory rhodopsin II (SRII), bacteriorhodopsin (BR), and halorhodopsin (HR). Spectral comparison of the hydrogen out-of-plane (HOOP) vibrations of the retinal chromophore in the K intermediates shows that extended choromophore distortion takes place in SrSRI and HsSRI, as well as in SRII, whereas the distortion is localized in the Schiff base region in BR and HR. It appears that sensor and pump functions are distinguishable from the spectral feature of HOOP modes. The HOOP band at 864 cm(-1) in SRII, important for negative phototaxis, is absent in SrSRI, suggesting differences in signal transfer mechanism between SRI and SRII. The strongly hydrogen-bound water molecule, important for proton pumps, is observed at 2172 cm(-1) in SrSRI, as well as in BR and SRII. The formation of the M intermediate accompanies the appearance of peaks at 1753 (+) and 1743 (-) cm(-1), which can be interpreted as the protonation signal of the counterion (Asp72) and the proton release signal from an unidentified carboxylic acid, respectively. The structure and structural changes of SrSRI are discussed on the basis of the present infrared spectral comparisons with other rhodopsins.

  8. A Deeper Look at Leo IV: Star Formation History and Extended Structure

    NASA Astrophysics Data System (ADS)

    Sand, David J.; Seth, Anil; Olszewski, Edward W.; Willman, Beth; Zaritsky, Dennis; Kallivayalil, Nitya

    2010-07-01

    We present MMT/Megacam imaging of the Leo IV dwarf galaxy in order to investigate its structure and star formation history, and to search for signs of association with the recently discovered Leo V satellite. Based on parameterized fits, we find that Leo IV is round, with epsilon < 0.23 (at the 68% confidence limit) and a half-light radius of rh ~= 130 pc. Additionally, we perform a thorough search for extended structures in the plane of the sky and along the line of sight. We derive our surface brightness detection limit by implanting fake structures into our catalog with stellar populations identical to that of Leo IV. We show that we are sensitive to stream-like structures with surface brightness μ r <~ 29.6 mag arcsec-2, and at this limit we find no stellar bridge between Leo IV (out to a radius of ~0.5 kpc) and the recently discovered, nearby satellite Leo V. Using the color-magnitude fitting package StarFISH, we determine that Leo IV is consistent with a single age (~14 Gyr), single metallicity ([Fe/H] ~ -2.3) stellar population, although we cannot rule out a significant spread in these values. We derive a luminosity of MV = -5.5 ± 0.3. Studying both the spatial distribution and frequency of Leo IV's "blue plume" stars reveals evidence for a young (~2 Gyr) stellar population which makes up ~2% of its stellar mass. This sprinkling of star formation, only detectable in this deep study, highlights the need for further imaging of the new Milky Way satellites along with theoretical work on the expected, detailed properties of these possible "reionization fossils." Observations reported here were obtained at the MMT observatory, a joint facility of the Smithsonian Institution and the University of Arizona.

  9. A DEEPER LOOK AT LEO IV: STAR FORMATION HISTORY AND EXTENDED STRUCTURE

    SciTech Connect

    Sand, David J.; Seth, Anil; Olszewski, Edward W.; Zaritsky, Dennis; Willman, Beth; Kallivayalil, Nitya

    2010-07-20

    We present MMT/Megacam imaging of the Leo IV dwarf galaxy in order to investigate its structure and star formation history, and to search for signs of association with the recently discovered Leo V satellite. Based on parameterized fits, we find that Leo IV is round, with {epsilon} < 0.23 (at the 68% confidence limit) and a half-light radius of r{sub h} {approx_equal} 130 pc. Additionally, we perform a thorough search for extended structures in the plane of the sky and along the line of sight. We derive our surface brightness detection limit by implanting fake structures into our catalog with stellar populations identical to that of Leo IV. We show that we are sensitive to stream-like structures with surface brightness {mu}{sub r} {approx}< 29.6 mag arcsec{sup -2}, and at this limit we find no stellar bridge between Leo IV (out to a radius of {approx}0.5 kpc) and the recently discovered, nearby satellite Leo V. Using the color-magnitude fitting package StarFISH, we determine that Leo IV is consistent with a single age ({approx}14 Gyr), single metallicity ([Fe/H] {approx} -2.3) stellar population, although we cannot rule out a significant spread in these values. We derive a luminosity of M{sub V} = -5.5 {+-} 0.3. Studying both the spatial distribution and frequency of Leo IV's 'blue plume' stars reveals evidence for a young ({approx}2 Gyr) stellar population which makes up {approx}2% of its stellar mass. This sprinkling of star formation, only detectable in this deep study, highlights the need for further imaging of the new Milky Way satellites along with theoretical work on the expected, detailed properties of these possible 'reionization fossils'.

  10. 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

  11. 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

  12. 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.

  13. STRUCTURE FORMATION BY FIFTH FORCE: POWER SPECTRUM FROM N-BODY SIMULATIONS

    SciTech Connect

    Zhao Hongsheng; Feix, Martin; Maccio, Andrea V.; Li Baojiu; Hoekstra, Henk

    2010-04-01

    We lay out the framework to numerically study nonlinear structure formation in the context of scalar-field-coupled cold dark matter models ({psi}CDM models) where the scalar field {psi} serves as dynamical dark energy. Adopting parameters for the scalar field that leave negligible effects on the cosmic microwave background (CMB) spectrum, we generate the initial conditions for our N-body simulations. The simulations follow the spatial distributions of dark matter and the scalar field, solving their equations of motion using a multilevel adaptive grid technique. We show that the spatial configuration of the scalar field depends sensitively on the local density field. The {psi}CDM model differs from standard {lambda}CDM at small scales with observable modifications of, e.g., the mass function of halos as well as the matter power spectrum. Nevertheless, the predictions of both models for the Hubble expansion and the CMB spectrum are virtually indistinguishable. Hence, galaxy cluster counts and weak lensing observations, which probe structure formation at small scales, are needed to falsify this class of models.

  14. 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

  15. Synthesis, structural characterization and formation mechanism of ferroelectric bismuth vanadate nanotubes.

    PubMed

    Singh, Satyendra; Kumari, Neelam; Varma, K B R; Krupanidhi, S B

    2009-11-01

    We report the synthesis and structural characterization of ferroelectric bismuth vanadate (Bi2VO5.5) (BVO) nanotubes within the nanoporous anodic aluminum oxide (AAO) templates via sol-gel method. The as-prepared BVO nanotubes were characterized by X-ray powder diffraction (XRD), Scanning Electron Microscope (SEM), High-Resolution Transmission Electron Microscope (HRTEM) and the stoichiometry of the nanotubes was established by energy-dispersive X-ray spectroscopy (EDX). Postannealed (675 degrees C for 1 h), BVO nanotubes were a polycrystalline and the XRD studies confirmed the crystal structure to be orthorhombic. The uniformity in diameter and length of the nanotubes as reveled by the TEM and SEM suggested that these were influenced to a guest extent by the thickness and pore diameter of the nanoporous AAO template. EDX analysis demonstrated the formation of stoichiometric Bi2VO5.5 phase. HRTEM confirmed that the obtained BVO nanotubes were made up of nanoparticles of 5-9 nm range. The possible formation mechanism of nanotubes was elucidated.

  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. Mode of formation and structural features of DNA-cationic liposome complexes used for transfection.

    PubMed

    Gershon, H; Ghirlando, R; Guttman, S B; Minsky, A

    1993-07-20

    Complexes formed between cationic liposomes and nucleic acids represent a highly efficient vehicle for delivery of DNA and RNA molecules into a large variety of eukaryotic cells. By using fluorescence, gel electrophoresis, and metal-shadowing electron microscopy techniques, the factors that affect the, yet unclear, interactions between DNA and cationic liposomes as well as the structural features of the resulting complexes have been elucidated. A model is suggested according to which cationic liposomes bind initially to DNA molecules to form clusters of aggregated vesicles along the nucleic acids. At a critical liposome density, two processes occur, namely, DNA-induced membrane fusion, indicated by lipid mixing studies, and liposome-induced DNA collapse, pointed out by the marked cooperativity of the encapsulation processes, by their modulations by DNA-condensing agents, and also by their conspicuous independence upon DNA length. The DNA collapse leads to the formation of condensed structures which can be completely encapsulated within the fused lipid bilayers in a fast, highly cooperative process since their exposed surface is substantially smaller than that of extended DNA molecules. The formation of the transfecting DNA-liposome complexes in which the nucleic acids are fully encapsulated within a positively-charged lipid bilayer is proposed, consequently, to be dominated by mutual effects exerted by the DNA and the cationic liposomes, leading to interrelated lipid fusion and DNA collapse.

  18. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Lagrangian theory for cosmic structure formation with vorticity: Newtonian and post-Friedmann approximations

    NASA Astrophysics Data System (ADS)

    Rampf, Cornelius; Villa, Eleonora; Bertacca, Daniele; Bruni, Marco

    2016-10-01

    We study the nonlinear gravitational dynamics of a universe filled with a pressureless fluid and a cosmological constant Λ in the context of Newtonian gravity, and in the relativistic post-Friedmann approach proposed in paper I [I. Milillo et al., Phys. Rev. D 92, 023519 (2015)]. The post-Friedmann approximation scheme is based on the 1 /c expansion of the space-time metric and the energy-momentum tensor, and includes nonlinear Newtonian cosmology. Here we establish the nonlinear post-Friedmann framework in the Lagrangian-coordinates approach for structure formation. For this we first identify a Lagrangian gauge which is suitable for incorporating nonzero vorticity. We analyze our results in two limits: at the leading order we recover the fully nonlinear Newtonian cosmological equations in the Lagrangian formulation, and we provide a space-time metric consistent from the perspective of general relativity. We then linearize our expressions and recover the relativistic results at first order in cosmological perturbation theory. Therefore, the introduced approximation scheme provides a unified treatment for the two leading-order regimes, from the small scales described by Newtonian gravity to the large linear scale, where first-order relativistic cosmological perturbation theory gives a very good description of structure formation.

  20. The well-defined structure of boxy bulges Implications for the Milky Way bulge formation

    NASA Astrophysics Data System (ADS)

    Di Matteo, P.

    Some results of idealized, dissipationless, N-body simulations which follow the formation and subsequent buckling of a stellar bar are presented in this contribution, and compared to the properties of the stellar populations in the Milky Way bulge. We find that: (i) the redistribution of stars in the disk initiated at the epoch of bar formation implies that it is the whole stellar disk that contributes to the boxy/peanut shaped structure; (ii) the contribution of stars to the local bulge density depends on their birth radius: stars born in the innermost disk tend to dominate the innermost regions of the boxy bulge, while outer stars become dominant in the external part of the boxy/peanut structure. As detailed in \\citet{dimatteo14}, stellar birth radii are imprinted in the bulge kinematics, that is the higher the birth radius of stars ending up in the bulge, the larger their rotational support and their line-of-sight velocity dispersions. On the basis of their chemical and kinematic characteristics, we suggest that the populations A, B and C, as defined by the ARGOS survey, can be associated, respectively, to the inner thin disk, to the young thick and to the old thick disk, following the nomenclature recently suggested for solar neighborhood stars by Haywood et al. (2013).

  1. Modeling the influence of alkane molecular structure on secondary organic aerosol formation.

    PubMed

    Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha

    2013-01-01

    Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors.

  2. 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.

  3. Formation of laser induced periodic surface structures (LIPSS) on Ti upon double fs pulse exposure

    NASA Astrophysics Data System (ADS)

    Gemini, Laura; Hashida, Masaki; Nishii, Takaya; Miyasaka, Yasuhiro; Inoue, Shunsuke; Limpouch, Jiri; Mocek, Tomas; Sakabe, Shuji

    2015-03-01

    Recently a parametric decay model was proposed in order to foresee LIPSS interspaces, and experimental results are in reasonable agreement. To confirm the possibility assumed by the model of pre-formed plasma generation, Ti surface was irradiated by a femtosecond (fs) laser beam composed by double fs pulses, with a fixed delay of 160 fs. The fluence of the first pulse (FPP), responsible for surface plasma formation, was varied in the range 10-50 mJ cm-2 and always kept below the LIPSS formation threshold fluence (FLIPSS) of Ti for 50-single-shots exposure. The fluence of the delayed pulse (FLP), responsible for LIPSS formation, was varied in the range 60-150 mJ cm-2 and always kept above FLIPSS. Regardless the specific fluence FLP of the delayed pulse, the interspace of the grating structures increases with the increase of FPP, that is the increase of the surface plasma density. This tendency suggests that a variation of the surface plasma density, due to a variation of FPP, actually leads to a modification of the grating features, highlighting the driving role of the first pulse in LIPSS formation. Moreover, we observed that the LIPSS periodicities after double pulse exposures are in quite good agreement with data on LIPSS periodicities after single 160 fs pulse irradiations on Ti surface and with the curve predicted by the parametric decay model. This experimental result suggests that the preformed plasma might be produced in the rising edge of the temporal profile of the laser pulse.

  4. Cloud-scale ISM Structure and Star Formation in M51

    NASA Astrophysics Data System (ADS)

    Leroy, Adam K.; Schinnerer, Eva; Hughes, Annie; Kruijssen, J. M. Diederik; Meidt, Sharon; Schruba, Andreas; Sun, Jiayi; Bigiel, Frank; Aniano, Gonzalo; Blanc, Guillermo A.; Bolatto, Alberto; Chevance, Mélanie; Colombo, Dario; Gallagher, Molly; Garcia-Burillo, Santiago; Kramer, Carsten; Querejeta, Miguel; Pety, Jerome; Thompson, Todd A.; Usero, Antonio

    2017-09-01

    We compare the structure of molecular gas at 40 pc resolution to the ability of gas to form stars across the disk of the spiral galaxy M51. We break the PAWS survey into 370 pc and 1.1 kpc resolution elements, and within each we estimate the molecular gas depletion time ({τ }{Dep}{mol}), the star-formation efficiency per free-fall time ({ε }{ff}), and the mass-weighted cloud-scale (40 pc) properties of the molecular gas: surface density, Σ, line width, σ, and b\\equiv {{Σ }}/{σ }2\\propto {α }{vir}-1, a parameter that traces the boundedness of the gas. We show that the cloud-scale surface density appears to be a reasonable proxy for mean volume density. Applying this, we find a typical star-formation efficiency per free-fall time, {ε }{ff}(< {{{Σ }}}40{pc}> )∼ 0.3 % {--}0.36 % , lower than adopted in many models and found for local clouds. Furthermore, the efficiency per free-fall time anti-correlates with both Σ and σ, in some tension with turbulent star-formation models. The best predictor of the rate of star formation per unit gas mass in our analysis is b\\equiv {{Σ }}/{σ }2, tracing the strength of self-gravity, with {τ }{Dep}{mol}\\propto {b}-0.9. The sense of the correlation is that gas with stronger self-gravity (higher b) forms stars at a higher rate (low {τ }{Dep}{mol}). The different regions of the galaxy mostly overlap in {τ }{Dep}{mol} as a function of b, so that low b explains the surprisingly high {τ }{Dep}{mol} found toward the inner spiral arms found by Meidt et al. (2013).

  5. Resonance Raman spectroscopic measurements delineate the structural changes that occur during tau fibril formation.

    PubMed

    Ramachandran, Gayathri; Milán-Garcés, Erix A; Udgaonkar, Jayant B; Puranik, Mrinalini

    2014-10-21

    The aggregation of the microtubule-associated protein, tau, into amyloid fibrils is a hallmark of neurodegenerative diseases such as the tauopathies and Alzheimer's disease. Since monomeric tau is an intrinsically disordered protein and the polymeric fibrils possess an ordered cross-β core, the aggregation process is known to involve substantial conformational conversion besides growth. The aggregation mechanism of tau in the presence of inducers such as heparin, deciphered using probes such as thioflavin T/S fluorescence, light scattering, and electron microscopy assays, has been shown to conform to ligand-induced nucleation-dependent polymerization. These probes do not, however, distinguish between the processes of conformational conversion and fibril growth. In this study, UV resonance Raman spectroscopy is employed to look directly at signatures of changes in secondary structure and side-chain packing during fibril formation by the four repeat functional domain of tau in the presence of the inducer heparin, at pH 7 and at 37 °C. Changes in the positions and intensities of the amide Raman bands are shown to occur in two distinct stages during the fibril formation process. The first stage of UVRR spectral changes corresponds to the transformation of monomer into early fibrillar aggregates. The second stage corresponds to the transformation of these early fibrillar aggregates into the final, ordered, mature fibrils and during this stage; the processes of conformational conversion and the consolidation of the fibril core occur simultaneously. Delineation of these secondary structural changes accompanying the formation of tau fibrils holds significance for the understanding of generic and tau-specific principles of amyloid assembly.

  6. 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.

  7. Structural, thermal, dielectric and phonon properties of perovskite-like imidazolium magnesium formate.

    PubMed

    Mączka, Mirosław; Marinho Costa, Nathalia Leal; Gągor, Anna; Paraguassu, Waldeci; Sieradzki, Adam; Hanuza, Jerzy

    2016-05-18

    We report the synthesis and characterisation of a magnesium formate framework templated by protonated imidazole. Single-crystal X-ray diffraction data showed that this compound crystallizes in the monoclinic structure in the P21/n space group with lattice parameters a = 12.1246(4) Å, b = 12.2087(5) Å, c = 12.4991(4) Å and β = 91.39(1)°. The antiparallel arrangement of the dipole moments associated with imidazolium cations suggests the antiferroelectric character of the room-temperature phase. The studied compound undergoes a structural phase transition at 451 K associated with a halving of the c lattice parameter and the disappearance of the antiferroelectric order. The monoclinic symmetry is preserved and the new metrics are a = 12.261(7) Å, b = 12.290(4) Å, c = 6.280(4) Å, and β = 90.62(5)°. Raman and IR data are consistent with the X-ray diffraction data. They also indicate that the disorder of imidazolium cations plays a significant role in the mechanism of the phase transition. Dielectric data show that the phase transition is associated with a relaxor nature of electric ordering. We also report high-pressure Raman scattering studies of this compound that revealed the presence of two pressure-induced phase transitions near 3 and 7 GPa. The first transition is most likely associated with a rearrangement of the imidazolium cations without any significant distortion of these cations and the magnesium formate framework, whereas the second transition leads to strong distortion of both the framework and imidazolium cations. High-pressure data also show that imidazolium magnesium formate does not show any signs of amorphization up to 11.4 GPa.

  8. Two-dimensional colloidal crystal assisted formation of conductive porous gold films with flexible structural controllability.

    PubMed

    Lu, Zhicheng; Liu, Chen; Han, Heyou

    2015-01-01

    Two-dimensional (2D) colloidal crystals of polystyrene (PS) particles were used as a structure-controlling template to fabricate conductive Au films with an ordered array of nanoholes. The fabrication mainly involved the functionalization of the supporting substrate with polyelectrolyte (PE) functional layers, self-assembly of Au nanoparticles, and electroless deposition of gold. The self-assembly of Au nanoparticles and electroless deposition of gold were macroscopically monitored using ultraviolet-visible (UV-vis) spectroscopy based on the changes in both the extinction spectra of Au nanoparticles and the optical responses of ordered arrays of PS particles. By scanning electron microscopy (SEM) characterization, it was found that Au nanoparticles were assembled into a film structure with orderly dispersed nanoholes and the deposition of gold was confined to the preformed Au nanoparticle films. During the formation of Au films, PE layer structure, Au nanoparticle size and heating treatment applied to the PS template could influence the structures of conductive porous Au films such as the hole diameter, film thickness, and hole diameter/wall thickness ratio (D/W). In addition, this paper also described electrochemical cyclic voltammetry (CV) employed to demonstrate the porosity of the ultimate Au films. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Secondary structure formations of conotoxin genes: a possible role in mediating variability.

    PubMed

    Dewan, Kalyan Kumar

    2006-10-20

    Small venomous peptides called conotoxins produced by the predatory marine snail (genus Conus) present an interesting case for mutational studies. They have a high degree of amino acid variability among them yet they possess highly conserved structural elements that are defined by cysteine residues forming disulfide bridges along the length of the mature peptide. It has been observed that codons specifying these cysteines are also highly conserved. It is unknown how such codon conservation is maintained within the mature conotoxin gene since this entire region undergoes an accelerated rate of mutation. There is evidence suggesting that nucleic acids wield some influence in mechanisms that dictate the region and frequency where mutations occur in DNA. Nucleic acids exert this effect primarily through secondary structures that bring about local peaks and troughs in the energy relief of these transient formations. Secondary structure predictions of several conotoxin genes were analyzed to see if there was any correspondence between the highly variable regions of the conotoxin. Regions of the DNA encompassing the conserved Cys codons (and several other conserved amino acid codons) have been found to correspond to predicted secondary structures of higher stabilities. In stark contrast the regions of the conotoxin that have a higher degree of variation correlate to regions of lower stability. This striking co-relation allows for a simple model of inaccessibility of a mutator to these highly conserved regions of the conotoxin gene allowing them a relative degree of resistance towards change.

  10. CERAMIDE CHANNELS: INFLUENCE OF MOLECULAR STRUCTURE ON CHANNEL FORMATION IN MEMBRANES

    PubMed Central

    Perera, Meenu N.; Ganesan, Vidyaramanan; Siskind, Leah J.; Szulc, Zdzislaw M.; Bielawski, Jacek; Bielawska, Alicja; Bittman, Robert; Colombini, Marco

    2012-01-01

    The sphingolipid, ceramide, self-assembles in the mitochondrial outer membrane (MOM), forming large channels capable of translocating proteins. These channels are believed to be involved in protein release from mitochondria, a key decision-making step. Synthetic analogs of ceramide, bearing modifications in each of the major structural features of ceramide were used to probe the molecular basis for the stability of ceramide channels. Channel stability and mitochondrial permeabilization were disrupted by methylation of the C1-hydroxyl group whereas modifications of the C3 allylic hydroxyl group were well tolerated. A change in chirality at C2 that would influence the orientation of the C1-hydroxyl group resulted in a strong reduction of channel-forming ability. Similarly, methylation of the amide nitrogen is also detrimental to channel formation. Many changes in the degree, location and nature of the unsaturation of ceramide had little effect on mitochondrial permeabilization. Competition experiments between ceramide and analogs resulted in synergy with structures compatible with the ceramide channel model and antagonism with incompatible structures. The results are consistent with ceramide channels being highly organized structures, stabilized by specific inter-molecular interactions, similar to the interactions responsible for protein folding. PMID:22365970

  11. 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.

  12. ETHOS—an effective theory of structure formation: From dark particle physics to the matter distribution of the Universe

    NASA Astrophysics Data System (ADS)

    Cyr-Racine, Francis-Yan; Sigurdson, Kris; Zavala, Jesús; Bringmann, Torsten; Vogelsberger, Mark; Pfrommer, Christoph

    2016-06-01

    We formulate an effective theory of structure formation (ETHOS) that enables cosmological structure formation to be computed in almost any microphysical model of dark matter physics. This framework maps the detailed microphysical theories of particle dark matter interactions into the physical effective parameters that shape the linear matter power spectrum and the self-interaction transfer cross section of nonrelativistic dark matter. These are the input to structure formation simulations, which follow the evolution of the cosmological and galactic dark matter distributions. Models with similar effective parameters in ETHOS but with different dark particle physics would nevertheless result in similar dark matter distributions. We present a general method to map an ultraviolet complete or effective field theory of low-energy dark matter physics into parameters that affect the linear matter power spectrum and carry out this mapping for several representative particle models. We further propose a simple but useful choice for characterizing the dark matter self-interaction transfer cross section that parametrizes self-scattering in structure formation simulations. Taken together, these effective parameters in ETHOS allow the classification of dark matter theories according to their structure formation properties rather than their intrinsic particle properties, paving the way for future simulations to span the space of viable dark matter physics relevant for structure formation.

  13. Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa.

    PubMed

    Yang, Xinmei; Matsui, Takashi; Kodama, Takeshi; Mori, Takahiro; Zhou, Xiaoxi; Taura, Futoshi; Noguchi, Hiroshi; Abe, Ikuro; Morita, Hiroyuki

    2016-03-01

    In polyketide biosynthesis, ring formation is one of the key diversification steps. Olivetolic acid cyclase (OAC) from Cannabis sativa, involved in cannabinoid biosynthesis, is the only known plant polyketide cyclase. In addition, it is the only functionally characterized plant α+β barrel (DABB) protein that catalyzes the C2-C7 aldol cyclization of the linear pentyl tetra-β-ketide CoA as the substrate, to generate olivetolic acid (OA). Herein, we solved the OAC apo and OAC-OA complex binary crystal structures at 1.32 and 1.70 Å resolutions, respectively. The crystal structures revealed that the enzyme indeed belongs to the DABB superfamily, as previously proposed, and possesses a unique active-site cavity containing the pentyl-binding hydrophobic pocket and the polyketide binding site, which have never been observed among the functionally and structurally characterized bacterial polyketide cyclases. Furthermore, site-directed mutagenesis studies indicated that Tyr72 and His78 function as acid/base catalysts at the catalytic center. Structural and/or functional studies of OAC suggested that the enzyme lacks thioesterase and aromatase activities. These observations demonstrated that OAC employs unique catalytic machinery utilizing acid/base catalytic chemistry for the formation of the precursor of OA. The structural and functional insights obtained in this work thus provide the foundation for analyses of the plant polyketide cyclases that will be discovered in the future. Structural data reported in this paper are available in the Protein Data Bank under the accession numbers 5B08 for the OAC apo, 5B09 for the OAC-OA binary complex and 5B0A, 5B0B, 5B0C, 5B0D, 5B0E, 5B0F and 5B0G for the OAC His5Q, Ile7F, Tyr27F, Tyr27W, Val59M, Tyr72F and His78S mutant enzymes, respectively. © 2016 Federation of European Biochemical Societies.

  14. 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.

  15. The new discussion of a neutrino mass and issues in the formation of large-scale structure

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.

    1991-01-01

    It is argued that the discrepancy between the large-scale structure predicted by cosmological models with neutrino mass (hot dark matter) do not differ drastically from the observed structure. Evidence from the correlation amplitude, nonlinearity and the onset of galaxy formation, large-scale streaming velocities, and the topology of large-scale structure is considered. Hot dark matter models seem to be as accurate predictors of the large-scale structure as are cold dark matter models.

  16. 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.

  17. Controlling Agglomeration of Protein Aggregates for Structure Formation in Liquid Oil: A Sticky Business

    PubMed Central

    2017-01-01

    Proteins are known to be effective building blocks when it comes to structure formation in aqueous environments. Recently, we have shown that submicron colloidal protein particles can also be used to provide structure to liquid oil and form so-called oleogels (de VriesA.J. Colloid Interface Sci.2017, 486, 75−83)27693552. To prevent particle agglomeration, a solvent exchange procedure was used to transfer the aggregates from water to the oil phase. The aim of the current paper was to elucidate on the enhanced stability against agglomeration of heat-set whey protein isolate (WPI) aggregates to develop an alternative for the solvent exchange procedure. Protein aggregates were transferred from water to several solvents differing in polarity to investigate the effect on agglomeration and changes in protein composition. We show that after drying protein aggregates by evaporation from solvents with a low polarity (e.g., hexane), the protein powder shows good dispersibility in liquid oil compared to powders dried from solvents with a high polarity. This difference in dispersibility could not be related to changes in protein composition or conformation but was instead related to the reduction of attractive capillary forces between the protein aggregates during drying. Following another route, agglomeration was also prevented by applying high freezing rates prior to freeze-drying. The rheological properties of the oleogels prepared with such freeze-dried protein aggregates were shown to be similar to that of oleogels prepared using a solvent exchange procedure. This Research Article provides valuable insights in how to tune the drying process to control protein agglomeration to allow for subsequent structure formation of proteins in liquid oil. PMID:28225592

  18. Controlling Agglomeration of Protein Aggregates for Structure Formation in Liquid Oil: A Sticky Business.

    PubMed

    de Vries, Auke; Lopez Gomez, Yuly; Jansen, Bas; van der Linden, Erik; Scholten, Elke

    2017-03-22

    Proteins are known to be effective building blocks when it comes to structure formation in aqueous environments. Recently, we have shown that submicron colloidal protein particles can also be used to provide structure to liquid oil and form so-called oleogels ( de Vries , A. J. Colloid Interface Sci. 2017 , 486 , 75 - 83 ) . To prevent particle agglomeration, a solvent exchange procedure was used to transfer the aggregates from water to the oil phase. The aim of the current paper was to elucidate on the enhanced stability against agglomeration of heat-set whey protein isolate (WPI) aggregates to develop an alternative for the solvent exchange procedure. Protein aggregates were transferred from water to several solvents differing in polarity to investigate the effect on agglomeration and changes in protein composition. We show that after drying protein aggregates by evaporation from solvents with a low polarity (e.g., hexane), the protein powder shows good dispersibility in liquid oil compared to powders dried from solvents with a high polarity. This difference in dispersibility could not be related to changes in protein composition or conformation but was instead related to the reduction of attractive capillary forces between the protein aggregates during drying. Following another route, agglomeration was also prevented by applying high freezing rates prior to freeze-drying. The rheological properties of the oleogels prepared with such freeze-dried protein aggregates were shown to be similar to that of oleogels prepared using a solvent exchange procedure. This Research Article provides valuable insights in how to tune the drying process to control protein agglomeration to allow for subsequent structure formation of proteins in liquid oil.

  19. Tryptophan fluorescence monitors structural changes accompanying signalling state formation in the photocycle of photoactive yellow protein.

    PubMed

    Gensch, Thomas; Hendriks, Johnny; Hellingwerf, Klaas J

    2004-06-01

    Photoactive yellow protein, a small, water-soluble blue-light absorbing photoreceptor protein from Ectothiorhodospira(Halorhodospira)[space]halophila has a structure with two hydrophobic cores, of which the main one houses its light-sensitive chromophore (p-coumaric acid), separated by a central [small beta]-sheet. This photoreceptor protein contains a single tryptophan residue (W119) that is situated at the interface between the central beta-sheet and its N-terminal cap. The fluorescence properties of W119 in the dark state pG (lambda(max)= 328 nm; Phi(fl)= 0.01; nearly pH-independent) are typical for a buried tryptophan in a hydrophobic environment with significant quenching by nearby amino acid residues. Signalling state formation leads to pH-dependent fluorescence changes: At pH values <6.5 the fluorescence emission increases, with a minor blue shift of the emission maximum. Above this pH, the emission maximum of the tryptophan shifts considerably to the red, whereas its total intensity decreases. These results further support the contention that signalling state formation in PYP leads to significant changes in the structure of this protein, even at sites that are at a considerable distance from the chromophore. The nature of these changes in pB, however, depend upon the pH imposed upon the protein: At slightly alkaline pH, which presumably is closest to the pH to which this protein is exposed in vivo, these changes lead to an exposure of the part of the central beta-sheet harbouring W119. At slightly acidic pH the polarity of the environment of W119 is hardly affected by the formation of the signalling state but the quenching of its fluorescence emission, possibly by nearby amino acids, is reduced. On the other hand, its accessibility for quenching by small molecules in the solution is enhanced at acidic and alkaline pH in the signalling state (pB) compared to the dark state (pG). This latter observation points towards a more flexible structure of the N

  20. Magnetic Structures of Heterometallic M(II)-M(III) Formate Compounds.

    PubMed

    Mazzuca, Lidia; Cañadillas-Delgado, Laura; Rodríguez-Velamazán, J Alberto; Fabelo, Oscar; Scarrozza, Marco; Stroppa, Alessandro; Picozzi, Silvia; Zhao, Jiong-Peng; Bu, Xian-He; Rodríguez-Carvajal, Juan

    2017-01-03

    A study of the magnetic structure of the [NH2(CH3)2]n[Fe(III)M(II)(HCOO)6]n niccolite-like compounds, with M(II) = Co(II) (2) and Mn(II) (3) ions, has been carried out using neutron diffraction and compared with the previously reported Fe(II)-containing compound (1). The inclusion of two different metallic atoms into the niccolite-like structure framework leads to the formation of isostructural compounds with very different magnetic behaviors due to the compensation or not of the different spins involved in each lattice. Below TN, the magnetic order in these compounds varies from ferrimagnetic behavior for 1 and 2 to an antiferromagnetic behavior with a weak spin canting for 3. Structure refinements of 2 and 3 at low temperature (45 K) have been carried out combining synchrotron X-ray and high-resolution neutron diffraction in a multipattern approach. The magnetic structures have been determined from the difference patterns between the neutron data in the paramagnetic and the magnetically ordered regions. These difference patterns have been analyzed using a simulated annealing protocol and symmetry analysis techniques. The obtained magnetic structures have been further rationalized by means of ab initio DFT calculations. The direction of the magnetic moment of each compound has been determined. The easy axis of the M(II) for compound 1 (Fe(II)) is along the c axis; for compound 2 (Co(II)), the moments are mainly within the ab plane; finally, for compound 3 (Mn(II)), the calculations show that the moments have components both in the ab plane and along the c axis.

  1. Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica

    PubMed Central

    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

  2. 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

  3. Impact of enhanced ultraviolet-B irradiance on maize yield formation and structure: a field evaluation

    NASA Astrophysics Data System (ADS)

    Gao, Wei; Zheng, Youfei; Slusser, James R.; He, Yuhong; Zhang, Ronggang

    2003-11-01

    Stratospheric ozone depletion and enhanced solar ultraviolet-B (UV-B) irradiance may have adverse impacts on the productivity of agricultural crops. Though only a small portion of the total solar electromagnetic spectrum, UV-B irradiance has a disproportionately large photobiological effect, largely because it is readily absorbed by important macromolecules such as proteins and nucleic acids. Numerous investigations have demonstrated that the effect of UV-B enhancements on plants includes a reduction in grain yield, alteration in species competition, susceptibility to disease, and changes in plant structure and pigmentation. Many experiments examining UV-B radiation effects on plants were conducted in growth chambers or greenhouses. It has been questioned if the effect of UV-B radiation on plants can be extrapolated to field responses from indoor studies because of the unnaturally high ratios of UV-B/UV-A and UV-B/PAR in many indoor studies. Field studies on UV-B radiation effect on plants have been recommended in order to use the UV and PAR irradiance provided by natural light. This study found the maize yield formation and yield structural elements responded to enhanced UV-B radiation under field conditions. Enhanced UV-B radiation caused a significant reduction of the dry matter accumulation and the maize grain yield in turn was affected. Analysis of yield structure indicates that the maize yield decreased with increased UV-B radiation and was evidently related to the decreased kernel weight and kernel number per ear.

  4. Internal structures of sandwaves in a tide-storm interactive system: Proterozoic Lower Quartzite Formation, India

    NASA Astrophysics Data System (ADS)

    Chakraborty, Chandan; Bose, Pradip K.

    1990-04-01

    A Proterozoic sandstone sequence belonging to the Lower Quartzite Formation of Vindhyan Supergroup, India, reveals the internal structures of near-symmetrical subtidal sandwaves formed in an area of strong tidal currents, occasionally interfered by wind-induced currents of varying magnitude. Internally, the sandwaves show decimetre-scale, herring-bone cross-laminated sets with inclined and horizontal set boundaries representing accretion on the gently inclined (around 5°) lee and stoss surfaces of the sandwaves respectively. The internal structures suggest oblique upbuilding of the sandwaves with almost equal contributions from the two reversing current modes of the tidal flow. Evidently, the sandwaves were maintained by bedload transport through migration of megaripples superimposed on the sandwaves. Occasional superimposition of short-lived, wind-induced currents on the tidal flow caused appreciable suspension transport of sand-sized sediments and led to the development of successive low-angle, unidirectional, mud-draped, cross-laminated bundles interwoven with the tide-generated structures. However, the dominant sediment type introduced during the period of wind-induced currents was in the size range of mud as reflected in the presence of exceptionally thick exotic mud layers in juxtaposition with the cross-laminated bundles. During the periods of vigorous storm currents, significant volumes of sand-sized sediments were introduced in the form of density flows, deposition from which led to the burial of tidal sandwaves. Renewal of the fair-weather tidal regime caused the development of new sandwaves.

  5. Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation

    PubMed Central

    Blaise, Mickaël; Bailly, Marc; Frechin, Mathieu; Behrens, Manja Annette; Fischer, Frédéric; Oliveira, Cristiano L P; Becker, Hubert Dominique; Pedersen, Jan Skov; Thirup, Søren; Kern, Daniel

    2010-01-01

    Four out of the 22 aminoacyl-tRNAs (aa-tRNAs) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the tRNA followed by tRNA-dependent conversion of the non-cognate amino acid. During tRNA-dependent asparagine formation, tRNAAsn promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-tRNA from non-discriminating aspartyl-tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 Å resolution reveals a particle formed by two GatCABs, two dimeric ND-AspRSs and four tRNAsAsn molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl-tRNAAsn without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer-ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine. PMID:20717102

  6. 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.

  7. Distribution and formation of the mesothermal structure (temperature inversions) in the North Pacific subarctic region

    NASA Astrophysics Data System (ADS)

    Ueno, Hiromichi; Yasuda, Ichiro

    2000-07-01

    The distribution and formation of mesothermal structure (temperature inversions) in the North Pacific subarctic region are investigated through analysis of climatological hydrographic data. It is suggested that the heat and salt that maintain the mesothermal water and thus the halocline in the density range of 26.7-27.2σθ are transported as a crossgyre flow from the transition domain just east of Japan, where the waters are influenced by the subtropical gyre water mass, to the eastern subarctic region. Along the transport route the isopycnal potential temperature and thus salinity are well conserved. In the western subarctic gyre, the Bering Sea, and the northern Gulf of Alaska, the temperature reaches its minimum at the surface in winter and the areal coverage agrees well with the distribution of the mesothermal structure. In the southeastern part of the zonally distributed mesothermal structure in the area of 170°E-150°W and 45°-50°N, where the winter sea surface temperature is higher than that in the deeper layer, dichothermal water is formed by subsurface intrusion of the low-temperature and low-salinity water that outcropped in the previous winter over the warm and saline water transported from the transition domain.

  8. 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

  9. 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

  10. Electrohydrodynamic pressure enhanced by free space charge for electrically induced structure formation with high aspect ratio.

    PubMed

    Tian, Hongmiao; Wang, Chunhui; Shao, Jinyou; Ding, Yucheng; Li, Xiangming

    2014-10-28

    Electrically induced structure formation (EISF) is an interesting and unique approach for generating a microstructured duplicate from a rheological polymer by a spatially modulated electric field induced by a patterned template. Most of the research on EISF have so far used various dielectric polymers (with an electrical conductivity smaller than 10(-10) S/m that can be considered a perfect dielectric), on which the electric field induces a Maxwell stress only due to the dipoles (or bounded charges) in the polymer molecules, leading to a structure with a small aspect ratio. This paper presents a different approach for improving the aspect ratio allowed in EISF by doping organic salt into the perfect dielectric polymer, i.e., turning the perfect dielectric into a leaky dielectric, considering the fact that the free space charges enriched in the leaky dielectric polymer can make an additional contribution to the Maxwell stress, i.e., electrohydrodynamic pressure, which is desirable for high aspect ratio structuring. Our numerical simulations and experimental tests have shown that a leaky dielectric polymer, with a small conductivity comparable to that of deionized water, can be much more effective at being electrohydrodynamically deformed into a high aspect ratio in comparison with a perfect dielectric polymer when both of them have roughly the same dielectric constant.

  11. Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

    SciTech Connect

    Liu Fengxiang; Liu Rangsu Hou Zhaoyang; Liu Hairong; Tian Zean; Zhou Lili

    2009-02-15

    The rapid solidification processes of Al{sub 50}Mg{sub 50} liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method-cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, .... The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

  12. [Schizotypal Personality Questionnaire-Brief - Likert format: Factor structure analysis in general population in France].

    PubMed

    Ferchiou, A; Todorov, L; Lajnef, M; Baudin, G; Pignon, B; Richard, J-R; Leboyer, M; Szöke, A; Schürhoff, F

    2016-09-16

    The main objective of the study was to explore the factorial structure of the French version of the Schizotypal Personality Questionnaire-Brief (SPQ-B) in a Likert format, in a representative sample of the general population. In addition, differences in the dimensional scores of schizotypy according to gender and age were analyzed. As the study in the general population of schizotypal traits and its determinants has been recently proposed as a way toward the understanding of aetiology and pathophysiology of schizophrenia, consistent self-report tools are crucial to measure psychometric schizotypy. A shorter version of the widely used Schizotypal Personality Questionnaire (SPQ-Brief) has been extensively investigated in different countries, particularly in samples of students or clinical adolescents, and more recently, a few studies used a Likert-type scale format which allows partial endorsement of items and reduces the risk of defensive answers. A sample of 233 subjects representative of the adult population from an urban area near Paris (Créteil) was recruited using the "itinerary method". They completed the French version of the SPQ-B with a 5-point Likert-type response format (1=completely disagree; 5=completely agree). We examined the dimensional structure of the French version of the SPQ-B with a Principal Components Analysis (PCA) followed by a promax rotation. Factor selection was based on Eigenvalues over 1.0 (Kaiser's criterion), Cattell's Scree-plot test, and interpretability of the factors. Items with loadings greater than 0.4 were retained for each dimension. The internal consistency estimate of the dimensions was calculated with Cronbach's α. In order to study the influence of age and gender, we carried out a simple linear regression with the subscales as dependent variables. Our sample was composed of 131 women (mean age=52.5±18.2 years) and 102 men (mean age=53±18.1 years). SPQ-B Likert total scores ranged from 22 to 84 points (mean=43.6

  13. 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.

  14. Structural geochemistry of Taconic slates, evidence for and against volume loss during cleavage formation

    SciTech Connect

    Goldstein, A. . Dept. of Geology)

    1993-03-01

    Arguments for and against volume loss during formation of salty cleavage abound in the literature. Most commonly, a geometric approach utilizing strain analysis suggests that volumes between 20% and 60% have been lost. The geochemical approach seeks to find the signature of that loss and most commonly will not lead to similar conclusions. In general, slates have very similar compositions to shales. In the few instances where one can trace the same stratigraphic unit or interval from uncleaved to cleaved, compositional variations are not sufficiently different to suggest major volume loss. These problems are encapsulated in the