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Sample records for fractal structure filaments

  1. Fractal intermediates in the self-assembly of silicatein filaments

    PubMed Central

    Murr, Meredith M.; Morse, Daniel E.

    2005-01-01

    Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges; they are the constituents of macroscopic protein filaments that are found occluded within the silica needles made by Tethya aurantia. Self-assembly of the silicatein monomers and oligomers is shown to form fibrous structures by a mechanism that is fundamentally different from any previously described filament-assembly process. This assembly proceeds through the formation of diffusion-limited, fractally patterned aggregates on the path to filament formation. The driving force for this self-assembly is suggested to be entropic, mediated by the interaction of hydrophobic patches on the surfaces of the silicatein subunits that are not found on highly homologous congeners that do not form filaments. Our results are consistent with a model in which silicatein monomers associate into oligomers that are stabilized by intermolecular disulfide bonds. These oligomeric units assemble into a fractal network that subsequently condenses and organizes into a filamentous structure. These results represent a potentially general mechanism for protein fiber self-assembly. PMID:16091468

  2. Fractal structures and processes

    SciTech Connect

    Bassingthwaighte, J.B.; Beard, D.A.; Percival, D.B.; Raymond, G.M.

    1996-06-01

    Fractals and chaos are closely related. Many chaotic systems have fractal features. Fractals are self-similar or self-affine structures, which means that they look much of the same when magnified or reduced in scale over a reasonably large range of scales, at least two orders of magnitude and preferably more (Mandelbrot, 1983). The methods for estimating their fractal dimensions or their Hurst coefficients, which summarize the scaling relationships and their correlation structures, are going through a rapid evolutionary phase. Fractal measures can be regarded as providing a useful statistical measure of correlated random processes. They also provide a basis for analyzing recursive processes in biology such as the growth of arborizing networks in the circulatory system, airways, or glandular ducts. {copyright} {ital 1996 American Institute of Physics.}

  3. Modeling of fractal intermediates in the self-assembly of silicatein filaments

    NASA Astrophysics Data System (ADS)

    Murr, Meredith; Thakur, Gunjan; Mezic, Igor; Morse, Daniel

    2006-03-01

    Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges, Self-assembly of the silicatein monomers and oligomers was previously shown experimentally (Murr and Morse 2005) to form fibrous structures through the formation of diffusion limited, fractally patterned aggregates on the path to filament formation. We present a diffusion-limited aggregation (DLA) based model that is capable of capturing the basic properties of this self-assembly process. The Silicatein oligomer is modeled with three sites of attachment. Rules of attachment are specified that allow for specific interaction between these sites when oligomers are in proximity. The process differs from a DLA process in the following: 1) The process of aggregation is continued dynamically, i.e. the growing structures are spatially distributed and keep diffusing as they are growing 2) The molecules are oriented. Thus rotational diffusion is important. 3) The attachment can happen at more than 1 site and the strength of the active sites can be varied. We show that the self-assembled structures have a good level of similarity with the in-vitro experimental results. We quantify this by comparing the fractal dimension of the experimental data and the model output.

  4. Filament wound structure and method

    DOEpatents

    Dritt, William S.; Gerth, Howard L.; Knight, Jr., Charles E.; Pardue, Robert M.

    1977-01-01

    The present invention relates to a filament wound spherical structure comprising a plurality of filament band sets disposed about the surface of a mandrel with each band of each set formed of a continuous filament circumferentially wound about the mandrel a selected number of circuits and with each circuit of filament being wound parallel to and contiguous with an immediate previously wound circuit. Each filament band in each band set is wound at the same helix angle from the axis of revolution of the mandrel and all of the bands of each set are uniformly distributed about the mandrel circumference. The pole-to-equator wall thickness taper associated with each band set, as several contiguous band sets are wound about the mandrel starting at the poles, is accumulative as the band sets are nested to provide a complete filament wound sphere of essentially uniform thickness.

  5. Fractal Dimensions of Macromolecular Structures

    PubMed Central

    Todoroff, Nickolay; Kunze, Jens; Schreuder, Herman; Hessler, Gerhard; Baringhaus, Karl-Heinz; Schneider, Gisbert

    2014-01-01

    Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less-explored geometric features of macromolecules is molecular surface irregularity, or ‘roughness’, which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified the surface roughnesses of biological macromolecules in a large-scale survey that revealed D values between 2.0 and 2.4. The results of our study imply that surface patches involved in molecular interactions, such as ligand-binding pockets and protein-protein interfaces, exhibit greater local fluctuations in their fractal dimensions than ‘inert’ surface areas. We expect approximately 22 % of a protein’s surface outside of the crystallographically known ligand binding sites to be ligandable. These findings provide a fresh perspective on macromolecular structure and have considerable implications for drug design as well as chemical and systems biology. PMID:26213587

  6. Recurrence Quantification of Fractal Structures

    PubMed Central

    Webber, Charles L.

    2012-01-01

    By definition, fractal structures possess recurrent patterns. At different levels repeating patterns can be visualized at higher magnifications. The purpose of this chapter is threefold. First, general characteristics of dynamical systems are addressed from a theoretical mathematical perspective. Second, qualitative and quantitative recurrence analyses are reviewed in brief, but the reader is directed to other sources for explicit details. Third, example mathematical systems that generate strange attractors are explicitly defined, giving the reader the ability to reproduce the rich dynamics of continuous chaotic flows or discrete chaotic iterations. The challenge is then posited for the reader to study for themselves the recurrent structuring of these different dynamics. With a firm appreciation of the power of recurrence analysis, the reader will be prepared to turn their sights on real-world systems (physiological, psychological, mechanical, etc.). PMID:23060808

  7. Fractals and cosmological large-scale structure

    NASA Technical Reports Server (NTRS)

    Luo, Xiaochun; Schramm, David N.

    1992-01-01

    Observations of galaxy-galaxy and cluster-cluster correlations as well as other large-scale structure can be fit with a 'limited' fractal with dimension D of about 1.2. This is not a 'pure' fractal out to the horizon: the distribution shifts from power law to random behavior at some large scale. If the observed patterns and structures are formed through an aggregation growth process, the fractal dimension D can serve as an interesting constraint on the properties of the stochastic motion responsible for limiting the fractal structure. In particular, it is found that the observed fractal should have grown from two-dimensional sheetlike objects such as pancakes, domain walls, or string wakes. This result is generic and does not depend on the details of the growth process.

  8. Fractal-like structures in colloid science.

    PubMed

    Lazzari, S; Nicoud, L; Jaquet, B; Lattuada, M; Morbidelli, M

    2016-09-01

    The present work aims at reviewing our current understanding of fractal structures in the frame of colloid aggregation as well as the possibility they offer to produce novel structured materials. In particular, the existing techniques to measure and compute the fractal dimension df are critically discussed based on the cases of organic/inorganic particles and proteins. Then the aggregation conditions affecting df are thoroughly analyzed, pointing out the most recent literature findings and the limitations of our current understanding. Finally, the importance of the fractal dimension in applications is discussed along with possible directions for the production of new structured materials. PMID:27233526

  9. A simultaneous one pot synthesis of two fractal structures via swapping two fractal reaction kinetic states.

    PubMed

    Ghosh, Subrata; Dutta, Mrinal; Ray, Kanad; Fujita, Daisuke; Bandyopadhyay, Anirban

    2016-06-01

    We introduce a new class of fractal reaction kinetics wherein two or more distinct fractal structures are synthesized as parts of a singular cascade reaction in a single chemical beaker. Two examples: sphere ↔ spiral & triangle ↔ square fractals, grow 10(6) orders from a single dendrimer (8 nm) to the visible scale. PMID:27166589

  10. Structural investigations of fat fractals using small-angle scattering

    NASA Astrophysics Data System (ADS)

    Anitas, Eugen M.

    2015-01-01

    Experimental small-angle scattering (SAS) data characterized, on a double logarithmic scale, by a succession of power-law decays with decreasing values of scattering exponents, can be described in terms of fractal structures with positive Lebesgue measure (fat fractals). Here we present a theoretical model for fat fractals and show how one can extract structural information about the underlying fractal using SAS method, for the well known fractals existing in the literature: Vicsek and Menger sponge. We calculate analytically the fractal structure factor and study its properties in momentum space. The models allow us to obtain the fractal dimension at each structural level inside the fractal, the number of particles inside the fractal and about the most common distances between the center of mass of the particles.

  11. Fractal structures in casting films from chlorophyll

    NASA Astrophysics Data System (ADS)

    Pedro, G. C.; Gorza, F. D. S.; de Souza, N. C.; Silva, J. R.

    2014-04-01

    Chlorophyll (Chl) molecules are important because they can act as natural light-harvesting devices during the photosynthesis. In addition, they have potential for application as component of solar cell. In this work, we have prepared casting films from chlorophyll (Chl) and demonstrated the occurrence of fractal structures when the films were submitted to different concentrations. By using optical microscopy and the box-count method, we have found that the fractal dimension is Df = 1.55. This value is close to predicted by the diffusion-limited aggregation (DLA) model. This suggests that the major mechanism - which determines the growth of the fractal structures from Chl molecules - is the molecular diffusion. Since the efficiencies of solar cells depend on the morphology of their interfaces, these finds can be useful to improve this kind of device.

  12. The fractal structure of the mitochondrial genomes

    NASA Astrophysics Data System (ADS)

    Oiwa, Nestor N.; Glazier, James A.

    2002-08-01

    The mitochondrial DNA genome has a definite multifractal structure. We show that loops, hairpins and inverted palindromes are responsible for this self-similarity. We can thus establish a definite relation between the function of subsequences and their fractal dimension. Intriguingly, protein coding DNAs also exhibit palindromic structures, although they do not appear in the sequence of amino acids. These structures may reflect the stabilization and transcriptional control of DNA or the control of posttranscriptional editing of mRNA.

  13. Dimension of a fractal streamer structure

    NASA Astrophysics Data System (ADS)

    Lehtinen, Nikolai G.; Østgaard, Nikolai

    2015-04-01

    Streamer corona plays an important role in formation of leader steps in lightning. In order to understand its dynamics, the streamer front velocity is calculated in a 1D model with curvature. We concentrate on the role of photoionization mechanism in the propagation of the streamer ionization front, the other important mechanisms being electron drift and electron diffusion. The results indicate, in particular, that the effect of photoionization on the streamer velocity for both positive and negative streamers is mostly determined by the photoionization length, with a weaker dependence on the amount of photoionization, and that the velocity is decreased for positive curvature, i.e., convex fronts. These results are used in a fractal model in which the front propagation velocity is simulated as the cluster growth probability [Niemeyer et al, 1984, doi:10.1103/PhysRevLett.52.1033]. Monte Carlo simulations of the cluster growth for various ratios of background electric field E to the breakdown field Eb show that the emerging transverse size of the streamers is of the order of the photoionization length, and at the larger scale the streamer structure is a fractal similar to the one obtained in a diffusion-limited aggregation (DLA) system. In the absence of electron attachment (Eb = 0), the fractal dimension is the same (D ˜ 1.67) as in the DLA model, and is reduced, i.e., the fractal has less branching, for Eb > 0.

  14. Fractal Structure in Human Cerebellum Measured by MRI

    NASA Astrophysics Data System (ADS)

    Zhang, Luduan; Yue, Guang; Brown, Robert; Liu, Jingzhi

    2003-10-01

    Fractal dimension has been used to quantify the structures of a wide range of objects in biology and medicine. We measured fractal dimension of human cerebellum (CB) in magnetic resonance images of 24 healthy young subjects (12 men, 12 women). CB images were resampled to a series of image sets with different three-dimensional resolutions. At each resolution, the skeleton of the CB white matter was obtained and the number of pixels belonging to the skeleton was determined. Fractal dimension of the CB skeleton was calculated using the box-counting method. The results indicated that the CB skeleton is a highly fractal structure, with a fractal dimension of 2.57+/-0.01. No significant difference in the CB fractal dimension was observed between men and women. Fractal dimension may serve as a quantitative index for structural complexity of the CB at its developmental, degenerative, or evolutionary stages.

  15. Probing the Physical Structures of Dense Filaments

    NASA Astrophysics Data System (ADS)

    Li, Di

    2015-08-01

    Filament is a common feature in cosmological structures of various scales, ranging from dark matter cosmic web, galaxy clusters, inter-galactic gas flows, to Galactic ISM clouds. Even within cold dense molecular cores, filaments have been detected. Theories and simulations with (or without) different combination of physical principles, including gravity, thermal balance, turbulence, and magnetic field, can reproduce intriguing images of filaments. The ubiquity of filaments and the similarity in simulated ones make physical parameters, beyond dust column density, a necessity for understanding filament evolution. I report three projects attempting to measure physical parameters of filaments. We derive the volume density of a dense Taurus filament based on several cyanoacetylene transitions observed by GBT and ART. We measure the gas temperature of the OMC 2-3 filament based on combined GBT+VLA ammonia images. We also measured the sub-millimeter polarization vectors along OMC3. These filaments were found to be likely a cylinder-type structure, without dynamic heating, and likely accreting mass along the magnetic field lines.

  16. Fractal structure enables temporal prediction in music.

    PubMed

    Rankin, Summer K; Fink, Philip W; Large, Edward W

    2014-10-01

    1/f serial correlations and statistical self-similarity (fractal structure) have been measured in various dimensions of musical compositions. Musical performances also display 1/f properties in expressive tempo fluctuations, and listeners predict tempo changes when synchronizing. Here the authors show that the 1/f structure is sufficient for listeners to predict the onset times of upcoming musical events. These results reveal what information listeners use to anticipate events in complex, non-isochronous acoustic rhythms, and this will entail innovative models of temporal synchronization. This finding could improve therapies for Parkinson's and related disorders and inform deeper understanding of how endogenous neural rhythms anticipate events in complex, temporally structured communication signals. PMID:25324107

  17. Structure of Flexible Filamentous Plant Viruses

    SciTech Connect

    Kendall, Amy; McDonald, Michele; Bian, Wen; Bowles, Timothy; Baumgarten, Sarah C.; Shi, Jian; Stewart, Phoebe L.; Bullitt, Esther; Gore, David; Irving, Thomas C.; Havens, Wendy M.; Ghabrial, Said A.; Wall, Joseph S.; Stubbs, Gerald

    2008-10-23

    Flexible filamentous viruses make up a large fraction of the known plant viruses, but in comparison with those of other viruses, very little is known about their structures. We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to determine the symmetry of a potyvirus, soybean mosaic virus; to confirm the symmetry of a potexvirus, potato virus X; and to determine the low-resolution structures of both viruses. We conclude that these viruses and, by implication, most or all flexible filamentous plant viruses share a common coat protein fold and helical symmetry, with slightly less than 9 subunits per helical turn.

  18. Vortex-ring-fractal Structure of Atom and Molecule

    SciTech Connect

    Osmera, Pavel

    2010-06-17

    This chapter is an attempt to attain a new and profound model of the nature's structure using a vortex-ring-fractal theory (VRFT). Scientists have been trying to explain some phenomena in Nature that have not been explained so far. The aim of this paper is the vortex-ring-fractal modeling of elements in the Mendeleev's periodic table, which is not in contradiction to the known laws of nature. We would like to find some acceptable structure model of the hydrogen as a vortex-fractal-coil structure of the proton and a vortex-fractal-ring structure of the electron. It is known that planetary model of the hydrogen atom is not right, the classical quantum model is too abstract. Our imagination is that the hydrogen is a levitation system of the proton and the electron. Structures of helium, oxygen, and carbon atoms and a hydrogen molecule are presented too.

  19. Process for applying control variables having fractal structures

    DOEpatents

    Bullock, IV, Jonathan S.; Lawson, Roger L.

    1996-01-01

    A process and apparatus for the application of a control variable having a fractal structure to a body or process. The process of the present invention comprises the steps of generating a control variable having a fractal structure and applying the control variable to a body or process reacting in accordance with the control variable. The process is applicable to electroforming where first, second and successive pulsed-currents are applied to cause the deposition of material onto a substrate, such that the first pulsed-current, the second pulsed-current, and successive pulsed currents form a fractal pulsed-current waveform.

  20. Process for applying control variables having fractal structures

    DOEpatents

    Bullock, J.S. IV; Lawson, R.L.

    1996-01-23

    A process and apparatus are disclosed for the application of a control variable having a fractal structure to a body or process. The process of the present invention comprises the steps of generating a control variable having a fractal structure and applying the control variable to a body or process reacting in accordance with the control variable. The process is applicable to electroforming where first, second and successive pulsed-currents are applied to cause the deposition of material onto a substrate, such that the first pulsed-current, the second pulsed-current, and successive pulsed currents form a fractal pulsed-current waveform. 3 figs.

  1. Fractal Bread.

    ERIC Educational Resources Information Center

    Esbenshade, Donald H., Jr.

    1991-01-01

    Develops the idea of fractals through a laboratory activity that calculates the fractal dimension of ordinary white bread. Extends use of the fractal dimension to compare other complex structures as other breads and sponges. (MDH)

  2. Fractal structure of the interplanetary magnetic field

    NASA Technical Reports Server (NTRS)

    Burlaga, L. F.; Klein, L. W.

    1985-01-01

    Under some conditions, time series of the interplanetary magnetic field strength and components have the properties of fractal curves. Magnetic field measurements made near 8.5 AU by Voyager 2 from June 5 to August 24, 1981 were self-similar over time scales from approximately 20 sec to approximately 3 x 100,000 sec, and the fractal dimension of the time series of the strength and components of the magnetic field was D = 5/3, corresponding to a power spectrum P(f) approximately f sup -5/3. Since the Kolmogorov spectrum for homogeneous, isotropic, stationary turbulence is also f sup -5/3, the Voyager 2 measurements are consistent with the observation of an inertial range of turbulence extending over approximately four decades in frequency. Interaction regions probably contributed most of the power in this interval. As an example, one interaction region is discussed in which the magnetic field had a fractal dimension D = 5/3.

  3. Fractal Particles: Titan's Thermal Structure and IR Opacity

    NASA Technical Reports Server (NTRS)

    McKay, C. P.; Rannou, P.; Guez, L.; Young, E. F.; DeVincenzi, Donald (Technical Monitor)

    1998-01-01

    Titan's haze particles are the principle opacity at solar wavelengths. Most past work in modeling these particles has assumed spherical particles. However, observational evidence strongly favors fractal shapes for the haze particles. We consider the implications of fractal particles for the thermal structure and near infrared opacity of Titan's atmosphere. We find that assuming fractal particles with the optical properties based on laboratory tholin material and with a production rate that allows for a match to the geometric albedo results in warmer troposphere and surface temperatures compared to spherical particles. In the near infrared (1-3 microns) the predicted opacity of the fractal particles is up to a factor of two less than for spherical particles. This has implications for the ability of Cassini to image Titan's surface at 1 micron.

  4. The analysis of the influence of fractal structure of stimuli on fractal dynamics in fixational eye movements and EEG signal

    PubMed Central

    Namazi, Hamidreza; Kulish, Vladimir V.; Akrami, Amin

    2016-01-01

    One of the major challenges in vision research is to analyze the effect of visual stimuli on human vision. However, no relationship has been yet discovered between the structure of the visual stimulus, and the structure of fixational eye movements. This study reveals the plasticity of human fixational eye movements in relation to the ‘complex’ visual stimulus. We demonstrated that the fractal temporal structure of visual dynamics shifts towards the fractal dynamics of the visual stimulus (image). The results showed that images with higher complexity (higher fractality) cause fixational eye movements with lower fractality. Considering the brain, as the main part of nervous system that is engaged in eye movements, we analyzed the governed Electroencephalogram (EEG) signal during fixation. We have found out that there is a coupling between fractality of image, EEG and fixational eye movements. The capability observed in this research can be further investigated and applied for treatment of different vision disorders. PMID:27217194

  5. The analysis of the influence of fractal structure of stimuli on fractal dynamics in fixational eye movements and EEG signal.

    PubMed

    Namazi, Hamidreza; Kulish, Vladimir V; Akrami, Amin

    2016-01-01

    One of the major challenges in vision research is to analyze the effect of visual stimuli on human vision. However, no relationship has been yet discovered between the structure of the visual stimulus, and the structure of fixational eye movements. This study reveals the plasticity of human fixational eye movements in relation to the 'complex' visual stimulus. We demonstrated that the fractal temporal structure of visual dynamics shifts towards the fractal dynamics of the visual stimulus (image). The results showed that images with higher complexity (higher fractality) cause fixational eye movements with lower fractality. Considering the brain, as the main part of nervous system that is engaged in eye movements, we analyzed the governed Electroencephalogram (EEG) signal during fixation. We have found out that there is a coupling between fractality of image, EEG and fixational eye movements. The capability observed in this research can be further investigated and applied for treatment of different vision disorders. PMID:27217194

  6. The analysis of the influence of fractal structure of stimuli on fractal dynamics in fixational eye movements and EEG signal

    NASA Astrophysics Data System (ADS)

    Namazi, Hamidreza; Kulish, Vladimir V.; Akrami, Amin

    2016-05-01

    One of the major challenges in vision research is to analyze the effect of visual stimuli on human vision. However, no relationship has been yet discovered between the structure of the visual stimulus, and the structure of fixational eye movements. This study reveals the plasticity of human fixational eye movements in relation to the ‘complex’ visual stimulus. We demonstrated that the fractal temporal structure of visual dynamics shifts towards the fractal dynamics of the visual stimulus (image). The results showed that images with higher complexity (higher fractality) cause fixational eye movements with lower fractality. Considering the brain, as the main part of nervous system that is engaged in eye movements, we analyzed the governed Electroencephalogram (EEG) signal during fixation. We have found out that there is a coupling between fractality of image, EEG and fixational eye movements. The capability observed in this research can be further investigated and applied for treatment of different vision disorders.

  7. Filamentous structures in skeletal muscle: anchors for the subsarcolemmal space.

    PubMed

    Khairani, Astrid Feinisa; Tajika, Yuki; Takahashi, Maiko; Ueno, Hitoshi; Murakami, Tohru; Soenggono, Arifin; Yorifuji, Hiroshi

    2015-03-01

    In skeletal muscle fibers, intermediate filaments and actin filaments provide structural support to the myofibrils and the sarcolemma. For many years, it was poorly understood from ultrastructural observations that how these filamentous structures were kept anchored. The present study was conducted to determine the architecture of filamentous anchoring structures in the subsarcolemmal space and the intermyofibrils. The diaphragms (Dp) of adult wild type and mdx mice (mdx is a model for Duchenne muscular dystrophy) were subjected to tension applied perpendicular to the long axis of the muscle fibers, with or without treatment with 1% Triton X-100 or 0.03% saponin. These experiments were conducted to confirm the presence and integrity of the filamentous anchoring structures. Transmission electron microscopy revealed that these structures provide firm transverse connections between the sarcolemma and peripheral myofibrils. Most of the filamentous structures appeared to be inserted into subsarcolemmal densities, forming anchoring connections between the sarcolemma and peripheral myofibrils. In some cases, actin filaments were found to run longitudinally in the subsarcolemmal space to connect to the sarcolemma or in some cases to connect to the intermyofibrils as elongated thin filaments. These filamentous anchoring structures were less common in the mdx Dp. Our data suggest that the transverse and longitudinal filamentous structures form an anchoring system in the subsarcolemmal space and the intermyofibrils. PMID:24519712

  8. Fractal structure of equipotential curves on a continuum percolation model

    NASA Astrophysics Data System (ADS)

    Matsutani, Shigeki; Shimosako, Yoshiyuki; Wang, Yunhong

    2012-12-01

    We numerically investigate the electric potential distribution over a two-dimensional continuum percolation model between the electrodes. The model consists of overlapped conductive particles on the background with an infinitesimal conductivity. Using the finite difference method, we solve the generalized Laplace equation and show that in the potential distribution, there appear quasi-equipotential clusters which approximately and locally have the same values as steps and stairs. Since the quasi-equipotential clusters have the fractal structure, we compute the fractal dimension of equipotential curves and its dependence on the volume fraction over [0,1]. The fractal dimension in [1.00, 1.246] has a peak at the percolation threshold pc.

  9. Synthesis of Cobalt Oxides Thin Films Fractal Structures by Laser Chemical Vapor Deposition

    PubMed Central

    Haniam, P.; Kunsombat, C.; Chiangga, S.; Songsasen, A.

    2014-01-01

    Thin films of cobalt oxides (CoO and Co3O4) fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures. PMID:24672354

  10. Synthesis of cobalt oxides thin films fractal structures by laser chemical vapor deposition.

    PubMed

    Haniam, P; Kunsombat, C; Chiangga, S; Songsasen, A

    2014-01-01

    Thin films of cobalt oxides (CoO and Co3O4) fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures. PMID:24672354

  11. Protozoan community structure in a fractal soil environment.

    PubMed

    Finlay, B J; Fenchel, T

    2001-09-01

    Protozoan abundance was quantified, and 365 protozoan species were recorded, in 150 soil samples from an upland grassland in Scotland. Across the entire size range (2-200 pm) protozoan species richness varied by a factor of two, whereas abundance increased by a factor of 20 with decreasing body size. As the soil had fractal structure, the relatively flat species curve can be explained if spatial heterogeneity determines species number--for in a fractal environment, heterogeneity will be the same at all spatial scales. Community structure appeared to approach a temporary steady-state about six days after re-hydration of dried soil. A simple model based on combining the fractal character of increasing habitat area at smaller spatial scales, with the weight-specific energy requirements of protozoa, provided theoretical curves of abundance and biovolume on body size which provide a reasonable fit to real data. We suggest two possibilities--that the apparent competence of the theoretical model is fortuitous and the product of poorly understood dynamic elements of the trophic structure in the community; or that key elements of protozoan community structure in a fractal soil environment may be largely explained in terms of habitat space and energy requirements. PMID:11693659

  12. Fractal free energy landscapes in structural glasses.

    PubMed

    Charbonneau, Patrick; Kurchan, Jorge; Parisi, Giorgio; Urbani, Pierfrancesco; Zamponi, Francesco

    2014-01-01

    Glasses are amorphous solids whose constituent particles are caged by their neighbours and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers. Here we show, using theory and numerical simulation, that the landscape is much rougher than is classically assumed. Deep in the glass, it undergoes a 'roughness transition' to fractal basins, which brings about isostaticity and marginal stability on approaching jamming. Critical exponents for the basin width, the weak force distribution and the spatial spread of quasi-contacts near jamming can be analytically determined. Their value is found to be compatible with numerical observations. This advance incorporates the jamming transition of granular materials into the framework of glass theory. Because temperature and pressure control what features of the landscape are experienced, glass mechanics and transport are expected to reflect the features of the topology we discuss here. PMID:24759041

  13. Fractal structures in stenoses and aneurysms in blood vessels

    PubMed Central

    Schelin, Adriane B.; Károlyi, György; de Moura, Alessandro P. S.; Booth, Nuala A.; Grebogi, Celso

    2010-01-01

    Recent advances in the field of chaotic advection provide the impetus to revisit the dynamics of particles transported by blood flow in the presence of vessel wall irregularities. The irregularity, being either a narrowing or expansion of the vessel, mimicking stenoses or aneurysms, generates abnormal flow patterns that lead to a peculiar filamentary distribution of advected particles, which, in the blood, would include platelets. Using a simple model, we show how the filamentary distribution depends on the size of the vessel wall irregularity, and how it varies under resting or exercise conditions. The particles transported by blood flow that spend a long time around a disturbance either stick to the vessel wall or reside on fractal filaments. We show that the faster flow associated with exercise creates widespread filaments where particles can get trapped for a longer time, thus allowing for the possible activation of such particles. We argue, based on previous results in the field of active processes in flows, that the non-trivial long-time distribution of transported particles has the potential to have major effects on biochemical processes occurring in blood flow, including the activation and deposition of platelets. One aspect of the generality of our approach is that it also applies to other relevant biological processes, an example being the coexistence of plankton species investigated previously. PMID:21078637

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

    PubMed

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

    2009-07-01

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

  15. Ubiquitination and filamentous structure of cytidine triphosphate synthase.

    PubMed

    Pai, Li-Mei; Wang, Pei-Yu; Lin, Wei-Cheng; Chakraborty, Archan; Yeh, Chau-Ting; Lin, Yu-Hung

    2016-07-01

    Living organisms respond to nutrient availability by regulating the activity of metabolic enzymes. Therefore, the reversible post-translational modification of an enzyme is a common regulatory mechanism for energy conservation. Recently, cytidine-5'-triphosphate (CTP) synthase was discovered to form a filamentous structure that is evolutionarily conserved from flies to humans. Interestingly, induction of the formation of CTP synthase filament is responsive to starvation or glutamine depletion. However, the biological roles of this structure remain elusive. We have recently shown that ubiquitination regulates CTP synthase activity by promoting filament formation in Drosophila ovaries during endocycles. Intriguingly, although the ubiquitination process was required for filament formation induced by glutamine depletion, CTP synthase ubiquitination was found to be inversely correlated with filament formation in Drosophila and human cell lines. In this article, we discuss the putative dual roles of ubiquitination, as well as its physiological implications, in the regulation of CTP synthase structure. PMID:27116391

  16. Baby universes and fractal structure of 2d gravity

    NASA Astrophysics Data System (ADS)

    Thorleifsson, Gudmar

    1994-04-01

    We extract the string susceptibility exponent γstr by measuring the distribution of baby universes on surfaces in the case of various matter fields coupled to discrete 2d quantum gravity. For c <= 1 the results are in good agreement with the KPZ-formula, if logarithmic corrections are taken into account for c = 1. For c > 1 it is not as clear how to extract γstr but universality with respect to c is observed in the fractal structure.

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

    SciTech Connect

    Alekseev, A.D.; Vasilenko, T.A.; Kirillov, A.K.

    2008-05-15

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

  18. Stochastic Erosion of Fractal Structure in Nonlinear Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Agarwal, S.; Wettlaufer, J. S.

    2014-12-01

    We analyze the effects of stochastic noise on the Lorenz-63 model in the chaotic regime to demonstrate a set of general issues arising in the interpretation of data from nonlinear dynamical systems typical in geophysics. The model is forced using both additive and multiplicative, white and colored noise and it is shown that, through a suitable choice of the noise intensity, both additive and multiplicative noise can produce similar dynamics. We use a recently developed measure, histogram distance, to show the similarity between the dynamics produced by additive and multiplicative forcing. This phenomenon, in a nonlinear fractal structure with chaotic dynamics can be explained by understanding how noise affects the Unstable Periodic Orbits (UPOs) of the system. For delta-correlated noise, the UPOs erode the fractal structure. In the presence of memory in the noise forcing, the time scale of the noise starts to interact with the period of some UPO and, depending on the noise intensity, stochastic resonance may be observed. This also explains the mixing in dissipative dynamical systems in presence of white noise; as the fractal structure is smoothed, the decay of correlations is enhanced, and hence the rate of mixing increases with noise intensity.

  19. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  20. Observation of two different fractal structures in nanoparticle, protein and surfactant complexes

    SciTech Connect

    Mehan, Sumit Kumar, Sugam Aswal, V. K.

    2014-04-24

    Small angle neutron scattering has been carried out from a complex of nanoparticle, protein and surfactant. Although all the components are similarly (anionic) charged, we have observed strong interactions in their complex formation. It is characterized by the coexistence of two different mass fractal structures. The first fractal structure is originated from the protein and surfactant interaction and second from the depletion effect of first fractal structure leading the nanoparticle aggregation. The fractal structure of protein-surfactant complex represents to bead necklace structure of micelle-like clusters of surfactant formed along the unfolded protein chain. Its fractal dimension depends on the surfactant to protein ratio (r) and decreases with the increase in r. However, fractal dimension of nanoparticle aggregates in nanoparticle-protein complex is found to be independent of protein concentration and governed by the diffusion limited aggregation like morphology.

  1. Observation of two different fractal structures in nanoparticle, protein and surfactant complexes

    NASA Astrophysics Data System (ADS)

    Mehan, Sumit; Kumar, Sugam; Aswal, V. K.

    2014-04-01

    Small angle neutron scattering has been carried out from a complex of nanoparticle, protein and surfactant. Although all the components are similarly (anionic) charged, we have observed strong interactions in their complex formation. It is characterized by the coexistence of two different mass fractal structures. The first fractal structure is originated from the protein and surfactant interaction and second from the depletion effect of first fractal structure leading the nanoparticle aggregation. The fractal structure of protein-surfactant complex represents to bead necklace structure of micelle-like clusters of surfactant formed along the unfolded protein chain. Its fractal dimension depends on the surfactant to protein ratio (r) and decreases with the increase in r. However, fractal dimension of nanoparticle aggregates in nanoparticle-protein complex is found to be independent of protein concentration and governed by the diffusion limited aggregation like morphology.

  2. Dynamics of solar filaments. IV - Structure and mass flow of an active region filament

    NASA Technical Reports Server (NTRS)

    Schmieder, B.; Malherbe, J. M.; Simon, G.; Poland, A. I.

    1985-01-01

    An active region filament near the center of the solar disk was observed on September 29-30, 1980, with the Multichannel Subtractive Double Pass Spectrograph of the Meudon solar tower and the UV Spectrograph and Polarimeter aboard the SMM satellite. H-alpha and C IV measurements are presently used to study brightness and material velocity in the 10,000 and 100,000 K temperature ranges, and photospheric magnetograms are used to investigate the underlying magnetic field. Attention is given to the constraints imposed on possible filament structures by observations, as well as the expected MHD relationships.

  3. Surface fractal analysis of pore structure of high-volume fly-ash cement pastes

    NASA Astrophysics Data System (ADS)

    Zeng, Qiang; Li, Kefei; Fen-Chong, Teddy; Dangla, Patrick

    2010-11-01

    The surface fractal dimensions of high-volume fly-ash cement pastes are evaluated for their hardening processes on the basis of mercury intrusion porosimetry (MIP) data. Two surface fractal models are retained: Neimark's model with cylindrical pore hypothesis and Zhang's model without pore geometry assumption. From both models, the logarithm plots exhibit the scale-dependent fractal properties and three distinct fractal regions (I, II, III) are identified for the pore structures. For regions I and III, corresponding to the large (capillary) and small (C-S-H inter-granular) pore ranges respectively, the pore structure shows strong fractal property and the fractal dimensions are evaluated as 2.592-2.965 by Neimark's model and 2.487-2.695 by Zhang's model. The fractal dimension of region I increases with w/ b ratio and hardening age but decreases with fly-ash content by its physical filling effect; the fractal dimension of region III does not evolve much with these factors. The region II of pore size range, corresponding to small capillary pores, turns out to be a transition region and show no clear fractal properties. The range of this region is much influenced by fly-ash content in the pastes. Finally, the correlation between the obtained fractal dimensions and pore structure evolution is discussed in depth.

  4. Structural design criteria for filament-wound composite shells

    NASA Technical Reports Server (NTRS)

    Hahn, H. T.; Jensen, D. W.; Claus, S. J.; Pai, S. P.; Hipp, P. A.

    1994-01-01

    Advanced composite cylinders, manufactured by filament winding, provide a cost effective solution to many present structural applications; however, the compressive performance of filament-wound cylinders is lower than comparable shells fabricated from unidirectional tape. The objective of this study was to determine the cause of this reduction in thin filament-wound cylinders by relating the manufacturing procedures to the quality of the cylinder and to its compressive performance. The experiments on cylinder buckling were complemented by eigenvalue buckling analysis using a detailed geometric model in a finite element analysis. The applicability of classical buckling analyses was also investigated as a design tool.

  5. Fractal structure of films deposited in a tokamak

    NASA Astrophysics Data System (ADS)

    Budaev, V. P.; Khimchenko, L. N.

    2007-04-01

    The surface of amorphous films deposited in the T-10 tokamak was studied in a scanning tunnel microscope. The surface relief on a scale from 10 nm to 100 μm showed a stochastic surface topography and revealed a hierarchy of grains. The observed variety of irregular structures of the films was studied within the framework of the concept of scale invariance using the methods of fractal geometry and statistical physics. The experimental probability density distribution functions of the surface height variations are close in shape to the Cauchy distribution. The stochastic surface topography of the films is characterized by a Hurst parameter of H = 0.68-0.85, which is evidence of a nontrivial self-similarity of the film structure. The fractal character and porous structure of deposited irregular films must be considered as an important issue related to the accumulation of tritium in the ITER project. The process of film growth on the surface of tokamak components exposed to plasma has been treated within the framework of the general concept of inhomogeneous surface growth. A strong turbulence of the edge plasma in tokamaks can give rise to fluctuations in the incident flux of particles, which leads to the growth of fractal films with grain dimensions ranging from nano-to micrometer scale. The shape of the surface of some films found in the T-10 tokamak has been interpreted using a model of diffusion-limited aggregation (DLA). The growth of films according to the discrete DLA model was simulated using statistics of fluctuations observed in a turbulent edge plasma of the T-10 tokamak. The modified DLA model reproduces well the main features of the surface of some films deposited in tokamaks.

  6. Method for preparing metallated filament-wound structures

    DOEpatents

    Peterson, George R.

    1979-01-01

    Metallated graphite filament-wound structures are prepared by coating a continuous multi-filament carbon yarn with a metal carbide, impregnating the carbide coated yarn with a polymerizable carbon precursor, winding the resulting filament about a mandrel, partially curing the impregnation in air, subjecting the wound composite to heat and pressure to cure the carbon precursor, and thereafter heating the composite in a sizing die at a pressure loading of at least 1000 psi for graphitizing the carbonaceous material in the composite. The carbide in the composite coalesces into rod-like shapes which are disposed in an end-to-end relationship parallel with the filaments to provide resistance to erosion in abrasive laden atmospheres.

  7. Chlordecone retention in the fractal structure of volcanic clay.

    PubMed

    Woignier, Thierry; Clostre, Florence; Macarie, Hervé; Jannoyer, Magalie

    2012-11-30

    Chlordecone (CHLD), a soil and foodstuff pollutant, as well as an environmentally persistent organochlorine insecticide, was used intensively in banana fields. The chlordecone uptake of three crops was measured for two types of polluted soils: allophanic and non-allophanic. The uptake is lower for allophanic soils even if their chlordecone content is higher than with non-allophanic soils. The fractal structure of the allophane aggregates was characterized at the nanoscale by small angle X-rays scattering, pore size distribution and transmission electron microscopy. We showed that clay microstructures should be an important physico-chemical factor governing the fate of chlordecone in the environment. Allophanic clays result in two counterintuitive findings: higher contaminant trappings yet lower contaminant availability. We propose that this specific, tortuous structure, along with its associated low accessibility, partly explains the low availability of chlordecone confined in allophanic soils. Capsule The fractal and tortuous microstructure of allophane clay favours the chlordecone retention in soils and disfavours the crop uptake. PMID:23062511

  8. Fractal analysis of bone structure with applications to osteoporosis and microgravity effects

    SciTech Connect

    Acharya, R.S.; Swarnarkar, V.; Krishnamurthy, R.; Hausman, E.; LeBlanc, A.; Lin, C.; Shackelford, L.

    1995-12-31

    The authors characterize the trabecular structure with the aid of fractal dimension. The authors use Alternating Sequential filters to generate a nonlinear pyramid for fractal dimension computations. The authors do not make any assumptions of the statistical distributions of the underlying fractal bone structure. The only assumption of the scheme is the rudimentary definition of self similarity. This allows them the freedom of not being constrained by statistical estimation schemes. With mathematical simulations, the authors have shown that the ASF methods outperform other existing methods for fractal dimension estimation. They have shown that the fractal dimension remains the same when computed with both the X-Ray images and the MRI images of the patella. They have shown that the fractal dimension of osteoporotic subjects is lower than that of the normal subjects. In animal models, the authors have shown that the fractal dimension of osteoporotic rats was lower than that of the normal rats. In a 17 week bedrest study, they have shown that the subject`s prebedrest fractal dimension is higher than that of the postbedrest fractal dimension.

  9. TRANSIENT CHAOS AND FRACTAL STRUCTURES IN PLANETARY FEEDING ZONES

    SciTech Connect

    Kovács, T.; Regály, Zs.

    2015-01-01

    The circular restricted three-body problem is investigated in the context of accretion and scattering processes. In our model, a large number of identical non-interacting mass-less planetesimals are considered in the planar case orbiting a star-planet system. This description allows us to investigate the gravitational scattering and possible capture of the particles by the forming planetary embryo in a dynamical systems approach. Although the problem serves a large variety of complex motions, the results can be easily interpreted because of the low dimensionality of the phase space. We show that initial conditions define isolated regions of the disk, where planetesimals accrete or escape, which have, in fact, a fractal structure. The fractal geometry of these ''basins'' implies that the dynamics is very complex. Based on the calculated escape rates and escape times, it is also demonstrated that the planetary accretion rate is exponential for short times and follows a power law for longer integration. A new numerical calculation of the maximum mass that a planet can reach (described by the expression of the isolation mass) is also derived.

  10. Transient Chaos and Fractal Structures in Planetary Feeding Zones

    NASA Astrophysics Data System (ADS)

    Kovács, T.; Regály, Zs.

    2015-01-01

    The circular restricted three-body problem is investigated in the context of accretion and scattering processes. In our model, a large number of identical non-interacting mass-less planetesimals are considered in the planar case orbiting a star-planet system. This description allows us to investigate the gravitational scattering and possible capture of the particles by the forming planetary embryo in a dynamical systems approach. Although the problem serves a large variety of complex motions, the results can be easily interpreted because of the low dimensionality of the phase space. We show that initial conditions define isolated regions of the disk, where planetesimals accrete or escape, which have, in fact, a fractal structure. The fractal geometry of these "basins" implies that the dynamics is very complex. Based on the calculated escape rates and escape times, it is also demonstrated that the planetary accretion rate is exponential for short times and follows a power law for longer integration. A new numerical calculation of the maximum mass that a planet can reach (described by the expression of the isolation mass) is also derived.

  11. Structural Dynamics of Filament-Wound Booster Rockets

    NASA Technical Reports Server (NTRS)

    Bugg, F. M.

    1987-01-01

    Report summarizes program of measurements and calculations of vibrations in filament-wound composite models of Space Shuttle solid-rocket boosters. Vibrational behavior predicted by finite-element computer model of structural dynamics correlates well with data from tests on full- and quarter-scale models. Computer model developed with NASTRAN general-purpose structural-analysis computer code.

  12. Surface structures of equilibrium restricted curvature model on two fractal substrates

    NASA Astrophysics Data System (ADS)

    Song, Li-Jian; Tang, Gang; Zhang, Yong-Wei; Han, Kui; Xun, Zhi-Peng; Xia, Hui; Hao, Da-Peng; Li, Yan

    2014-01-01

    With the aim to probe the effects of the microscopic details of fractal substrates on the scaling of discrete growth models, the surface structures of the equilibrium restricted curvature (ERC) model on Sierpinski arrowhead and crab substrates are analyzed by means of Monte Carlo simulations. These two fractal substrates have the same fractal dimension df, but possess different dynamic exponents of random walk zrw. The results show that the surface structure of the ERC model on fractal substrates are related to not only the fractal dimension df, but also to the microscopic structures of the substrates expressed by the dynamic exponent of random walk zrw. The ERC model growing on the two substrates follows the well-known Family—Vicsek scaling law and satisfies the scaling relations 2α + df asymp z asymp 2zrw. In addition, the values of the scaling exponents are in good agreement with the analytical prediction of the fractional Mullins—Herring equation.

  13. Self-Structured Conductive Filament Nanoheater for Chalcogenide Phase Transition.

    PubMed

    You, Byoung Kuk; Byun, Myunghwan; Kim, Seungjun; Lee, Keon Jae

    2015-06-23

    Ge2Sb2Te5-based phase-change memories (PCMs), which undergo fast and reversible switching between amorphous and crystalline structural transformation, are being utilized for nonvolatile data storage. However, a critical obstacle is the high programming current of the PCM cell, resulting from the limited pattern size of the optical lithography-based heater. Here, we suggest a facile and scalable strategy of utilizing self-structured conductive filament (CF) nanoheaters for Joule heating of chalcogenide materials. This CF nanoheater can replace the lithographical-patterned conventional resistor-type heater. The sub-10 nm contact area between the CF and the phase-change material achieves significant reduction of the reset current. In particular, the PCM cell with a single Ni filament nanoheater can be operated at an ultralow writing current of 20 μA. Finally, phase-transition behaviors through filament-type nanoheaters were directly observed by using transmission electron microscopy. PMID:26039415

  14. Aliasing removing of hyperspectral image based on fractal structure matching

    NASA Astrophysics Data System (ADS)

    Wei, Ran; Zhang, Ye; Zhang, Junping

    2015-05-01

    Due to the richness on high frequency components, hyperspectral image (HSI) is more sensitive to distortion like aliasing. Many methods aiming at removing such distortion have been proposed. However, seldom of them are suitable to HSI, due to low spatial resolution characteristic of HSI. Fortunately, HSI contains plentiful spectral information, which can be exploited to overcome such difficulties. Motivated by this, we proposed an aliasing removing method for HSI. The major differences between proposed and current methods is that proposed algorithm is able to utilize fractal structure information, thus the dilemma originated from low-resolution of HSI is solved. Experiments on real HSI data demonstrated subjectively and objectively that proposed method can not only remove annoying visual effect brought by aliasing, but also recover more high frequency component.

  15. Structural Basis of Actin Filament Nucleation by Tandem W Domains

    PubMed Central

    Chen, Xiaorui; Ni, Fengyun; Tian, Xia; Kondrashkina, Elena; Wang, Qinghua; Ma, Jianpeng

    2013-01-01

    SUMMARY Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization. PMID:23727244

  16. Application of fractal dimensions to study the structure of flocs formed in lime softening process.

    PubMed

    Vahedi, Arman; Gorczyca, Beata

    2011-01-01

    The use of fractal dimensions to study the internal structure and settling of flocs formed in lime softening process was investigated. Fractal dimensions of flocs were measured directly on floc images and indirectly from their settling velocity. An optical microscope with a motorized stage was used to measure the fractal dimensions of lime softening flocs directly on their images in 2 and 3D space. The directly determined fractal dimensions of the lime softening flocs were 1.11-1.25 for floc boundary, 1.82-1.99 for cross-sectional area and 2.6-2.99 for floc volume. The fractal dimension determined indirectly from the flocs settling rates was 1.87 that was different from the 3D fractal dimension determined directly on floc images. This discrepancy is due to the following incorrect assumptions used for fractal dimensions determined from floc settling rates: linear relationship between square settling velocity and floc size (Stokes' Law), Euclidean relationship between floc size and volume, constant fractal dimensions and one primary particle size describing entire population of flocs. Floc settling model incorporating variable floc fractal dimensions as well as variable primary particle size was found to describe the settling velocity of large (>50 μm) lime softening flocs better than Stokes' Law. Settling velocities of smaller flocs (<50 μm) could still be quite well predicted by Stokes' Law. The variation of fractal dimensions with lime floc size in this study indicated that two mechanisms are involved in the formation of these flocs: cluster-cluster aggregation for small flocs (<50 μm) and diffusion-limited aggregation for large flocs (>50 μm). Therefore, the relationship between the floc fractal dimension and floc size appears to be determined by floc formation mechanisms. PMID:20937512

  17. On filament structure and propagation within a commercial plasma globe

    SciTech Connect

    Burin, M. J.; Simmons, G. G.; Ceja, H. G.; Zweben, S. J.; Nagy, A.; Brunkhorst, C.

    2015-05-15

    The filamentary discharge seen within commercial plasma globes is commonly enjoyed yet not well understood. Here, we investigate the discharge properties of a plasma globe using a variable high voltage amplifier. We find that increasing voltage magnitude increases the number of filaments while leaving their individual structure basically unchanged, a result typical of dielectric barrier discharges. The frequency of the voltage also affects filament population but more significantly changes filament structure, with more diffuse filaments seen at lower frequencies. Voltage polarity is observed to be important, especially at lower frequencies, where for negative-gradient voltages the discharge is more diffuse, not filamentary. At late stages of the discharge circular structures appear and expand on the glass boundaries. We find no trend of discharge speed with respect to voltage variables, though this may be due to manufacturer sample-to-sample variation. Each voltage cycle the discharge expands outward at ∼10–15 km/s, a speed significantly higher than the estimated electron drift yet considerably lower than that observed for most streamers. We discuss the physics of these observations and their relation to similar discharges that can be found within nature and industry.

  18. Filamented ion tail structures at Titan: A hybrid simulation study

    NASA Astrophysics Data System (ADS)

    Feyerabend, Moritz; Simon, Sven; Motschmann, Uwe; Liuzzo, Lucas

    2015-11-01

    This study investigates the processes that lead to the detection of split signatures in ion density during several crossings of the Cassini spacecraft through Titan's mid-range plasma tail (T9, T63, and T75). During each of these flybys, the Cassini Plasma Spectrometer detected Titan's ionospheric ion population twice; i.e., the spacecraft passed through two spatially separated regions where cold ions were detected, with the regions also being dominated by ions of different masses in the case of T9. Whether this filamented tail structure is an omnipresent feature of Titan's plasma interaction or a result of non-stationary upstream conditions during specific flybys is still unclear. To explain these features, we apply the hybrid simulation code AIKEF (kinetic ions and fluid electrons). Our model includes chemical reactions as well as a realistic photoionization model for a sophisticated description of the ionospheric composition of Titan. Our simulations show that the filamentation of Titan's tail is indeed a common feature of the moon's plasma interaction. Light ionospheric species escape along draped magnetic field lines to form a parabolically shaped filament structure, which is mainly seen in planes that contain the upstream magnetospheric magnetic field and the upstream flow direction. In addition, transport of ions of all species from the ramside towards downstream produces a cone structure behind Titan, with a region of decreased density inside and filaments of 1-2 RT (RT=2575 km) thickness and enhanced density at the surface of the cone. Spacecraft trajectories that penetrate these structures allow for the detection of split signatures in the tail. The orientation of the upstream magnetic field and plasma flow as well as local time effects (i.e., Titan's orbital position) influence the location of the filaments in the tail and can also cause asymmetries in their sizes and densities. The detection of the split signatures along a spacecraft trajectory may

  19. Filament Structure, Organization, and Dynamics in MreB Sheets*

    PubMed Central

    Popp, David; Narita, Akihiro; Maeda, Kayo; Fujisawa, Tetsuro; Ghoshdastider, Umesh; Iwasa, Mitsusada; Maéda, Yuichiro; Robinson, Robert C.

    2010-01-01

    In vivo fluorescence microscopy studies of bacterial cells have shown that the bacterial shape-determining protein and actin homolog, MreB, forms cable-like structures that spiral around the periphery of the cell. The molecular structure of these cables has yet to be established. Here we show by electron microscopy that Thermatoga maritime MreB forms complex, several μm long multilayered sheets consisting of diagonally interwoven filaments in the presence of either ATP or GTP. This architecture, in agreement with recent rheological measurements on MreB cables, may have superior mechanical properties and could be an important feature for maintaining bacterial cell shape. MreB polymers within the sheets appear to be single-stranded helical filaments rather than the linear protofilaments found in the MreB crystal structure. Sheet assembly occurs over a wide range of pH, ionic strength, and temperature. Polymerization kinetics are consistent with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation. Steady-state TIRF microscopy studies of MreB suggest filament treadmilling while high pressure small angle x-ray scattering measurements indicate that the stability of MreB polymers is similar to that of F-actin filaments. In the presence of ADP or GDP, long, thin cables formed in which MreB was arranged in parallel as linear protofilaments. This suggests that the bacterial cell may exploit various nucleotides to generate different filament structures within cables for specific MreB-based functions. PMID:20223832

  20. Filament structure, organization, and dynamics in MreB sheets.

    PubMed

    Popp, David; Narita, Akihiro; Maeda, Kayo; Fujisawa, Tetsuro; Ghoshdastider, Umesh; Iwasa, Mitsusada; Maéda, Yuichiro; Robinson, Robert C

    2010-05-21

    In vivo fluorescence microscopy studies of bacterial cells have shown that the bacterial shape-determining protein and actin homolog, MreB, forms cable-like structures that spiral around the periphery of the cell. The molecular structure of these cables has yet to be established. Here we show by electron microscopy that Thermatoga maritime MreB forms complex, several mum long multilayered sheets consisting of diagonally interwoven filaments in the presence of either ATP or GTP. This architecture, in agreement with recent rheological measurements on MreB cables, may have superior mechanical properties and could be an important feature for maintaining bacterial cell shape. MreB polymers within the sheets appear to be single-stranded helical filaments rather than the linear protofilaments found in the MreB crystal structure. Sheet assembly occurs over a wide range of pH, ionic strength, and temperature. Polymerization kinetics are consistent with a cooperative assembly mechanism requiring only two steps: monomer activation followed by elongation. Steady-state TIRF microscopy studies of MreB suggest filament treadmilling while high pressure small angle x-ray scattering measurements indicate that the stability of MreB polymers is similar to that of F-actin filaments. In the presence of ADP or GDP, long, thin cables formed in which MreB was arranged in parallel as linear protofilaments. This suggests that the bacterial cell may exploit various nucleotides to generate different filament structures within cables for specific MreB-based functions. PMID:20223832

  1. Fractal Dimension Analysis of Subcortical Gray Matter Structures in Schizophrenia

    PubMed Central

    Sehatpour, Pejman; Long, Jun; Gui, Weihua; Qiao, Jianping; Javitt, Daniel C.; Wang, Zhishun

    2016-01-01

    A failure of adaptive inference—misinterpreting available sensory information for appropriate perception and action—is at the heart of clinical manifestations of schizophrenia, implicating key subcortical structures in the brain including the hippocampus. We used high-resolution, three-dimensional (3D) fractal geometry analysis to study subtle and potentially biologically relevant structural alterations (in the geometry of protrusions, gyri and indentations, sulci) in subcortical gray matter (GM) in patients with schizophrenia relative to healthy individuals. In particular, we focus on utilizing Fractal Dimension (FD), a compact shape descriptor that can be computed using inputs with irregular (i.e., not necessarily smooth) surfaces in order to quantify complexity (of geometrical properties and configurations of structures across spatial scales) of subcortical GM in this disorder. Probabilistic (entropy-based) information FD was computed based on the box-counting approach for each of the seven subcortical structures, bilaterally, as well as the brainstem from high-resolution magnetic resonance (MR) images in chronic patients with schizophrenia (n = 19) and age-matched healthy controls (n = 19) (age ranges: patients, 22.7–54.3 and healthy controls, 24.9–51.6 years old). We found a significant reduction of FD in the left hippocampus (median: 2.1460, range: 2.07–2.18 vs. median: 2.1730, range: 2.15–2.23, p<0.001; Cohen’s effect size, U3 = 0.8158 (95% Confidence Intervals, CIs: 0.6316, 1.0)), the right hippocampus (median: 2.1430, range: 2.05–2.19 vs. median: 2.1760, range: 2.12–2.21, p = 0.004; U3 = 0.8421 (CIs: 0.5263, 1)), as well as left thalamus (median: 2.4230, range: 2.40–2.44, p = 0.005; U3 = 0.7895 (CIs: 0.5789, 0.9473)) in schizophrenia patients, relative to healthy individuals. Our findings provide in-vivo quantitative evidence for reduced surface complexity of hippocampus, with reduced FD indicating a less complex, less regular GM

  2. Fractal Dimension Analysis of Subcortical Gray Matter Structures in Schizophrenia.

    PubMed

    Zhao, Guihu; Denisova, Kristina; Sehatpour, Pejman; Long, Jun; Gui, Weihua; Qiao, Jianping; Javitt, Daniel C; Wang, Zhishun

    2016-01-01

    A failure of adaptive inference-misinterpreting available sensory information for appropriate perception and action-is at the heart of clinical manifestations of schizophrenia, implicating key subcortical structures in the brain including the hippocampus. We used high-resolution, three-dimensional (3D) fractal geometry analysis to study subtle and potentially biologically relevant structural alterations (in the geometry of protrusions, gyri and indentations, sulci) in subcortical gray matter (GM) in patients with schizophrenia relative to healthy individuals. In particular, we focus on utilizing Fractal Dimension (FD), a compact shape descriptor that can be computed using inputs with irregular (i.e., not necessarily smooth) surfaces in order to quantify complexity (of geometrical properties and configurations of structures across spatial scales) of subcortical GM in this disorder. Probabilistic (entropy-based) information FD was computed based on the box-counting approach for each of the seven subcortical structures, bilaterally, as well as the brainstem from high-resolution magnetic resonance (MR) images in chronic patients with schizophrenia (n = 19) and age-matched healthy controls (n = 19) (age ranges: patients, 22.7-54.3 and healthy controls, 24.9-51.6 years old). We found a significant reduction of FD in the left hippocampus (median: 2.1460, range: 2.07-2.18 vs. median: 2.1730, range: 2.15-2.23, p<0.001; Cohen's effect size, U3 = 0.8158 (95% Confidence Intervals, CIs: 0.6316, 1.0)), the right hippocampus (median: 2.1430, range: 2.05-2.19 vs. median: 2.1760, range: 2.12-2.21, p = 0.004; U3 = 0.8421 (CIs: 0.5263, 1)), as well as left thalamus (median: 2.4230, range: 2.40-2.44, p = 0.005; U3 = 0.7895 (CIs: 0.5789, 0.9473)) in schizophrenia patients, relative to healthy individuals. Our findings provide in-vivo quantitative evidence for reduced surface complexity of hippocampus, with reduced FD indicating a less complex, less regular GM surface detected in

  3. Lattice Boltzmann simulation of multicomponent noncontinuum diffusion in fractal porous structures

    NASA Astrophysics Data System (ADS)

    Ma, Qiang; Chen, Zhenqian

    2015-07-01

    A lattice Boltzmann method (LBM) of multicomponent diffusion is developed to examine multicomponent, noncontinuum mass diffusion in porous media. An additional collision interaction is proposed to mimic the Knudsen diffusion caused by the collision interaction between gas molecules and solid pore walls. Using the improved LBM model, the ternary mixtures diffusion is simulated in fractal porous structures which are reconstructed by the random midpoint displacement algorithm. The effects of fractal characteristics and Knudsen diffusion resistance on the multicomponent diffusion in porous structures are investigated and discussed. The results indicate that the smaller fractal dimension enhances the diffusion rate of gas mixtures in fractal porous structures. When the dimensionless Knudsen diffusion coefficient is less than 20, the presence of Knudsen diffusion resistance reduces the rate of mass diffusion in porous structures obviously, especially for the species with larger molecular weight.

  4. Flexible filamentous virus structure from fiber diffraction

    SciTech Connect

    Stubbs, Gerald; Kendall, Amy; McDonald, Michele; Bian, Wen; Bowles, Timothy; Baumgarten, Sarah; McCullough, Ian; Shi, Jian; Stewart, Phoebe; Bullitt, Esther; Gore, David; Ghabrial, Said

    2008-10-24

    Fiber diffraction data have been obtained from Narcissus mosaic virus, a potexvirus from the family Flexiviridae, and soybean mosaic virus (SMV), a potyvirus from the family Potyviridae. Analysis of the data in conjunction with cryo-electron microscopy data allowed us to determine the symmetry of the viruses and to make reconstructions of SMV at 19 {angstrom} resolution and of another potexvirus, papaya mosaic virus, at 18 {angstrom} resolution. These data include the first well-ordered data ever obtained for the potyviruses and the best-ordered data from the potexviruses, and offer the promise of eventual high resolution structure determinations.

  5. Structure and mechanical properties of liquid crystalline filaments

    SciTech Connect

    Eremin, Alexey; Nemes, Alexandru; Stannarius, Ralf; Schulz, Mario; Nadasi, Hajnalka; Weissflog, Wolfgang

    2005-03-01

    The formation of stable freely suspended filaments is an interesting peculiarity of some liquid crystal phases. So far, little is known about their structure and stability. Similarly to free-standing smectic films, an internal molecular structure of the mesophase stabilizes these macroscopically well-ordered objects with length to diameter ratios of 10{sup 3} and above. In this paper, we report observations of smectic liquid crystal fibers formed by bent-shaped molecules in different mesophases. Our study, employing several experimental techniques, focuses on mechanical and structural aspects of fiber formation such as internal structure, stability, and mechanical and optical properties.

  6. An Early Cretaceous heterodontosaurid dinosaur with filamentous integumentary structures.

    PubMed

    Zheng, Xiao-Ting; You, Hai-Lu; Xu, Xing; Dong, Zhi-Ming

    2009-03-19

    Ornithischia is one of the two major groups of dinosaurs, with heterodontosauridae as one of its major clades. Heterodontosauridae is characterized by small, gracile bodies and a problematic phylogenetic position. Recent phylogenetic work indicates that it represents the most basal group of all well-known ornithischians. Previous heterodontosaurid records are mainly from the Early Jurassic period (205-190 million years ago) of Africa. Here we report a new heterodontosaurid, Tianyulong confuciusi gen. et sp. nov., from the Early Cretaceous period (144-99 million years ago) of western Liaoning Province, China. Tianyulong extends the geographical distribution of heterodontosaurids to Asia and confirms the clade's previously questionable temporal range extension into the Early Cretaceous period. More surprisingly, Tianyulong bears long, singular and unbranched filamentous integumentary (outer skin) structures. This represents the first confirmed report, to our knowledge, of filamentous integumentary structures in an ornithischian dinosaur. PMID:19295609

  7. An investigation into the feasibility of implementing fractal paradigms to simulate cancellous bone structure.

    PubMed

    Haire, T J; Ganney, P S; Langton, C M

    2001-01-01

    Cancellous bone consists of a framework of solid trabeculae interspersed with bone marrow. The structure of the bone tissue framework is highly convoluted and complex, being fractal and statistically self-similar over a limited range of magnifications. To date, the structure of natural cancellous bone tissue has been defined using 2D and 3D imaging, with no facility to modify and control the structure. The potential of four computer-generated paradigms has been reviewed based upon knowledge of other fractal structures and chaotic systems, namely Diffusion Limited Aggregation (DLA), Percolation and Epidemics, Cellular Automata, and a regular Grid with randomly relocated nodes. The resulting structures were compared for their ability to create realistic structures of cancellous bone rather than reflecting growth and form processes. Although the creation of realistic computer-generated cancellous bone structures is difficult, it should not be impossible. Future work considering the combination of fractal and chaotic paradigms is underway. PMID:11328644

  8. Magnetohydrodynamics of fractal media

    SciTech Connect

    Tarasov, Vasily E.

    2006-05-15

    The fractal distribution of charged particles is considered. An example of this distribution is the charged particles that are distributed over the fractal. The fractional integrals are used to describe fractal distribution. These integrals are considered as approximations of integrals on fractals. Typical turbulent media could be of a fractal structure and the corresponding equations should be changed to include the fractal features of the media. The magnetohydrodynamics equations for fractal media are derived from the fractional generalization of integral Maxwell equations and integral hydrodynamics (balance) equations. Possible equilibrium states for these equations are considered.

  9. Novel actin-like filament structure from Clostridium tetani.

    PubMed

    Popp, David; Narita, Akihiro; Lee, Lin Jie; Ghoshdastider, Umesh; Xue, Bo; Srinivasan, Ramanujam; Balasubramanian, Mohan K; Tanaka, Toshitsugu; Robinson, Robert C

    2012-06-15

    Eukaryotic F-actin is constructed from two protofilaments that gently wind around each other to form a helical polymer. Several bacterial actin-like proteins (Alps) are also known to form F-actin-like helical arrangements from two protofilaments, yet with varied helical geometries. Here, we report a unique filament architecture of Alp12 from Clostridium tetani that is constructed from four protofilaments. Through fitting of an Alp12 monomer homology model into the electron microscopy data, the filament was determined to be constructed from two antiparallel strands, each composed of two parallel protofilaments. These four protofilaments form an open helical cylinder separated by a wide cleft. The molecular interactions within single protofilaments are similar to F-actin, yet interactions between protofilaments differ from those in F-actin. The filament structure and assembly and disassembly kinetics suggest Alp12 to be a dynamically unstable force-generating motor involved in segregating the pE88 plasmid, which encodes the lethal tetanus toxin, and thus a potential target for drug design. Alp12 can be repeatedly cycled between states of polymerization and dissociation, making it a novel candidate for incorporation into fuel-propelled nanobiopolymer machines. PMID:22514279

  10. Robustness of the fractal regime for the multiple-scattering structure factor

    NASA Astrophysics Data System (ADS)

    Katyal, Nisha; Botet, Robert; Puri, Sanjay

    2016-08-01

    In the single-scattering theory of electromagnetic radiation, the fractal regime is a definite range in the photon momentum-transfer q, which is characterized by the scaling-law behavior of the structure factor: S(q) ∝ 1 /q df. This allows a straightforward estimation of the fractal dimension df of aggregates in Small-Angle X-ray Scattering (SAXS) experiments. However, this behavior is not commonly studied in optical scattering experiments because of the lack of information on its domain of validity. In the present work, we propose a definition of the multiple-scattering structure factor, which naturally generalizes the single-scattering function S(q). We show that the mean-field theory of electromagnetic scattering provides an explicit condition to interpret the significance of multiple scattering. In this paper, we investigate and discuss electromagnetic scattering by three classes of fractal aggregates. The results obtained from the TMatrix method show that the fractal scaling range is divided into two domains: (1) a genuine fractal regime, which is robust; (2) a possible anomalous scaling regime, S(q) ∝ 1 /qδ, with exponent δ independent of df, and related to the way the scattering mechanism uses the local morphology of the scatterer. The recognition, and an analysis, of the latter domain is of importance because it may result in significant reduction of the fractal regime, and brings into question the proper mechanism in the build-up of multiple-scattering.

  11. The fractal structure of glycogen: A clever solution to optimize cell metabolism.

    PubMed

    Meléndez, R; Meléndez-Hevia, E; Canela, E I

    1999-09-01

    Fractal objects are complex structures built with a simple procedure involving very little information. This has an obvious interest for living beings, because they are splendid examples of optimization to achieve the most efficient structure for a number of goals by means of the most economic way. The lung alveolar structure, the capillary network, and the structure of several parts of higher plant organization, such as ears, spikes, umbels, etc., are supposed to be fractals, and, in fact, mathematical functions based on fractal geometry algorithms can be developed to simulate them. However, the statement that a given biological structure is fractal should imply that the iterative process of its construction has a real biological meaning, i.e., that its construction in nature is achieved by means of a single genetic, enzymatic, or biophysical mechanism successively repeated; thus, such an iterative process should not be just an abstract mathematical tool to reproduce that object. This property has not been proven at present for any biological structure, because the mechanisms that build the objects mentioned above are unknown in detail. In this work, we present results that show that the glycogen molecule could be the first known real biological fractal structure. PMID:10465745

  12. Fabrication of 3D fractal structures using nanoscale anisotropic etching of single crystalline silicon

    NASA Astrophysics Data System (ADS)

    Berenschot, Erwin J. W.; Jansen, Henri V.; Tas, Niels R.

    2013-05-01

    When it comes to high-performance filtration, separation, sunlight collection, surface charge storage or catalysis, the effective surface area is what counts. Highly regular fractal structures seem to be the perfect candidates, but manufacturing can be quite cumbersome. Here it is shown--for the first time—that complex 3D fractals can be engineered using a recursive operation in conventional micromachining of single crystalline silicon. The procedure uses the built-in capability of the crystal lattice to form self-similar octahedral structures with minimal interference of the constructor. The silicon fractal can be used directly or as a mold to transfer the shape into another material. Moreover, they can be dense, porous, or like a wireframe. We demonstrate, after four levels of processing, that the initial number of octahedral structures is increased by a factor of 625. Meanwhile the size decreases 16 times down to 300 nm. At any level, pores of less than 100 nm can be fabricated at the octahedral vertices of the fractal. The presented technique supports the design of fractals with Hausdorff dimension D free of choice and up to D = 2.322.

  13. Filamentary structures in dense plasma focus: Current filaments or vortex filaments?

    SciTech Connect

    Soto, Leopoldo Pavez, Cristian; Moreno, José; Castillo, Fermin; Veloso, Felipe; Auluck, S. K. H.

    2014-07-15

    Recent observations of an azimuthally distributed array of sub-millimeter size sources of fusion protons and correlation between extreme ultraviolet (XUV) images of filaments with neutron yield in PF-1000 plasma focus have re-kindled interest in their significance. These filaments have been described variously in literature as current filaments and vortex filaments, with very little experimental evidence in support of either nomenclature. This paper provides, for the first time, experimental observations of filaments on a table-top plasma focus device using three techniques: framing photography of visible self-luminosity from the plasma, schlieren photography, and interferometry. Quantitative evaluation of density profile of filaments from interferometry reveals that their radius closely agrees with the collision-less ion skin depth. This is a signature of relaxed state of a Hall fluid, which has significant mass flow with equipartition between kinetic and magnetic energy, supporting the “vortex filament” description. This interpretation is consistent with empirical evidence of an efficient energy concentration mechanism inferred from nuclear reaction yields.

  14. Fractal flame structure due to the hydrodynamic Darrieus-Landau instability.

    PubMed

    Yu, Rixin; Bai, Xue-Song; Bychkov, Vitaly

    2015-12-01

    By using large scale numerical simulations, we obtain fractal structure, which develops at originally planar flame fronts due to the hydrodynamic Darrieus-Landau (DL) instability bending the fronts. We clarify some important issues regarding the DL fractal flames, which have been debated for a long time. We demonstrate an increase of the flame propagation speed with the hypothetic channel width, which controls the length scale of the instability development. We show that this increase may be fitted by a power law indicating the mean fractal properties of the flame front structure. The power exponent in this law is found to be not a universal constant, rather it depends on the flame properties-on the density drop at the front. Using box counting on the simulated flame front shapes we show the fractal flame dimension at the intermediate scale is smaller than the one given by the power law, but it has a similar dependency on the density drop. We also obtain a formation of pockets at the DL fractal flame fronts, which previously has been associated only with turbulent burning. PMID:26764824

  15. Fractal-based morphological image processing approach to analyzing complex structures characterized by closed domains

    NASA Astrophysics Data System (ADS)

    Bonifazi, Giuseppe

    2002-05-01

    Fractal geometry concerns the study of non-Euclidean geometrical figures generated by a recursive sequence of mathematical operations. These figures show self-similar features in the sense that their shape, at a certain scale, is equal to, or at least 'similar' to, the same shape of the figure at a different scale or resolution. This property of scale invariance often occurs also in some natural events. The basis of the method is the very comparison of the space covering of one of those geometrical constructions, the 'Sierpinski Carpet,' and the particles location and size distribution in the portion of surface acquired in the images. Fractal analysis method, consists in the study of the size distribution structure and disposition modalities. Such an approach was presented in this paper with reference to the characterization of airborne dust produced in working environment through the evaluation of particle size disposition and distribution over a surface. Such a behavior, in fact, was assumed to be strictly correlated with 1) material surface physical characteristics and 2) on the modalities by which the material is 'shot' on the dust sample holder (glass support). To get this goal, a 2D-Fractal extractor has been used, calibrated to different area thresholding values, as a result binary sample image changes, originating different fractal resolutions plotted for the residual background area (Richardson plot). Changing the lower size thresholding value of the 2D-Fractal extractor algorithm, means to change the starting point of fractal measurements; in such way, it has been looked for possible differences of powders in the lower dimensional classes. The rate by which the lowest part of the plot goes down to residual area equal to zero, together with fractal dimensions (low and high, depending on average material curve) and their precision (R2) of 'zero curve' (Richardson Plot with area thresholding value equal to zero, i.e. whole fractal distribution), can be used

  16. Structure and flow of dense suspensions of protein fractal aggregates in comparison with microgels.

    PubMed

    Inthavong, Walailuk; Kharlamova, Anna; Chassenieux, Christophe; Nicolai, Taco

    2016-03-14

    Solutions of the globular whey protein β-lactoglobulin (β-lg) were heated at different protein concentrations leading to the formation of polydisperse fractal aggregates with different average sizes. The structure of the solutions was analyzed with light scattering as a function of the protein concentration. The osmotic compressibility and the dynamic correlation length decreased with increasing concentration and became independent of the aggregate size in dense suspensions. The results obtained for different aggregate sizes could be superimposed after normalizing the concentration with the overlap concentration. Dense suspensions of fractal protein aggregates are strongly interpenetrated and can be visualized as an ensemble of fractal 'blobs'. The viscosity of the heated β-lg solutions increased extremely sharply above 80 g L(-1) and diverged at 98 g L(-1), mainly due to the sharply increasing aggregate size. At a fixed aggregate size, the viscosity increased initially exponentially with increasing concentration and then diverged. The increase was stronger when the aggregates were larger, but the dependence of the viscosity on the aggregate size was weaker than that of the osmotic compressibility and the dynamic correlation length. The concentration dependence of the viscosity of solutions of fractal β-lg aggregates is much stronger than that of homogeneous β-lg microgels. The behavior of fractal aggregates formed by whey protein isolates was similar. PMID:26864954

  17. Fractal structures for the Jacobi Hamiltonian of restricted three-body problem

    NASA Astrophysics Data System (ADS)

    Rollin, G.; Lages, J.; Shepelyansky, D. L.

    2016-08-01

    We study the dynamical chaos and integrable motion in the planar circular restricted three-body problem and determine the fractal dimension of the spiral strange repeller set of non-escaping orbits at different values of mass ratio of binary bodies and of Jacobi integral of motion. We find that the spiral fractal structure of the Poincaré section leads to a spiral density distribution of particles remaining in the system. We also show that the initial exponential drop of survival probability with time is followed by the algebraic decay related to the universal algebraic statistics of Poincaré recurrences in generic symplectic maps.

  18. Investigation of changes in fractal dimension from layered retinal structures of healthy and diabetic eyes with optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Gao, Wei; Zakharov, Valery P.; Myakinin, Oleg O.; Bratchenko, Ivan A.; Artemyev, Dmitry N.; Kornilin, Dmitry V.

    2015-07-01

    Optical coherence tomography (OCT) is usually employed for the measurement of retinal thickness characterizing the structural changes of tissue. However, fractal dimension (FD) could also character the structural changes of tissue. Therefore, fractal dimension changes may provide further information regarding cellular layers and early damage in ocular diseases. We investigated the possibility of OCT in detecting changes in fractal dimension from layered retinal structures. OCT images were obtained from diabetic patients without retinopathy (DM, n = 38 eyes) or mild diabetic retinopathy (MDR, n = 43 eyes) and normal healthy subjects (Controls, n = 74 eyes). Fractal dimension was calculated using the differentiate box counting methodology. We evaluated the usefulness of quantifying fractal dimension of layered structures in the detection of retinal damage. Generalized estimating equations considering within-subject intereye relations were used to test for differences between the groups. A modified p value of <0.001 was considered statistically significant. Receiver operating characteristic (ROC) curves were constructed to describe the ability of fractal dimension to discriminate between the eyes of DM, MDR and healthy eyes. Significant decreases of fractal dimension were observed in all layers in the MDR eyes compared with controls except in the inner nuclear layer (INL). Significant decreases of fractal dimension were also observed in all layers in the MDR eyes compared with DM eyes. The highest area under receiver operating characteristic curve (AUROC) values estimated for fractal dimension were observed for the outer plexiform layer (OPL) and outer segment photoreceptors (OS) when comparing MDR eyes with controls. The highest AUROC value estimated for fractal dimension were also observed for the retinal nerve fiber layer (RNFL) and OS when comparing MDR eyes with DM eyes. Our results suggest that fractal dimension of the intraretinal layers may provide useful

  19. Structure of the ParM filament at 8.5 Å resolution

    PubMed Central

    Gayathri, Pananghat; Fujii, Takashi; Namba, Keiichi; Löwe, Jan

    2013-01-01

    The actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5 Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric crystal structures of ParM provides insights into dynamic instability of ParM filaments. The structural analysis suggests that a ParM conformation, corresponding to a metastable state, is held within the filament by intrafilament contacts. This filament conformation of ParM can be attained only from the ATP-bound state, and induces a change in conformation of the bound nucleotide. The structural analysis also provides a rationale for the observed stimulation of hydrolysis upon polymerisation into the filament. PMID:23462100

  20. Structural and Fractal Dimensions are Reliable Determinants of Grain Yield in Soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reliable models are needed to describe plants with complex geometric structures, quantify the impact of management strategies on the plant’s geometric distribution in space and time, and predict yield as a function of fractal dimension. We measured growth and development variables on single soybean ...

  1. Cytokeratin intermediate filaments of rat hepatocytes: different cytoskeletal domains and their three-dimensional structure.

    PubMed

    Katsuma, Y; Marceau, N; Ohta, M; French, S W

    1988-01-01

    A new method of visualizing the three-dimensional architecture of the cytokeratin filaments of the intact rat hepatocyte in situ has been achieved. Frozen sections of liver cut 10 micron thick were serially extracted to remove all elements of the cells except the intermediate filaments. Parallel sections were stained with monoclonal antibodies to the two main cytokeratins found in bile duct and liver cells. Immunofluorescent antibody and immunogold electron microscopy techniques were used to identify the proteins morphologically. Several new observations resulted from these studies. The pericanalicular sheath of intermediate filaments was visualized using steropairs as an uninterrupted branching tubular structure composed of cytokeratins located in the cell cortex of adjacent hepatocytes. Intermediate filaments in the cell cortex formed a distinct sheet of matted filaments which enveloped the entire hepatocyte. The cortical intermediate filaments were in continuity with the pericanalicular sheath and the filaments located within the cytoplasm. The intermediate filaments are attached to the centrioles and appeared to tent the nuclear lamina-pore complex at points of contact. Monoclonal antibodies to rat liver intermediate filament cytokeratins (CK49 and CK55) each stained intermediate filaments located in the cell cortex, within the cytoplasm and at the nucleus. By immunogold staining, some of the intermediate filament filaments were shown to contain both cytokeratins. Filaments which did not stain were thought to be either actin at the cell periphery or nuclear lamins around the nucleus. It is concluded that the cytokeratins form a specialized framework for the cell cortex, canaliculus, centrioles and the nucleus of hepatocytes. The filaments run continuously throughout the cytoplasm without terminating. PMID:2453432

  2. Flow around new wind fence with multi-scale fractal structure in an atmospheric boundary layer

    NASA Astrophysics Data System (ADS)

    McClure, Sarah; Lee, Sang-Joon; Zhang, Wei

    2015-11-01

    Understanding and controlling atmospheric boundary-layer flows with engineered structures, such as porous wind fences or windbreaks, has been of great interest to the fluid mechanics and wind engineering community. Previous studies found that the regular mono-scale grid fence of 50% porosity and a bottom gap of 10% of the fence height are considered to be optimal over a flat surface. Significant differences in turbulent flow structure have recently been noted behind multi-scale fractal wind fences, even with the same porosity. In this study, wind-tunnel tests on the turbulent flow and the turbulence kinetic energy transport of 1D and 2D multi-scale fractal fences under atmospheric boundary-layer were conducted. Velocity fields around the fractal fences were systematically measured using Particle Image Velocimetry to uncover effects of key parameters on turbulent flows around the fences at a Reynolds number of approximately 3.6x104 based on the free-stream speed and fence height. The turbulent flow structures induced by specific 1D/2D multi-scale fractal wind fences were compared to those of a conventional grid fence. The present results would contribute to the design of new-generation wind fences to reduce snow/sand deposition on critical infrastructure such as roads and bridges.

  3. Structure of the Intermediate Filament-Binding Region of Desmoplakin

    PubMed Central

    Kang, Hyunook; Weiss, Thomas M.; Bang, Injin; Weis, William I.; Choi, Hee-Jung

    2016-01-01

    Desmoplakin (DP) is a cytoskeletal linker protein that connects the desmosomal cadherin/plakoglobin/plakophilin complex to intermediate filaments (IFs). The C-terminal region of DP (DPCT) mediates IF binding, and contains three plakin repeat domains (PRDs), termed PRD-A, PRD-B and PRD-C. Previous crystal structures of PRDs B and C revealed that each is formed by 4.5 copies of a plakin repeat (PR) and has a conserved positively charged groove on its surface. Although PRDs A and B are linked by just four amino acids, B and C are separated by a 154 residue flexible linker, which has hindered crystallographic analysis of the full DPCT. Here we present the crystal structure of a DPCT fragment spanning PRDs A and B, and elucidate the overall architecture of DPCT by small angle X-ray scattering (SAXS) analysis. The structure of PRD-A is similar to that of PRD-B, and the two domains are arranged in a quasi-linear arrangement, and separated by a 4 amino acid linker. Analysis of the B-C linker region using secondary structure prediction and the crystal structure of a homologous linker from the cytolinker periplakin suggests that the N-terminal ~100 amino acids of the linker form two PR-like motifs. SAXS analysis of DPCT indicates an elongated but non-linear shape with Rg = 51.5 Å and Dmax = 178 Å. These data provide the first structural insights into an IF binding protein containing multiple PRDs and provide a foundation for studying the molecular basis of DP-IF interactions. PMID:26808545

  4. Exhaled Aerosol Pattern Discloses Lung Structural Abnormality: A Sensitivity Study Using Computational Modeling and Fractal Analysis

    PubMed Central

    Xi, Jinxiang; Si, Xiuhua A.; Kim, JongWon; Mckee, Edward; Lin, En-Bing

    2014-01-01

    Background Exhaled aerosol patterns, also called aerosol fingerprints, provide clues to the health of the lung and can be used to detect disease-modified airway structures. The key is how to decode the exhaled aerosol fingerprints and retrieve the lung structural information for a non-invasive identification of respiratory diseases. Objective and Methods In this study, a CFD-fractal analysis method was developed to quantify exhaled aerosol fingerprints and applied it to one benign and three malign conditions: a tracheal carina tumor, a bronchial tumor, and asthma. Respirations of tracer aerosols of 1 µm at a flow rate of 30 L/min were simulated, with exhaled distributions recorded at the mouth. Large eddy simulations and a Lagrangian tracking approach were used to simulate respiratory airflows and aerosol dynamics. Aerosol morphometric measures such as concentration disparity, spatial distributions, and fractal analysis were applied to distinguish various exhaled aerosol patterns. Findings Utilizing physiology-based modeling, we demonstrated substantial differences in exhaled aerosol distributions among normal and pathological airways, which were suggestive of the disease location and extent. With fractal analysis, we also demonstrated that exhaled aerosol patterns exhibited fractal behavior in both the entire image and selected regions of interest. Each exhaled aerosol fingerprint exhibited distinct pattern parameters such as spatial probability, fractal dimension, lacunarity, and multifractal spectrum. Furthermore, a correlation of the diseased location and exhaled aerosol spatial distribution was established for asthma. Conclusion Aerosol-fingerprint-based breath tests disclose clues about the site and severity of lung diseases and appear to be sensitive enough to be a practical tool for diagnosis and prognosis of respiratory diseases with structural abnormalities. PMID:25105680

  5. Efficient RF energy harvesting by using a fractal structured rectenna system

    NASA Astrophysics Data System (ADS)

    Oh, Sechang; Ramasamy, Mouli; Varadan, Vijay K.

    2014-04-01

    A rectenna system delivers, collects, and converts RF energy into direct current to power the electronic devices or recharge batteries. It consists of an antenna for receiving RF power, an input filter for processing energy and impedance matching, a rectifier, an output filter, and a load resistor. However, the conventional rectenna systems have drawback in terms of power generation, as the single resonant frequency of an antenna can generate only low power compared to multiple resonant frequencies. A multi band rectenna system is an optimal solution to generate more power. This paper proposes the design of a novel rectenna system, which involves developing a multi band rectenna with a fractal structured antenna to facilitate an increase in energy harvesting from various sources like Wi-Fi, TV signals, mobile networks and other ambient sources, eliminating the limitation of a single band technique. The usage of fractal antennas effects certain prominent advantages in terms of size and multiple resonances. Even though, a fractal antenna incorporates multiple resonances, controlling the resonant frequencies is an important aspect to generate power from the various desired RF sources. Hence, this paper also describes the design parameters of the fractal antenna and the methods to control the multi band frequency.

  6. Nonlinear enhancement of the fractal structure in the escape dynamics of Bose-Einstein condensates

    SciTech Connect

    Mitchell, Kevin A.; Ilan, Boaz

    2009-10-15

    We consider the escape dynamics of an ensemble of Bose-Einstein-condensed atoms from an optical-dipole trap consisting of two overlapping Gaussian wells. Earlier theoretical studies (based on a model of quantum evolution using ensembles of classical trajectories) predicted that self-similar fractal features could be visible in this system by measuring the escaping flux as a function of time for varying initial conditions. Here, direct numerical quantum simulations show the clear influence of quantum interference on the escape data. Fractal features are still evident in the data, albeit with interference fringes superposed. Furthermore, the nonlinear influence of atom-atom interactions is also considered, in the context of the (2+1)-dimensional Gross-Pitaevskii equation. Of particular note is that an attractive nonlinear interaction enhances the resolution of fractal structures in the escape data. Thus, the interplay between nonlinear focusing and dispersion results in dynamics that resolve the underlying classical fractal more faithfully than the noninteracting quantum (or classical) dynamics.

  7. Fractal structure of the distributions of air dose rates in Koriyama city in Fukushima.

    PubMed

    Ishihara, Masamichi

    2014-10-01

    The authors investigated the fractal structure of the distributions of air dose rates in Koriyama city in Fukushima using data published by the Fukushima Prefectural and Koriyama City governments. Relative frequency data of air dose rates (strength distribution) could be well fitted with a q-distribution. In the present analysis, the relative frequency decreases approximately as s for high air dose rate values, where the quantity s represents air dose rate. The fractal dimension is a function of the threshold sth of air dose rate. The fractal dimension is approximately 1.59 when sth is the average of the air dose rates in Koriyama (0.9 μSv h) and decreases with increasing the threshold: it is approximately 1.97 for sth = 0.6 μSv h and 1.40 for sth = 1.2 μSv h. These results confirm that the strength distribution behaves like a power function for high air dose rate values and that the fallout pattern can be described as a fractal. PMID:25162424

  8. Ultrasonic analysis of Kevlar-epoxy filament wound structures

    NASA Astrophysics Data System (ADS)

    Brosey, W. D.

    1985-07-01

    Composite structures are often desirable for their strength and weight characteristics. Since composites are not as well characterized mechanically as metallic or ceramic structures, much work has been performed at the Oak Ridge Y-12 Plant to obtain that characterization and to develop methods of determining the mechanical properties of a composite nondestructively. Most of the work to date has been performed on nonenclosed structures. One notable exception has been the holographic evaluation of spherical Kevlar-epoxy composite pressure vessels. Several promising nondestructive evaluation techniques have been used to locate flaws and predict the integrity of the composite. Several of these include thermography, Moire interferometry, ultrasonic stress wave factor, ultrasonic C-scan image enhancement, radiography, and nuclear magnetic resonance. As a first step in this transfer and development of NDE techniques, known defects were placed within spherical Kevlar-epoxy, filament-wound test specimens to determine the extent to which they could be detected. These defects included Teflon shim-simulated delaminations, macrosphere-simulated voids, dry-band sets, variable tension, Kevlar 29 fiber instead of the higher strength Kevlar 40 fiber, and an alternate high-void-content winding pattern. Ultrasonic waveform analysis was performed in both the time and frequency domains to determine the detectability and locatability of structural flaws within the composite. Preparation has been made at Virginia Polytechnic Institute and State University and at the University of Delaware, to examine the specimens using various NDE techniques. This work is a compilation of interim project reports in partial fulfillment of the contracts between Virginia Polytechnic Institute and State University, the University of Delaware, and Y-12 Plant.

  9. Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography

    SciTech Connect

    Norlen, Lars . E-mail: lars.norlen@ki.se; Masich, Sergej; Goldie, Kenneth N.; Hoenger, Andreas

    2007-06-10

    Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly {alpha}-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

  10. Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure

    PubMed Central

    González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.

    2014-01-01

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166

  11. Fractal images induce fractal pupil dilations and constrictions.

    PubMed

    Moon, P; Muday, J; Raynor, S; Schirillo, J; Boydston, C; Fairbanks, M S; Taylor, R P

    2014-09-01

    Fractals are self-similar structures or patterns that repeat at increasingly fine magnifications. Research has revealed fractal patterns in many natural and physiological processes. This article investigates pupillary size over time to determine if their oscillations demonstrate a fractal pattern. We predict that pupil size over time will fluctuate in a fractal manner and this may be due to either the fractal neuronal structure or fractal properties of the image viewed. We present evidence that low complexity fractal patterns underlie pupillary oscillations as subjects view spatial fractal patterns. We also present evidence implicating the autonomic nervous system's importance in these patterns. Using the variational method of the box-counting procedure we demonstrate that low complexity fractal patterns are found in changes within pupil size over time in millimeters (mm) and our data suggest that these pupillary oscillation patterns do not depend on the fractal properties of the image viewed. PMID:24978815

  12. Fractal structures of dendrites in GaSe crystals

    NASA Astrophysics Data System (ADS)

    Kolesnikov, N. N.; Borisenko, E. B.; Borisenko, D. N.; Bozhko, S. I.

    2008-07-01

    Solidification of melts at substantial supercooling is associated with instability on the growth front. This causes growth of dendrites, which form as a branched tree in a crystal. In the layered melt-grown GaSe crystals dendrites are observed, if growth rates are rather high [N.N. Kolesnikov, E.B. Borisenko, D.N. Borisenko, V.K. Gartman, Influence of growth conditions on microstructure and properties of GaSe crystals, J. Crystal Growth 300 (2) (2007) 294-298]. Models based on solution of the thermal diffusion problem are traditionally used to describe dendrite growth. Solution of this problem requires information about several physical parameters, such as diffusion coefficient, heat conductivity coefficient and supercooling at the solid/liquid interface. The study of scale invariance of dendrites formed in a crystal provides a new approach to solution of the dynamic growth problem. The calculated fractal dimensionality of the experimentally observed dendrites in GaSe crystals is D=1.7. It coincides with dimensionality of the clusters obtained through computer simulation in terms of the model of diffusion-limited aggregation (DLA). This result provides a new approach to description of the dynamics of dendrite growth. We have shown that the dendrite growth mechanism in the layered semiconductor crystals can be described by a two-dimensional DLA model. It is shown that probabilistic simulation can be used to show the development of a dendrite in any material. In contrast to the classical theories of dendrite growth, this approach does not require information on physical parameters.

  13. Frealix: model-based refinement of helical filament structures from electron micrographs.

    PubMed

    Rohou, Alexis; Grigorieff, Nikolaus

    2014-05-01

    The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1-40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1-40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ∼8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments. PMID:24657230

  14. Frealix: Model-based refinement of helical filament structures from electron micrographs

    PubMed Central

    Rohou, Alexis; Grigorieff, Nikolaus

    2014-01-01

    The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent “single particles”, yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1–40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1–40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ~8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments. PMID:24657230

  15. Characterization and structural investigation of fractal porous-silica over an extremely wide scale range of pore size.

    PubMed

    Ono, Yusuke; Mayama, Hiroyuki; Furó, István; Sagidullin, Alexander I; Matsushima, Keiichiro; Ura, Haruo; Uchiyama, Tomoyuki; Tsujii, Kaoru

    2009-08-01

    We have succeeded in creating Menger sponge-like fractal body, i.e., porous-silica samples with Menger sponge-like fractal geometries, by a novel template method utilizing template particles of alkylketene dimer (AKD) and a sol-gel synthesis of tetramethyl orthosilicate (TMOS). We report here the first experimental results on characterization and structural investigations of the fractal porous-silica samples prepared with various conditions such as calcination temperature and packing condition of the template particles. In order to characterize the fractal porous-silica samples, pore volume distribution, porosity and specific surface area were measured over an extremely wide scale from 1 nm to 100 microm by means of mercury porosimetry, (1)H NMR cryoporometry, nitrogen gas adsorption experiments together with direct evaluations of cross-sectional fractal dimension D(cs), and size limits of D(cs). We have found that the pore volume distribution and specific surface area of the fractal porous-silica samples can be discussed in terms of different fractal porous structures at different scale regions. PMID:19406424

  16. Estimation of the adequacy of the fractal model of the atomic structure of amorphous silicon

    SciTech Connect

    Golodenko, A. B.

    2010-01-15

    A method of constructing a fractal model of noncrystalline solid substance is considered using the example of amorphous silicon. In systems of iteration functions, the physical meaning of dihedral and valence angles of the elementary crystallographic cell is assigned to arguments. The model adequacy is estimated by the radial distribution function, the atomic structure density, the distribution of valence and dihedral angles, and the density of dangling interatomic bonds.

  17. Fractal analysis of the structural complexity of the connective tissue in human carotid bodies

    PubMed Central

    Guidolin, Diego; Porzionato, Andrea; Tortorella, Cinzia; Macchi, Veronica; De Caro, Raffaele

    2014-01-01

    The carotid body (CB) may undergo different structural changes during perinatal development, aging, or in response to environmental stimuli. In the previous literature, morphometric approaches to evaluate these changes have considered quantitative first order parameters, such as volumes or densities, while changes in spatial disposition and/or complexity of structural components have not yet been considered. In the present study, different strategies for addressing morphological complexity of CB, apart from the overall amount of each tissue component, were evaluated and compared. In particular, we considered the spatial distribution of connective tissue in the carotid bodies of young control subjects, young opiate-related deaths and aged subjects, through analysis of dispersion (Morisita's index), gray level co-occurrence matrix (entropy, angular second moment, variance, correlation), and fractal analysis (fractal dimension, lacunarity). Opiate-related deaths and aged subjects showed a comparable increase in connective tissue with respect to young controls. However, the Morisita's index (p < 0.05), angular second moment (p < 0.05), fractal dimension (p < 0.01), and lacunarity (p < 0.01) permitted to identify significant differences in the disposition of the connective tissue between these two series. A receiver operating characteristic (ROC) curve was also calculated to evaluate the efficiency of each parameter. The fractal dimension and lacunarity, with areas under the ROC curve of 0.9651 (excellent accuracy) and 0.8835 (good accuracy), respectively, showed the highest discriminatory power. They evidenced higher level of structural complexity in the carotid bodies of opiate-related deaths than old controls, due to more complex branching of intralobular connective tissue. Further analyses will have to consider the suitability of these approaches to address other morphological features of the CB, such as different cell populations, vascularization, and innervation

  18. [Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography].

    PubMed

    Lu, Xiao-long; Zheng, Qin; Yin, Xian-zhen; Xiao, Guang-qing; Liao, Zu-hua; Yang, Ming; Zhang, Ji-wen

    2015-06-01

    The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new

  19. Characterization of microgravity effects on bone structure and strength using fractal analysis

    NASA Technical Reports Server (NTRS)

    Acharya, Raj S.; Shackelford, Linda

    1995-01-01

    The effect of micro-gravity on the musculoskeletal system has been well studied. Significant changes in bone and muscle have been shown after long term space flight. Similar changes have been demonstrated due to bed rest. Bone demineralization is particularly profound in weight bearing bones. Much of the current techniques to monitor bone condition use bone mass measurements. However, bone mass measurements are not reliable to distinguish Osteoporotic and Normal subjects. It has been shown that the overlap between normals and osteoporosis is found for all of the bone mass measurement technologies: single and dual photon absorptiometry, quantitative computed tomography and direct measurement of bone area/volume on biopsy as well as radiogrammetry. A similar discordance is noted in the fact that it has not been regularly possible to find the expected correlation between severity of osteoporosis and degree of bone loss. Structural parameters such as trabecular connectivity have been proposed as features for assessing bone conditions. In this report, we use fractal analysis to characterize bone structure. We show that the fractal dimension computed with MRI images and X-Ray images of the patella are the same. Preliminary experimental results show that the fractal dimension computed from MRI images of vertebrae of human subjects before bedrest is higher than during bedrest.

  20. Fractal Structures on Fe3O4 Ferrofluid: A Small-Angle Neutron Scattering Study

    NASA Astrophysics Data System (ADS)

    Giri Rachman Putra, Edy; Seong, Baek Seok; Shin, Eunjoo; Ikram, Abarrul; Ani, Sistin Ari; Darminto

    2010-10-01

    A small-angle neutron scattering (SANS) which is a powerful technique to reveal the large scale structures was applied to investigate the fractal structures of water-based Fe3O4ferrofluid, magnetic fluid. The natural magnetite Fe3O4 from iron sand of several rivers in East Java Province of Indonesia was extracted and purified using magnetic separator. Four different ferrofluid concentrations, i.e. 0.5, 1.0, 2.0 and 3.0 Molar (M) were synthesized through a co-precipitation method and then dispersed in tetramethyl ammonium hydroxide (TMAH) as surfactant. The fractal aggregates in ferrofluid samples were observed from their SANS scattering distributions confirming the correlations to their concentrations. The mass fractal dimension changed from about 3 to 2 as ferrofluid concentration increased showing a deviation slope at intermediate scattering vector q range. The size of primary magnetic particle as a building block was determined by fitting the scattering profiles with a log-normal sphere model calculation. The mean average size of those magnetic particles is about 60 - 100 Å in diameter with a particle size distribution σ = 0.5.

  1. Structure determination of helical filaments by solid-state NMR spectroscopy

    PubMed Central

    Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

    2016-01-01

    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

  2. Correlated Percolation, Fractal Structures, and Scale-Invariant Distribution of Clusters in Natural Images

    PubMed Central

    Saremi, Saeed; Sejnowski, Terrence J.

    2016-01-01

    Natural images are scale invariant with structures at all length scales. We formulated a geometric view of scale invariance in natural images using percolation theory, which describes the behavior of connected clusters on graphs. We map images to the percolation model by defining clusters on a binary representation for images. We show that critical percolating structures emerge in natural images and study their scaling properties by identifying fractal dimensions and exponents for the scale-invariant distributions of clusters. This formulation leads to a method for identifying clusters in images from underlying structures as a starting point for image segmentation. PMID:26415153

  3. Correlated Percolation, Fractal Structures, and Scale-Invariant Distribution of Clusters in Natural Images.

    PubMed

    Saremi, Saeed; Sejnowski, Terrence J

    2016-05-01

    Natural images are scale invariant with structures at all length scales.We formulated a geometric view of scale invariance in natural images using percolation theory, which describes the behavior of connected clusters on graphs.We map images to the percolation model by defining clusters on a binary representation for images. We show that critical percolating structures emerge in natural images and study their scaling properties by identifying fractal dimensions and exponents for the scale-invariant distributions of clusters. This formulation leads to a method for identifying clusters in images from underlying structures as a starting point for image segmentation. PMID:26415153

  4. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits.

    PubMed

    Hocky, Glen M; Baker, Joseph L; Bradley, Michael J; Sinitskiy, Anton V; De La Cruz, Enrique M; Voth, Gregory A

    2016-05-26

    Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the "stiffness site" affects filament mechanical properties. Incorporating a magnesium ion in the "polymerization site" does not seem to require any large-scale change to an actin subunit's conformation. Binding of a magnesium ion in the "stiffness site" adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids. PMID:27146246

  5. Bridging Three Orders of Magnitude: Multiple Scattered Waves Sense Fractal Microscopic Structures via Dispersion

    NASA Astrophysics Data System (ADS)

    Lambert, Simon A.; Näsholm, Sven Peter; Nordsletten, David; Michler, Christian; Juge, Lauriane; Serfaty, Jean-Michel; Bilston, Lynne; Guzina, Bojan; Holm, Sverre; Sinkus, Ralph

    2015-08-01

    Wave scattering provides profound insight into the structure of matter. Typically, the ability to sense microstructure is determined by the ratio of scatterer size to probing wavelength. Here, we address the question of whether macroscopic waves can report back the presence and distribution of microscopic scatterers despite several orders of magnitude difference in scale between wavelength and scatterer size. In our analysis, monosized hard scatterers 5 μ m in radius are immersed in lossless gelatin phantoms to investigate the effect of multiple reflections on the propagation of shear waves with millimeter wavelength. Steady-state monochromatic waves are imaged in situ via magnetic resonance imaging, enabling quantification of the phase velocity at a voxel size big enough to contain thousands of individual scatterers, but small enough to resolve the wavelength. We show in theory, experiments, and simulations that the resulting coherent superposition of multiple reflections gives rise to power-law dispersion at the macroscopic scale if the scatterer distribution exhibits apparent fractality over an effective length scale that is comparable to the probing wavelength. Since apparent fractality is naturally present in any random medium, microstructure can thereby leave its fingerprint on the macroscopically quantifiable power-law exponent. Our results are generic to wave phenomena and carry great potential for sensing microstructure that exhibits intrinsic fractality, such as, for instance, vasculature.

  6. Bridging Three Orders of Magnitude: Multiple Scattered Waves Sense Fractal Microscopic Structures via Dispersion.

    PubMed

    Lambert, Simon A; Näsholm, Sven Peter; Nordsletten, David; Michler, Christian; Juge, Lauriane; Serfaty, Jean-Michel; Bilston, Lynne; Guzina, Bojan; Holm, Sverre; Sinkus, Ralph

    2015-08-28

    Wave scattering provides profound insight into the structure of matter. Typically, the ability to sense microstructure is determined by the ratio of scatterer size to probing wavelength. Here, we address the question of whether macroscopic waves can report back the presence and distribution of microscopic scatterers despite several orders of magnitude difference in scale between wavelength and scatterer size. In our analysis, monosized hard scatterers 5  μm in radius are immersed in lossless gelatin phantoms to investigate the effect of multiple reflections on the propagation of shear waves with millimeter wavelength. Steady-state monochromatic waves are imaged in situ via magnetic resonance imaging, enabling quantification of the phase velocity at a voxel size big enough to contain thousands of individual scatterers, but small enough to resolve the wavelength. We show in theory, experiments, and simulations that the resulting coherent superposition of multiple reflections gives rise to power-law dispersion at the macroscopic scale if the scatterer distribution exhibits apparent fractality over an effective length scale that is comparable to the probing wavelength. Since apparent fractality is naturally present in any random medium, microstructure can thereby leave its fingerprint on the macroscopically quantifiable power-law exponent. Our results are generic to wave phenomena and carry great potential for sensing microstructure that exhibits intrinsic fractality, such as, for instance, vasculature. PMID:26371655

  7. Fractal structures in two-metal electrodeposition systems I: Pb and Zn

    SciTech Connect

    Nakouzi, Elias; Sultan, Rabih

    2011-12-15

    Pattern formation in two-metal electrochemical deposition has been scarcely explored in the chemical literature. In this paper, we report new experiments on zinc-lead fractal co-deposition. Electrodeposits are grown in special cells at a fixed large value of the zinc ion concentration, while that of the lead ion is increased gradually. A very wide diversity of morphologies are obtained and classified. Most of the deposited domains are almost exclusively Pb or Zn. But certain regions originating at the base cathode, ranging from a short grass alley to dense, grown-up bushes or shrubs, manifest a combined Pb-Zn composition. Composition is determined using scanning electron microscopy/energy dispersive x ray measurements as well atomic absorption spectroscopy. Pb domains are characterized by shiny leaf-like and dense deposits as well as flowers with round, balloon-like corollas. The Zn zones display a greater variety of morphologies such as thick trunks and thin and fine branching, in addition to minute ''cigar flower'' structures. The various morphologies are analyzed and classified from the viewpoint of fractal nature, characterized by the box-count fractal dimension. Finally, macroscopic spatial alternation between two different characteristic morphologies is observed under certain conditions.

  8. Long-Range Order and Fractality in the Structure and Organization of Eukaryotic Genomes

    NASA Astrophysics Data System (ADS)

    Polychronopoulos, Dimitris; Tsiagkas, Giannis; Athanasopoulou, Labrini; Sellis, Diamantis; Almirantis, Yannis

    2014-12-01

    The late Professor J.S. Nicolis always emphasized, both in his writings and in presentations and discussions with students and friends, the relevance of a dynamical systems approach to biology. In particular, viewing the genome as a "biological text" captures the dynamical character of both the evolution and function of the organisms in the form of correlations indicating the presence of a long-range order. This genomic structure can be expressed in forms reminiscent of natural languages and several temporal and spatial traces l by the functioning of dynamical systems: Zipf laws, self-similarity and fractality. Here we review several works of our group and recent unpublished results, focusing on the chromosomal distribution of biologically active genomic components: Genes and protein-coding segments, CpG islands, transposable elements belonging to all major classes and several types of conserved non-coding genomic elements. We report the systematic appearance of power-laws in the size distribution of the distances between elements belonging to each of these types of functional genomic elements. Moreover, fractality is also found in several cases, using box-counting and entropic scaling.We present here, for the first time in a unified way, an aggregative model of the genomic dynamics which can explain the observed patterns on the grounds of known phenomena accompanying genome evolution. Our results comply with recent findings about a "fractal globule" geometry of chromatin in the eukaryotic nucleus.

  9. Slender Vortex Filament with Slowly Varying Core Structure

    NASA Technical Reports Server (NTRS)

    Ting, Lu; Tung, Chee

    2000-01-01

    We give a brief review of the asymptotic theory of slender vortex filaments with emphases on the choices of scalings characterizing the physical problems and the corresponding assumptions and/or restrictions introduced in the formation of the asymptotic theory of Callegari and Ting (1978) and its extension by Klein and Ting (1992). In particular, the slender filaments considered are assumed to be forming loops or tori. Because of this restriction, the theory is not applicable to the trailing vortex system of a rotorcraft. We describe the multiple length scales characterizing the vortex system, formulate the expansion scheme, derive the governing equations and then identify the assumptions or restrictions inherent in the multi-scale analysis and needed for the validity of the asymptotic theory of the trailing vortex system.

  10. Thin Filament Structure and the Steric Blocking Model.

    PubMed

    Lehman, William

    2016-04-01

    By interacting with the troponin-tropomyosin complex on myofibrillar thin filaments, Ca2+ and myosin govern the regulatory switching processes influencing contractile activity of mammalian cardiac and skeletal muscles. A possible explanation of the roles played by Ca2+ and myosin emerged in the early 1970s when a compelling "steric model" began to gain traction as a likely mechanism accounting for muscle regulation. In its most simple form, the model holds that, under the control of Ca2+ binding to troponin and myosin binding to actin, tropomyosin strands running along thin filaments either block myosin-binding sites on actin when muscles are relaxed or move away from them when muscles are activated. Evidence for the steric model was initially based on interpretation of subtle changes observed in X-ray fiber diffraction patterns of intact skeletal muscle preparations. Over the past 25 years, electron microscopy coupled with three-dimensional reconstruction directly resolved thin filament organization under many experimental conditions and at increasingly higher resolution. At low-Ca2+, tropomyosin was shown to occupy a "blocked-state" position on the filament, and switched-on in a two-step process, involving first a movement of tropomyosin away from the majority of the myosin-binding site as Ca2+ binds to troponin and then a further movement to fully expose the site when small numbers of myosin heads bind to actin. In this contribution, basic information on Ca2+-regulation of muscle contraction is provided. A description is then given relating the voyage of discovery taken to arrive at the present understanding of the steric regulatory model. PMID:27065174

  11. Electron Microscopic Observations on the Structure of Treponema zuelzerae and Its Axial Filaments

    PubMed Central

    Bharier, M. A.; Eiserling, F. A.; Rittenberg, S. C.

    1971-01-01

    The fine structure of the spirochete Treponema zuelzerae, and particularly of its axial filaments, was investigated by using the electron microscope. The cell consists of a protoplasmic core surrounded by two concentric envelopes, each approximately 12 nm in width. Between these envelopes are two axial filaments, one originating at each pole of the cell, which overlap and lie side by side in the central region of the cell. The diameter of the axial filaments is 18.0 to 18.5 nm. The terminal region of each filament at its proximal end consists of a hook-like structure, very similar in appearance to the proximal end of a bacterial flagellum. The outer envelope of the cell is readily disrupted with distilled water, and this treatment often results in the release of the filaments from their axial position. A sheath is seen surrounding the filaments when cells are treated with distilled water for no more than 1 min and fixed immediately with osmium tetroxide or glutaraldehyde. This sheath has a striated fine structure and a diameter of 46 nm. Images PMID:5541022

  12. Structural Architecture of the CARMA1/Bcl10/MALT1 Signalosome: Nucleation-Induced Filamentous Assembly

    PubMed Central

    Qiao, Qi; Yang, Chenghua; Zheng, Chao; Fontán, Lorena; David, Liron; Yu, Xiong; Bracken, Clay; Rosen, Monica; Melnick, Ari; Egelman, Edward H.; Wu, Hao

    2014-01-01

    SUMMARY The CARMA1/Bcl10/MALT1 (CBM) signalosome mediates antigen receptor-induced NF-κB signaling to regulate multiple lymphocyte functions. While CARMA1 and Bcl10 contain caspase recruitment domains (CARDs), MALT1 is a paracaspase with structural similarity to caspases. Here we show that the reconstituted CBM signalosome is a helical filamentous assembly in which substoichiometric CARMA1 nucleates Bcl10 filaments. Bcl10 filament formation is a highly cooperative process whose threshold is sensitized by oligomerized CARMA1 upon receptor activation. In cells, both cotransfected CARMA1/Bcl10 complex and the endogenous CBM signalosome are filamentous morphologically. Combining crystallography, nuclear magnetic resonance, and electron microscopy, we reveal the structure of the Bcl10 CARD filament and the mode of interaction between CARMA1 and Bcl10. Structure-guided mutagenesis confirmed the observed interfaces in Bcl10 filament assembly and MALT1 activation in vitro and NF-κB activation in cells. These data support a paradigm of nucleation-induced signal transduction with threshold response due to cooperativity and signal amplification by polymerization. PMID:24074955

  13. Turbulence structure and turbulence kinetic energy transport in multiscale/fractal-generated turbulence

    NASA Astrophysics Data System (ADS)

    Nagata, Kouji; Sakai, Yasuhiko; Inaba, Takuto; Suzuki, Hiroki; Terashima, Osamu; Suzuki, Hiroyuki

    2013-06-01

    The turbulence structure and turbulence kinetic energy transport in multiscale/fractal-generated turbulence in a wind tunnel are investigated. A low-blockage, space-filling square-type (i.e., fractal elements with square shapes) fractal grid is placed at the inlet of the test section. On the basis of the thickness of the biggest grid bar, t0, and the inflow velocity U∞, the Reynolds numbers (Re0) are set to 5900 and 11 400; these values are the same as those considered in previous experiments [D. Hurst and J. C. Vassilicos, "Scalings and decay of fractal-generated turbulence," Phys. Fluids 19, 035103 (2007), 10.1063/1.2676448; N. Mazellier and J. C. Vassilicos, "Turbulence without Richardson-Kolmogorov cascade," Phys. Fluids 22, 075101 (2010), 10.1063/1.3453708]. The turbulence characteristics are measured using hot-wire anemometry with I- and X-type probes. Generally, good agreements are observed despite the difference in the size of the test sections used: The longitudinal integral length-scale Lu and the Taylor microscale λ, and their ratio Lu/λ, are approximately constant during decay and are independent of the turbulent Reynolds number Reλ. Centerline statistical results support the finding of Mazellier and Vassilicos, namely, that the classical scaling of Lu/λ ˜ Reλ and the Richardson-Kolmogorov cascade are not universal to all boundary-free weakly sheared/strained turbulence. The cross-sectional profiles show that in the entire cross section of the tunnel, Lu/λ hardly changes in the decay region of the rms velocity, which implies that the turbulent field is self-similar. The production and transport of turbulence kinetic energy K in fractal grid turbulence are also investigated from cross-sectional profiles of the advection A^*, production P^*, triple-correlation transport T^*, pressure transport Π*, viscous diffusion D^*, and dissipation ɛ terms in the K transport equation. In the upstream region, turbulence produced by the biggest grid bar is

  14. Thermal properties of composite materials with a complex fractal structure

    NASA Astrophysics Data System (ADS)

    Cervantes-Álvarez, F.; Reyes-Salgado, J. J.; Dossetti, V.; Carrillo, J. L.

    2014-06-01

    In this work, we report the thermal characterization of platelike composite samples made of polyester resin and magnetite inclusions. By means of photoacoustic spectroscopy and thermal relaxation, the thermal diffusivity, conductivity and volumetric heat capacity of the samples were experimentally measured. The volume fraction of the inclusions was systematically varied in order to study the changes in the effective thermal conductivity of the composites. For some samples, a static magnetic field was applied during the polymerization process, resulting in anisotropic inclusion distributions. Our results show a decrease in the thermal conductivity of some of the anisotropic samples, compared to the isotropic randomly distributed ones. Our analysis indicates that the development of elongated inclusion structures leads to the formation of magnetite and resin domains, causing this effect. We correlate the complexity of the inclusion structure with the observed thermal response through a multifractal and lacunarity analysis. All the experimental data are contrasted with the well known Maxwell-Garnett effective media approximation for composite materials.

  15. The N-terminal domain of MuB protein has striking structural similarity to DNA-binding domains and mediates MuB filament-filament interactions.

    PubMed

    Dramićanin, Marija; López-Méndez, Blanca; Boskovic, Jasminka; Campos-Olivas, Ramón; Ramón-Maiques, Santiago

    2015-08-01

    MuB is an ATP-dependent DNA-binding protein that regulates the activity of MuA transposase and delivers the target DNA for transposition of phage Mu. Mechanistic insight into MuB function is limited to its AAA+ ATPase module, which upon ATP binding assembles into helical filaments around the DNA. However, the structure and function of the flexible N-terminal domain (NTD) appended to the AAA+ module remains uncharacterized. Here we report the solution structure of MuB NTD determined by NMR spectroscopy. The structure reveals a compact domain formed by four α-helices connected by short loops, and confirms the presence of a helix-turn-helix motif. High structural similarity and sequence homology with λ repressor-like DNA-binding domains suggest a possible role of MuB NTD in DNA binding. We also demonstrate that the NTD directly mediates the ability of MuB to establish filament-filament interactions. These findings lead us to a model in which the NTD interacts with the AAA+ spirals and perhaps also with the DNA bound within the filament, favoring MuB polymerization and filament clustering. We propose that the MuB NTD-dependent filament interactions might be an effective mechanism to bridge distant DNA regions during Mu transposition. PMID:26169224

  16. Engineering the shape and structure of materials by fractal cut.

    PubMed

    Cho, Yigil; Shin, Joong-Ho; Costa, Avelino; Kim, Tae Ann; Kunin, Valentin; Li, Ju; Lee, Su Yeon; Yang, Shu; Han, Heung Nam; Choi, In-Suk; Srolovitz, David J

    2014-12-01

    In this paper we discuss the transformation of a sheet of material into a wide range of desired shapes and patterns by introducing a set of simple cuts in a multilevel hierarchy with different motifs. Each choice of hierarchical cut motif and cut level allows the material to expand into a unique structure with a unique set of properties. We can reverse-engineer the desired expanded geometries to find the requisite cut pattern to produce it without changing the physical properties of the initial material. The concept was experimentally realized and applied to create an electrode that expands to >800% the original area with only very minor stretching of the underlying material. The generality of our approach greatly expands the design space for materials so that they can be tuned for diverse applications. PMID:25422433

  17. Engineering the shape and structure of materials by fractal cut

    PubMed Central

    Cho, Yigil; Shin, Joong-Ho; Costa, Avelino; Kim, Tae Ann; Kunin, Valentin; Li, Ju; Lee, Su Yeon; Yang, Shu; Han, Heung Nam; Choi, In-Suk; Srolovitz, David J.

    2014-01-01

    In this paper we discuss the transformation of a sheet of material into a wide range of desired shapes and patterns by introducing a set of simple cuts in a multilevel hierarchy with different motifs. Each choice of hierarchical cut motif and cut level allows the material to expand into a unique structure with a unique set of properties. We can reverse-engineer the desired expanded geometries to find the requisite cut pattern to produce it without changing the physical properties of the initial material. The concept was experimentally realized and applied to create an electrode that expands to >800% the original area with only very minor stretching of the underlying material. The generality of our approach greatly expands the design space for materials so that they can be tuned for diverse applications. PMID:25422433

  18. Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology

    PubMed Central

    Slaymaker, Ian M.; Fu, Yang; Toso, Daniel B.; Ranatunga, Nimna; Brewster, Aaron; Forsburg, Susan L.; Zhou, Z. Hong; Chen, Xiaojiang S.

    2013-01-01

    Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins during G1 and S phases. Here, we report an unusually wide left-handed filament structure for an archaeal MCM, as determined by X-ray and electron microscopy. The crystal structure reveals that an α-helix bundle formed between two neighboring subunits plays a critical role in filament formation. The filament has a remarkably strong electro-positive surface spiraling along the inner filament channel for DNA binding. We show that this MCM filament binding to DNA causes dramatic DNA topology change. This newly identified function of MCM to change DNA topology may imply a wider functional role for MCM in DNA metabolisms beyond helicase function. Finally, using yeast genetics, we show that the inter-subunit interactions, important for MCM filament formation, play a role for cell growth and survival. PMID:23361460

  19. Swirling around filaments: are large-scale structure vortices spinning up dark haloes?

    NASA Astrophysics Data System (ADS)

    Laigle, C.; Pichon, C.; Codis, S.; Dubois, Y.; Le Borgne, D.; Pogosyan, D.; Devriendt, J.; Peirani, S.; Prunet, S.; Rouberol, S.; Slyz, A.; Sousbie, T.

    2015-01-01

    The kinematic analysis of dark matter and hydrodynamical simulations suggests that the vorticity in large-scale structure is mostly confined to, and predominantly aligned with, their filaments, with an excess of probability of 20 per cent to have the angle between vorticity and filaments direction lower than 60° relative to random orientations. The cross-sections of these filaments are typically partitioned into four quadrants with opposite vorticity sign, arising from multiple flows, originating from neighbouring walls. The spins of haloes embedded within these filaments are consistently aligned with this vorticity for any halo mass, with a stronger alignment for the most massive structures up to an excess of probability of 165 per cent. The global geometry of the flow within the cosmic web is therefore qualitatively consistent with a spin acquisition for smaller haloes induced by this large-scale coherence, as argued in Codis et al. In effect, secondary anisotropic infall (originating from the vortex-rich filament within which these lower-mass haloes form) dominates the angular momentum budget of these haloes. The transition mass from alignment to orthogonality is related to the size of a given multi-flow region with a given polarity. This transition may be reconciled with the standard tidal torque theory if the latter is augmented so as to account for the larger scale anisotropic environment of walls and filaments.

  20. Fractal-like dependence in the designs of efficient pressure-bearing structures

    NASA Astrophysics Data System (ADS)

    Rayneau-Kirkhope, D.; Farr, R. S.; Mao, Y.

    2011-02-01

    By analysing the possible failure modes at each level, we propose a hierarchical design for highly efficient mechanical structures to withstand hydrostatic crush pressure, which becomes fractal in the limit of zero pressure. We deduce the Hausdorff dimension of these designs (over the range of length scales where this applies), and show that through changing the number of hierarchical levels, the power law scaling relation between applied external pressure and volume of material required can be altered in a systematic way. The design can be applied to arbitrary shapes, but for clarity we present two examples (cylinder and sphere).

  1. Formation of fractal-like structures driven by carbon nanotubes-based collapsed hollow capsules.

    PubMed

    Salgueiriño-Maceira, Verónica; Hoppe, Cristina E; Correa-Duarte, Miguel A

    2007-01-18

    Carbon nanotubes (CNTs) based hollow capsules were obtained by degradation under acidic conditions of core-shell nanocomposites build up upon adsorption of multilayers of CNTs (shell) onto melamine-formaldehyde (MF) spheres (core). By evaporation of the dispersions obtained, polymeric fractal patterns from the degradation products of the MF core were formed onto silicon wafers. The proposed mechanism for the formation of these structures is based on the role of the capsules as arrangements of heterogeneities that facilitate the dewetting of the liquid polymeric films. PMID:17214481

  2. Monitoring the integrity of filament-wound structures using built-in sensor networks

    NASA Astrophysics Data System (ADS)

    Lin, Mark; Kumar, Amrita; Qing, Xinlin; Beard, Shawn J.; Russell, Samuel S.; Walker, James L.; Delay, Thomas K.

    2003-08-01

    Monitoring the integrity of filament wound composite structures such as solid rocket motors and liquid fuel bottles is important in order to prevent catastrophic failures and to prolong the service life of these structures. To ensure the safety and reliability of rocket components, they require frequent inspection for structural damages that might have occurred during manufacturing, transportation, and storage. The timely and accurate detection, characterization and monitoring of structural cracking, delamination, debonding and other types of damage is a major concern in the operational environment. Utilization of a sensor network system integrated with the structure itself can greatly reduce this inspection burden through fast in-situ data collection and processing. Acellent Technologies, Inc. is currently developing integrated structural monitoring tools for continuous monitoring of composite and metal structures on aircraft and spacecraft. Acellent's integrated structural monitoring system consists of a flexible sensor/actuator network layer called the SMART Layer, supporting diagnostic hardware, and data processing/analysis software. Recently, Acellent has been working with NASA Marshall Space Flight Center to develop ways of embedding the SMART Layer inside filament wound composite bottles. SMART Layers were designed and manufactured for the filament wound bottles and embedded in them during the filament winding process. Acellent has been working on developing a complete structural health monitoring system for the filament wound bottles including data processing tools to interpret the changes in sensor signal caused by changes in the structural condition or material property. A prototype of a filament wound composite bottle with an embedded sensor network has been fabricated and preliminary data analysis tools have been developed.

  3. Fractal image compression

    NASA Technical Reports Server (NTRS)

    Barnsley, Michael F.; Sloan, Alan D.

    1989-01-01

    Fractals are geometric or data structures which do not simplify under magnification. Fractal Image Compression is a technique which associates a fractal to an image. On the one hand, the fractal can be described in terms of a few succinct rules, while on the other, the fractal contains much or all of the image information. Since the rules are described with less bits of data than the image, compression results. Data compression with fractals is an approach to reach high compression ratios for large data streams related to images. The high compression ratios are attained at a cost of large amounts of computation. Both lossless and lossy modes are supported by the technique. The technique is stable in that small errors in codes lead to small errors in image data. Applications to the NASA mission are discussed.

  4. Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits.

    PubMed

    Harbage, David; Kondev, Jané

    2016-07-01

    Self-assembling filamentous structures made of protein subunits are ubiquitous in cell biology. These structures are often highly dynamic, with subunits in a continuous state of flux, binding to and falling off of filaments. In spite of this constant turnover of their molecular parts, many cellular structures seem to maintain a well-defined size over time, which is often required for their proper functioning. One widely discussed mechanism of size regulation involves the cell maintaining a finite pool of protein subunits available for assembly. This finite pool mechanism can control the length of a single filament by having assembly proceed until the pool of free subunits is depleted to the point when assembly and disassembly are balanced. Still, this leaves open the question of whether the same mechanism can provide size control for multiple filamentous structures that are assembled from a common pool of protein subunits, as is often the case in cells. We address this question by solving the steady-state master equation governing the stochastic assembly and disassembly of multifilament structures made from a shared finite pool of subunits. We find that, while the total number of subunits within a multifilament structure is well-defined, individual filaments within the structure have a wide, power-law distribution of lengths. We also compute the phase diagram for two multifilament structures competing for the same pool of subunits and identify conditions for coexistence when both have a well-defined size. These predictions can be tested in cell experiments in which the size of the subunit pool or the number of filament nucleators is tuned. PMID:27135597

  5. Self-propelled worm-like filaments: spontaneous spiral formation, structure, and dynamics.

    PubMed

    Isele-Holder, Rolf E; Elgeti, Jens; Gompper, Gerhard

    2015-09-28

    Worm-like filaments that are propelled homogeneously along their tangent vector are studied by Brownian dynamics simulations. Systems in two dimensions are investigated, corresponding to filaments adsorbed to interfaces or surfaces. A large parameter space covering weak and strong propulsion, as well as flexible and stiff filaments is explored. For strongly propelled and flexible filaments, the free-swimming filaments spontaneously form stable spirals. The propulsion force has a strong impact on dynamic properties, such as the rotational and translational mean square displacement and the rate of conformational sampling. In particular, when the active self-propulsion dominates thermal diffusion, but is too weak for spiral formation, the rotational diffusion coefficient has an activity-induced contribution given by v(c)/ξ(P), where v(c) is the contour velocity and ξ(P) the persistence length. In contrast, structural properties are hardly affected by the activity of the system, as long as no spirals form. The model mimics common features of biological systems, such as microtubules and actin filaments on motility assays or slender bacteria, and artificially designed microswimmers. PMID:26256415

  6. Nanoscopic structural rearrangements of the Cu-filament in conductive-bridge memories.

    PubMed

    Celano, U; Giammaria, G; Goux, L; Belmonte, A; Jurczak, M; Vandervorst, W

    2016-07-21

    The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm(3). The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this work, a combination of two- and three-dimensional scanning probe microscopy (SPM) techniques are used to study the conductive filament (CF) formation, rupture and its nanoscopic structural rearrangements. The high spatial confinement of our approach enables to locally induce RS in a confined area and image it in 3D. A conical shape of the CF is consistently observed, indicating that the ion migration is the rate limiting step in the filament formation when using high quality dielectrics as switching layers. The sub-10 nm electrical contact size of the AFM tip is used to study the filament's dissolution and detect the hopping conduction of Cu during the CF rupture. We consistently observe a tunnel gap formation associated with the tip-induced filament reset. Finally, aiming to match the fundamental understanding with the integrated device operations, we apply scalpel SPM to failed memory cells and directly observe the appearance of filament multiplicity as a major source of failures and variability in CBRAM. PMID:27441315

  7. Structural basis for heteromeric assembly and perinuclear organization of keratin filaments

    PubMed Central

    Lee, Chang-Hun; Kim, Min-Sung; Chung, Byung Min; Leahy, Daniel J; Coulombe, Pierre A

    2013-01-01

    There is as yet no high-resolution data regarding the structure and organization of keratin intermediate filaments, which are obligate heteropolymers providing vital mechanical support in epithelia. We report the crystal structure of interacting 2B regions from the central coiled-coil domains of keratins 5 and 14 (K5 and K14), expressed in progenitor keratinocytes of epidermis. The interface of the K5–K14 coiled-coil heterodimer has asymmetric salt bridges, hydrogen bonds and hydrophobic contacts, and its surface exhibits a notable charge polarization. A trans-dimer homotypic disulfide bond involving Cys367 in K14's stutter region occurs in the crystal and in skin keratinocytes, where it is concentrated in a keratin filament cage enveloping the nucleus. We show that K14-Cys367 impacts nuclear shape in cultured keratinocytes and that mouse epidermal keratinocytes lacking K14 show aberrations in nuclear structure, highlighting a new function for keratin filaments. PMID:22705788

  8. Auditory-motor synchronization with temporally fluctuating sequences is dependent on fractal structure but not musical expertise

    PubMed Central

    Rankin, Summer K.; Limb, Charles J.

    2014-01-01

    Fractal structure is a ubiquitous property found in nature and biology, and has been observed in processes at different levels of organization, including rhythmic behavior and musical structure. A temporal process is characterized as fractal when serial long-term correlations and statistical self-similarity (scaling) are present. Previous studies of sensorimotor synchronization using isochronous (non-fractal) stimuli show that participants' errors exhibit persistent structure (positive long-term correlations), while their inter-tap intervals (ITIs) exhibit anti-persistent structure (negative long-term correlations). Auditory-motor synchronization has not been investigated with anti-persistent stimuli. In the current study, we systematically investigated whether the fractal structure of auditory rhythms was reflected in the responses of participants who were asked to coordinate their taps with each event. We asked musicians and non-musicians to tap with 12 different rhythms that ranged from anti-persistent to persistent. The scaling exponents of the ITIs were strongly correlated with the scaling exponents of the stimuli, showing that the long-term structure of the participants' taps scaled with the long-term structure of the stimuli. Surprisingly, the performance of the musicians was not significantly better than that of the non-musicians. Our results imply that humans are able to readily adapt (rather than simply react) to the overall statistical structure of temporally fluctuating stimuli, regardless of musical skill. PMID:25232347

  9. Dark Ribbons Propagating and Sweeping Across Extreme Ultraviolet Structures After Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Xiao, Junmin; Zhang, Jun; Li, Ting; Yang, Shuhong

    2015-05-01

    With observations from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we first report that dark ribbons (DRs) moved apart from the filament channel and swept across EUV structures after filament eruptions on 2013 June 23 and 2012 February 10 and 24, respectively. In the first event, the DR with a length of 168 Mm appeared at 100 Mm to the northwest of the filament channel, where the filament erupted 15 hr previously. The DR moved toward the northwest with the different sections having different velocities, ranging from 0.3 to 1.6 km s‑1. When the DR’s middle part swept across a strong EUV structure, the motion of this part was blocked, appearing to deflect the DR. With the DR propagation, the connection of the surrounding EUV structures gradually changed. After one day passed, the DR eventually disappeared. In the other two events, the dynamic evolution of the DRs was similar to that in the first event. Based on the observations, we speculate that the reconnection during the filament eruption changes the configuration of the surrounding magnetic fields systematically. During the reconnection process, magnetic fields are deflecting and the former arbitrarily distributed magnetic fields are rearranged along specific directions. The deflection of magnetic fields results in an instantaneous void region where the magnetic strength is smaller and the plasma density is lower. Consequently, the void region is observed as a DR and propagates outward with the reconnection developing.

  10. Dark Ribbons Propagating and Sweeping across Extreme Ultraviolet Structures after Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Xiao, Junmin; Zhang, Jun; Li, Ting; Yang, Shuhong

    2015-05-01

    With observations from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we first report that dark ribbons (DRs) moved apart from the filament channel and swept across EUV structures after filament eruptions on 2013 June 23 and 2012 February 10 and 24, respectively. In the first event, the DR with a length of 168 Mm appeared at 100 Mm to the northwest of the filament channel, where the filament erupted 15 hr previously. The DR moved toward the northwest with the different sections having different velocities, ranging from 0.3 to 1.6 km s-1. When the DR’s middle part swept across a strong EUV structure, the motion of this part was blocked, appearing to deflect the DR. With the DR propagation, the connection of the surrounding EUV structures gradually changed. After one day passed, the DR eventually disappeared. In the other two events, the dynamic evolution of the DRs was similar to that in the first event. Based on the observations, we speculate that the reconnection during the filament eruption changes the configuration of the surrounding magnetic fields systematically. During the reconnection process, magnetic fields are deflecting and the former arbitrarily distributed magnetic fields are rearranged along specific directions. The deflection of magnetic fields results in an instantaneous void region where the magnetic strength is smaller and the plasma density is lower. Consequently, the void region is observed as a DR and propagates outward with the reconnection developing.

  11. Fractal Geometry of Architecture

    NASA Astrophysics Data System (ADS)

    Lorenz, Wolfgang E.

    In Fractals smaller parts and the whole are linked together. Fractals are self-similar, as those parts are, at least approximately, scaled-down copies of the rough whole. In architecture, such a concept has also been known for a long time. Not only architects of the twentieth century called for an overall idea that is mirrored in every single detail, but also Gothic cathedrals and Indian temples offer self-similarity. This study mainly focuses upon the question whether this concept of self-similarity makes architecture with fractal properties more diverse and interesting than Euclidean Modern architecture. The first part gives an introduction and explains Fractal properties in various natural and architectural objects, presenting the underlying structure by computer programmed renderings. In this connection, differences between the fractal, architectural concept and true, mathematical Fractals are worked out to become aware of limits. This is the basis for dealing with the problem whether fractal-like architecture, particularly facades, can be measured so that different designs can be compared with each other under the aspect of fractal properties. Finally the usability of the Box-Counting Method, an easy-to-use measurement method of Fractal Dimension is analyzed with regard to architecture.

  12. Contribution of stratified extracellular polymeric substances to the gel-like and fractal structures of activated sludge.

    PubMed

    Yuan, D Q; Wang, Y L; Feng, J

    2014-06-01

    The gel-like and fractal structures of activated sludge (AS) before and after extracellular polymeric substances (EPS) extraction as well as different EPS fractions were investigated. The contributions of individual components in different EPS fractions to the gel-like behavior of sludge samples by enzyme treatment were examined as well. The centrifugation and ultrasound method was employed to stratify the EPS into slime, loosely and tightly bound EPS (LB- and TB-EPS). It was observed that all samples behaved as weak gels with weak-link. TB-EPS and AS after LB-EPS extraction showed the strongest elasticity in higher concentrations and highest mass fractal dimension, which may indicate the key role of TB-EPS in the gel-like and fractal structures of the sludge. Effects of protease or amylase on the gel-like property of sludge samples differed in the presence of different EPS fractions. PMID:24651018

  13. Helical filaments

    NASA Astrophysics Data System (ADS)

    Barbieri, Nicholas; Hosseinimakarem, Zahra; Lim, Khan; Durand, Magali; Baudelet, Matthieu; Johnson, Eric; Richardson, Martin

    2014-06-01

    The shaping of laser-induced filamenting plasma channels into helical structures by guiding the process with a non-diffracting beam is demonstrated. This was achieved using a Bessel beam superposition to control the phase of an ultrafast laser beam possessing intensities sufficient to induce Kerr effect driven non-linear self-focusing. Several experimental methods were used to characterize the resulting beams and confirm the observed structures are laser air filaments.

  14. Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

    SciTech Connect

    Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata; Leavis, Paul C.; Navaza, Jorge; Dominguez, Roberto

    2013-11-20

    Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin {beta}4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin {beta}4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  15. Structural characterization of a capping protein interaction motif defines a family of actin filament regulators

    PubMed Central

    Hernandez-Valladares, Maria; Kim, Taekyung; Kannan, Balakrishnan; Tung, Alvin; Aguda, Adeleke H; Larsson, Mårten; Cooper, John A; Robinson, Robert C

    2011-01-01

    Capping protein (CP) regulates actin dynamics by binding the barbed ends of actin filaments. Removal of CP may be one means to harness actin polymerization for processes such as cell movement and endocytosis. Here we structurally and biochemically investigated a CP interaction (CPI) motif present in the otherwise unrelated proteins CARMIL and CD2AP. The CPI motif wraps around the stalk of the mushroom-shaped CP at a site distant from the actin-binding interface, which lies on the top of the mushroom cap. We propose that the CPI motif may act as an allosteric modulator, restricting CP to a low-affinity, filament-binding conformation. Structure-based sequence alignments extend the CPI motif–containing family to include CIN85, CKIP-1, CapZIP and a relatively uncharacterized protein, WASHCAP (FAM21). Peptides comprising these CPI motifs are able to inhibit CP and to uncap CP-bound actin filaments. PMID:20357771

  16. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly

    PubMed Central

    Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca

    2015-01-01

    Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general. PMID:26181054

  17. Invertebrate muscles: thin and thick filament structure; molecular basis of contraction and its regulation, catch and asynchronous muscle

    PubMed Central

    Hooper, Scott L.; Hobbs, Kevin H.; Thuma, Jeffrey B.

    2008-01-01

    This is the second in a series of canonical reviews on invertebrate muscle. We cover here thin and thick filament structure, the molecular basis of force generation and its regulation, and two special properties of some invertebrate muscle, catch and asynchronous muscle. Invertebrate thin filaments resemble vertebrate thin filaments, although helix structure and tropomyosin arrangement show small differences. Invertebrate thick filaments, alternatively, are very different from vertebrate striated thick filaments and show great variation within invertebrates. Part of this diversity stems from variation in paramyosin content, which is greatly increased in very large diameter invertebrate thick filaments. Other of it arises from relatively small changes in filament backbone structure, which results in filaments with grossly similar myosin head placements (rotating crowns of heads every 14.5 nm) but large changes in detail (distances between heads in azimuthal registration varying from three to thousands of crowns). The lever arm basis of force generation is common to both vetebrates and invertebrates, and in some invertebrates this process is understood on the near atomic level. Invertebrate actomyosin is both thin (tropomyosin:troponin) and thick (primarily via direct Ca++ binding to myosin) filament regulated, and most invertebrate muscles are dually regulated. These mechanisms are well understood on the molecular level, but the behavioral utility of dual regulation is less so. The phosphorylation state of the thick filament associated giant protein, twitchin, has been recently shown to be the molecular basis of catch. The molecular basis of the stretch activation underlying asynchronous muscle activity, however, remains unresolved. PMID:18616971

  18. Multiparticle sintering dynamics: from fractal-like aggregates to compact structures.

    PubMed

    Eggersdorfer, Max L; Kadau, Dirk; Herrmann, Hans J; Pratsinis, Sotiris E

    2011-05-17

    Multiparticle sintering is encountered in almost all high temperature processes for material synthesis (titania, silica, and nickel) and energy generation (e.g., fly ash formation) resulting in aggregates of primary particles (hard- or sinter-bonded agglomerates). This mechanism of particle growth is investigated quantitatively by mass and energy balances during viscous sintering of amorphous aerosol materials (e.g., SiO(2) and polymers) that typically have a distribution of sizes and complex morphology. This model is validated at limited cases of sintering between two (equally or unequally sized) particles, and chains of particles. The evolution of morphology, surface area and radii of gyration of multiparticle aggregates are elucidated for various sizes and initial fractal dimension. For each of these structures that had been generated by diffusion limited (DLA), cluster-cluster (DLCA), and ballistic particle-cluster agglomeration (BPCA) the surface area evolution is monitored and found to scale differently than that of the radius of gyration (moment of inertia). Expressions are proposed for the evolution of fractal dimension and the surface area of aggregates undergoing viscous sintering. These expressions are important in design of aerosol processes with population balance equations (PBE) and/or fluid dynamic simulations for material synthesis or minimization and even suppression of particle formation. PMID:21488641

  19. Myosin light chain phosphorylation enhances contraction of heart muscle via structural changes in both thick and thin filaments

    PubMed Central

    Kampourakis, Thomas; Sun, Yin-Biao; Irving, Malcolm

    2016-01-01

    Contraction of heart muscle is triggered by calcium binding to the actin-containing thin filaments but modulated by structural changes in the myosin-containing thick filaments. We used phosphorylation of the myosin regulatory light chain (cRLC) by the cardiac isoform of its specific kinase to elucidate mechanisms of thick filament-mediated contractile regulation in demembranated trabeculae from the rat right ventricle. cRLC phosphorylation enhanced active force and its calcium sensitivity and altered thick filament structure as reported by bifunctional rhodamine probes on the cRLC: the myosin head domains became more perpendicular to the filament axis. The effects of cRLC phosphorylation on thick filament structure and its calcium sensitivity were mimicked by increasing sarcomere length or by deleting the N terminus of the cRLC. Changes in thick filament structure were highly cooperative with respect to either calcium concentration or extent of cRLC phosphorylation. Probes on unphosphorylated myosin heads reported similar structural changes when neighboring heads were phosphorylated, directly demonstrating signaling between myosin heads. Moreover probes on troponin showed that calcium sensitization by cRLC phosphorylation is mediated by the thin filament, revealing a signaling pathway between thick and thin filaments that is still present when active force is blocked by Blebbistatin. These results show that coordinated and cooperative structural changes in the thick and thin filaments are fundamental to the physiological regulation of contractility in the heart. This integrated dual-filament concept of contractile regulation may aid understanding of functional effects of mutations in the protein components of both filaments associated with heart disease. PMID:27162358

  20. Myosin light chain phosphorylation enhances contraction of heart muscle via structural changes in both thick and thin filaments.

    PubMed

    Kampourakis, Thomas; Sun, Yin-Biao; Irving, Malcolm

    2016-05-24

    Contraction of heart muscle is triggered by calcium binding to the actin-containing thin filaments but modulated by structural changes in the myosin-containing thick filaments. We used phosphorylation of the myosin regulatory light chain (cRLC) by the cardiac isoform of its specific kinase to elucidate mechanisms of thick filament-mediated contractile regulation in demembranated trabeculae from the rat right ventricle. cRLC phosphorylation enhanced active force and its calcium sensitivity and altered thick filament structure as reported by bifunctional rhodamine probes on the cRLC: the myosin head domains became more perpendicular to the filament axis. The effects of cRLC phosphorylation on thick filament structure and its calcium sensitivity were mimicked by increasing sarcomere length or by deleting the N terminus of the cRLC. Changes in thick filament structure were highly cooperative with respect to either calcium concentration or extent of cRLC phosphorylation. Probes on unphosphorylated myosin heads reported similar structural changes when neighboring heads were phosphorylated, directly demonstrating signaling between myosin heads. Moreover probes on troponin showed that calcium sensitization by cRLC phosphorylation is mediated by the thin filament, revealing a signaling pathway between thick and thin filaments that is still present when active force is blocked by Blebbistatin. These results show that coordinated and cooperative structural changes in the thick and thin filaments are fundamental to the physiological regulation of contractility in the heart. This integrated dual-filament concept of contractile regulation may aid understanding of functional effects of mutations in the protein components of both filaments associated with heart disease. PMID:27162358

  1. Characterization of Microgravity Effects on Bone Structure and Strength Using Fractal Analysis

    NASA Technical Reports Server (NTRS)

    Acharya, Raj S.; Shackelford, Linda

    1996-01-01

    Protecting humans against extreme environmental conditions requires a thorough understanding of the pathophysiological changes resulting from the exposure to those extreme conditions. Knowledge of the degree of medical risk associated with the exposure is of paramount importance in the design of effective prophylactic and therapeutic measures for space exploration. Major health hazards due o musculoskeletal systems include the signs and symptoms of hypercalciuria, lengthy recovery of lost bone tissue after flight, the possibility of irreversible trabecular bone loss, the possible effect of calcification in the soft tissues, and the possible increase in fracture potential. In this research, we characterize the trabecular structure with the aid of fractal analysis. Our research to relate local trabecular structural information to microgravity conditions is an important initial step in understanding the effect of microgravity and countermeasures on bone condition and strength. The proposed research is also closely linked with Osteoporosis and will benefit the general population.

  2. Fractal structure and the dynamics of aggregation of synthetic melanin in low pH aqueous solutions

    SciTech Connect

    Huang, J.S.; Sung, J.; Eisner, M.; Moss, S.C.; Gallas, J.

    1989-01-01

    We have used static and dynamic light scattering to study the dynamics of aggregation of synthetic melanin, an amorphous biopolymeric substance, in low pH aqueous solution. We have found that, depending on the final pH value of the solutions, there existed two regimes of the aggregation kinetics, one corresponding to diffusion limited aggregation (DLA), and the other corresponding to reaction limited aggregation (RLA). The precipitates formed in these two regimes can be characterized by fractal structures. We have found fractal dimensions of d/sub f/ = 1.8 for the DLA clusters and d/sub f/ = 2.2 for the RLA clusters. These results agree well with the proposed limits of the fractal dimensions of the gold aggregates formed in aqueous solutions by Weitz et al.

  3. Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure

    NASA Technical Reports Server (NTRS)

    Maniotis, A. J.; Chen, C. S.; Ingber, D. E.

    1997-01-01

    We report here that living cells and nuclei are hard-wired such that a mechanical tug on cell surface receptors can immediately change the organization of molecular assemblies in the cytoplasm and nucleus. When integrins were pulled by micromanipulating bound microbeads or micropipettes, cytoskeletal filaments reoriented, nuclei distorted, and nucleoli redistributed along the axis of the applied tension field. These effects were specific for integrins, independent of cortical membrane distortion, and were mediated by direct linkages between the cytoskeleton and nucleus. Actin microfilaments mediated force transfer to the nucleus at low strain; however, tearing of the actin gel resulted with greater distortion. In contrast, intermediate filaments effectively mediated force transfer to the nucleus under both conditions. These filament systems also acted as molecular guy wires to mechanically stiffen the nucleus and anchor it in place, whereas microtubules acted to hold open the intermediate filament lattice and to stabilize the nucleus against lateral compression. Molecular connections between integrins, cytoskeletal filaments, and nuclear scaffolds may therefore provide a discrete path for mechanical signal transfer through cells as well as a mechanism for producing integrated changes in cell and nuclear structure in response to changes in extracellular matrix adhesivity or mechanics.

  4. The Filament Sensor for Near Real-Time Detection of Cytoskeletal Fiber Structures

    PubMed Central

    Eltzner, Benjamin; Wollnik, Carina; Gottschlich, Carsten; Huckemann, Stephan; Rehfeldt, Florian

    2015-01-01

    A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the understanding of the underlying fiber arrangement processes. In this paper, we propose the filament sensor (FS), a fast and robust processing sequence which detects and records location, orientation, length, and width for each single filament of an image, and thus allows for the above described analysis. The extraction of these features has previously not been possible with existing methods. We evaluate the performance of the proposed FS in terms of accuracy and speed in comparison to three existing methods with respect to their limited output. Further, we provide a benchmark dataset of real cell images along with filaments manually marked by a human expert as well as simulated benchmark images. The FS clearly outperforms existing methods in terms of computational runtime and filament extraction accuracy. The implementation of the FS and the benchmark database are available as open source. PMID:25996921

  5. Dynamics of permanent structural transformations in ZBLAN induced by self-channeled plasma filament

    NASA Astrophysics Data System (ADS)

    Cho, Sung-Hak; Kumagai, Hiroshi; Midorikawa, Katsumi

    2004-06-01

    The time-resolved dynamics of permanent structural transformations in the ZBLAN (fluoride glass) induced by self-channeled plasma filament were first observed in situ using a high-intensity femtosecond (110 fs) Ti: sapphire laser ( λp=800 nm). Self-channeled plasma filament would be induced in ZBLAN glass at the irradiation higher than input intensity of 1.0 × 10 12 W/cm 2 and photoinduce either the refractive index modification or optical crack modification. At the domain of refractive index modification, the lifetime of induced self-channeled plasma filament was 30 ps and structural transition time for forming the refractive index change was 40 ps. At the domain of optical cracks, however, the lifetime of induced self-channeled plasma filament was 70 ps and structural transition time for forming the optical cracks was 70 ps. A maximum value of refractive index change (Δ n) was measured to be 1.3 × 10 -2. The intensity profile of the output beam transmitted through the refractive index modification showed that the bulk modification produced a permanent structure of optical waveguide.

  6. New structural approach for determining load carrying capability of filament wound composite materials

    NASA Technical Reports Server (NTRS)

    Armstrong, W. H.; Yang, P. B.

    1970-01-01

    Metal lined boron and graphite composites exhibit high strength and minimum weight, making them superior to aluminum cylindrical shell structures and to steel or aluminum constructed pressure vessels. S glass filament-epoxy resin matrix with aluminum liner is suitable for cryogenic tanks.

  7. Structural basis for the prion-like MAVS filaments in antiviral innate immunity

    PubMed Central

    Xu, Hui; He, Xiaojing; Zheng, Hui; Huang, Lily J; Hou, Fajian; Yu, Zhiheng; de la Cruz, Michael Jason; Borkowski, Brian; Zhang, Xuewu; Chen, Zhijian J; Jiang, Qiu-Xing

    2014-01-01

    Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001 PMID:24569476

  8. Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

    NASA Astrophysics Data System (ADS)

    Qin, Zhao

    Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association

  9. The structure of the chorion and associated surface filaments in Oryzias--evidence for the presence of extracellular tubules.

    PubMed

    Hart, N H; Pietri, R; Donovan, M

    1984-05-01

    The structure of the chorion with its associated surface filaments has been examined in Oryzias latipes using several techniques, including scanning and transmission electron microscopy, enzymatic digestion, and sodium dodecylsulfate-polyacrylamide gel electrophoresis. The chorion of the recently fertilized egg was found to be organized into three zones: an outer, fuzzy electron-lucent zone that was continuous over the surface of filaments, a middle, homogeneous electron-dense zone, and an inner zone of ten to 12 horizontal, fibrous lamellae. Two topographically distinct types of filaments were found on the chorionic surface: nonattaching and attaching. Nonattaching filaments showed a regular spatial distribution over the chorion with an interfilament distance of about 60-70 microns. Attaching filaments originated from a localized portion of the chorion and united with those of neighboring eggs to anchor the egg cluster to the gonoduct of the female. Both nonattaching and attaching filaments were morphologically regionalized into basal and distal segments. Internally, nonattaching and attaching filaments were constructed of unbranched, packed tubules with an average outside diameter of approximately 19.5 and 18.8 nm, respectively. Using the attaching filament for further study, it was determined by rotational analysis (Markham et al., '63) that the wall of each tubule was a cylinder composed of 14 globular subunits. Two structural types of attaching filaments were identified. The type I attaching filament was similar in internal organization to the nonattaching filament and consisted of only tubules. The type II attaching filament, however, showed a highly osmiophilic, electron-dense bar surrounded by packed tubules. Tubules of attaching filaments of the adult were resistant to the action of Triton X-100 and colchicine, but sensitive to a 0.1% protease solution. However, colchicine-treated ovary tissue showed an absence and pattern of disorganization of tubules at

  10. The effect of residual silk sericin on the structure and mechanical property of regenerated silk filament.

    PubMed

    Ki, Chang Seok; Kim, Jong Wook; Oh, Han Jin; Lee, Ki Hoon; Park, Young Hwan

    2007-08-01

    In this study, we elucidated the effect of residual silk sericin (SS) on structure and mechanical properties of regenerated silk filament as well as on fiber formation. The dope viscosity markedly increased with increasing residual SS content in dope solution which was prepared by dissolving the silk protein in formic acid. As a result of FTIR, (13)C NMR, and XRD, a small amount of SS (9.6%) contained in the filament showed highest content of beta-sheet conformation and maximum crystallinity. It seems that the SS affects the structural change of SF up to a certain level by inducing the beta-transition easily. The tenacity of the filaments, containing 9.6-18.9% SS, was in the range of 2.1-2.4 gf/d, which was about 50% higher than the filament without SS (pure SF). Consequently, with the enhancement of spinnability in wet spinning process, the SS can play an important role for developing the crystalline structure of SF as well as for improving mechanical properties of the regenerated silk fiber. PMID:17573107

  11. Generic fractal structure of finite parts of trajectories of piecewise smooth Hamiltonian systems

    NASA Astrophysics Data System (ADS)

    Hildebrand, R.; Lokutsievskiy, L. V.; Zelikin, M. I.

    2013-03-01

    Piecewise smooth Hamiltonian systems with tangent discontinuity are studied. A new phenomenon is discovered, namely, the generic chaotic behavior of finite parts of trajectories. The approach is to consider the evolution of Poisson brackets for smooth parts of the initial Hamiltonian system. It turns out that, near second-order singular points lying on a discontinuity stratum of codimension two, the system of Poisson brackets is reduced to the Hamiltonian system of the Pontryagin Maximum Principle. The corresponding optimization problem is studied and the topological structure of its optimal trajectories is constructed (optimal synthesis). The synthesis contains countably many periodic solutions on the quotient space by the scale group and a Cantor-like set of nonwandering points (NW) having fractal Hausdorff dimension. The dynamics of the system is described by a topological Markov chain. The entropy is evaluated, together with bounds for the Hausdorff and box dimension of (NW).

  12. Correlation of Resistance with Fractal Structure for Different Single-walled Carbon Nanotube Networks

    NASA Astrophysics Data System (ADS)

    Liu, Bingbing; Sundqvist, Bertil; Olsson, Eva; Zhu, Xiao-Mei; Zou, Guangtian

    2001-03-01

    The temperature dependence of resistance and magnetoresistance for bulk samples of single-walled nanotubes treated in different ways have been studied systematically and compared with that of pristine nanotubes synthesized with Ce/Ni as catalyst. The resistance of samples pressurized under a hydrostatic pressure of 1.5 GPa shows a 2D Variable range hopping behavior, similar to that for as-grown samples and for samples partly purified by treatment in nitric acid for a short time. A pressed sample composed of small pieces of as-grown mats follows a 3D VRH, similar to that for samples treated in nitric acid for a long time. The correlation between the conduction dimension and the nanotube morphology is well explained by a fractal structure model. The results indicate that 2D VRH is a characteristic transport behavior for nanotubes.

  13. Time scale defined by the fractal structure of the price fluctuations in foreign exchange markets

    NASA Astrophysics Data System (ADS)

    Kumagai, Yoshiaki

    2010-04-01

    In this contribution, a new time scale named C-fluctuation time is defined by price fluctuations observed at a given resolution. The intraday fractal structures and the relations of the three time scales: real time (physical time), tick time and C-fluctuation time, in foreign exchange markets are analyzed. The data set used is trading prices of foreign exchange rates; US dollar (USD)/Japanese yen (JPY), USD/Euro (EUR), and EUR/JPY. The accuracy of the data is one minute and data within a minute are recorded in order of transaction. The series of instantaneous velocity of C-fluctuation time flowing are exponentially distributed for small C when they are measured by real time and for tiny C when they are measured by tick time. When the market is volatile, for larger C, the series of instantaneous velocity are exponentially distributed.

  14. Nanoscopic structural rearrangements of the Cu-filament in conductive-bridge memories

    NASA Astrophysics Data System (ADS)

    Celano, U.; Giammaria, G.; Goux, L.; Belmonte, A.; Jurczak, M.; Vandervorst, W.

    2016-07-01

    The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm3. The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this work, a combination of two- and three-dimensional scanning probe microscopy (SPM) techniques are used to study the conductive filament (CF) formation, rupture and its nanoscopic structural rearrangements. The high spatial confinement of our approach enables to locally induce RS in a confined area and image it in 3D. A conical shape of the CF is consistently observed, indicating that the ion migration is the rate limiting step in the filament formation when using high quality dielectrics as switching layers. The sub-10 nm electrical contact size of the AFM tip is used to study the filament's dissolution and detect the hopping conduction of Cu during the CF rupture. We consistently observe a tunnel gap formation associated with the tip-induced filament reset. Finally, aiming to match the fundamental understanding with the integrated device operations, we apply scalpel SPM to failed memory cells and directly observe the appearance of filament multiplicity as a major source of failures and variability in CBRAM.The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm3. The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this

  15. How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability?

    PubMed

    Xu, Liang; Zheng, Jie; Margittai, Martin; Nussinov, Ruth; Ma, Buyong

    2016-05-18

    Tau proteins are hyperphosphorylated at common sites in their N- and C-terminal domains in at least three neurodegenerative diseases, Parkinson, dementia with Lewy bodies, and Alzheimer's, suggesting specific pathology but general mechanism. Full-length human tau filament comprises a rigid core and a two-layered fuzzy coat. Tau is categorized into two groups of isoforms, with either four repeats (R1-R4) or three repeats (R1, R3, and R4); their truncated constructs are respectively called K18 and K19. Using multiscale molecular dynamics simulations, we explored the conformational consequences of hyperhposphorylation on tau's repeats. Our lower conformational energy filament models suggest a rigid filament core with a radius of ∼30 to 40 Å and an outer layer with a thickness of ∼140 Å consisting of a double-layered polyelectrolyte. The presence of the phosphorylated terminal domains alters the relative stabilities in the K18 ensemble, thus shifting the populations of the full-length filaments. However, the structure with the straight repeats in the core region is still the most stable, similar to the truncated K18 peptide species without the N- and C-terminus. Our simulations across different scales of resolution consistently reveal that hyperphosphorylation of the two terminal domains decreases the attractive interactions among the N- and C-terminus and repeat domain. To date, the relationship on the conformational level between phosphorylation and aggregation has not been understood. Our results suggest that the exposure of the repeat domain upon hyperphosphorylation could enhance tau filament aggregation. Thus, we discovered that even though these neurodegenerative diseases vary and their associated tau filaments are phosphorylated to different extents, remarkably, the three pathologies appear to share a common tau aggregation mechanism. PMID:26854860

  16. Fine-scale structures and material flows of quiescent filaments observed by the New Vacuum Solar Telescope

    NASA Astrophysics Data System (ADS)

    Yan, Xiao-Li; Xue, Zhi-Ke; Xiang, Yong-Yuan; Yang, Li-Heng

    2015-10-01

    Study of the small-scale structures and material flows associated with solar quiescent filaments is very important for understanding the formation and equilibrium of solar filaments. Using high resolution Hα data observed by the New Vacuum Solar Telescope, we present the structures of barbs and material flows along the threads across the spine in two quiescent filaments on 2013 September 29 and on 2012 November 2, respectively. During the evolution of the filament barb, several parallel tube-shaped structures formed and the width of the structures ranged from about 2.3 Mm to 3.3 Mm. The parallel tube-shaped structures merged together accompanied by material flows from the spine to the barb. Moreover, the boundary between the barb and surrounding atmosphere was very neat. The counter-streaming flows were not found to appear alternately in the adjacent threads of the filament. However, the large-scale patchy counter-streaming flows were detected in the filament. The flows in one patch of the filament have the same direction but flows in the adjacent patch have opposite direction. The patches of two opposite flows with a size of about 10″ were alternately exhibited along the spine of the filament. The velocity of these material flows ranged from 5.6 km s-1 to 15.0 km s-1. The material flows along the threads of the filament did not change their direction for about two hours and fourteen minutes during the evolution of the filament. Our results confirm that the large-scale counter-streaming flows with a certain width along the threads of solar filaments exist and are coaligned well with the threads.

  17. Hybrid stent device of flow-diverting effect and stent-assisted coil embolization formed by fractal structure.

    PubMed

    Kojima, Masahiro; Irie, Keiko; Masunaga, Kouhei; Sakai, Yasuhiko; Nakajima, Masahiro; Takeuchi, Masaru; Fukuda, Toshio; Arai, Fumihito; Negoro, Makoto

    2016-05-01

    This paper presents a novel hybrid medical stent device. This hybrid stent device formed by fractal mesh structures provides a flow-diverting effect and stent-assisted coil embolization. Flow-diverter stents decrease blood flow into an aneurysm to prevent its rupture. In general, the mesh size of a flow-diverter stent needs to be small enough to prevent blood flow into the aneurysm. Conventional flow-diverter stents are not available for stent-assisted coil embolization, which is an effective method for aneurysm occlusion, because the mesh size is too small to insert a micro-catheter for coil embolization. The proposed hybrid stent device is capable of stent-assisted coil embolization while simultaneously providing a flow-diverting effect. The fractal stent device is composed of mesh structures with fine and rough mesh areas. The rough mesh area can be used to insert a micro-catheter for stent-assisted coil embolization. Flow-diverting effects of two fractal stent designs were composed to three commercially available stent designs. Flow-diverting effects were analyzed using computational fluid dynamics (CFD) analysis and particle image velocimetry (PIV) experiment. Based on the CFD and PIV results, the fractal stent devices reduce the flow velocity inside an aneurism just as much as the commercially available flow-diverting stents while allowing stent-assisted coil embolization. PMID:26438390

  18. Parameterizing liquid crystal variable retarder structural organization with a fractal-Born approximation model

    NASA Astrophysics Data System (ADS)

    Gladish, James C.; Duncan, Donald D.

    2016-05-01

    Liquid crystal variable retarders (LCVRs) are computer-controlled birefringent devices that contain nanometer-sized birefringent liquid crystals (LCs). These devices impart retardance effects through a global, uniform orientation change of the LCs, which is based on a user-defined drive voltage input. In other words, the LC structural organization dictates the device functionality. The LC structural organization also produces a spectral scatter component which exhibits an inverse power law dependence. We investigate LC structural organization by measuring the voltage-dependent LC spectral scattering signature with an integrating sphere and then relate this observable to a fractal-Born model based on the Born approximation and a Von Kármán spectrum. We obtain LCVR light scattering spectra at various drive voltages (i.e., different LC orientations) and then parameterize LCVR structural organization with voltage-dependent correlation lengths. The results can aid in determining performance characteristics of systems using LCVRs and can provide insight into interpreting structural organization measurements.

  19. Structural basis of thymosin-β4/profilin exchange leading to actin filament polymerization

    PubMed Central

    Xue, Bo; Leyrat, Cedric; Grimes, Jonathan M.; Robinson, Robert C.

    2014-01-01

    Thymosin-β4 (Tβ4) and profilin are the two major sequestering proteins that maintain the pool of monomeric actin (G-actin) within cells of higher eukaryotes. Tβ4 prevents G-actin from joining a filament, whereas profilin:actin only supports barbed-end elongation. Here, we report two Tβ4:actin structures. The first structure shows that Tβ4 has two helices that bind at the barbed and pointed faces of G-actin, preventing the incorporation of the bound G-actin into a filament. The second structure displays a more open nucleotide binding cleft on G-actin, which is typical of profilin:actin structures, with a concomitant disruption of the Tβ4 C-terminal helix interaction. These structures, combined with biochemical assays and molecular dynamics simulations, show that the exchange of bound actin between Tβ4 and profilin involves both steric and allosteric components. The sensitivity of profilin to the conformational state of actin indicates a similar allosteric mechanism for the dissociation of profilin during filament elongation. PMID:25313062

  20. Fullerenol Nanoparticles with Structural Activity Induce Variable Intracellular Actin Filament Morphologies.

    PubMed

    Jin, Junjiang; Dong, Ying; Wang, Ying; Xia, Lin; Gu, Weihong; Bai, Xue; Chang, Yanan; Zhang, Mingyi; Chen, Kui; Li, Juan; Zhao, Lina; Xing, Gengmei

    2016-06-01

    Fullerenol nanoparticles are promising for various biological applications; many studies have shown that they induce variable and diverse biological effects including side effects. Separation and purification of two fractions of fullerenols has demonstrated that they have varied chemical structures on the surfaces of their carbon cages. Actin is an important structural protein that is able to transform functional structures under varied physiological conditions. We assessed the abilities of the two fractions of fullerenols to attach to actin and induce variable morphological features in actin filament structures. Specifically the fullerenol fraction with a surface electric charge of -1.913 ± 0.008q (x10(-6) C) has percentages of C-OH and C=O on the carbon cage of 16.14 ± 0.60 and 17.55 ± 0.69. These features allow it to form intermolecular hydrogen bonds with actin at a stoichiometric ratio of four fullerenols per actin subunit. Molecular simulations revealed these specific binding sites and binding modes in atomic details in the interaction between the active fullerenol and actin filament. Conversely, these interactions were not possible for the other fraction of fullerenol with that percentages of C-OH and C=O on the carbon cage were 15.59 ± 0.01 and 1.94 ± 0.11. Neither sample induced appreciable cytotoxicity or acute cell death. After entering cells, active fullerenol binding to actin induces variable morphological features and may transform ATP-actin to ADP-actin. These changes facilitate the binding of ADF/cofilin, allowing cofilin to sever actin filaments to form cofilin/actin/fullerenol rods. Our findings suggest that fullerenol with structural activity binding disturbs actin filament structure, which may inhibit locomotion of cell or induce chronic side effects in to cells. PMID:27319217

  1. Protein Thermal Conductivity Measured in the Solid State Reveals Anharmonic Interactions of Vibrations in a Fractal Structure.

    PubMed

    Foley, Brian M; Gorham, Caroline S; Duda, John C; Cheaito, Ramez; Szwejkowski, Chester J; Constantin, Costel; Kaehr, Bryan; Hopkins, Patrick E

    2014-04-01

    Energy processes and vibrations in biological macromolecules such as proteins ultimately dictate biological, chemical, and physical functions in living materials. These energetic vibrations in the ribbon-like motifs of proteins interact on self-similar structures and fractal-like objects over a range of length scales of the protein (a few angstroms to the size of the protein itself, a few nanometers). In fact, the fractal geometries of protein molecules create a complex network of vibrations; therefore, proteins represent an ideal material system to study the underlying mechanisms driving vibrational thermal transport in a dense, fractal network. However, experimental studies of thermal energy transport in proteins have been limited to dispersive protein suspensions, which limits the knowledge that can be extracted about how vibrational energy is transferred in a pure protein solid. We overcome this by synthesizing solid, water-insoluble protein films for thermal conductivity measurements via time-domain thermoreflectance. We measure the thermal conductivity of bovine serum albumin and myoglobin solid films over a range of temperatures from 77 to 296 K. These temperature trends indicate that anharmonic coupling of vibrations in the protein is contributing to thermal conductivity. This first-ever observation of anharmonic-like trends in the thermal conductivity of a fully dense protein forms the basis of validation of seminal theories of vibrational energy-transfer processes in fractal objects. PMID:26274452

  2. Self-Elongation with Sequential Folding of a Filament of Bacterial Cells

    NASA Astrophysics Data System (ADS)

    Honda, Ryojiro; Wakita, Jun-ichi; Katori, Makoto

    2015-11-01

    Under hard-agar and nutrient-rich conditions, a cell of Bacillus subtilis grows as a single filament owing to the failure of cell separation after each growth and division cycle. The self-elongating filament of cells shows sequential folding processes, and multifold structures extend over an agar plate. We report that the growth process from the exponential phase to the stationary phase is well described by the time evolution of fractal dimensions of the filament configuration. We propose a method of characterizing filament configurations using a set of lengths of multifold parts of a filament. Systems of differential equations are introduced to describe the folding processes that create multifold structures in the early stage of the growth process. We show that the fitting of experimental data to the solutions of equations is excellent, and the parameters involved in our model systems are determined.

  3. Distribution of human single-nucleotide polymorphisms is approximated by the power law and represents a fractal structure.

    PubMed

    Gouda, Norio; Shiwa, Yuh; Akashi, Motohiro; Yoshikawa, Hirofumi; Kasahara, Ken; Furusawa, Mitsuru

    2016-05-01

    Single-nucleotide polymorphisms (SNPs) are one of the main causes of evolution. The distribution of human SNPs, which were examined in detail genomewide, was analyzed. Three discrete databases of human SNPs were used for this analysis, and similar results were obtained from these databases. It was found that the distribution of the distance between SNPs was approximated by the power law, and the shape of the regions including SNPs had the so-called fractal structure. Although the reason why the distribution of SNPs obeys such a certain law of physics is unclear, a speculation was attempted in connection with the three-dimensional structure of human chromatin which has a fractal structure. PMID:27030000

  4. Myopathy-inducing mutation H40Y in ACTA1 hampers actin filament structure and function.

    PubMed

    Chan, Chun; Fan, Jun; Messer, Andrew E; Marston, Steve B; Iwamoto, Hiroyuki; Ochala, Julien

    2016-08-01

    In humans, more than 200 missense mutations have been identified in the ACTA1 gene. The exact molecular mechanisms by which, these particular mutations become toxic and lead to muscle weakness and myopathies remain obscure. To address this, here, we performed a molecular dynamics simulation, and we used a broad range of biophysical assays to determine how the lethal and myopathy-related H40Y amino acid substitution in actin affects the structure, stability, and function of this protein. Interestingly, our results showed that H40Y severely disrupts the DNase I-binding-loop structure and actin filaments. In addition, we observed that normal and mutant actin monomers are likely to form distinctive homopolymers, with mutant filaments being very stiff, and not supporting proper myosin binding. These phenomena underlie the toxicity of H40Y and may be considered as important triggering factors for the contractile dysfunction, muscle weakness and disease phenotype seen in patients. PMID:27112274

  5. Persistence intervals of fractals

    NASA Astrophysics Data System (ADS)

    Máté, Gabriell; Heermann, Dieter W.

    2014-07-01

    Objects and structures presenting fractal like behavior are abundant in the world surrounding us. Fractal theory provides a great deal of tools for the analysis of the scaling properties of these objects. We would like to contribute to the field by analyzing and applying a particular case of the theory behind the P.H. dimension, a concept introduced by MacPherson and Schweinhart, to seek an intuitive explanation for the relation of this dimension and the fractality of certain objects. The approach is based on recently elaborated computational topology methods and it proves to be very useful for investigating scaling hidden in dimensions lower than the “native” dimension in which the investigated object is embedded. We demonstrate the applicability of the method with two examples: the Sierpinski gasket-a traditional fractal-and a two dimensional object composed of short segments arranged according to a circular structure.

  6. Structure of the Acidianus Filamentous Virus 3 and Comparative Genomics of Related Archaeal Lipothrixviruses▿

    PubMed Central

    Vestergaard, Gisle; Aramayo, Ricardo; Basta, Tamara; Häring, Monika; Peng, Xu; Brügger, Kim; Chen, Lanming; Rachel, Reinhard; Boisset, Nicolas; Garrett, Roger A.; Prangishvili, David

    2008-01-01

    Four novel filamentous viruses with double-stranded DNA genomes, namely, Acidianus filamentous virus 3 (AFV3), AFV6, AFV7, and AFV8, have been characterized from the hyperthermophilic archaeal genus Acidianus, and they are assigned to the Betalipothrixvirus genus of the family Lipothrixviridae. The structures of the approximately 2-μm-long virions are similar, and one of them, AFV3, was studied in detail. It consists of a cylindrical envelope containing globular subunits arranged in a helical formation that is unique for any known double-stranded DNA virus. The envelope is 3.1 nm thick and encases an inner core with two parallel rows of protein subunits arranged like a zipper. Each end of the virion is tapered and carries three short filaments. Two major structural proteins were identified as being common to all betalipothrixviruses. The viral genomes were sequenced and analyzed, and they reveal a high level of conservation in both gene content and gene order over large regions, with this similarity extending partly to the earlier described betalipothrixvirus Sulfolobus islandicus filamentous virus. A few predicted gene products of each virus, in addition to the structural proteins, could be assigned specific functions, including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators, and glycosyltransferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral genome, apparently resulting in phenotypic changes, as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include (i) large inverted terminal repeats exhibiting conserved, regularly spaced direct repeats; (ii) a highly conserved operon encoding the two major structural proteins; (iii) multiple overlapping open reading frames, which may be indicative of gene recoding; (iv) putative 12-bp genetic elements; and (v) partial gene

  7. A bacterial hydrogen-dependent CO2 reductase forms filamentous structures.

    PubMed

    Schuchmann, Kai; Vonck, Janet; Müller, Volker

    2016-04-01

    Interconversion of CO2 and formic acid is an important reaction in bacteria. A novel enzyme complex that directly utilizes molecular hydrogen as electron donor for the reversible reduction of CO2 has recently been identified in the Wood-Ljungdahl pathway of an acetogenic bacterium. This pathway is utilized for carbon fixation as well as energy conservation. Here we describe the further characterization of the quaternary structure of this enzyme complex and the unexpected behavior of this enzyme in polymerizing into filamentous structures. Polymerization of metabolic enzymes into similar structures has been observed only in rare cases but the increasing number of examples point towards a more general characteristic of enzyme functioning. Polymerization of the purified enzyme into ordered filaments of more than 0.1 μm in length was only dependent on the presence of divalent cations. Polymerization was a reversible process and connected to the enzymatic activity of the oxygen-sensitive enzyme with the filamentous form being the most active state. PMID:26833643

  8. Effect of calcium magnesium acetate on the forming property and fractal dimension of sludge pore structure during combustion.

    PubMed

    Zhang, Lihui; Duan, Feng; Huang, Yaji; Chyang, Chiensong

    2015-12-01

    The changes in pore structure characteristics of sewage sludge particles under effect of calcium magnesium acetate (CMA) during combustion were investigated, the samples were characterized by N2 isothermal absorption method, and the data were used to analyze the fractal properties of the obtained samples. Results show that reaction time and the mole ratio of calcium to sulfur (Ca/S ratio) have notable impact on the pore structure and morphology of solid sample. The Brunauer-Emmett-Teller (BET) specific surface area (SBET) of sample increases with Ca/S ratio, while significant decreases with reaction time. The fractal dimension D has the similar trend with that of SBET, indicating that the surface roughness of sludge increases under the effect of CMA adding, resulting in improved the sludge combustion and the desulfurization process. PMID:26342334

  9. Spherical cluster ensembles with fractal structure in LaSrMnO: New form of self-organization in solids

    NASA Astrophysics Data System (ADS)

    Okunev, V. D.; Samoilenko, Z. A.; Szymczak, H.; Szymczak, R.; Burkhovetski, V. V.; Lewandowski, S. J.

    2013-04-01

    The growth of La0.7Sr0.3MnO3 films in magnetron plasma, in special conditions, leads to the appearance of ensembles of micron-sized spherical crystalline clusters with fractal structure, which we consider to be a new form of self-organization in solids. Each ensemble contains 105-106 elementary clusters, 100-250 Å in diameter. Interaction of the clusters in the ensemble is realized through the interatomic chemical bonds, intrinsic to the manganites. Integration of peripheral areas of interacting clusters results in the formation of common intercluster medium in the ensemble. We argue that the ensembles with fractal structure built into paramagnetic disordered matrix have ferromagnetic properties. Absence of sharp borders between elementary clusters and the presence of common intercluster medium inside each ensemble permits to rearrange magnetic order and to change the volume of the ferromagnetic phase, providing automatically a high sensitivity of the material to the external field.

  10. Thermal properties of composite two-layer systems with a fractal inclusion structure

    NASA Astrophysics Data System (ADS)

    Reyes-Salgado, J. J.; Dossetti, V.; Bonilla-Capilla, B.; Carrillo, J. L.

    2015-01-01

    In this work, we study the thermal transport properties of platelike composite two-layer samples made of polyester resin and magnetite inclusions. By means of photoacoustic spectroscopy and thermal relaxation, their effective thermal diffusivity and conductivity were experimentally measured. The composite layers were prepared under the action of a static magnetic field, resulting in anisotropic (fractal) inclusion structures with the formation of chain-like magnetite aggregates parallel to the faces of the layers. In one kind of the bilayers, a composite layer was formed on top of a resin layer while their relative thickness was varied. These samples can be described by known models. In contrast, bilayers with the same concentration of inclusions and the same thickness on both sides, where only the angle between their inclusion structures was systematically varied, show a nontrivial behaviour of their thermal conductivity as a function of this angle. Through a multifractal and lacunarity analysis, we explain the observed thermal response in terms of the complexity of the interface between the layers.

  11. Intrinsic Safety Factors for Glass & Carbon Fibre Composite Filament Wound Structures

    NASA Astrophysics Data System (ADS)

    Bunsell, A. R.; Thionnet, A.; Chou, H. Y.

    2014-02-01

    The determination of intrinsic safety factors for glass and carbon fibre unidirectional composites and filament wound internally pressurised structures, is described. In such structures the fibres are placed on geodesic paths and the pressure induces tensile forces in them. The fibres ensure the strength of the composite and must break for it to fail. Failure is seen in such structures, to depend mainly on the accumulation of fibre breaks. These are initially randomly distributed but become critical when clusters of breaks develop. Long term behaviour of carbon fibre composites is controlled by the viscoelastic relaxation of the matrix around breaks, which can lead to further delayed fibre breaks. Failure in glass fibre structures can additionally be induced by stress corrosion of the glass fibres. This process does not seem to occur with carbon fibres and as the latter are increasingly used in critical structures emphasis is given to them. Until the development of clusters of fibre breaks, in a filament wound structure, no macroscopic changes in the composite behaviour are evident so that failure occurs in a sudden death manner. Multi-scale simulation, taking into account the characteristics of the composite components and scaling up their behaviour under load, accurately describes the overall behaviour of the composite structure. This approach not only allows the behaviour to be described, as a function of time, but also calculates the scatter which will occur in the behaviour of the structure. This allows the intrinsic safety factors of the composite structure to be quantified.

  12. Structural Polymorphism of the ParM Filament and Dynamic Instability

    PubMed Central

    Galkin, Vitold E.; Orlova, Albina; Rivera, Chris; Mullins, R. Dyche; Egelman, Edward H.

    2009-01-01

    Segregation of the R1 plasmid in bacteria relies on ParM, an actin homolog that segregates plasmids by switching between cycles of polymerization and depolymerization. We find similar polymerization kinetics and stability in the presence of either ATP or GTP and a 10-fold affinity preference for ATP over GTP. We used electron cryo-microscopy to evaluate the heterogeneity within ParM filaments. In addition to variable twist ParM has variable axial rise, and both parameters are coupled. Subunits in the same ParM filaments can exist in two different structural states, with the nucleotide-binding cleft closed or open, and the bound nucleotide biases the distribution of states. The interface between protomers is different between these states, and in neither state is it similar to F-actin. Our results suggest that the closed state of the cleft is required but not sufficient for ParM polymerization, and provide a structural basis for the dynamic instability of ParM filaments. PMID:19748346

  13. The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly.

    PubMed

    DiMattia, Michael A; Watts, Norman R; Cheng, Naiqian; Huang, Rick; Heymann, J Bernard; Grimes, Jonathan M; Wingfield, Paul T; Stuart, David I; Steven, Alasdair C

    2016-07-01

    HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes. PMID:27265851

  14. Functional complexity of intermediate filament cytoskeletons: from structure to assembly to gene ablation.

    PubMed

    Herrmann, Harald; Hesse, Michael; Reichenzeller, Michaela; Aebi, Ueli; Magin, Thomas M

    2003-01-01

    The cell biology of intermediate filament (IF) proteins and their filaments is complicated by the fact that the members of the gene family, which in humans amount to at least 65, are differentially expressed in very complex patterns during embryonic development. Thus, different tissues and cells express entirely different sets and amounts of IF proteins, the only exception being the nuclear B-type lamins, which are found in every cell. Moreover, in the course of evolution the individual members of this family have, within one species, diverged so much from each other with regard to sequence and thus molecular properties that it is hard to envision a unifying kind of function for them. The known epidermolytic diseases, caused by single point mutations in keratins, have been used as an argument for a role of IFs in mechanical "stress resistance," something one would not have easily ascribed to the beaded chain filaments, a special type of IF in the eye lens, or to nuclear lamins. Therefore, the power of plastic dish cell biology may be limited in revealing functional clues for these structural elements, and it may therefore be of interest to go to the extreme ends of the life sciences, i.e., from the molecular properties of individual molecules including their structure at the atomic level to targeted inactivation of their genes in living animals, mouse, and worm to define their role more precisely in metazoan cell physiology. PMID:12641211

  15. Structural modifications in fused silica induced by ultraviolet fs laser filaments

    NASA Astrophysics Data System (ADS)

    Zergioti, I.; Kyrkis, K. D.; Papazoglou, D. G.; Tzortzakis, S.

    2007-07-01

    It is shown that the tight focusing of short ultraviolet laser pulses (248 nm, 450 fs) in the bulk of high bandgap transparent solids (fused silica) can result in structural modifications in the material. These can vary from small changes of the refractive index to birefringence, cracks and voids. This restructuring of the medium is due to the high laser intensities attained, and the plasma that is generated through multi-photon processes. The restructuring comes in the form of a string, which is the result of the nonlinear propagation of the laser beam in the medium as a self-trapped filament. We resume the conditions for the generation of the different types of modifications and comment on the temporal evolution and the role of the plasma strings at the trail of the light filaments.

  16. Fractal dust grains in plasma

    SciTech Connect

    Huang, F.; Peng, R. D.; Liu, Y. H.; Chen, Z. Y.; Ye, M. F.; Wang, L.

    2012-09-15

    Fractal dust grains of different shapes are observed in a radially confined magnetized radio frequency plasma. The fractal dimensions of the dust structures in two-dimensional (2D) horizontal dust layers are calculated, and their evolution in the dust growth process is investigated. It is found that as the dust grains grow the fractal dimension of the dust structure decreases. In addition, the fractal dimension of the center region is larger than that of the entire region in the 2D dust layer. In the initial growth stage, the small dust particulates at a high number density in a 2D layer tend to fill space as a normal surface with fractal dimension D = 2. The mechanism of the formation of fractal dust grains is discussed.

  17. Freely Suspended Smectic Filaments and the Structure of the B7 Phase of MHOBOW

    NASA Technical Reports Server (NTRS)

    Clark, N.; Link, D. R.; Maclennan, J. E.

    2000-01-01

    Our recent discovery of the spontaneous formation of chiral domains in fluid smectic phases of achiral bow-shaped molecules opens up a wide variety of possibilities for new liquid crystal phases and phenomena. The basic, spontaneously chiral layer structure of the highest temperature fluid smectic phases, the B2 and B7, are shown. One of the most intriguing aspects of this structure is the plethora of possible phases coming from different stacking sequences of the polar ordering and tilt directions. The four possibilities of next-nearest neighbor alternation are shown. In the original material studied, NOBOW, the ground states found are antiferroelectric, either the racemic SmC(sub S)P(sub A) or the chiral SmC(sub A)P(sub A). We are currently studying MHOBOW, synthesized by D. Walba which, by virtue of its methyl hexyloxy tail has a tendency to form anticlinic layer interfaces, in the hope of finding a phase with a ferroelectric ground state, either SmC(sub A)P(sub S) or SmC(sub S)P(sub A), which can be obtained in NOBOW only by applying a field. Preliminary observations of MHO-BOW have made its study, from the point of view of understanding novel LC structures, extremely high priority. The following truly remarkable characteristics have been revealed: (i) The smectic phase grows out of the isotropic in the form of helical ribbons. The resulting planar aligned textures of focal conics with layers normal to glass plates exhibit bizarre modulations, including stripes and checker-boards. These have also been seen in other materials suggesting that this is a new phase (tentatively called B7), which is a fluid smectic with some kind of in-layer structure. (ii) It is virtually impossible to make freely suspended films of MHOBOW. Rather it makes the freely suspended filaments which preliminary x-ray scattering experiments reveal to have the nested cylinder layer structure indicated; (iii) The powder x-ray diffraction exhibits four resolution-limited smectic layering peaks

  18. Small-angle scattering from fat fractals

    NASA Astrophysics Data System (ADS)

    Anitas, Eugen M.

    2014-06-01

    A number of experimental small-angle scattering (SAS) data are characterized by a succession of power-law decays with arbitrarily decreasing values of scattering exponents. To describe such data, here we develop a new theoretical model based on 3D fat fractals (sets with fractal structure, but nonzero volume) and show how one can extract structural information about the underlying fractal structure. We calculate analytically the monodisperse and polydisperse SAS intensity (fractal form factor and structure factor) of a newly introduced model of fat fractals and study its properties in momentum space. The system is a 3D deterministic mass fractal built on an extension of the well-known Cantor fractal. The model allows us to explain a succession of power-law decays and respectively, of generalized power-law decays (GPLD; superposition of maxima and minima on a power-law decay) with arbitrarily decreasing scattering exponents in the range from zero to three. We show that within the model, the present analysis allows us to obtain the edges of all the fractal regions in the momentum space, the number of fractal iteration and the fractal dimensions and scaling factors at each structural level in the fractal. We applied our model to calculate an analytical expression for the radius of gyration of the fractal. The obtained quantities characterizing the fat fractal are correlated to variation of scaling factor with the iteration number.

  19. a Fractal Permeability Model for Shale Matrix with Multi-Scale Porous Structure

    NASA Astrophysics Data System (ADS)

    Sheng, Mao; Li, Gensheng; Tian, Shouceng; Huang, Zhongwei; Chen, Liqiang

    2016-01-01

    Nanopore structure and its multiscale feature significantly affect the shale-gas permeability. This paper employs fractal theory to build a shale-gas permeability model, particularly considering the effects of multiscale flow within a multiscale pore space. Contrary to previous studies which assume a bundle of capillary tubes with equal size, in this research, this model reflects various flow regimes that occur in multiscale pores and takes the measured pore-size distribution into account. The flow regime within different scales is individually determined by the Knudsen number. The gas permeability is an integral value of individual permeabilities contributed from pores of different scales. Through comparing the results of five shale samples, it is confirmed that the gas permeability varies with the pore-size distribution of the samples, even though their intrinsic permeabilities are the same. Due to consideration of multiscale flow, the change of gas permeability with pore pressure becomes more complex. Consequently, it is necessary to cover the effects of multiscale flow while determining shale-gas permeability.

  20. Fractal Movies.

    ERIC Educational Resources Information Center

    Osler, Thomas J.

    1999-01-01

    Because fractal images are by nature very complex, it can be inspiring and instructive to create the code in the classroom and watch the fractal image evolve as the user slowly changes some important parameter or zooms in and out of the image. Uses programming language that permits the user to store and retrieve a graphics image as a disk file.…

  1. Fractal electronic devices: simulation and implementation.

    PubMed

    Fairbanks, M S; McCarthy, D N; Scott, S A; Brown, S A; Taylor, R P

    2011-09-01

    Many natural structures have fractal geometries that exhibit useful functional properties. These properties, which exploit the recurrence of patterns at increasingly small scales, are often desirable in applications and, consequently, fractal geometry is increasingly employed in diverse technologies ranging from radio antennae to storm barriers. In this paper, we explore the application of fractal geometry to electrical devices. First, we lay the foundations for the implementation of fractal devices by considering diffusion-limited aggregation (DLA) of atomic clusters. Under appropriate growth conditions, atomic clusters of various elements form fractal patterns driven by DLA. We perform a fractal analysis of both simulated and physical devices to determine their spatial scaling properties and demonstrate their potential as fractal circuit elements. Finally, we simulate conduction through idealized and DLA fractal devices and show that their fractal scaling properties generate novel, nonlinear conduction properties in response to depletion by electrostatic gates. PMID:21841218

  2. Fractal electronic devices: simulation and implementation

    NASA Astrophysics Data System (ADS)

    Fairbanks, M. S.; McCarthy, D. N.; Scott, S. A.; Brown, S. A.; Taylor, R. P.

    2011-09-01

    Many natural structures have fractal geometries that exhibit useful functional properties. These properties, which exploit the recurrence of patterns at increasingly small scales, are often desirable in applications and, consequently, fractal geometry is increasingly employed in diverse technologies ranging from radio antennae to storm barriers. In this paper, we explore the application of fractal geometry to electrical devices. First, we lay the foundations for the implementation of fractal devices by considering diffusion-limited aggregation (DLA) of atomic clusters. Under appropriate growth conditions, atomic clusters of various elements form fractal patterns driven by DLA. We perform a fractal analysis of both simulated and physical devices to determine their spatial scaling properties and demonstrate their potential as fractal circuit elements. Finally, we simulate conduction through idealized and DLA fractal devices and show that their fractal scaling properties generate novel, nonlinear conduction properties in response to depletion by electrostatic gates.

  3. Predicting Structural Behavior of Filament Wound Composite Pressure Vessel Using Three Dimensional Shell Analysis

    NASA Astrophysics Data System (ADS)

    Madhavi, M.; Venkat, R.

    2014-01-01

    Fiber reinforced polymer composite materials with their higher specific strength, moduli and tailorability characteristics will result in reduction of weight of the structure. The composite pressure vessels with integrated end domes develop hoop stresses that are twice longitudinal stresses and when isotropic materials like metals are used for development of the hardware and the material is not fully utilized in the longitudinal/meridional direction resulting in over weight components. The determination of a proper winding angles and thickness is very important to decrease manufacturing difficulties and to increase structural efficiency. In the present study a methodology is developed to understand structural characteristics of filament wound pressure vessels with integrated end domes. Progressive ply wise failure analysis of composite pressure vessel with geodesic end domes is carried out to determine matrix crack failure, burst pressure values at various positions of the shell. A three dimensional finite element analysis is computed to predict the deformations and stresses in the composite pressure vessel. The proposed method could save the time to design filament wound structures, to check whether the ply design is safe for the given input conditions and also can be adapted to non-geodesic structures. The results can be utilized to understand structural characteristics of filament wound pressure vessels with integrated end domes. This approach can be adopted for various applications like solid rocket motor casings, automobile fuel storage tanks and chemical storage tanks. Based on the predictions a composite pressure vessel is designed and developed. Hydraulic test is performed on the composite pressure vessel till the burst pressure.

  4. Stochastic dislocation kinetics and fractal structures in deforming metals probed by acoustic emission and surface topography measurements

    SciTech Connect

    Vinogradov, A.; Yasnikov, I. S.; Estrin, Y.

    2014-06-21

    We demonstrate that the fractal dimension (FD) of the dislocation population in a deforming material is an important quantitative characteristic of the evolution of the dislocation structure. Thus, we show that peaking of FD signifies a nearing loss of uniformity of plastic flow and the onset of strain localization. Two techniques were employed to determine FD: (i) inspection of surface morphology of the deforming crystal by white light interferometry and (ii) monitoring of acoustic emission (AE) during uniaxial tensile deformation. A connection between the AE characteristics and the fractal dimension determined from surface topography measurements was established. As a common platform for the two methods, the dislocation density evolution in the bulk was used. The relations found made it possible to identify the occurrence of a peak in the median frequency of AE as a harbinger of plastic instability leading to necking. It is suggested that access to the fractal dimension provided by AE measurements and by surface topography analysis makes these techniques important tools for monitoring the evolution of the dislocation structure during plastic deformation—both as stand-alone methods and especially when used in tandem.

  5. Keratin intermediate filament structure. Crosslinking studies yield quantitative information on molecular dimensions and mechanism of assembly.

    PubMed

    Steinert, P M; Marekov, L N; Fraser, R D; Parry, D A

    1993-03-20

    One of the major obstacles to solving the full three-dimensional structure of keratin intermediate filaments (KIF) is the determination of the exact mode(s) of alignment of nearest-neighbor molecules; this in turn requires precise information of the lengths of the non-alpha-helical linker segments within the coiled-coil alpha-helical heterodimer molecule. In this study, we have induced lysine-lysine and cysteine-cysteine crosslinks between keratin intermediate filament molecules in small assembly-competent oligomers, isolated them and then characterized the natures and locations of the crosslinks. Of more than 100 found, 21 quantitatively major crosslinks were used to obtain the relative axial alignments of rod domain segments by least-squares fitting methods. Three dominant modes of alignment were found. In each case the molecules are antiparallel with the first involving molecules in approximate register (stagger = -0.2 nm), the second involving molecules staggered so as to bring the 1B segments into approximate alignment (stagger = -16.1 nm), and the third involving molecules staggered so as to bring the 2B segments into approximate alignment (stagger = 28.2 nm). In addition, the data enable quantitative estimates to be made for the first time of the lengths of the non-coiled-coil segments (L1 = 2.5 nm, L12 = 1.6 nm, L2 = 0.8 nm), and the total length of the rod domain (46.0 nm). Alignment of molecules according to these parameters permits construction of a two-dimensional surface lattice which displays a 1.6 nm (10 or 11 residue) overlap between similarly directed molecules. Together, the data predict six important overlapping sequence regions that recur about 16 times per 46 nm of filament length. Interestingly, synthetic peptides corresponding to these sequences, singly or in combination, significantly interfere with keratin filament structural integrity. These results thus represent the most significant set of structural constraints for KIF yet available and

  6. Effect of high-power laser divergence on the plasma structural parameters during multiple filamentation in air

    NASA Astrophysics Data System (ADS)

    Geints, Yu. E.; Zemlyanov, A. A.

    2016-06-01

    Multiple filamentation of an infrared high-power laser pulse in air is considered. Based on the numerical solution to the unidirectional pulse propagation equation, the effect of radiation external focusing on the spatial structure of the plasma area produced in the filamentation region is studied. We show that the number of generated plasma channels in the beam wake and the density of their spatial distribution over the filamentation region depend on the initial divergence of laser radiation. We found that in a specific range of beam focusing the number of produced plasma channels could be minimized due to the formation of a consolidated thick plasma bunch at the beam axis.

  7. Fractals in physiology and medicine

    NASA Technical Reports Server (NTRS)

    Goldberger, Ary L.; West, Bruce J.

    1987-01-01

    The paper demonstrates how the nonlinear concepts of fractals, as applied in physiology and medicine, can provide an insight into the organization of such complex structures as the tracheobronchial tree and heart, as well as into the dynamics of healthy physiological variability. Particular attention is given to the characteristics of computer-generated fractal lungs and heart and to fractal pathologies in these organs. It is shown that alterations in fractal scaling may underlie a number of pathophysiological disturbances, including sudden cardiac death syndromes.

  8. Wet spinning of silk polymer. II. Effect of drawing on the structural characteristics and properties of filament.

    PubMed

    Um, In Chul; Ki, Chang Seok; Kweon, HaeYong; Lee, Kwang Gill; Ihm, Dae Woo; Park, Young Hwan

    2004-04-01

    Regenerated silk fibroin (SF) filaments were prepared by the wet spinning technique. The rheological behavior of the SF dope solution prepared with formic acid was examined and the drawing effect on the structural characteristics and mechanical properties of SF filament was comparatively studied with those of natural silk fiber. SF dope exhibited shear thinning, but, as the dope concentration increased, the effect of shear thinning decreased, an indication that a higher concentration of dope solution will result in good spinnability. Wet-spun SF filaments exhibited a uniform and circular cross-sectional shape and dense morphology under SEM observation. X-ray diffraction (XRD) results revealed that the crystallinity of wet-spun regenerated filaments was hardly affected by the draw ratio, whereas the crystalline and amorphous orientation of regenerated SF filament showed different features depending on the drawing. The crystalline orientation of regenerated filaments increased with an increase of draw ratio and was lower than that of natural silk fiber. On the contrary, the amorphous orientation was constant throughout 1X-5X draw ratios, after an abrupt increase at 1X, and was higher than that of natural silk fiber. These differences in the orientation behaviors are attributed to the different spinning mechanisms involved. The tensile property was strongly dependent on the draw ratio. The breaking strength and elongation of the regenerated filament at 5X draw ratio were 2.2 g/day and 17%, respectively. PMID:15178015

  9. Fabrication of transparent antifouling thin films with fractal structure by atmospheric pressure cold plasma deposition.

    PubMed

    Miyagawa, Hayato; Yamauchi, Koji; Kim, Yoon-Kee; Ogawa, Kazufumi; Yamaguchi, Kenzo; Suzaki, Yoshifumi

    2012-12-21

    Antifouling surface with both superhydrophobicity and oil-repellency has been fabricated on glass substrate by forming fractal microstructure(s). The fractal microstructure was constituted by transparent silica particles of 100 nm diameter and transparent zinc-oxide columns grown on silica particles by atmospheric pressure cold plasma deposition. The sample surface was coated with a chemically adsorbed monomolecular layer. We found that one sample has the superhydrophobic ability with a water droplet contact angle of more than 150°, while another sample has a high transmittance of more than 85% in a wavelength range from 400 to 800 nm. PMID:23186100

  10. The Structure and Assembly Mechanism of a Novel Three-Stranded Tubulin Filament that Centers Phage DNA

    PubMed Central

    Zehr, Elena A.; Kraemer, James A.; Erb, Marcella L.; Coker, Joanna K.C.; Montabana, Elizabeth A.; Pogliano, Joe; Agard, David A.

    2014-01-01

    SUMMARY Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural diversity is poorly understood. Here, we determine a 7.1 Å cryo-EM reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins. PMID:24631461

  11. Searching for filaments and large-scale structure around DAFT/FADA clusters

    NASA Astrophysics Data System (ADS)

    Durret, F.; Márquez, I.; Acebrón, A.; Adami, C.; Cabrera-Lavers, A.; Capelato, H.; Martinet, N.; Sarron, F.; Ulmer, M. P.

    2016-04-01

    Context. Clusters of galaxies are located at the intersection of cosmic filaments and are still accreting galaxies and groups along these preferential directions. However, because of their relatively low contrast on the sky, filaments are difficult to detect (unless a large amount of spectroscopic data are available), and unambiguous detections have been limited until now to relatively low redshifts (z< ~ 0.3). Aims: This project is aimed at searching for extensions and filaments around clusters, traced by galaxies selected to be at the cluster redshift based on the red sequence. In the 0.4 filaments. Methods: We have searched for extensions and filaments around the thirty clusters of the DAFT/FADA survey for which we had deep wide field photometric data. For each cluster, based on a colour-magnitude diagram, we selected galaxies that were likely to belong to the red sequence, and hence to be at the cluster redshift, and built density maps. By computing the background for each of these maps and drawing 3σ contours, we estimated the elongations of the structures detected in this way. Whenever possible, we identified the other structures detected on the density maps with clusters listed in NED. Results: We find clear elongations in twelve clusters out of thirty, with sizes that can reach up to 7.6 Mpc. Eleven other clusters have neighbouring structures, but the zones linking them are not detected in the density maps at a 3σ level. Three clusters show no extended structure and no neighbours, and four clusters are of too low contrast to be clearly visible on our density maps. Conclusions: The simple method we have applied appears to work well to show the existence of filaments and/or extensions around a number of clusters in the redshift range 0.4

  12. Crystal structure of AFV1-102, a protein from the acidianus filamentous virus 1

    PubMed Central

    Keller, Jenny; Leulliot, Nicolas; Collinet, Bruno; Campanacci, Valerie; Cambillau, Christian; Pranghisvilli, David; van Tilbeurgh, Herman

    2009-01-01

    Viruses infecting hyperthermophilic archaea have intriguing morphologies and genomic properties. The vast majority of their genes do not have homologs other than in other hyperthermophilic viruses, and the biology of these viruses is poorly understood. As part of a structural genomics project on the proteins of these viruses, we present here the structure of a 102 amino acid protein from acidianus filamentous virus 1 (AFV1-102). The structure shows that it is made of two identical motifs that have poor sequence similarity. Although no function can be proposed from structural analysis, tight binding of the gateway tag peptide in a groove between the two motifs suggests AFV1-102 is involved in protein protein interactions. PMID:19319936

  13. Book review of "Biophysical Chemistry of Fractal Structures and Processes in Environmental Systems"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The editors are N. Senesi and K.J. Wilkinson, and the book is published in 2008 by John Wiley and Sons, with 323 pages. This book is part of the IUPAC series on “Analytical and physical chemistry of environmental systems.” Nineteen generally well-known fractal scientists have contributed to this vol...

  14. Direct observation of anodic dissolution and filament growth behavior in polyethylene-oxide-based atomic switch structures

    NASA Astrophysics Data System (ADS)

    Krishnan, Karthik; Tsuruoka, Tohru; Aono, Masakazu

    2016-06-01

    We directly observed anodic dissolution and subsequent filament growth behavior in a planar atomic switch structure with Ag salt incorporated polyethylene oxide (Ag-PEO) film using in situ optical microscopy and ex situ scanning electron microscopy. The high ionic conductivities of Ag-PEO films enable the investigation of filament formation under voltage bias, even in micrometer-scaled devices. It was found that the filament formation changes from unidirectional growth to dendritic growth, depending on its distance from the grounded electrode. Based on this understanding of filament growth dynamics in planar devices, highly stable resistive switching was achieved in an Ag/Ag-PEO/Pt stacked device with an Ag-PEO film thickness of 100 nm. The device showed repeated switching operations for more than 102 sweep cycles, with a high ON/OFF resistance ratio of 105.

  15. The Language of Fractals.

    ERIC Educational Resources Information Center

    Jurgens, Hartmut; And Others

    1990-01-01

    The production and application of images based on fractal geometry are described. Discussed are fractal language groups, fractal image coding, and fractal dialects. Implications for these applications of geometry to mathematics education are suggested. (CW)

  16. The primary structure of component 8c-1, a subunit protein of intermediate filaments in wool keratin. Relationships with proteins from other intermediate filaments.

    PubMed Central

    Dowling, L M; Crewther, W G; Inglis, A S

    1986-01-01

    Component 8c-1, one of four highly homologous component-8 subunit proteins present in the microfibrils of wool, was isolated as its S-carboxymethyl derivative and its amino acid sequence was determined. Large peptides were isolated after cleaving the protein chemically or enzymically and the sequence of each was determined with an automatic Sequenator. The peptides were ordered by sequence overlaps and, in some instances, by homology with known sequences from other component-8 subunits. The C-terminal residues were identified by three procedures. Full details of the various procedures used have been deposited as Supplementary Publication SUP 50133 (4 pp.) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1986) 233, 5. The result showed that the protein comprises 412 residues and has an Mr, including the N-terminal acetyl group, of 48,300. The sequence of residues 98-200 of component 8c-1 was found to correspond to the partial or complete sequences of four homologous type I helical segments previously isolated from helical fragments recovered from chymotryptic digests of microfibrillar proteins of wool [Crewther & Dowling (1971) Appl. Polym. Symp. 18, 1-20; Crewther, Gough, Inglis & McKern (1978) Text. Res. J. 48, 160-162; Gough, Inglis & Crewther (1978) Biochem. J. 173, 385]. Considered in relation to amino acid sequences of other intermediate-filament proteins, the sequence is in accord with the view that keratin filament proteins are of two types [Hanukoglu & Fuchs (1983) Cell (Cambridge, Mass.) 33, 915-924]. Filament proteins from non-keratinous tissues, such as desmin, vimentin, neurofilament proteins and the glial fibrillary acidic protein, which form monocomponent filaments, constitute a third type. It is suggested that as a whole the proteins from intermediate filaments be classed as filamentins, the three types at present identified forming

  17. Fractal dynamics of earthquakes

    SciTech Connect

    Bak, P.; Chen, K.

    1995-05-01

    Many objects in nature, from mountain landscapes to electrical breakdown and turbulence, have a self-similar fractal spatial structure. It seems obvious that to understand the origin of self-similar structures, one must understand the nature of the dynamical processes that created them: temporal and spatial properties must necessarily be completely interwoven. This is particularly true for earthquakes, which have a variety of fractal aspects. The distribution of energy released during earthquakes is given by the Gutenberg-Richter power law. The distribution of epicenters appears to be fractal with dimension D {approx} 1--1.3. The number of after shocks decay as a function of time according to the Omori power law. There have been several attempts to explain the Gutenberg-Richter law by starting from a fractal distribution of faults or stresses. But this is a hen-and-egg approach: to explain the Gutenberg-Richter law, one assumes the existence of another power-law--the fractal distribution. The authors present results of a simple stick slip model of earthquakes, which evolves to a self-organized critical state. Emphasis is on demonstrating that empirical power laws for earthquakes indicate that the Earth`s crust is at the critical state, with no typical time, space, or energy scale. Of course the model is tremendously oversimplified; however in analogy with equilibrium phenomena they do not expect criticality to depend on details of the model (universality).

  18. The topological insulator in a fractal space

    SciTech Connect

    Song, Zhi-Gang; Zhang, Yan-Yang; Li, Shu-Shen

    2014-06-09

    We investigate the band structures and transport properties of a two-dimensional model of topological insulator, with a fractal edge or a fractal bulk. A fractal edge does not affect the robust transport even when the fractal pattern has reached the resolution of the atomic-scale, because the bulk is still well insulating against backscattering. On the other hand, a fractal bulk can support the robust transport only when the fractal resolution is much larger than a critical size. Smaller resolution of bulk fractal pattern will lead to remarkable backscattering and localization, due to strong couplings of opposite edge states on narrow sub-edges which appear almost everywhere in the fractal bulk.

  19. Analysis of fractals with combined partition

    NASA Astrophysics Data System (ADS)

    Dedovich, T. G.; Tokarev, M. V.

    2016-03-01

    The space—time properties in the general theory of relativity, as well as the discreteness and non-Archimedean property of space in the quantum theory of gravitation, are discussed. It is emphasized that the properties of bodies in non-Archimedean spaces coincide with the properties of the field of P-adic numbers and fractals. It is suggested that parton showers, used for describing interactions between particles and nuclei at high energies, have a fractal structure. A mechanism of fractal formation with combined partition is considered. The modified SePaC method is offered for the analysis of such fractals. The BC, PaC, and SePaC methods for determining a fractal dimension and other fractal characteristics (numbers of levels and values of a base of forming a fractal) are considered. It is found that the SePaC method has advantages for the analysis of fractals with combined partition.

  20. Synchrosqueezed wavelet transform-fractality model for locating, detecting, and quantifying damage in smart highrise building structures

    NASA Astrophysics Data System (ADS)

    Amezquita-Sanchez, Juan P.; Adeli, Hojjat

    2015-06-01

    A new methodology is presented for (a) detecting, (b) locating, and (c) quantifying the damage severity in a smart highrise building structure. The methodology consists of three steps: In step 1, the synchrosqueezed wavelet transform is used to eliminate the noise in the signals. In step 2, a nonlinear dynamics measure based on the chaos theory, fractality dimension (FD), is employed to detect features to be used for damage detection. In step 3, a new structural damage index, based on the estimated FD values, is proposed as a measure of the condition of the structure. Further, the damage location is obtained using the changes of the estimated FD values. Three different FD algorithms for computing the fractality of time series signals are investigated. They are Katz’s FD, Higuchi’s FD, and box dimension. The usefulness and effectiveness of the proposed methodology are validated using the sensed data obtained experimentally for the 1:20 scaled model of a 38-storey concrete building structure.

  1. Tilt Angles of Quiescent Filaments and Filaments of Active Regions

    NASA Astrophysics Data System (ADS)

    Tlatov, A. G.; Kuzanyan, K. M.; Vasil'yeva, V. V.

    2016-04-01

    We carry out study of tilt angles of solar filaments using the data from the two observatories: Meudon Observatory and Kislovodsk Mountain Astronomical Station for the century-long period 1919-2014. We developed special software for digitization of the filaments structures on Hα synoptic maps. The filaments were vectorized in semi-automatic mode. The tilt angles of filaments with respect to the equator (τ) were analyzed. Approximately 2/3 of the filaments have positive angles τ >0, which is defined as when the eastern end of the filaments are closer to the poles than the western ones. We have separated tilts for the filaments which are close to the active region structures and those of quiescent filaments. We found that long quiescent filaments mainly have negative tilts. The filaments which are close to active regions mainly have positive tilt angles.

  2. Identification of a Gene Essential for Sheathed Structure Formation in Sphaerotilus natans, a Filamentous Sheathed Bacterium

    PubMed Central

    Suzuki, Toshihiko; Kanagawa, Takahiro; Kamagata, Yoichi

    2002-01-01

    Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in substrate-rich media it grows as single rod-shaped cells, whereas in substrate-limited media it grows as filaments. To identify genes responsible for sheath formation, we carried out transposon Tn5 mutagenesis. Of the approximately 20,000 mutants obtained, 7 did not form sheathed structures. Sequencing of the Tn5-flanking regions showed that five of the seven Tn5 insertions converged at the same open reading frame, designated sthA. The deduced amino acids encoded by sthA were found to be homologous to glycosyltransferase, which is known to be involved in linking sugars to lipid carriers during bacterial exopolysaccharide biosynthesis. Disruption of the gene of the wild-type strain by inserting a kanamycin resistance gene cassette also resulted in sheathless growth under either type of nutrient condition. These findings indicate that sthA is a crucial component responsible for sheath formation. PMID:11772646

  3. Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments

    PubMed Central

    Tang, Shaogeng; Henne, W Mike; Borbat, Peter P; Buchkovich, Nicholas J; Freed, Jack H; Mao, Yuxin; Fromme, J Christopher; Emr, Scott D

    2015-01-01

    The endosomal sorting complexes required for transport (ESCRTs) constitute hetero-oligomeric machines that catalyze multiple topologically similar membrane-remodeling processes. Although ESCRT-III subunits polymerize into spirals, how individual ESCRT-III subunits are activated and assembled together into a membrane-deforming filament remains unknown. Here, we determine X-ray crystal structures of the most abundant ESCRT-III subunit Snf7 in its active conformation. Using pulsed dipolar electron spin resonance spectroscopy (PDS), we show that Snf7 activation requires a prominent conformational rearrangement to expose protein-membrane and protein-protein interfaces. This promotes the assembly of Snf7 arrays with ~30 Å periodicity into a membrane-sculpting filament. Using a combination of biochemical and genetic approaches, both in vitro and in vivo, we demonstrate that mutations on these protein interfaces halt Snf7 assembly and block ESCRT function. The architecture of the activated and membrane-bound Snf7 polymer provides crucial insights into the spatially unique ESCRT-III-mediated membrane remodeling. DOI: http://dx.doi.org/10.7554/eLife.12548.001 PMID:26670543

  4. Hypothesis testing on the fractal structure of behavioral sequences: the Bayesian assessment of scaling methodology.

    PubMed

    Moscoso del Prado Martín, Fermín

    2013-12-01

    I introduce the Bayesian assessment of scaling (BAS), a simple but powerful Bayesian hypothesis contrast methodology that can be used to test hypotheses on the scaling regime exhibited by a sequence of behavioral data. Rather than comparing parametric models, as typically done in previous approaches, the BAS offers a direct, nonparametric way to test whether a time series exhibits fractal scaling. The BAS provides a simpler and faster test than do previous methods, and the code for making the required computations is provided. The method also enables testing of finely specified hypotheses on the scaling indices, something that was not possible with the previously available methods. I then present 4 simulation studies showing that the BAS methodology outperforms the other methods used in the psychological literature. I conclude with a discussion of methodological issues on fractal analyses in experimental psychology. PMID:24417750

  5. Quantitative multi-scale analysis of mineral distributions and fractal pore structures for a heterogeneous Junger Basin shale

    NASA Astrophysics Data System (ADS)

    Wang, Y. D.; Liu, K. Y.; Yang, Y. S.; Ren, Y. Q.; Hu, T.; Deng, B.; Xiao, T. Q.

    2016-04-01

    Three dimensional (3D) characterization of shales has recently attracted wide attentions in relation to the growing importance of shale oil and gas. Obtaining a complete 3D compositional distribution of shale has proven to be challenging due to its multi-scale characteristics. A combined multi-energy X-ray micro-CT technique and data-constrained modelling (DCM) approach has been used to quantitatively investigate the multi-scale mineral and porosity distributions of a heterogeneous shale from the Junger Basin, northwestern China by sub-sampling. The 3D sub-resolution structures of minerals and pores in the samples are quantitatively obtained as the partial volume fraction distributions, with colours representing compositions. The shale sub-samples from two areas have different physical structures for minerals and pores, with the dominant minerals being feldspar and dolomite, respectively. Significant heterogeneities have been observed in the analysis. The sub-voxel sized pores form large interconnected clusters with fractal structures. The fractal dimensions of the largest clusters for both sub-samples were quantitatively calculated and found to be 2.34 and 2.86, respectively. The results are relevant in quantitative modelling of gas transport in shale reservoirs.

  6. Filament winding

    NASA Astrophysics Data System (ADS)

    Shibley, A. M.

    The major aspects of filament winding are discussed, emphasizing basic reinforcement and matrix materials, winding procedures, process controls, and cured composite properties. Fiberglass (E-glass and S-glass strengths are 500,000 and 665,000 psi respectively) and polyester resins are the principal reinforcement constituent materials. Graphite and aramid reinforcements are being used more frequently, primarily for the more critical pressure vessels. Matrix systems are most commonly based on epoxy as it has superior mechanical properties, fatigue behavior, and heat resistance as compard with polyesters. A fiberglass overwrap of PVC pipe is an anticipated development in on-site winding and combination winding, and the compression molding of filament wound lay-ups will be investigated. The fabrication of weight-sensitive structural components may be achieved by using such moldings.

  7. Structural Dynamics of C-domain of Cardiac Troponin I Protein in Reconstituted Thin Filament*

    PubMed Central

    Zhou, Zhiqun; Li, King-Lun; Rieck, Daniel; Ouyang, Yexin; Chandra, Murali; Dong, Wen-Ji

    2012-01-01

    The regulatory function of cardiac troponin I (cTnI) involves three important contiguous regions within its C-domain: the inhibitory region (IR), the regulatory region (RR), and the mobile domain (MD). Within these regions, the dynamics of regional structure and kinetics of transitions in dynamic state are believed to facilitate regulatory signaling. This study was designed to use fluorescence anisotropy techniques to acquire steady-state and kinetic information on the dynamic state of the C-domain of cTnI in the reconstituted thin filament. A series of single cysteine cTnI mutants was generated, labeled with the fluorophore tetramethylrhodamine, and subjected to various anisotropy experiments at the thin filament level. The structure of the IR was found to be less dynamic than that of the RR and the MD, and Ca2+ binding induced minimal changes in IR dynamics: the flexibility of the RR decreased, whereas the MD became more flexible. Anisotropy stopped-flow experiments showed that the kinetics describing the transition of the MD and RR from the Ca2+-bound to the Ca2+-free dynamic states were significantly faster (53.2–116.8 s−1) than that of the IR (14.1 s−1). Our results support the fly casting mechanism, implying that an unstructured MD with rapid dynamics and kinetics plays a critical role to initiate relaxation upon Ca2+ dissociation by rapidly interacting with actin to promote the dissociation of the RR from the N-domain of cTnC. In contrast, the IR responds to Ca2+ signals with slow structural dynamics and transition kinetics. The collective findings suggested a fourth state of activation. PMID:22207765

  8. Fractal Electronic Circuits Assembled From Nanoclusters

    NASA Astrophysics Data System (ADS)

    Fairbanks, M. S.; McCarthy, D.; Taylor, R. P.; Brown, S. A.

    2009-07-01

    Many patterns in nature can be described using fractal geometry. The effect of this fractal character is an array of properties that can include high internal connectivity, high dispersivity, and enhanced surface area to volume ratios. These properties are often desirable in applications and, consequently, fractal geometry is increasingly employed in technologies ranging from antenna to storm barriers. In this paper, we explore the application of fractal geometry to electrical circuits, inspired by the pervasive fractal structure of neurons in the brain. We show that, under appropriate growth conditions, nanoclusters of Sb form into islands on atomically flat substrates via a process close to diffusion-limited aggregation (DLA), establishing fractal islands that will form the basis of our fractal circuits. We perform fractal analysis of the islands to determine the spatial scaling properties (characterized by the fractal dimension, D) of the proposed circuits and demonstrate how varying growth conditions can affect D. We discuss fabrication approaches for establishing electrical contact to the fractal islands. Finally, we present fractal circuit simulations, which show that the fractal character of the circuit translates into novel, non-linear conduction properties determined by the circuit's D value.

  9. Spherical cluster ensembles with fractal structure in LaSrMnO: New form of self-organization in solids

    SciTech Connect

    Okunev, V. D.; Samoilenko, Z. A.; Burkhovetski, V. V.; Szymczak, H.; Szymczak, R.; Lewandowski, S. J.

    2013-04-28

    The growth of La{sub 0.7}Sr{sub 0.3}MnO{sub 3} films in magnetron plasma, in special conditions, leads to the appearance of ensembles of micron-sized spherical crystalline clusters with fractal structure, which we consider to be a new form of self-organization in solids. Each ensemble contains 10{sup 5}-10{sup 6} elementary clusters, 100-250 A in diameter. Interaction of the clusters in the ensemble is realized through the interatomic chemical bonds, intrinsic to the manganites. Integration of peripheral areas of interacting clusters results in the formation of common intercluster medium in the ensemble. We argue that the ensembles with fractal structure built into paramagnetic disordered matrix have ferromagnetic properties. Absence of sharp borders between elementary clusters and the presence of common intercluster medium inside each ensemble permits to rearrange magnetic order and to change the volume of the ferromagnetic phase, providing automatically a high sensitivity of the material to the external field.

  10. Experimental validation of a signal-based approach for structural earthquake damage detection using fractal dimension of time frequency feature

    NASA Astrophysics Data System (ADS)

    Tao, Dongwang; Mao, Chenxi; Zhang, Dongyu; Li, Hui

    2014-12-01

    This article extends a signal-based approach formerly proposed by the authors, which utilizes the fractal dimension of time frequency feature (FDTFF) of displacements, for earthquake damage detection of moment resist frame (MRF), and validates the approach with shaking table tests. The time frequency feature (TFF) of the relative displacement at measured story is defined as the real part of the coefficients of the analytical wavelet transform. The fractal dimension (FD) is to quantify the TFF within the fundamental frequency band using box counting method. It is verified that the FDTFFs at all stories of the linear MRF are identical with the help of static condensation method and modal superposition principle, while the FDTFFs at the stories with localized nonlinearities due to damage will be different from those at the stories without nonlinearities using the reverse-path methodology. By comparing the FDTFFs of displacements at measured stories in a structure, the damage-induced nonlinearity of the structure under strong ground motion can be detected and localized. Finally shaking table experiments on a 1:8 scale sixteen-story three-bay steel MRF with added frictional dampers, which generate local nonlinearities, are conducted to validate the approach.

  11. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels.

    PubMed

    Fornander, Louise H; Frykholm, Karolin; Fritzsche, Joachim; Araya, Joshua; Nevin, Philip; Werner, Erik; Çakır, Ali; Persson, Fredrik; Garcin, Edwige B; Beuning, Penny J; Mehlig, Bernhard; Modesti, Mauro; Westerlund, Fredrik

    2016-08-23

    RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes. PMID:27479732

  12. Relation of the fractal structure of organic pigments to their performance

    NASA Astrophysics Data System (ADS)

    Skillas, G.; Agashe, N.; Kohls, D. J.; Ilavsky, J.; Jemian, P.; Clapp, L.; Schwartz, R. J.; Beaucage, G.

    2002-05-01

    Different pigments embedded in polymer matrices were examined by small angle scattering of x- rays over 3 wave number decades. The scattering intensities show differences both in the mass fractal dimension (varying between 1.4 and 2.67) and the size of the particles. The differences are pronounced between dry pigment powders and the same powders in a polymer matrix as well as between the pigments themselves. Further, a correlation of pigment geometrical configuration and pigment performance, as perceived by the human eye, shows how pigments with a maximum color brightness per pigment mass can be created.

  13. [Fractal structure and physicochemical characteristics analysis of aerobic sludge floc in A2/O process].

    PubMed

    Xuan, Ke-Jia; Wang, Yi-Li; Wei, Ke-Ji; Du, Jie-Di; Zhang, Tong

    2009-07-15

    Image analysis method, free settling test were performed to determine the morphology, particle size distribution, free setting velocity, effective density, porosity and fractal dimensions in different topological spaces of aerobic sludge flocs in A2/O process. Then the physicochemical indices, corresponding to the sludge properties such as: settleability, compressibility, dewaterability and stability, were measured. Besides these, the extra-cellular polymeric substances (EPS) were extracted from sludge and classified as different components. The results showed that the sludge floc with irregular morphology was high porous. The effective densities of these sludge flocs generally increased with the increase of their size, but the porosities within the flocs and their free settling velocities decreased accordingly. The median diameters of the sludge flocs at two different sampling times were 248.81 microm, 332.86 microm, respectively. Their corresponding average effective densities were 0.0040, 0.0072 g x cm(-3), and average free settling velocities were 2.67 mm x s(-1), 4.79 mm x s(-1), and giving the average porosities of0.94, 0.89. The dimensional analysis methods, based on power law correlations between floc perimeter, projected area and maximum length, were used to determine the one- and two-dimensional fractal dimensions (D1 and D2 ) of sludge flocs, giving D1 = 1.03 or 1.19, D2 = 1.64 or 1.84. The mass fractal dimensions (D(f)) of these sludge flocs were determined by the bi-logarithm relations of effective density (based on Logan empirical equation)-maximum diameter which equaled to 1.74 or 2.29. The above results demonstrated that the second sample of sludge flocs was larger and more compact, but smoother than the first sample. Moreover, the results also showed that the sludge flocs in A2/O process with high flocculating ability or high negative surface charge had high values of sludge volume index (SVI) and zone setting velocity (ZSV), and low values of

  14. The structure and poloidal dynamics of blob filaments in TJ-K

    NASA Astrophysics Data System (ADS)

    Garland, S.; Fuchert, G.; Ramisch, M.; Hirth, T.

    2016-04-01

    Relatively dense, field-aligned, filament-like structures (blobs) have been observed to propagate radially and poloidally through the scrape-off layer (SOL) in magnetically confined fusion plasmas, and contribute significantly to SOL transport. A detailed understanding of blob structure and dynamics, and their dependence on magnetic field geometry, is important in magnetic confinement physics for the prediction of heat loads on reactor wall facing components, as well as for understanding plasma confinement and neutral particle recycling. Experimentally deduced centre of mass poloidal blob velocity components, obtained using the conditional averaging technique, have been compared to an analytical blob model which has been simplified to express blob velocity in terms of the magnetic field curvature vector. Background flows are not incorporated into the analytical model, and must be added in to obtain good agreement with the experimental data. In addition, the 3D structure of blobs in TJ-K has been investigated using the conditional average of density fluctuations in two toroidally separated poloidal planes. Blobs are observed to be aligned to a flux tube near to the last closed flux surface, in the blob birth region. However at positions further along the blob trajectory, the structures do not deform according to the magnetic shear, rather they remain rigid, and retain their original form.

  15. Regulation of structure and function of sarcomeric actin filaments in striated muscle of the nematode Caenorhabditis elegans

    PubMed Central

    Ono, Shoichiro

    2014-01-01

    The nematode Caenorhabditis elegans has been used as a valuable system to study structure and function of striated muscle. The body wall muscle of C. elegans is obliquely striated muscle with highly organized sarcomeric assembly of actin, myosin, and other accessary proteins. Genetic and molecular biological studies in C. elegans have identified a number of genes encoding structural and regulatory components for the muscle contractile apparatuses, and many of them have counterparts in mammalian cardiac and skeletal muscles or striated muscles in other invertebrates. Applicability of genetics, cell biology, and biochemistry has made C. elegans an excellent system to study mechanisms of muscle contractility and assembly and maintenance of myofibrils. This review focuses on the regulatory mechanisms of structure and function of actin filaments in the C. elegans body wall muscle. Sarcomeric actin filaments in C. elegans muscle are associated with the troponin-tropomyosin system that regulates the actin-myosin interaction. Proteins that bind to the side and ends of actin filaments support ordered assembly of thin filaments. Furthermore, regulators of actin dynamics play important roles in initial assembly, growth, and maintenance of sarcomeres. The knowledge acquired in C. elegans can serve as bases to understand the basic mechanisms of muscle structure and function. PMID:25125169

  16. Crystal structure of the C-terminal half of tropomodulin and structural basis of actin filament pointed-end capping.

    PubMed Central

    Krieger, Inna; Kostyukova, Alla; Yamashita, Atsuko; Nitanai, Yasushi; Maéda, Yuichiro

    2002-01-01

    Tropomodulin is the unique pointed-end capping protein of the actin-tropomyosin filament. By blocking elongation and depolymerization, tropomodulin regulates the architecture and the dynamics of the filament. Here we report the crystal structure at 1.45-A resolution of the C-terminal half of tropomodulin (C20), the actin-binding moiety of tropomodulin. C20 is a leucine-rich repeat domain, and this is the first actin-associated protein with a leucine-rich repeat. Binding assays suggested that C20 also interacts with the N-terminal fragment, M1-M2-M3, of nebulin. Based on the crystal structure, we propose a model for C20 docking to the actin subunit at the pointed end. Although speculative, the model is consistent with the idea that a tropomodulin molecule competes with an actin subunit for a pointed end. The model also suggests that interactions with tropomyosin, actin, and nebulin are all possible sources of influences on the dynamic properties of pointed-end capping by tropomodulin. PMID:12414704

  17. A Brief Historical Introduction to Fractals and Fractal Geometry

    ERIC Educational Resources Information Center

    Debnath, Lokenath

    2006-01-01

    This paper deals with a brief historical introduction to fractals, fractal dimension and fractal geometry. Many fractals including the Cantor fractal, the Koch fractal, the Minkowski fractal, the Mandelbrot and Given fractal are described to illustrate self-similar geometrical figures. This is followed by the discovery of dynamical systems and…

  18. On the Structure and Evolution of a Polar Crown Prominence/Filament System

    NASA Astrophysics Data System (ADS)

    Panesar, N. K.; Innes, D. E.; Schmit, D. J.; Tiwari, S. K.

    2014-08-01

    Polar crown prominences, that partially circle the Sun's poles between 60° and 70° latitude, are made of chromospheric plasma. We aim to diagnose the 3D dynamics of a polar crown prominence using high-cadence EUV images from the Solar Dynamics Observatory (SDO)/AIA at 304, 171, and 193 Å and the Ahead spacecraft of the Solar Terrestrial Relations Observatory (STEREO-A)/EUVI at 195 Å. Using time series across specific structures, we compare flows across the disk in 195 Å with the prominence dynamics seen on the limb. The densest prominence material forms vertical columns that are separated by many tens of Mm and connected by dynamic bridges of plasma that are clearly visible in 304/171 Å two-colour images. We also observe intermittent but repetitious flows with velocity 15 km s-1 in the prominence that appear to be associated with EUV bright points on the solar disk. The boundary between the prominence and the overlying cavity appears as a sharp edge. We discuss the structure of the coronal cavity seen both above and around the prominence. SDO/HMI and GONG magnetograms are used to infer the underlying magnetic topology. The evolution and structure of the prominence with respect to the magnetic field seems to agree with the filament-linkage model.

  19. Filament-Level Modeling of Aramid-Based High-Performance Structural Materials

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Bell, W. C.; Glomski, P. S.; Pandurangan, B.; Yen, C.-F.; Cheeseman, B. A.

    2011-11-01

    Molecular statics and molecular dynamics are employed to study the effects of various microstructural and topological defects (e.g., chain ends, axial chain misalignment, inorganic solvent impurities, and sheet stacking faults) on the strength, ductility, and stiffness of p-phenylene terephthalamide (PPTA) fibers/filaments. These fibers can be considered as prototypes for advanced high strength/high-stiffness fibers like Kevlar®, Twaron®, New Star®, etc. While modeling these fibers, it was taken into account that they are essentially crystalline materials consisting of stacks of sheets, with each sheet containing an array of nearly parallel hydrogen-bonded molecules/chains. The inter-sheet bonding, on the other hand, was considered as mainly being of van der Waals or p-electron character. The effects of various deviations of the PPTA fiber structure from that of the perfectly crystalline structure (i.e., microstructural/topological defects) on the material's mechanical properties are then considered. The results obtained show that while the presence of these defects decreases all the mechanical properties of PPTA fibers, specific properties display an increased level of sensitivity to the presence of certain defects. For example, longitudinal tensile properties are found to be most sensitive to the presence of chain ends, in-sheet transverse properties to the presence of chain misalignments, while cross-sheet transverse properties are found to be most affected by the presence of sheet stacking faults.

  20. An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages.

    PubMed Central

    Marzec, C J; Day, L A

    1994-01-01

    A model is presented that treats the symmetry matching problem in structures made of two interacting coaxial helices of point charges. The charges are sources of a potential field that mediates a non-specific attractive interaction between the helices. The problem is represented in Fourier space, which affords the most generality. It is found that coaxial helices with optimally mated symmetries can lock into spatial resonance configurations that maximize their interaction. The resonances are represented as vectors in a discrete three-dimensional space. Two algebraic relations are given for the four symmetry parameters of two helices in resonance. One-start inner helices interacting with coaxial one-start or NR-start outer helices are considered. Applications are made to the filamentous bacteriophages Ff, Pf1, Xf, and Pf3. The interaction given by the linearized Poisson-Boltzmann equation is calculated in this formalism to allow comparison of the electrostatic free energy of interaction of different resonance structures. Experimental nucleotide/subunit ratios are accounted for, and models for the DNA-protein interfaces are presented, with particular emphasis on Pf1. PMID:7696463

  1. Conservation of the structure of keratin intermediate filaments: molecular mechanism by which different keratin molecules integrate into preexisting keratin intermediate filaments during differentiation.

    PubMed

    Steinert, P M; Marekov, L N; Parry, D A

    1993-09-28

    During development and differentiation, the intermediate filament component of the cytoskeleton of many cells and tissues is rebuilt by a dynamic exchange process in which one set of protein chains is replaced by another, without recourse to creation of a new network. One major example is the replacement of keratin 5/keratin 14 (K5/K14) keratin intermediate filaments (KIFs) by K1/K10 KIFs during terminal differentiation in the epidermis. The present work was undertaken to explore how this may occur. We have induced lysine-lysine cross-links with disulfosuccinimidyl tartrate in K5/K14 KIFs in order to determine the axial dimensions and relative axial alignments of the K5/K14 molecules. Many of the cross-links induced in subfilamentous oligomers containing one, two, or three molecules were also found in the intact KIF, indicating that the body of data thus generated provides physiologically relevant information on the structural organization in the KIF. A least-squares analysis using as data the positions of lysine residues involved in 23 induced cross-links has allowed the axial alignments of the various coiled-coil segments in the rod domain to be determined. Three modes of antiparallel alignment of two neighboring molecules were found: A11 (staggered by -16.7 nm), A22 (staggered by 28.8 nm), and A12 (almost in register; staggered by only 0.3 nm). Since the axial repeat length is about 1 nm less than the molecular length, the data require a fourth mode of molecule alignment, termed ACN, in which similarly directed molecules are overlapped by the equivalent of about 5-10 residues.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7691168

  2. The structural basis for the intrinsic disorder of the actin filament: the "lateral slipping" model.

    PubMed

    Bremer, A; Millonig, R C; Sütterlin, R; Engel, A; Pollard, T D; Aebi, U

    1991-11-01

    Three-dimensional (3-D) helical reconstructions computed from electron micrographs of negatively stained dispersed F-actin filaments invariably revealed two uninterrupted columns of mass forming the "backbone" of the double-helical filament. The contact between neighboring subunits along the thus defined two long-pitch helical strands was spatially conserved and of high mass density, while the intersubunit contact between them was of lower mass density and varied among reconstructions. In contrast, phalloidinstabilized F-actin filaments displayed higher and spatially more conserved mass density between the two long-pitch helical strands, suggesting that this bicyclic hepta-peptide toxin strengthens the intersubunit contact between the two strands. Consistent with this distinct intersubunit bonding pattern, the two long-pitch helical strands of unstabilized filaments were sometimes observed separated from each other over a distance of two to six subunits, suggesting that the intrastrand intersubunit contact is also physically stronger than the interstrand contact. The resolution of the filament reconstructions, extending to 2.5 nm axially and radially, enabled us to reproducibly "cut out" the F-actin subunit which measured 5.5 nm axially by 6.0 nm tangentially by 3.2 nm radially. The subunit is distinctly polar with a massive "base" pointing towards the "barbed" end of the filament, and a slender "tip" defining its "pointed" end (i.e., relative to the "arrowhead" pattern revealed after stoichiometric decoration of the filaments with myosin subfragment 1). Concavities running approximately parallel to the filament axis both on the inner and outer face of the subunit define a distinct cleft separating the subunit into two domains of similar size: an inner domain confined to radii less than or equal to 2.5-nm forms the uninterrupted backbone of the two long-pitch helical strands, and an outer domain placed at radii of 2-5-nm protrudes radially and thus predominantly

  3. Music and fractals

    NASA Astrophysics Data System (ADS)

    Wuorinen, Charles

    2015-03-01

    Any of the arts may produce exemplars that have fractal characteristics. There may be fractal painting, fractal poetry, and the like. But these will always be specific instances, not necessarily displaying intrinsic properties of the art-medium itself. Only music, I believe, of all the arts possesses an intrinsically fractal character, so that its very nature is fractally determined. Thus, it is reasonable to assert that any instance of music is fractal...

  4. Role of lattice structure and low temperature resistivity in fast-electron-beam filamentation in carbon

    NASA Astrophysics Data System (ADS)

    Dance, R. J.; Butler, N. M. H.; Gray, R. J.; MacLellan, D. A.; Rusby, D. R.; Scott, G. G.; Zielbauer, B.; Bagnoud, V.; Xu, H.; Robinson, A. P. L.; Desjarlais, M. P.; Neely, D.; McKenna, P.

    2016-01-01

    The influence of low temperature (eV to tens-of-eV) electrical resistivity on the onset of the filamentation instability in fast-electron transport is investigated in targets comprising of layers of ordered (diamond) and disordered (vitreous) carbon. It is shown experimentally and numerically that the thickness of the disordered carbon layer influences the degree of filamentation of the fast-electron beam. Strong filamentation is produced if the thickness is of the order of 60 μm or greater, for an electron distribution driven by a sub-picosecond, mid-1020 Wcm‑2 laser pulse. It is shown that the position of the vitreous carbon layer relative to the fast-electron source (where the beam current density and background temperature are highest) does not have a strong effect because the resistive filamentation growth rate is high in disordered carbon over a wide range of temperatures up to the Spitzer regime.

  5. Construction of fractal nanostructures based on Kepler-Shubnikov nets

    NASA Astrophysics Data System (ADS)

    Ivanov, V. V.; Talanov, V. M.

    2013-05-01

    A system of information codes for deterministic fractal lattices and sets of multifractal curves is proposed. An iterative modular design was used to obtain a series of deterministic fractal lattices with generators in the form of fragments of 2 D structures and a series of multifractal curves (based on some Kepler-Shubnikov nets) having Cantor set properties. The main characteristics of fractal structures and their lacunar spectra are determined. A hierarchical principle is formulated for modules of regular fractal structures.

  6. Construction of fractal nanostructures based on Kepler-Shubnikov nets

    SciTech Connect

    Ivanov, V. V. Talanov, V. M.

    2013-05-15

    A system of information codes for deterministic fractal lattices and sets of multifractal curves is proposed. An iterative modular design was used to obtain a series of deterministic fractal lattices with generators in the form of fragments of 2D structures and a series of multifractal curves (based on some Kepler-Shubnikov nets) having Cantor set properties. The main characteristics of fractal structures and their lacunar spectra are determined. A hierarchical principle is formulated for modules of regular fractal structures.

  7. The Rapid Formation of a Filament Caused by Magnetic Reconnection between Two Sets of Dark Threadlike Structures

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Yu, Shunping; Xu, Zhe

    2016-01-01

    Taking advantage of the high spatiotemporal resolution observations from the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we present rare observations of the rapid formation of a filament caused by magnetic reconnection between two sets of dark threadlike structures. The two sets of dark threadlike structures belong to distinct flux systems with their adjacent ends anchored in an opposite-polarity magnetic field region, where the calculated photospheric velocity field shows that converging flows dominate there. Due to the converging flows, opposite-polarity magnetic flux converged and then canceled, leading to the formation of extreme ultraviolet (EUV) brightening that spread in opposite directions along the spine of the dark threadlike structures. Meanwhile, very weak remote brightening in the other terminals of the dark threadlike structures, as well as EUV loops, which rooted in the opposite-polarity magnetic field region, appeared. In addition, all of the AIA Fe line observations reveal that a flux rope was formed and underwent a rolling motion during the fadeaway of the EUV brightening. Soon after, as the EUV brightening disappeared, a filament that is very likely composed of two sets of intertwined dark threadlike structures was formed. Via differential emission measure (EM) analysis, it is found that both the EM and temperature of the plasma around the flux-canceling site increased during the brightening, implying that there, magnetic reconnection may occur to heat the plasma. These observations provide evidence that the filament is formed by magnetic reconnection associated with flux convergence and cancellation, and the magnetic structure of the filament is most likely a flux rope.

  8. Isolation and characterization of Candida albicans morphological mutants derepressed for the formation of filamentous hypha-type structures

    SciTech Connect

    Gil, C.; Pomes, R.; Nombela, C. )

    1990-05-01

    Several Candida albicans morphological mutants were obtained by a procedure based on a combined treatment with nitrous acid plus UV irradiation and a double-enrichment step to increase the proportion of mutants growing as long filamentous structures. Altered cell morphogenesis in these mutants correlated with an altered colonial phenotype. Two of these mutants, C. albicans NEL102 and NEL103, were selected and characterized. Mutant blastoconidia initiated budding but eventually gave rise to filamentous hypha-type formations. These filaments were long and septate, and they branched very regularly at positions near septa. Calcofluor white (which is known to bind chitin-rich areas) stained septa, branching zones, and filament tips very intensely, as observed under the fluorescence microscope. Wild-type hybrids were obtained by fusing protoplasts of strain NEL102 with B14, another morphological mutant previously described as being permanently pseudomycelial, indicating that genetic determinants responsible for the two altered phenotypes are different. The mutants characterized in this work seemed to sequentially express the morphogenic characteristics of C. albicans, from blastoconidia to hyphae, in the absence of any inducer. Further characterization of these strains could be relevant to gain understanding of the genetic control of dimorphism in this species.

  9. Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

    SciTech Connect

    Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

    2010-11-07

    Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

  10. Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

    NASA Astrophysics Data System (ADS)

    Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

    2010-11-01

    Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

  11. Fractal analysis of Mesoamerican pyramids.

    PubMed

    Burkle-Elizondo, Gerardo; Valdez-Cepeda, Ricardo David

    2006-01-01

    A myth of ancient cultural roots was integrated into Mesoamerican cult, and the reference to architecture denoted a depth religious symbolism. The pyramids form a functional part of this cosmovision that is centered on sacralization. The space architecture works was an expression of the ideological necessities into their conception of harmony. The symbolism of the temple structures seems to reflect the mathematical order of the Universe. We contemplate two models of fractal analysis. The first one includes 16 pyramids. We studied a data set that was treated as a fractal profile to estimate the Df through variography (Dv). The estimated Fractal Dimension Dv = 1.383 +/- 0.211. In the second one we studied a data set to estimate the Dv of 19 pyramids and the estimated Fractal Dimension Dv = 1.229 +/- 0.165. PMID:16393505

  12. The Small Heat Shock Protein Hsp27 Affects Assembly Dynamics and Structure of Keratin Intermediate Filament Networks

    PubMed Central

    Kayser, Jona; Haslbeck, Martin; Dempfle, Lisa; Krause, Maike; Grashoff, Carsten; Buchner, Johannes; Herrmann, Harald; Bausch, Andreas R.

    2013-01-01

    The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation. PMID:24138853

  13. Chaos recognition and fractal analysis in the term structure of Shanghai Interbank Offered Rate

    NASA Astrophysics Data System (ADS)

    Gu, Rongbao; Chen, Xi; Li, Xinjie

    2014-10-01

    In this paper, we investigate the Shanghai Interbank Offered Rate (SHIBOR) employing the chaos recognition and fractal analysis. We find that all interest rates of SHIBOR are chaotic systems with multifractal nature. The volatilities of the short-term interest rates are larger than the medium- and long-term interest rates and the magnitudes of these fluctuations decrease with the term increases. The smaller fluctuations of all interest rates have long-term memory property. The larger fluctuations of medium- or long-term interest rates have also long-term memory property but not for those of short-term rates. Moreover, there is long-term memory property between the two interest rates of SHIBOR with one medium- or long-term, but not for both short-term interest rates. Especially, there is also long-term memory between SHIBOR and USD LIBOR. These findings are beneficial not only to understand well the SHIBOR's running but also to price accurately financial products.

  14. FRET study of the structural and kinetic effects of PKC phosphomimetic cardiac troponin T mutants on thin filament regulation.

    PubMed

    Schlecht, William; Zhou, Zhiqun; Li, King-Lun; Rieck, Daniel; Ouyang, Yexin; Dong, Wen-Ji

    2014-05-15

    FRET was used to investigate the structural and kinetic effects that PKC phosphorylations exert on Ca(2+) and myosin subfragment-1 dependent conformational transitions of the cardiac thin filament. PKC phosphorylations of cTnT were mimicked by glutamate substitution. Ca(2+) and S1-induced distance changes between the central linker of cTnC and the switch region of cTnI (cTnI-Sr) were monitored in reconstituted thin filaments using steady state and time resolved FRET, while kinetics of structural transitions were determined using stopped flow. Thin filament Ca(2+) sensitivity was found to be significantly blunted by the presence of the cTnT(T204E) mutant, whereas pseudo-phosphorylation at additional sites increased the Ca(2+)-sensitivity. The rate of Ca(2+)-dissociation induced structural changes was decreased in the C-terminal end of cTnI-Sr in the presence of pseudo-phosphorylations while remaining unchanged at the N-terminal end of this region. Additionally, the distance between cTnI-Sr and cTnC was decreased significantly for the triple and quadruple phosphomimetic mutants cTnT(T195E/S199E/T204E) and cTnT(T195E/S199E/T204E/T285E), which correlated with the Ca(2+)-sensitivity increase seen in these same mutants. We conclude that significant changes in thin filament Ca(2+)-sensitivity, structure and kinetics are brought about through PKC phosphorylation of cTnT. These changes can either decrease or increase Ca(2+)-sensitivity and likely play an important role in cardiac regulation. PMID:24708997

  15. FRET Study of the Structural and Kinetic Effects of PKC Phosphomimetic Cardiac Troponin T Mutants on Thin Filament Regulation

    PubMed Central

    Schlecht, William; Zhou, Zhiqun; Li, King-Lun; Rieck, Daniel; Ouyang, Yexin; Dong, Wen-Ji

    2014-01-01

    FRET was used to investigate the structural and kinetic effects that PKC phosphorylations exert on Ca2+ and myosin subfragment-1 dependent conformational transitions of the cardiac thin filament. PKC phosphorylations of cTnT were mimicked by glutamate substitution. Ca2+ and S1-induced distance changes between the central linker of cTnC and the switch region of cTnI (cTnI-Sr) were monitored in reconstituted thin filaments using steady state and time resolved FRET, while kinetics of structural transitions were determined using stopped flow. Thin filament Ca2+ sensitivity was found to be significantly blunted by the presence of the cTnT(T204E) mutant, whereas pseudo-phosphorylation at additional sites increased the Ca2+-sensitivty. The rate of Ca2+-dissociation induced structural changes was decreased in the C-terminal end of cTnI-Sr in the presence of pseudo-phosphorylations while remaining unchanged at the N-terminal end of this region. Additionally, the distance between cTnI-Sr and cTnC was decreased significantly for the triple and quadruple phosphomimetic mutants cTnT(T195E/S199E/T204E) and cTnT(T195E/S199E/T204E/T285E), which correlated with the Ca2+-sensitivity increase seen in these same mutants. We conclude that significant changes in thin filament Ca2+-sensitivity, structure and kinetics are brought about through PKC phosphorylation of cTnT. These changes can either decrease or increase Ca2+-sensitivity and likely play an important role in cardiac regulation. PMID:24708997

  16. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization

    SciTech Connect

    Lebedev, D. V. Filatov, M. V.; Kuklin, A. I.; Islamov, A. Kh.; Stellbrink, J.; Pantina, R. A.; Denisov, Yu. Yu.; Toperverg, B. P.; Isaev-Ivanov, V. V.

    2008-01-15

    The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10{sup -1} to 10{sup -4} A{sup -1} with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 {mu}m and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm.

  17. A new RHQT Nb3Al superconducting wire with a Ta/Cu/Ta three-layer filament-barrier structure

    NASA Astrophysics Data System (ADS)

    Takeuchi, Takao; Tsuchiya, Kiyosumi; Nakagawa, Kazuhiko; Nimori, Shigeki; Banno, Nobuya; Iijima, Yasuo; Kikuchi, Akihiro; Nakamoto, Tatsushi

    2012-06-01

    To suppress the low-magnetic-field instability (flux jumps in low magnetic fields) of a rapid-heating, quenching and transformation (RHQT) processed Nb3Al superconductor, we had previously modified the cross-sectional design of an RHQT Nb3Al by adopting a Ta filament-barrier structure. Unlike Nb barriers, Ta barriers are not superconducting in magnetic fields at 4.2 K so that they electromagnetically decouple filaments. However, small flux jumps still occurred at 1.8 K, which is a typical operating temperature for the magnets used in high-energy particle accelerators. Furthermore, poor bonding at the Ta/Ta interface between neighboring Ta-coated jelly-roll (JR) filaments frequently caused precursor wires to break during drawing. To overcome these problems, we fabricated a new RHQT Nb3Al wire with a Ta/Cu/Ta three-layer filament-barrier structure for which an internal stabilization technique (Cu rods encased in Ta are dispersed in the wire cross section) was extended. Removing the Ta/Ta interface in the interfilamentary barrier (JR filament/Ta/Cu/Ta/JR filament) allowed precursor wires to be drawn without breaking. Furthermore, the Cu filament barrier electromagnetically decoupled filaments to suppress flux jumps at 1.8 K. The ductile Cu layer also improved the bending strain tolerance of RHQT Nb3Al.

  18. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly

    PubMed Central

    Shen, Qing-Tao; Schuh, Amber L.; Zheng, Yuqing; Quinney, Kyle; Wang, Lei; Hanna, Michael; Mitchell, Julie C.; Otegui, Marisa S.; Ahlquist, Paul; Cui, Qiang

    2014-01-01

    The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers. ESCRT-III (endosomal sorting complex required for transport III) filaments mediate membrane scission during the ostensibly disparate processes of multivesicular endosome biogenesis, cytokinesis, and retroviral budding. However, mechanisms by which ESCRT-III subunits assemble into a polymer remain unknown. Using cryogenic electron microscopy (cryo-EM), we found that the full-length ESCRT-III subunit Vps32/CHMP4B spontaneously forms single-stranded spiral filaments. The resolution afforded by two-dimensional cryo-EM combined with molecular dynamics simulations revealed that individual Vps32/CHMP4B monomers within a filament are flexible and able to accommodate a range of bending angles. In contrast, the interface between monomers is stable and refractory to changes in conformation. We additionally found that the carboxyl terminus of Vps32/CHMP4B plays a key role in restricting the lateral association of filaments. Our findings highlight new mechanisms by which ESCRT-III filaments assemble to generate a unique polymer capable of membrane remodeling in multiple cellular contexts. PMID:25202029

  19. USING CORONAL CELLS TO INFER THE MAGNETIC FIELD STRUCTURE AND CHIRALITY OF FILAMENT CHANNELS

    SciTech Connect

    Sheeley, N. R. Jr.; Warren, H. P.; Martin, S. F.; Panasenco, O.

    2013-08-01

    Coronal cells are visible at temperatures of {approx}1.2 MK in Fe XII coronal images obtained from the Solar Dynamics Observatory and Solar Terrestrial Relations Observatory spacecraft. We show that near a filament channel, the plumelike tails of these cells bend horizontally in opposite directions on the two sides of the channel like fibrils in the chromosphere. Because the cells are rooted in magnetic flux concentrations of majority polarity, these observations can be used with photospheric magnetograms to infer the direction of the horizontal field in filament channels and the chirality of the associated magnetic field. This method is similar to the procedure for inferring the direction of the magnetic field and the chirality of the fibril pattern in filament channels from H{alpha} observations. However, the coronal cell observations are easier to use and provide clear inferences of the horizontal field direction for heights up to {approx}50 Mm into the corona.

  20. Fractal vector optical fields.

    PubMed

    Pan, Yue; Gao, Xu-Zhen; Cai, Meng-Qiang; Zhang, Guan-Lin; Li, Yongnan; Tu, Chenghou; Wang, Hui-Tian

    2016-07-15

    We introduce the concept of a fractal, which provides an alternative approach for flexibly engineering the optical fields and their focal fields. We propose, design, and create a new family of optical fields-fractal vector optical fields, which build a bridge between the fractal and vector optical fields. The fractal vector optical fields have polarization states exhibiting fractal geometry, and may also involve the phase and/or amplitude simultaneously. The results reveal that the focal fields exhibit self-similarity, and the hierarchy of the fractal has the "weeding" role. The fractal can be used to engineer the focal field. PMID:27420485

  1. Multifractal formalism for fractal signals: The structure-function approach versus the wavelet-transform modulus-maxima method

    NASA Astrophysics Data System (ADS)

    Muzy, J. F.; Bacry, E.; Arneodo, A.

    1993-02-01

    Several attempts have been made recently to generalize the multifractal formalism, originally introduced for singular measures, to fractal signals. We report on a systematic comparison between the structure-function approach, pioneered by Parisi and Frisch [in 2 Proceedings of the International School on Turbulence and Predictability in Geophysical Fluid Dynamics and Climate Dynamics, edited by M. Ghil, R. Benzi, and G. Parisi (North-Holland, Amsterdam, 1985), p. 84] to account for the multifractal nature of fully developed turbulent signals, and an alternative method we have developed within the framework of the wavelet-transform analysis. We comment on the intrinsic limitations of the structure-function approach; this technique has fundamental drawbacks and does not provide a full characterization of the singularities of a signal in many cases. We demonstrate that our method, based on the wavelet-transform modulus-maxima representation, works in most situations and is likely to be the ground of a unified multifractal description of self-affine distributions. Our theoretical considerations are both illustrated on pedagogical examples and supported by numerical simulations.

  2. Safety evaluation design of filament wound structures - Cases of pressure vessels and pipes

    NASA Astrophysics Data System (ADS)

    Kawahara, Masanori; Mori, Takao; Hirase, Yosihiro; Katoh, Akihiko; Ishihara, Toshio

    Procedures are presented for the safety-related evaluation of filament-wound composite products, such as pressure vessels and pipes. In order to increase the fatigue strength of pressure vessel metallic liners subject to cyclic internal pressures, by controlling residual stresses, the 'autofrettage' overpressuring treatment has been devised.

  3. RUI: Structure and Behavior of RF-Driven Plasma Filaments in High-Pressure Gases

    SciTech Connect

    Burin, Michael

    2014-11-18

    The filamentary discharge seen within commercial plasma globes is commonly enjoyed, yet not well understood. We investigate filament properties in a plasma globe using a variable high voltage amplifier. Results from the 3-year grant period and their physics are discussed.

  4. Human development VII: a spiral fractal model of fine structure of physical energy could explain central aspects of biological information, biological organization and biological creativity.

    PubMed

    Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Rald, Erik; Nielsen, Maj Lyck; Merrick, Joav

    2006-01-01

    In this paper we have made a draft of a physical fractal essence of the universe, a sketch of a new cosmology, which we believe to lay at the root of our new holistic biological paradigm. We present the fractal roomy spiraled structures and the energy-rich dancing "infinite strings" or lines of the universe that our hypothesis is based upon. The geometric language of this cosmology is symbolic and both pre-mathematical and pre-philosophical. The symbols are both text and figures, and using these we step by step explain the new model that at least to some extent is able to explain the complex informational system behind morphogenesis, ontogenesis, regeneration and healing. We suggest that it is from this highly dynamic spiraled structure that organization of cells, organs, and the wholeness of the human being including consciousness emerge. The model of "dancing fractal spirals" carries many similarities to premodern cultures descriptions of the energy of the life and universe. Examples are the Native American shamanistic descriptions of their perception of energy and the old Indian Yogis descriptions of the life-energy within the body and outside. Similar ideas of energy and matter are found in the modern superstring theories. The model of the informational system of the organism gives new meaning to Bateson's definition of information: "A difference that makes a difference", and indicates how information-directed self-organization can exist on high structural levels in living organisms, giving birth to their subjectivity and consciousness. PMID:17115083

  5. Order-fractal transitions in abstract paintings

    NASA Astrophysics Data System (ADS)

    de la Calleja, E. M.; Cervantes, F.; de la Calleja, J.

    2016-08-01

    In this study, we determined the degree of order for 22 Jackson Pollock paintings using the Hausdorff-Besicovitch fractal dimension. Based on the maximum value of each multi-fractal spectrum, the artworks were classified according to the year in which they were painted. It has been reported that Pollock's paintings are fractal and that this feature was more evident in his later works. However, our results show that the fractal dimension of these paintings ranges among values close to two. We characterize this behavior as a fractal-order transition. Based on the study of disorder-order transition in physical systems, we interpreted the fractal-order transition via the dark paint strokes in Pollock's paintings as structured lines that follow a power law measured by the fractal dimension. We determined self-similarity in specific paintings, thereby demonstrating an important dependence on the scale of observations. We also characterized the fractal spectrum for the painting entitled Teri's Find. We obtained similar spectra for Teri's Find and Number 5, thereby suggesting that the fractal dimension cannot be rejected completely as a quantitative parameter for authenticating these artworks.

  6. a Type of Fractal Interpolation Functions and Their Fractional Calculus

    NASA Astrophysics Data System (ADS)

    Liang, Yong-Shun; Zhang, Qi

    2016-05-01

    Combine Chebyshev systems with fractal interpolation, certain continuous functions have been approximated by fractal interpolation functions unanimously. Local structure of these fractal interpolation functions (FIF) has been discussed. The relationship between order of Riemann-Liouville fractional calculus and Box dimension of FIF has been investigated.

  7. A CapG gain-of-function mutant reveals critical structural and functional determinants for actin filament severing

    PubMed Central

    Zhang, Y; Vorobiev, Sergey M; Gibson, Bruce G; Hao, Binghua; Sidhu, Gurjit S; Mishra, Vishnu S; Yarmola, Elena G; Bubb, Michael R; Almo, Steven C; Southwick, Frederick S

    2006-01-01

    CapG is the only member of the gelsolin family unable to sever actin filaments. Changing amino acids 84–91 (severing domain) and 124–137 (WH2-containing segment) simultaneously to the sequences of gelsolin results in a mutant, CapG-sev, capable of severing actin filaments. The gain of severing function does not alter actin filament capping, but is accompanied by a higher affinity for monomeric actin, and the capacity to bind and sequester two actin monomers. Analysis of CapG-sev crystal structure suggests a more loosely folded inactive conformation than gelsolin, with a shorter S1–S2 latch. Calcium binding to S1 opens this latch and S1 becomes separated from a closely interfaced S2–S3 complex by an extended arm consisting of amino acids 118–137. Modeling with F-actin predicts that the length of this WH2-containing arm is critical for severing function, and the addition of a single amino acid (alanine or histidine) eliminates CapG-sev severing activity, confirming this prediction. We conclude that efficient severing utilizes two actin monomer-binding sites, and that the length of the WH2-containing segment is a critical functional determinant for severing. PMID:16977317

  8. Fractal kinetics in drug release from finite fractal matrices

    NASA Astrophysics Data System (ADS)

    Kosmidis, Kosmas; Argyrakis, Panos; Macheras, Panos

    2003-09-01

    We have re-examined the random release of particles from fractal polymer matrices using Monte Carlo simulations, a problem originally studied by Bunde et al. [J. Chem. Phys. 83, 5909 (1985)]. A certain population of particles diffuses on a fractal structure, and as particles reach the boundaries of the structure they are removed from the system. We find that the number of particles that escape from the matrix as a function of time can be approximated by a Weibull (stretched exponential) function, similar to the case of release from Euclidean matrices. The earlier result that fractal release rates are described by power laws is correct only at the initial stage of the release, but it has to be modified if one is to describe in one picture the entire process for a finite system. These results pertain to the release of drugs, chemicals, agrochemicals, etc., from delivery systems.

  9. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8

    PubMed Central

    Nagayoshi, Yuko; Kumagae, Kenta; Mori, Kazuki; Tashiro, Kosuke; Nakamura, Ayano; Fujino, Yasuhiro; Hiromasa, Yasuaki; Iwamoto, Takeo; Kuhara, Satoru; Ohshima, Toshihisa; Doi, Katsumi

    2016-01-01

    A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell. PMID:26941711

  10. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8.

    PubMed

    Nagayoshi, Yuko; Kumagae, Kenta; Mori, Kazuki; Tashiro, Kosuke; Nakamura, Ayano; Fujino, Yasuhiro; Hiromasa, Yasuaki; Iwamoto, Takeo; Kuhara, Satoru; Ohshima, Toshihisa; Doi, Katsumi

    2016-01-01

    A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell. PMID:26941711

  11. Analysis of the structure and subcellular location of filamentous phage pIV.

    PubMed Central

    Russel, M; Kaźmierczak, B

    1993-01-01

    The gene IV protein of filamentous bacteriophages is an integral membrane protein required for phage assembly and export. A series of gene IV::phoA fusion, gene IV deletion, and gene IV missense mutations have been isolated and characterized. The alkaline phosphatase activity of the fusion proteins suggests that pIV lacks a cytoplasmic domain. Cell fractionation studies indicate that the carboxy-terminal half of pIV mediates its assembly into the membrane, although there is no single, discrete membrane localization domain. The properties of gene IV missense and deletion mutants, combined with an analysis of the similarities between pIVs from various filamentous phage and related bacterial export-mediating proteins, suggest that the amino-terminal half of pIV consists of a periplasmic substrate-binding domain that confers specificity to the assembly-export system. Images PMID:8320216

  12. Spectro-polarimetric observation of the fine structure of a quiescent filament

    NASA Astrophysics Data System (ADS)

    Zong, W. G.; Tang, Y. H.; Fang, C.; Mein, P.; Mein, N.; Xu, A. A.

    2003-12-01

    This paper presents the spectro-polarimetric measurements of a big quiescent filament observed by the MSDP mode of the THEMIS on August 24, 2000. The Hα , CaII 8542 and NaI D2 line profiles of a segment of the filament were obtained. By use of the Hα images with high spatial resolution, the two barb endpoints were identified. The parameters at the barbs' endpoints, including intensity, velocity and longitudinal magnetic field were measured. Using the data with high spatial resolution (0.16'' per pixel), we have found the following results. 1) There was mass motion at the barb endpoints in the chromosphere, the values and the directions of the mass motion at the barb endpoints change in several minutes. 2) The two barb endpoints are located between the majority polarities and the minority polarities.

  13. The identification of filaments on far-infrared and submillimiter images: Morphology, physical conditions and relation with star formation of filamentary structure

    SciTech Connect

    Schisano, E.; Carey, S.; Paladini, R.; Rygl, K. L. J.; Molinari, S.; Elia, D.; Pestalozzi, M.; Busquet, G.; Billot, N.; Noriega-Crespo, A.; Moore, T. J. T.; Plume, R.; Glover, S. C. O.; Vázquez-Semadeni, E.

    2014-08-10

    Observations of molecular clouds reveal a complex structure, with gas and dust often arranged in filamentary, rather than spherical geometries. The association of pre- and proto-stellar cores with the filaments suggests a direct link with the process of star formation. Any study of the properties of such filaments requires representative samples from different environments for an unbiased detection method. We developed such an approach using the Hessian matrix of a surface-brightness distribution to identify filaments and determine their physical and morphological properties. After testing the method on simulated, but realistic, filaments, we apply the algorithms to column-density maps computed from Herschel observations of the Galactic plane obtained by the Hi-GAL project. We identified ∼500 filaments, in the longitude range of l = 216.°5 to l = 225.°5, with lengths from ∼1 pc up to ∼30 pc and widths between 0.1 pc and 2.5 pc. Average column densities are between 10{sup 20} cm{sup –2} and 10{sup 22} cm{sup –2}. Filaments include the majority of dense material with N{sub H{sub 2}} > 6 × 10{sup 21} cm{sup –2}. We find that the pre- and proto-stellar compact sources already identified in the same region are mostly associated with filaments. However, surface densities in excess of the expected critical values for high-mass star formation are only found on the filaments, indicating that these structures are necessary to channel material into the clumps. Furthermore, we analyze the gravitational stability of filaments and discuss their relationship with star formation.

  14. The Identification of Filaments on Far-infrared and Submillimiter Images: Morphology, Physical Conditions and Relation with Star Formation of Filamentary Structure

    NASA Astrophysics Data System (ADS)

    Schisano, E.; Rygl, K. L. J.; Molinari, S.; Busquet, G.; Elia, D.; Pestalozzi, M.; Polychroni, D.; Billot, N.; Carey, S.; Paladini, R.; Noriega-Crespo, A.; Moore, T. J. T.; Plume, R.; Glover, S. C. O.; Vázquez-Semadeni, E.

    2014-08-01

    Observations of molecular clouds reveal a complex structure, with gas and dust often arranged in filamentary, rather than spherical geometries. The association of pre- and proto-stellar cores with the filaments suggests a direct link with the process of star formation. Any study of the properties of such filaments requires representative samples from different environments for an unbiased detection method. We developed such an approach using the Hessian matrix of a surface-brightness distribution to identify filaments and determine their physical and morphological properties. After testing the method on simulated, but realistic, filaments, we apply the algorithms to column-density maps computed from Herschel observations of the Galactic plane obtained by the Hi-GAL project. We identified ~500 filaments, in the longitude range of l = 216.°5 to l = 225.°5, with lengths from ~1 pc up to ~30 pc and widths between 0.1 pc and 2.5 pc. Average column densities are between 1020 cm-2 and 1022 cm-2. Filaments include the majority of dense material with N_H_{2} > 6 × 1021 cm-2. We find that the pre- and proto-stellar compact sources already identified in the same region are mostly associated with filaments. However, surface densities in excess of the expected critical values for high-mass star formation are only found on the filaments, indicating that these structures are necessary to channel material into the clumps. Furthermore, we analyze the gravitational stability of filaments and discuss their relationship with star formation.

  15. Randomness in fractals, connectivity dimensions, and percolation

    NASA Astrophysics Data System (ADS)

    Perreau, M.; Levy, J. C. S.

    1989-10-01

    The structural properties of random fractals embedded in a d-dimensional Euclidean space are studied by means of transfer-matrix formalism of fractal sets. For d=1, both global and local approaches have been investigated, leading to the definition of a subdimension that is different from the fractal dimension and depends on the probability distribution. This subdimension is shown to be identical for the global and local approaches; then, the scaling corrections involved in this subdimension are the same for both these approaches. For d>1, only the local approach can be generalized, characterizing the connectivity properties of these structures. There are exactly d subdimensions called connectivity dimensions that prove to be useful to describe percolation properties of these fractals. Several percolation thresholds are shown, and the fractal dimension of the sets at the percolation threshold are related to the connectivity dimensions.

  16. Structural CNT Composites. Part I; Developing a Carbon Nanotube Filament Winder

    NASA Technical Reports Server (NTRS)

    Sauti, Godfrey; Kim, Jae-Woo; Wincheski, Russell A.; Antczak, Andrew; Campero, Jamie C.; Luong, Hoa H.; Shanahan, Michelle H.; Stelter, Christopher J.; Siochi, Emilie J.

    2015-01-01

    Carbon nanotube (CNT) based materials promise advances in the production of high strength and multifunctional components for aerospace and other applications. Specifically, in tension dominated applications, the latest CNT based filaments are yielding composite properties comparable to or exceeding composites from more established fibers such as Kevlar and carbon fiber. However, for the properties of these materials to be fully realized at the component level, suitable manufacturing processes have to be developed. These materials handle differently from conventional fibers, with different wetting characteristics and behavior under load. The limited availability of bulk forms also requires that the equipment be scaled down accordingly to tailor the process development approach to material availability. Here, the development of hardware and software for filament winding of carbon nanotube based tapes and yarns is described. This hardware features precision guidance of the CNT material and control of the winding tension over a wide range in an open architecture that allows for effective process control and troubleshooting during winding. Use of the filament winder to develop CNT based Composite Overwrapped Pressure Vessels (COPVs) shall also be discussed.

  17. Fine Structure of Chromospheric Brightenings above a Light Bridge and Penumbral Filaments

    NASA Astrophysics Data System (ADS)

    Bharti, Lokesh

    We present simultaneous photospheric and chromospheric observations of the trailing sunspot in NOAA 10904. At the limit of the instrumental spatial resolution Ca II H images show jet-like brightenings above a lightbridge and a penumbral filament that intrudes into the umbra. The observations were carried out with the Swedish Solar Telescope (SST) on 13 August 2006. The Solar Optical Universal Polarimeter (SOUP) filter was used to scan the Fe I 6302.5 ˚ line at A 6 wavelength positions. Full Stokes polarimetry was performed and the magnetic field vector was obtained by means of a Milne-Eddington inversion of the radiative transfer equation. The data reveal a more inclined field in the light bridge and penumbral filament than in the umbra with a vertical current density higher than 200 mA m-2 . Also opposite polarity patches were found in the light bridge. Such a magnetic configuration indicates low altitude reconnection. A similar mechanism causes penumbral microjets which were also observed along other penumbral filaments.

  18. Filament disappearances

    NASA Technical Reports Server (NTRS)

    Wagner, William J.

    1986-01-01

    The phenomenon of the sudden filament disappearance (Disparition Brusque) is a familiar one to observers at H alpha telescopes. Nevertherless, the importance in Disparition Brusques (DB) continues to grow for several reasons which are cited in the discussion. It is reported that there seems to be more interest on building and maintain filaments than in destroying them. As a consequence, this sub-group is smaller than most of the others. All the same, progress in this area of filament disapperences seems steady and assured. The importance and interest in DBs is discussed and future directions are indicated.

  19. Solid friction between soft filaments.

    PubMed

    Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A W C; Vitelli, Vincenzo; Mahadevan, L; Dogic, Zvonimir

    2015-06-01

    Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments' overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes's drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament's elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials. PMID:25730393

  20. The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: the nature of the repeating unit.

    PubMed

    Fraser, R D B; Parry, David A D

    2006-08-01

    Recently, the spatial distribution of the crosslinks induced between lysine residues in trichocyte (alpha-) keratin intermediate filaments (IF) using disulfosuccinimidyl tartrate was analyzed in detail and the results used to provide information about the three-dimensional structure of the IF [Fraser, R.D.B., Parry, D.A.D., 2005. The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: features of the molecular packing deduced from the sites of induced crosslinks. J. Struct. Biol. 151, 171-181.] The presence of small amounts of 0--> +/-4 crosslinkages between molecular strands four distant in the network implied that the three-dimensional network of interacting molecules must be deeply puckered, but no specific suggestions were made about the nature of the puckering. Whilst it was recognized that there may be more than one type of molecular environment in the structural repeat the initial analysis was confined to the simplest case in which all molecules had the same environment, that is to say the asymmetric unit comprised a single molecule. Further studies reported here suggest that it is likely that the asymmetric unit consists of at least two and possibly as many as four molecules and the implications of this for modeling the structure of trichocyte IF are discussed. PMID:16890455

  1. Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant

    SciTech Connect

    Chen, Jianhong; Villanueva, Nicolas; Rould, Mark A.; Morrical, Scott W.

    2010-09-03

    Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To investigate, we characterized yeast Rad51 H352A and H352Y mutants, and solved the structure of H352Y. H352A forms catalytically competent but salt-labile complexes on ssDNA. In contrast, H352Y forms salt-resistant complexes on ssDNA, but is defective in nucleotide exchange, RPA displacement and strand exchange with full-length DNA substrates. The 2.5 {angstrom} crystal structure of H352Y reveals a right-handed helical filament in a high-pitch (130 {angstrom}) conformation with P61 symmetry. The catalytic core and dimer interface regions of H352Y closely resemble those of DNA-bound Escherichia coli RecA protein. The H352Y mutation stabilizes Phe187 from the adjacent subunit in a position that interferes with the {gamma}-phosphate-binding site of the Walker A motif/P-loop, potentially explaining the limited catalysis observed. Comparison of Rad51 H352Y, RecA-DNA and related structures reveals that the presence of bound DNA correlates with the isomerization of a conserved cis peptide near Walker B to the trans configuration, which appears to prime the catalytic glutamate residue for ATP hydrolysis.

  2. Fractal nanoparticle plasmonics: the Cayley tree.

    PubMed

    Gottheim, Samuel; Zhang, Hui; Govorov, Alexander O; Halas, Naomi J

    2015-03-24

    There has been strong, ongoing interest over the past decade in developing strategies to design and engineer materials with tailored optical properties. Fractal-like nanoparticles and films have long been known to possess a remarkably broad-band optical response and are potential nanoscale components for realizing spectrum-spanning optical effects. Here we examine the role of self-similarity in a fractal geometry for the design of plasmon line shapes. By computing and fabricating simple Cayley tree nanostructures of increasing fractal order N, we are able to identify the principle behind how the multimodal plasmon spectrum of this system develops as the fractal order is increased. With increasing N, the fractal structure acquires an increasing number of modes with certain degeneracies: these modes correspond to plasmon oscillations on the different length scales inside a fractal. As a result, fractals with large N exhibit broad, multipeaked spectra from plasmons with large degeneracy numbers. The Cayley tree serves as an example of a more general, fractal-based route for the design of structures and media with highly complex optical line shapes. PMID:25727720

  3. The fractal aggregation of asphaltenes.

    PubMed

    Hoepfner, Michael P; Fávero, Cláudio Vilas Bôas; Haji-Akbari, Nasim; Fogler, H Scott

    2013-07-16

    This paper discusses time-resolved small-angle neutron scattering results that were used to investigate asphaltene structure and stability with and without a precipitant added in both crude oil and model oil. A novel approach was used to isolate the scattering from asphaltenes that are insoluble and in the process of aggregating from those that are soluble. It was found that both soluble and insoluble asphaltenes form fractal clusters in crude oil and the fractal dimension of the insoluble asphaltene clusters is higher than that of the soluble clusters. Adding heptane also increases the size of soluble asphaltene clusters without modifying the fractal dimension. Understanding the process of insoluble asphaltenes forming fractals with higher fractal dimensions will potentially reveal the microscopic asphaltene destabilization mechanism (i.e., how a precipitant modifies asphaltene-asphaltene interactions). It was concluded that because of the polydisperse nature of asphaltenes, no well-defined asphaltene phase stability envelope exists and small amounts of asphaltenes precipitated even at dilute precipitant concentrations. Asphaltenes that are stable in a crude oil-precipitant mixture are dispersed on the nanometer length scale. An asphaltene precipitation mechanism is proposed that is consistent with the experimental findings. Additionally, it was found that the heptane-insoluble asphaltene fraction is the dominant source of small-angle scattering in crude oil and the previously unobtainable asphaltene solubility at low heptane concentrations was measured. PMID:23808932

  4. Chaos, Fractals, and Polynomials.

    ERIC Educational Resources Information Center

    Tylee, J. Louis; Tylee, Thomas B.

    1996-01-01

    Discusses chaos theory; linear algebraic equations and the numerical solution of polynomials, including the use of the Newton-Raphson technique to find polynomial roots; fractals; search region and coordinate systems; convergence; and generating color fractals on a computer. (LRW)

  5. Chaos and Fractals.

    ERIC Educational Resources Information Center

    Barton, Ray

    1990-01-01

    Presented is an educational game called "The Chaos Game" which produces complicated fractal images. Two basic computer programs are included. The production of fractal images by the Sierpinski gasket and the Chaos Game programs is discussed. (CW)

  6. Dark Filaments, Clouds and Cores: A Multiband IR Study of the Early Stages of Star Formation in Extended Structures

    NASA Astrophysics Data System (ADS)

    Smith, Howard

    Star formation typically begins in cold, dark clouds that are not spherically symmetric, but elongated as infrared dark clouds or long linear filaments. Their star-forming characteristics are thought to be sensitive to the geometries. We propose a systematic, detailed study of a sample of 168 of these dark clouds spanning a wide range of parameters using new archival data from Herschel and Spitzer. Archival Herschel photometry in particular enables for the first time a sensitive, systematic study of the full far-infrared continuum of these objects. We have distance determinations and ancillary molecule line measurements for all of our sources. Ten-band photometry (from 3.5um to 500um) will let us determine the luminosities, spectral energy distributions (SEDs), and estimate masses of these cold structures as functions of their star-formation activity. We will produce dust temperature and optical depth maps that will enable statistical studies of filaments and their cores; we expect statistics on over 500 protostellar cores. Our selected sources span a range of physical conditions: distances from 1 to 8 kpc, lengths from 0.1 to 80 pc, aspect ratios from below 2 to above 8, nominal core masses from about 1 to 500 Mo, and a range of geometries including linear, branching, hub-filament, and network configurations. We plan to use the extended Robitaille YSO models and SUNRISE radiative transfer models for prestellar cores to analyze a generic set of the most common objects, and then test their applicability across the sample. We will also bring other data to bear (WISE; 2MASS, millimeter) as is useful. We address three current, multi-faceted problems: (1) What are the density, temperature and optical depth structures of filaments and their cores? How do these parameters vary spatially for cores and the inter-core regions? How do these parameters correlate to filamentary or environmental properties? (2) What is the statistical distribution of these properties; in

  7. Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining.

    PubMed

    Ropars, Virginie; Drevet, Pascal; Legrand, Pierre; Baconnais, Sonia; Amram, Jeremy; Faure, Guilhem; Márquez, José A; Piétrement, Olivier; Guerois, Raphaël; Callebaut, Isabelle; Le Cam, Eric; Revy, Patrick; de Villartay, Jean-Pierre; Charbonnier, Jean-Baptiste

    2011-08-01

    Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X4(1-157)-Cernunnos(1-224) complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X4(1-157) and Cernunnos(1-224) homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4-Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4-Cernunnos interface. We identified four X4 residues (Glu(55), Asp(58), Met(61), and Phe(106)) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step. PMID:21768349

  8. Fractal Surfaces of Molecular Crystals Mimicking Lotus Leaf with Phototunable Double Roughness Structures.

    PubMed

    Nishimura, Ryo; Hyodo, Kengo; Sawaguchi, Haruna; Yamamoto, Yoshiaki; Nonomura, Yoshimune; Mayama, Hiroyuki; Yokojima, Satoshi; Nakamura, Shinichiro; Uchida, Kingo

    2016-08-17

    Double roughness structure, the origin of the lotus effect of natural lotus leaf, was successfully reproduced on a diarylethene microcrystalline surface. Static superwater-repellency and dynamic water-drop-bouncing were observed on the surface, in the manner of natural lotus leaves. Double roughness structure was essential for water-drop-bouncing. This ability was not observed on a single roughness microcrystalline surface showing the lotus effect of the same diarylethene derivative. The double roughness structure was reversibly controlled by alternating irradiation with UV and visible light. PMID:27455376

  9. [Fractal analysis of liver fibrosis].

    PubMed

    Soda, G; Nardoni, S; Bosco, D; Grizzi, F; Dioguardi, N; Melis, M

    2003-04-01

    This study realized by two different study groups use of Fractal geometry to quantify the complex collagen deposition during chronic liver disease. Thirty standard needle liver biopsy specimens were obtained from patients with chronic HCV-related disease. Three mu-thick sections were cut and stained by means of Picrosirius stain, in order to visualise collagen matrix. The degree of fibrosis was measured using a quantitative scoring system based on the computer-assisted evaluation of the fractal dimension of the deposited collagen surface. The obtained results by both study groups, show that the proposed method is reproducible, rapid and inexpensive. The complex distribution of its collagenous components can be quantified using a single numerical score. This study demonstrated that it is possible to quantify the collagen's irregularity in an objective manner, and that the study of the fractal properties of the collagen shapes is likely to reveal more about its structure and the complex behaviour of its development. PMID:12768879

  10. Spatial structure of scrape-off-layer filaments near the midplane and X-point regions of Alcator C-Mod

    SciTech Connect

    Terry, J L; Zweben, S J; Umansky, M V; Cziegler, I; Grulke, O; LaBombard, B; Stotler, D P

    2008-05-22

    Movies of edge turbulence at both the outboard midplane and the region outboard of the typical lower X-point location in C-Mod have been obtained using Gas-Puff-Imaging together with fast-framing cameras. Intermittent turbulent structures, typically referred to as blobs or filaments, are observed in both locations. Near the midplane the filaments are roughly circular in cross-section, while in the X-point region they are highly elongated. Filament velocities in this region are {approx}3x faster than the radial velocities at the midplane, in a direction roughly normal to the local flux surfaces. The observations are consistent with the picture that the filaments arise in outboard region and, as a consequence of the rapid parallel diffusion of the potential perturbations, map along field lines. A simulation using the 3D BOUT turbulence code has been made, with the result that reproduces many of the spatial features observed in the experiment.

  11. Fractals in the Classroom

    ERIC Educational Resources Information Center

    Fraboni, Michael; Moller, Trisha

    2008-01-01

    Fractal geometry offers teachers great flexibility: It can be adapted to the level of the audience or to time constraints. Although easily explained, fractal geometry leads to rich and interesting mathematical complexities. In this article, the authors describe fractal geometry, explain the process of iteration, and provide a sample exercise.…

  12. Fractal Model of a Compact Intracloud Discharge. I. Features of the Structure and Evolution

    NASA Astrophysics Data System (ADS)

    Iudin, D. I.; Davydenko, S. S.

    2015-12-01

    We propose a new model of a compact intracloud discharge considered as the result of interaction between two (or more) bipolar streamer structures formed in a strong large-scale electric field of a thundercloud. The model assumes two stages of the compact discharge development. At the preliminary stage, two or more bipolar streamer structures appear successively in the thundercloud in the region of a strong electric field (at the boundaries between the regions of the main positive and the main negative electric charges or between the main positive charge region and the top negative screening layer). The time of development of such structures is determined by the characteristics of the conducting channels that form them and can reach tens of milliseconds. Spatiotemporal synchronization of the bipolar streamer structures is provided by the altitude modulation of the electric field, which, in particular, can originate from a large-scale turbulence of the cloud medium or the stream instability. It is shown that a single bipolar streamer structure accumulates significant electric charges of different signs at its ends as it develops. The start of the main stage of a compact intracloud discharge corresponds to the occurrence of the conducting channel (breakdown of the gap) between the mature streamer structures. The electric charge accumulated at the adjacent ends of the structures at this stage is neutralized over a time much shorter than the duration of the preliminary stage. The parameters of the current pulse are in good agreement with the estimates of the current of a compact intracloud discharge which were obtained in the transmission-line approximation.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2016-12-01

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

  15. Experimental evidence of how the fractal structure controls the hydrodynamic resistance on granular aggregates moving through water

    NASA Astrophysics Data System (ADS)

    Maggi, Federico

    2015-09-01

    A comprehensive set of experiments was carried out to investigate the effect of the fractal architecture of granular aggregates on the free-fall acceleration through a still water column. Test aggregates were first generated numerically with a method that allowed to control the fractal dimension d and, next, three stochastic replicates were lithographically fabricated for each of six values of d ranging between 1.9 and 2.7. The recorded position, velocity and acceleration served to analyze their dynamics in the Reynolds and Galilei number space, and to calculate the momentum rate of change and the intensity of drag (viscous and impact) and inertial forces (added mass and Basset-Bousinnesq). Analysis of these forces highlighted a strong dependence on d; additionally, integration of these forces in the particle momentum equation allowed to identify an additional resistance Rx that showed a strong correlation with d. A correlation analysis of Rx with various scaling laws combining velocity and acceleration suggested that Rx could be described by a nonlinear drag force and a force intermediate between drag and inertia. It was therefore concluded that irregular granular fractal aggregates accelerating in water are subject to highly complex and nonlinear hydrodynamic effects caused by surface roughness and volume porosity, and that these effects have tight connection with the internal and external fractal characteristics of the aggregates.

  16. Formation of dense structures induced by filament collisions. Correlation of density, kinematics, and magnetic field in the Pipe nebula

    NASA Astrophysics Data System (ADS)

    Frau, P.; Girart, J. M.; Alves, F. O.; Franco, G. A. P.; Onishi, T.; Román-Zúñiga, C. G.

    2015-02-01

    Context. The Pipe nebula is a molecular cloud that lacks star formation feedback and has a relatively simple morphology and velocity structure. This makes it an ideal target for testing cloud evolution through collisions. Aims: We aim at drawing a comprehensive picture of this relatively simple cloud to better understand the formation and evolution of molecular clouds on large scales. Methods: We use archival data to compare the optical polarization properties, the visual extinction, and the 13CO velocities and linewidths of the entire cloud in order to identify trends among the observables. Results: The Pipe nebula can be roughly divided into two filaments with different orientations and gas velocity ranges: E-W at 2-4 km s-1 and N-S at 6-7 km s-1. The two filaments overlap at the bowl, where the gas shows a velocity gradient spanning from 2 to 7 km s-1. Compared to the rest of the Pipe nebula, the bowl gas appears to be denser and exhibits larger linewidths. In addition, the polarization data at the bowl shows lower angular dispersion and higher polarization degree. Cores in the bowl tend to cluster in space and to follow the 13CO velocity gradient. In the stem, cores tend to cluster in regions with properties similar to those of the bowl. Conclusions: The velocity pattern points to a collision between the filaments in the bowl region. The magnetic field seems to be compressed and strengthened in the shocked region. The proportional increase in density and magnetic field strength by a factor similar to the Alfvénic Mach number suggests a continuous shock at low Alfvénic Mach number under the flux-freezing condition. Shocked regions seem to enhance the formation and clustering of dense cores. A movie associated to Fig. 2 is available at http://www.aanda.org

  17. Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal

    PubMed Central

    Dreyer, Thiago R.; Freitas, Fernanda Z.; Bertolini, Maria Célia; Fontes, Marcos R. M.

    2015-01-01

    Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site. PMID:26091498

  18. Reorganization of actin filaments by ADF/cofilin is involved in formation of microtubule structures during Xenopus oocyte maturation

    PubMed Central

    Yamagishi, Yuka; Abe, Hiroshi

    2015-01-01

    We examined the reorganization of actin filaments and microtubules during Xenopus oocyte maturation. Surrounding the germinal vesicle (GV) in immature oocytes, the cytoplasmic actin filaments reorganized to accumulate beneath the vegetal side of the GV, where the microtubule-organizing center and transient microtubule array (MTOC-TMA) assembled, just before GV breakdown (GVBD). Immediately after GVBD, both Xenopus ADF/cofilin (XAC) and its phosphatase Slingshot (XSSH) accumulated into the nuclei and intranuclear actin filaments disassembled from the vegetal side with the shrinkage of the GV. As the MTOC-TMA developed well, cytoplasmic actin filaments were retained at the MTOC-TMA base region. Suppression of XAC dephosphorylation by anti-XSSH antibody injection inhibited both actin filament reorganization and proper formation and localization of both the MTOC-TMA and meiotic spindles. Stabilization of actin filaments by phalloidin also inhibited formation of the MTOC-TMA and disassembly of intranuclear actin filaments without affecting nuclear shrinkage. Nocodazole also caused the MTOC-TMA and the cytoplasmic actin filaments at its base region to disappear, which further impeded disassembly of intranuclear actin filaments from the vegetal side. XAC appears to reorganize cytoplasmic actin filaments required for precise assembly of the MTOC and, together with the MTOC-TMA, regulate the intranuclear actin filament disassembly essential for meiotic spindle formation. PMID:26424802

  19. Nonvolatile conductive filaments resistive switching behaviors in Ag/GaO x /Nb:SrTiO3/Ag structure

    NASA Astrophysics Data System (ADS)

    Li, P. G.; Zhi, Y. S.; Wang, P. C.; Sun, Z. B.; Li, L. H.; An, Y. H.; Guo, D. Y.; Tang, W. H.; Xiao, J. H.

    2016-07-01

    Ag/GaO x /NSTO/Ag structures were fabricated, and the electrical properties measurement results show that the device behaviors a unipolar resistance switching characteristic with bi-stable resistance ratio of three orders. In the positive voltage region, the dominant conducting mechanism of high resistance state obeys Poole-Frenkel emission rules, while in the negative region, that obeys space-charge-limited current mechanism. Both the I- V curves of ON and OFF states and temperature-dependent variation resistances indicate that the unipolar resistance switching behavior can be explained by the formation/rupture of conductive filaments, which composed of oxygen vacancies. The stable switching results demonstrated that the structure can be applied in resistance random access memory devices.

  20. Structural Analysis of Helios Filament-Wound Tanks Subjected to Internal Pressure and Cooling

    NASA Technical Reports Server (NTRS)

    Ko, William L

    2005-01-01

    A finite-element stress analysis is performed on Helios filament-wound hydrogen tanks to examine the stress field and effect of end dome geometry on the stress field. Each tank is composed of a central circular cylindrical section with either geodesic or hemispherical end domes, which have metallic polar bosses. The tanks are subjected to combined and separate internal pressure and temperature loading conditions, and the stress contributions of each loading component are examined. The tank-wall-polar-boss interfacial meridional tensile stress in the hemispherical dome is found to be approximately 27 percent lower than that in the geodesic dome. The effects of both material anisotropy and the aluminum lining on the intensities of tensile meridional stress at the tank-wall-polar-boss bonding interface are examined.

  1. Fractal Poisson processes

    NASA Astrophysics Data System (ADS)

    Eliazar, Iddo; Klafter, Joseph

    2008-09-01

    The Central Limit Theorem (CLT) and Extreme Value Theory (EVT) study, respectively, the stochastic limit-laws of sums and maxima of sequences of independent and identically distributed (i.i.d.) random variables via an affine scaling scheme. In this research we study the stochastic limit-laws of populations of i.i.d. random variables via nonlinear scaling schemes. The stochastic population-limits obtained are fractal Poisson processes which are statistically self-similar with respect to the scaling scheme applied, and which are characterized by two elemental structures: (i) a universal power-law structure common to all limits, and independent of the scaling scheme applied; (ii) a specific structure contingent on the scaling scheme applied. The sum-projection and the maximum-projection of the population-limits obtained are generalizations of the classic CLT and EVT results - extending them from affine to general nonlinear scaling schemes.

  2. Structural changes of the regulatory proteins bound to the thin filaments in skeletal muscle contraction by X-ray fiber diffraction

    SciTech Connect

    Sugimoto, Yasunobu Takezawa, Yasunori; Matsuo, Tatsuhito; Ueno, Yutaka; Minakata, Shiho; Tanaka, Hidehiro; Wakabayashi, Katsuzo

    2008-04-25

    In order to clarify the structural changes related to the regulation mechanism in skeletal muscle contraction, the intensity changes of thin filament-based reflections were investigated by X-ray fiber diffraction. The time course and extent of intensity changes of the first to third order troponin (TN)-associated meridional reflections with a basic repeat of 38.4 nm were different for each of these reflections. The intensity of the first and second thin filament layer lines changed in a reciprocal manner both during initial activation and during the force generation process. The axial spacings of the TN-meridional reflections decreased by {approx}0.1% upon activation relative to the relaxing state and increased by {approx}0.24% in the force generation state, in line with that of the 2.7-nm reflection. Ca{sup 2+}-binding to TN triggered the shortening and a change in the helical symmetry of the thin filaments. Modeling of the structural changes using the intensities of the thin filament-based reflections suggested that the conformation of the globular core domain of TN altered upon activation, undergoing additional conformational changes at the tension plateau. The tail domain of TN moved together with tropomyosin during contraction. The results indicate that the structural changes of regulatory proteins bound to the actin filaments occur in two steps, the first in response to the Ca{sup 2+}-binding and the second induced by actomyosin interaction.

  3. Fractality à la carte: a general particle aggregation model

    PubMed Central

    Nicolás-Carlock, J. R.; Carrillo-Estrada, J. L.; Dossetti, V.

    2016-01-01

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters’ fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension. PMID:26781204

  4. Fractality à la carte: a general particle aggregation model

    NASA Astrophysics Data System (ADS)

    Nicolás-Carlock, J. R.; Carrillo-Estrada, J. L.; Dossetti, V.

    2016-01-01

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters’ fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension.

  5. Fractality à la carte: a general particle aggregation model.

    PubMed

    Nicolás-Carlock, J R; Carrillo-Estrada, J L; Dossetti, V

    2016-01-01

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters' fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension. PMID:26781204

  6. Fractal statistics of cloud fields

    NASA Technical Reports Server (NTRS)

    Cahalan, Robert F.; Joseph, Joachim H.

    1989-01-01

    Landsat Multispectral Scanner (MSS) and Thematic Mapper (TM) data, with 80 and 30 m spatial resolution, respectively, have been employed to study the spatial structure of boundary-layer and intertropical convergence zone (ITCZ) clouds. The probability distributions of cloud areas and cloud perimeters are found to approximately follow a power-law, with a different power (i.e., fractal dimension) for each cloud type. They are better approximated by a double power-law behavior, indicating a change in the fractal dimension at a characteristic size which depends upon cloud type. The fractal dimension also changes with threshold. The more intense cloud areas are found to have a higher perimeter fractal dimension, perhaps indicative of the increased turbulence at cloud top. A detailed picture of the inhomogeneous spatial structure of various cloud types will contribute to a better understanding of basic cloud processes, and also has implications for the remote sensing of clouds, for their effects on remote sensing of other parameters, and for the parameterization of clouds in general circulation models, all of which rely upon plane-parallel radiative transfer algorithms.

  7. Three-dimensional structure of the M-region (bare zone) of vertebrate striated muscle myosin filaments by single-particle analysis.

    PubMed

    Al-Khayat, Hind A; Kensler, Robert W; Morris, Edward P; Squire, John M

    2010-11-12

    The rods of anti-parallel myosin molecules overlap at the centre of bipolar myosin filaments to produce an M-region (bare zone) that is free of myosin heads. Beyond the M-region edges, myosin molecules aggregate in a parallel fashion to yield the bridge regions of the myosin filaments. Adjacent myosin filaments in striated muscle A-bands are cross-linked by the M-band. Vertebrate striated muscle myosin filaments have a 3-fold rotational symmetry around their long axes. In addition, at the centre of the M-region, there are three 2-fold axes perpendicular to the filament long axis, giving the whole filament dihedral 32-point group symmetry. Here we describe the three-dimensional structure obtained by a single-particle analysis of the M-region of myosin filaments from goldfish skeletal muscle under relaxing conditions and as viewed in negative stain. This is the first single-particle reconstruction of isolated M-regions. The resulting three-dimensional reconstruction reveals details to about 55 Å resolution of the density distribution in the five main nonmyosin densities in the M-band (M6', M4', M1, M4 and M6) and in the myosin head crowns (P1, P2 and P3) at the M-region edges. The outermost crowns in the reconstruction were identified specifically by their close similarity to the corresponding crown levels in our previously published bridge region reconstructions. The packing of myosin molecules into the M-region structure is discussed, and some unidentified densities are highlighted. PMID:20851129

  8. Streptococcus salivarius Fimbriae Are Composed of a Glycoprotein Containing a Repeated Motif Assembled into a Filamentous Nondissociable Structure

    PubMed Central

    Lévesque, Céline; Vadeboncoeur, Christian; Chandad, Fatiha; Frenette, Michel

    2001-01-01

    Streptococcus salivarius, a gram-positive bacterium found in the human oral cavity, expresses flexible peritrichous fimbriae. In this paper, we report purification and partial characterization of S. salivarius fimbriae. Fimbriae were extracted by shearing the cell surface of hyperfimbriated mutant A37 (a spontaneous mutant of S. salivarius ATCC 25975) with glass beads. Preliminary experiments showed that S. salivarius fimbriae did not dissociate when they were incubated at 100°C in the presence of sodium dodecyl sulfate. This characteristic was used to separate them from other cell surface components by successive gel filtration chromatography procedures. Fimbriae with molecular masses ranging from 20 × 106 to 40 × 106 Da were purified. Examination of purified fimbriae by electron microscopy revealed the presence of filamentous structures up to 1 μm long and 3 to 4 nm in diameter. Biochemical studies of purified fimbriae and an amino acid sequence analysis of a fimbrial internal peptide revealed that S. salivarius fimbriae were composed of a glycoprotein assembled into a filamentous structure resistant to dissociation. The internal amino acid sequence was composed of a repeated motif of two amino acids alternating with two modified residues: A/X/T-E-Q-M/φ, where X represents a modified amino acid residue and φ represents a blank cycle. Immunolocalization experiments also revealed that the fimbriae were associated with a wheat germ agglutinin-reactive carbohydrate. Immunolabeling experiments with antifimbria polyclonal antibodies showed that antigenically related fimbria-like structures were expressed in two other human oral streptococcal species, Streptococcus mitis and Streptococcus constellatus. PMID:11292790

  9. Extracellular matrix of adipogenically differentiated mesenchymal stem cells reveals a network of collagen filaments, mostly interwoven by hexagonal structural units.

    PubMed

    Ullah, Mujib; Sittinger, Michael; Ringe, Jochen

    2013-01-01

    Extracellular matrix (ECM) is the non-cellular component of tissues, which not only provides biological shelter but also takes part in the cellular decisions for diverse functions. Every tissue has an ECM with unique composition and topology that governs the process of determination, differentiation, proliferation, migration and regeneration of cells. Little is known about the structural organization of matrix especially of MSC-derived adipogenic ECM. Here, we particularly focus on the composition and architecture of the fat ECM to understand the cellular behavior on functional bases. Thus, mesenchymal stem cells (MSC) were adipogenically differentiated, then, were transferred to adipogenic propagation medium, whereas they started the release of lipid droplets leaving bare network of ECM. Microarray analysis was performed, to indentify the molecular machinery of matrix. Adipogenesis was verified by Oil Red O staining of lipid droplets and by qPCR of adipogenic marker genes PPARG and FABP4. Antibody staining demonstrated the presence of collagen type I, II and IV filaments, while alkaline phosphatase activity verified the ossified nature of these filaments. In the adipogenic matrix, the hexagonal structures were abundant followed by octagonal structures, whereas they interwoven in a crisscross manner. Regarding molecular machinery of adipogenic ECM, the bioinformatics analysis revealed the upregulated expression of COL4A1, ITGA7, ITGA7, SDC2, ICAM3, ADAMTS9, TIMP4, GPC1, GPC4 and downregulated expression of COL14A1, ADAMTS5, TIMP2, TIMP3, BGN, LAMA3, ITGA2, ITGA4, ITGB1, ITGB8, CLDN11. Moreover, genes associated with integrins, glycoproteins, laminins, fibronectins, cadherins, selectins and linked signaling pathways were found. Knowledge of the interactive-language between cells and matrix could be beneficial for the artificial designing of biomaterials and bioscaffolds. PMID:23851162

  10. A ROBUST MEASURE OF COSMIC STRUCTURE BEYOND THE POWER SPECTRUM: COSMIC FILAMENTS AND THE TEMPERATURE OF DARK MATTER

    SciTech Connect

    Obreschkow, D.; Power, C.; Bruderer, M.; Bonvin, C.

    2013-01-10

    We discover that the mass of dark matter particles m {sub DM} is imprinted in phase correlations of the cosmic density field more significantly than in the two-point correlation. In particular, phase correlations trace m {sub DM} out to scales about five times larger than the two-point correlation. This result relies on a new estimator l(r) of pure phase information in Fourier space, which can be interpreted as a parameter-free and scale-invariant tracer of filament-like structure. Based on simulated density fields, we show how m {sub DM} can, in principle, be measured using l(r), given a suitably reconstructed density field.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. Collagen-like glycoprotein BclS is involved in the formation of filamentous structures of the Lysinibacillus sphaericus exosporium.

    PubMed

    Zhao, Ni; Ge, Yong; Shi, Tingyu; Hu, Xiaomin; Yuan, Zhiming

    2014-11-01

    Lysinibacillus sphaericus produces mosquitocidal binary toxins (Bin toxins) deposited within a balloon-like exosporium during sporulation. Unlike Bacillus cereus group strains, the exosporium of L. sphaericus is usually devoid of the hair-like nap, an external filamentous structure formed by a collagen-like protein, BclA. In this study, a new collagen-like exosporium protein encoded by Bsph_0411 (BclS) from L. sphaericus C3-41 was characterized. Thin-section electron microscopy revealed that deletion of bclS resulted in the loss of the filamentous structures that attach to the exosporium basal layer and spread through the interspace of spores. In vivo visualization of BclS-green fluorescent protein (GFP)/mCherry fusion proteins revealed a dynamic pattern of fluorescence that encased the spore from the mother cell-distal (MCD) pole of the forespore, and the BclS-GFP fusions were found to be located in the interspace of the spore, as confirmed by three-dimensional (3D) superresolution fluorescence microscopy. Further studies demonstrated that the bclS mutant spores were more sensitive to wet-heat treatment and germinated at a lower rate than wild-type spores and that these phenotypes were significantly restored in the bclS-complemented strain. These results suggested novel roles of collagen-like protein in exosporium assembly and spore germination, providing a hint for a further understanding of the genetic basis of the high level of persistence of Bin toxins in nature. PMID:25149519

  13. Collagen-Like Glycoprotein BclS Is Involved in the Formation of Filamentous Structures of the Lysinibacillus sphaericus Exosporium

    PubMed Central

    Zhao, Ni; Ge, Yong; Shi, Tingyu; Hu, Xiaomin

    2014-01-01

    Lysinibacillus sphaericus produces mosquitocidal binary toxins (Bin toxins) deposited within a balloon-like exosporium during sporulation. Unlike Bacillus cereus group strains, the exosporium of L. sphaericus is usually devoid of the hair-like nap, an external filamentous structure formed by a collagen-like protein, BclA. In this study, a new collagen-like exosporium protein encoded by Bsph_0411 (BclS) from L. sphaericus C3-41 was characterized. Thin-section electron microscopy revealed that deletion of bclS resulted in the loss of the filamentous structures that attach to the exosporium basal layer and spread through the interspace of spores. In vivo visualization of BclS-green fluorescent protein (GFP)/mCherry fusion proteins revealed a dynamic pattern of fluorescence that encased the spore from the mother cell-distal (MCD) pole of the forespore, and the BclS-GFP fusions were found to be located in the interspace of the spore, as confirmed by three-dimensional (3D) superresolution fluorescence microscopy. Further studies demonstrated that the bclS mutant spores were more sensitive to wet-heat treatment and germinated at a lower rate than wild-type spores and that these phenotypes were significantly restored in the bclS-complemented strain. These results suggested novel roles of collagen-like protein in exosporium assembly and spore germination, providing a hint for a further understanding of the genetic basis of the high level of persistence of Bin toxins in nature. PMID:25149519

  14. Embedded fiber optic sensor arrays for structural health monitoring of filament wound composite pressure vessels

    NASA Astrophysics Data System (ADS)

    Foedinger, Richard C.; Rea, David L.; Sirkis, James S.; Baldwin, Christopher S.; Troll, John R.; Grande, Robert; Davis, Craig S.; Vandiver, Terry L.

    1999-05-01

    Optical Fiber Bragg Grating (FBG) strain and temperature sensors were embedded into four carbon/epoxy, filament-wound 5.75' diameter Standard Testing and Evaluation Bottles (STEBs). These sensors were used to monitor temperature and strain during cure and pressurization of the pressure vessels. Preliminary to this work, micrographs were made of embedded fiber, showing good incorporation of the fiber into the material and no degradation of the optical fiber's acrylate coating. A survey was also made of different ingress/egress techniques to protecting the fiber as in enters the bottle and preventing attenuation and power fluctuation, with Tefzel tubing proving to be the most effective method. The FBGs were embedded parallel to the reinforcing fibers, in the hoop and helical directions, and also in the axial direction. The sensors showed close agreement with surface-mounted Resistance Strain Gages (RSGs),as well as finite element modeling. Sensors in the hoop direction embedded at mid-cylinder showed the closest agreement (-1.2%), while agreement for hoop- direction sensors embedded near the ends of the bottle (11%) was not as close. The agreement was also better for helically directed sensors embedded at mid-cylinder (-1.6%?) than for those embedded near the ends (-24%). Some preliminary impact testing was conducted that indicated FBG sensors would be appropriate for sensing impact damage.

  15. Exploring Fractals in the Classroom.

    ERIC Educational Resources Information Center

    Naylor, Michael

    1999-01-01

    Describes an activity involving six investigations. Introduces students to fractals, allows them to study the properties of some famous fractals, and encourages them to create their own fractal artwork. Contains 14 references. (ASK)

  16. ZnS:Cr Nanostructures Building Fractals and Their Properties

    SciTech Connect

    Gogoi, D. P.; Das, U.; Mohanta, D.; Ahmed, G. A.; Choudhury, A.

    2010-10-04

    Cr doped ZnS nanostructures have been fabricated through colloidal solution route by using Polyvinyl alcohol (-C{sub 2}H{sub 4}O){sub n} and Polyvinyl pyrrolidone k30 (C{sub 6}H{sub 9}NO){sub x} as dielectric hosts. Growth of fractal structures have been observed through Transmission Electron Microscopy. Higher magnification TEM study reveals that these fractals actually a organize structure of ZnS:Cr nanostructures. The structural study of these nanostructures in the fractals is done by X-Ray Diffraction, UV-Visible spectroscopy, Photoluminescence spectroscopy AFM and MFM. These investigations allow us to form a comprehensive explanation of fractal as well as nanostructure growth. We have done dimensional study of these fractals and the reason behind the formation of these fractals.

  17. Fractals: To Know, to Do, to Simulate.

    ERIC Educational Resources Information Center

    Talanquer, Vicente; Irazoque, Glinda

    1993-01-01

    Discusses the development of fractal theory and suggests fractal aggregates as an attractive alternative for introducing fractal concepts. Describes methods for producing metallic fractals and a computer simulation for drawing fractals. (MVL)

  18. Multifractal parametrization for the volume of space forms on surfaces of Zn x Cd1- x Te-Si(111) heterocompositions and estimating the energy of a surface with fractal structure

    NASA Astrophysics Data System (ADS)

    Moskvin, P. P.; Krizhanovskii, V. B.; Rashkovetskii, L. V.; Vuichik, N. V.

    2016-05-01

    Multifractal (MF) analysis is used to describe the volume of space forms on the surfaces of structures in the solid solution of a Zn x Cd1- x Te-Si(111) substrate. AFM images of film surfaces have been are used for MF analysis. The parameters of MF spectra are determined for the distribution of volume of surface nanoforms. Based on the formal approach and data on the parameters of the fractal state for the volume and surfaces of nanoforms, an equation is proposed that considers the contribution from the fractal structure of the surface to its surface energy. The behavior of the system's surface energy, depending on fractal parameters that describe states of the volume and surfaces of nanoforms is discussed.

  19. Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state.

    PubMed

    Sousa, Duncan R; Stagg, Scott M; Stroupe, M Elizabeth

    2013-11-15

    Tropomyosin (Tm) is a key factor in the molecular mechanisms that regulate the binding of myosin motors to actin filaments (F-Actins) in most eukaryotic cells. This regulation is achieved by the azimuthal repositioning of Tm along the actin (Ac):Tm:troponin (Tn) thin filament to block or expose myosin binding sites on Ac. In striated muscle, including involuntary cardiac muscle, Tm regulates muscle contraction by coupling Ca(2+) binding to Tn with myosin binding to the thin filament. In smooth muscle, the switch is the posttranslational modification of the myosin. Depending on the activation state of Tn and the binding state of myosin, Tm can occupy the blocked, closed, or open position on Ac. Using native cryogenic 3DEM (three-dimensional electron microscopy), we have directly resolved and visualized cardiac and gizzard muscle Tm on filamentous Ac in the position that corresponds to the closed state. From the 8-Å-resolution structure of the reconstituted Ac:Tm filament formed with gizzard-derived Tm, we discuss two possible mechanisms for the transition from closed to open state and describe the role Tm plays in blocking myosin tight binding in the closed-state position. PMID:24021812

  20. Temperature-sensitive intermediate filament assembly. Alternative structures of Xenopus laevis vimentin in vitro and in vivo.

    PubMed

    Herrmann, H; Eckelt, A; Brettel, M; Grund, C; Franke, W W

    1993-11-01

    In assembly assays of intermediate filaments (IFs) from vimentin of the amphibian species Xenopus laevis we have observed the formation of so far unknown structures at temperatures above 28 degrees C. Upon assembly in vitro at temperatures above 34 degrees C massive aggregates, partly with a protofilamentous substructure, were found and their formation correlated with drastically reduced end-viscosity. Large spheroidal, dense aggregates with a complex suborganization were also seen to form at 37 degrees C in the cytoplasm of living mammalian cells devoid of endogenous vimentin upon transfection with cDNA encoding the amphibian vimentin, and this was also true for vimentin forced to accumulate in the nucleoplasm by the introduction of a "nuclear localization signal". Upon shift from the non-permissive (37 degrees C) to the permissive (28 degrees C) temperature, such aggregates of non-IF vimentin structures gradually disappeared and a normal-looking IF meshwork formed. The results, which are discussed in relation to other structures assembled by IF proteins, indicate a marked thermosensitivity in the amino acid sequence of the vimentin which seems to have been reduced during evolution of warm-blooded animals. They further show that members of the multigene gene family of IF proteins can occur in structures totally different from IFs. PMID:8230211

  1. Predicting Solar Filament Eruptions with HEK Filament Metadata

    NASA Astrophysics Data System (ADS)

    Aggarwal, A.; Reeves, K.; Schanche, N.

    2015-12-01

    Solar filaments are cool, dark channels of partially-ionized plasma that lie above the chromosphere. Their structure follows the neutral line between local regions of opposite magnetic polarity. Previous research (e.g. Schmieder et al. 2013) has shown a positive correlation (80%) between the occurrence of filament eruptions and coronal mass ejections (CME's). If certain filament properties, such as length, chirality, and tilt, indicate a tendency towards filament eruptions, one may be able to further predict an oncoming CME. Towards this end, we present a novel algorithm based on spatiotemporal analysis that systematically correlates filament eruptions documented in the Heliophysics Event Knowledgebase (HEK) with HEK filaments that have been grouped together using a tracking algorithm developed at Georgia State University (e.g. Kempton et al. 2014). We also find filament tracks that are not correlated with eruptions to form a null data set in a similar fashion. Finally, we compare the metadata from erupting and non-erupting filament tracks to discover which filament properties may present signs of an eruption onset. Through statistical methods such as the two-sample Kolmogorov-Smirnov test and Random Forest Classifier, we find that a filament that is increasing in length or changing in tilt with respect to the equator may be a useful gauge to predict a filament eruption. However, the average values of length and tilt for both datasets follow similar distributions, leading us to conclude that these parameters do not indicate an eruption event. This work is supported by the NSF-REU solar physics program at SAO, grant number AGS-1263241, and NSF DIBBS grant number ACI-1443061.

  2. Fractal dimension and surface topography on the diamond deposition of seeded WC-Co substrates

    NASA Astrophysics Data System (ADS)

    Chou, C.-C.; Lin, H.-H.

    2010-04-01

    Diamond thin films were deposited on WC-Co substrates by hot filament chemical vapor deposition to improve the tribological performance. The influence of the substrate surface topography was found to play an important role during the nucleation stage and the later growth rate as well. In this study, we systematically investigated the relation between substrate surface irregularity, which was evaluated by fractal dimension as well as statistical roughness parameters and the quality of the later deposited diamond film. Preseeding processes, in diamond acetone suspensions with two particle diameters, by supersonic vibrator were also implemented to investigate the effect of particular size on diamond nucleation. The original surfaces were measured with a stylus profiler and contact-mode atomic force microscopy. The diamond deposited substrates were examined by scanning electron microscopy, x-ray diffractometry, Raman spectroscopy, and Rockwell-C indentation to study substrate topography, crystalline structure of the coating, the composition of diamond films, and adhesion between deposited layers and substrates, respectively. The synergetic influence of the substrate's fractal dimension and the particular size of pre-seeding diamond suspension were studied and addressed. The deposited film of a WC-Co substrate with higher surface fractal dimension (>2.50), preseeded by fine diamond suspension (4-12 nm particle size) in advance, has a high diamond-rich composition and adhesion strength.

  3. Fractal structure and predictive strategy of the daily extreme temperature residuals at Fabra Observatory (NE Spain, years 1917-2005)

    NASA Astrophysics Data System (ADS)

    Lana, X.; Burgueño, A.; Serra, C.; Martínez, M. D.

    2015-07-01

    A compilation of daily extreme temperatures recorded at the Fabra Observatory (Catalonia, NE Spain) since 1917 up to 2005 has permitted an exhaustive analysis of the fractal behaviour of the daily extreme temperature residuals, DTR, defined as the difference between the observed daily extreme temperature and the daily average value. The lacunarity characterises the lag distribution on the residual series for several thresholds. Hurst, H, and Hausdorff, Ha, exponents, together with the exponent β of the decaying power law, describing the evolution of power spectral density with frequency, permit to characterise the persistence, antipersistence or randomness of the residual series. The self-affine character of DTR series is verified, and additionally, they are simulated by means of fractional Gaussian noise, fGn. The reconstruction theorem leads to the quantification of the complexity (correlation dimension, μ*, and Kolmogorov entropy, κ) and predictive instability (Lyapunov exponents, λ, and Kaplan-Yorke dimension, D KY) of the residual series. All fractal parameters are computed for consecutive and independent segments of 5-year lengths. This strategy permits to obtain a high enough number of fractal parameter samples to estimate time trends, including their statistical significance. Comparisons are made between results of predictive algorithms based on fGn models and an autoregressive autoregressive integrated moving average (ARIMA) process, with the latter leading to slightly better results than the former. Several dynamic atmospheric mechanisms and local effects, such as local topography and vicinity to the Mediterranean coast, are proposed to explain the complex and instable predictability of DTR series. The memory of the physical system (Kolmogorov entropy) would be attributed to the interaction with the Mediterranean Sea.

  4. Periodic colour-centre structure formed under filamentation of mid-IR femtosecond laser radiation in a LiF crystal

    NASA Astrophysics Data System (ADS)

    Kuznetsov, A. V.; Kompanets, V. O.; Dormidonov, A. E.; Chekalin, S. V.; Shlenov, S. A.; Kandidov, V. P.

    2016-04-01

    A colour-centre structure formed in a LiF crystal under filamentation of a femtosecond mid-IR laser pulse with a power slightly exceeding the critical power for self-focusing has been experimentally and theoretically investigated. Strictly periodic oscillations have been detected for the first time for the density of the colour centres induced in an isotropic LiF crystal under filamentation of a laser beam with a wavelength tuned in the range from 2600 to 3350 nm. The structure period is found to be about 30 μm. With an increase in the laser radiation wavelength, the period of the oscillations decreases and their amplitude increases. The maximum colour centre density, observed under filamentation of a 3100-nm beam, is related to the increased contribution of the direct generation of colour centres as a result of the absorption of an integer number of photons by the exciton band. It is numerically shown that the formation of a periodic colour-centre structure in LiF is due to the periodic change in the light field amplitude in the light bullet (1.5 optical periods long) formed under filamentation.

  5. Fractal energy carpets in non-Hermitian Hofstadter quantum mechanics.

    PubMed

    Chernodub, Maxim N; Ouvry, Stéphane

    2015-10-01

    We study the non-Hermitian Hofstadter dynamics of a quantum particle with biased motion on a square lattice in the background of a magnetic field. We show that in quasimomentum space, the energy spectrum is an overlap of infinitely many inequivalent fractals. The energy levels in each fractal are space-filling curves with Hausdorff dimension 2. The band structure of the spectrum is similar to a fractal spider web in contrast to the Hofstadter butterfly for unbiased motion. PMID:26565163

  6. Fractal energy carpets in non-Hermitian Hofstadter quantum mechanics

    NASA Astrophysics Data System (ADS)

    Chernodub, Maxim N.; Ouvry, Stéphane

    2015-10-01

    We study the non-Hermitian Hofstadter dynamics of a quantum particle with biased motion on a square lattice in the background of a magnetic field. We show that in quasimomentum space, the energy spectrum is an overlap of infinitely many inequivalent fractals. The energy levels in each fractal are space-filling curves with Hausdorff dimension 2. The band structure of the spectrum is similar to a fractal spider web in contrast to the Hofstadter butterfly for unbiased motion.

  7. Solid friction between soft filaments

    NASA Astrophysics Data System (ADS)

    Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A. W. C.; Vitelli, Vincenzo; Mahadevan, L.; Dogic, Zvonimir

    2015-06-01

    Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

  8. Role of Intermediate Filaments in Vesicular Traffic

    PubMed Central

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  9. Role of Intermediate Filaments in Vesicular Traffic.

    PubMed

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  10. Fractal Metrology for biogeosystems analysis

    NASA Astrophysics Data System (ADS)

    Torres-Argüelles, V.; Oleschko, K.; Tarquis, A. M.; Korvin, G.; Gaona, C.; Parrot, J.-F.; Ventura-Ramos, E.

    2010-11-01

    The solid-pore distribution pattern plays an important role in soil functioning being related with the main physical, chemical and biological multiscale and multitemporal processes of this complex system. In the present research, we studied the aggregation process as self-organizing and operating near a critical point. The structural pattern is extracted from the digital images of three soils (Chernozem, Solonetz and "Chocolate" Clay) and compared in terms of roughness of the gray-intensity distribution quantified by several measurement techniques. Special attention was paid to the uncertainty of each of them measured in terms of standard deviation. Some of the applied methods are known as classical in the fractal context (box-counting, rescaling-range and wavelets analyses, etc.) while the others have been recently developed by our Group. The combination of these techniques, coming from Fractal Geometry, Metrology, Informatics, Probability Theory and Statistics is termed in this paper Fractal Metrology (FM). We show the usefulness of FM for complex systems analysis through a case study of the soil's physical and chemical degradation applying the selected toolbox to describe and compare the structural attributes of three porous media with contrasting structure but similar clay mineralogy dominated by montmorillonites.

  11. Inverse cascade in the structure of substorm aurora and non-linear dynamics of field-aligned current filaments

    NASA Astrophysics Data System (ADS)

    Kozelov, B. V.; Golovchanskaya, I. V.; Mingalev, O. V.

    2011-08-01

    We investigate time evolution of scaling index αA that characterizes auroral luminosity fluctuations at the beginning of substorm expansion. With the use of UVI images from the Polar satellite, it is shown that αA typically varies from values less than unity to ~1.5, increasing with breakup progress. Similar scaling features were previously reported for fluctuations at smaller scales from all-sky TV observations. If this signature is interpreted in terms of non-linear interactions between scales, it means that the power of small-scale fluctuations is transferred with time to larger scales, a kind of the inverse cascade. Scaling behavior in the aurora during substorm activity is compared with that in the field-aligned currents simulated numerically in the model of non-linear interactions of Alfvénic coherent structures, according to the Chang et al. (2004) scenario. This scenario also suggests an inverse cascade, manifesting in clustering of small-scale field-aligned current filaments of the same polarity and formation of "coarse-grained" structures of field-aligned currents.

  12. The structure and ionization of the extended emission-line filaments surrounding the QSO MR 2251-178

    SciTech Connect

    Macchetto, F.; Colina, L.; Golombek, D.; Perryman, M.A.C.; Di Serego Alighieri, S. ESA, Astrophysics Div., Noordwijk ESA, Space Telescope European Coordinating Facility, Garching )

    1990-06-01

    This paper presents new VLA radio maps, at 6 cm and 20 cm, of the QSO MR 2251-178, together with deep high-spatial-resolution images in the O II forbidden 3727-A line in the O III forbidden 5007-A line, and H-alpha emission lines, showing the presence of extended emission-line filaments surrounding the MR 2251-178. The morphology of the circumnuclear emission-line regions and an extended system of filaments in different ionization states are shown. The physical characteristics, such as luminosities, densities, mass, and ionization parameters of different filaments are derived. 48 refs.

  13. Fractal dimension analysis of complexity in Ligeti piano pieces

    NASA Astrophysics Data System (ADS)

    Bader, Rolf

    2005-04-01

    Fractal correlation dimensional analysis has been performed with whole solo piano pieces by Gyrgy Ligeti at every 50ms interval of the pieces. The resulting curves of development of complexity represented by the fractal dimension showed up a very reasonable correlation with the perceptional density of events during these pieces. The seventh piece of Ligeti's ``Musica ricercata'' was used as a test case. Here, each new part of the piece was followed by an increase of the fractal dimension because of the increase of information at the part changes. The second piece ``Galamb borong,'' number seven of the piano Etudes was used, because Ligeti wrote these Etudes after studying fractal geometry. Although the piece is not fractal in the strict mathematical sense, the overall structure of the psychoacoustic event-density as well as the detailed event development is represented by the fractal dimension plot.

  14. Electromagnetic fields in fractal continua

    NASA Astrophysics Data System (ADS)

    Balankin, Alexander S.; Mena, Baltasar; Patiño, Julián; Morales, Daniel

    2013-04-01

    Fractal continuum electrodynamics is developed on the basis of a model of three-dimensional continuum ΦD3⊂E3 with a fractal metric. The generalized forms of Maxwell equations are derived employing the local fractional vector calculus related to the Hausdorff derivative. The difference between the fractal continuum electrodynamics based on the fractal metric of continua with Euclidean topology and the electrodynamics in fractional space Fα accounting the fractal topology of continuum with the Euclidean metric is outlined. Some electromagnetic phenomena in fractal media associated with their fractal time and space metrics are discussed.

  15. Fractals, malware, and data models

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Potter, Andrew N.; Williams, Deborah; Handley, James W.

    2012-06-01

    We examine the hypothesis that the decision boundary between malware and non-malware is fractal. We introduce a novel encoding method derived from text mining for converting disassembled programs first into opstrings and then filter these into a reduced opcode alphabet. These opcodes are enumerated and encoded into real floating point number format and used for characterizing frequency of occurrence and distribution properties of malware functions to compare with non-malware functions. We use the concept of invariant moments to characterize the highly non-Gaussian structure of the opcode distributions. We then derive Data Model based classifiers from identified features and interpolate and extrapolate the parameter sample space for the derived Data Models. This is done to examine the nature of the parameter space classification boundary between families of malware and the general non-malware category. Preliminary results strongly support the fractal boundary hypothesis, and a summary of our methods and results are presented here.

  16. FAST TRACK COMMUNICATION: Weyl law for fat fractals

    NASA Astrophysics Data System (ADS)

    Spina, María E.; García-Mata, Ignacio; Saraceno, Marcos

    2010-10-01

    It has been conjectured that for a class of piecewise linear maps the closure of the set of images of the discontinuity has the structure of a fat fractal, that is, a fractal with positive measure. An example of such maps is the sawtooth map in the elliptic regime. In this work we analyze this problem quantum mechanically in the semiclassical regime. We find that the fraction of states localized on the unstable set satisfies a modified fractal Weyl law, where the exponent is given by the exterior dimension of the fat fractal.

  17. Magnetically driven filament probe.

    PubMed

    Schmid, A; Herrmann, A; Rohde, V; Maraschek, M; Müller, H W

    2007-05-01

    A radially movable probe has been developed for studies of filamentary transport in ASDEX Upgrade during edge localized modes (ELMs) by means of Langmuir tips and magnetic pickup coils. The probe is permanently installed at the low field side in the ASDEX Upgrade vacuum vessel and is not subject to limitations in probe size, as, for example, probes on a shared manipulator are. The probe is moved by a magnetic drive, which allows for easy installation in the vessel, and has moderate machine requirements, as it will only require an electric feedthrough and an external power supply. The drive gives a linear motion with a radial range of 5 cm within 50 ms, where range and velocity can be largely scaled according to experimental requirements. The probe has been installed in the outer midplane of the ASDEX Upgrade vessel, where ELM filaments are expected to have their maximum amplitude. Filaments are coherent substructures within an ELM, carrying a fraction of the ELM released energy towards the wall. The new probe allows to measure the structure of these filaments, in particular, parameters such as filament rotation (by time delay measurements) and size (by peak width analysis). Activating the drive moves the probe from a safe position behind the limiter to a position in front of the limiters, i.e., exposes the Langmuir pins to the scrape-off layer plasma. PMID:17552815

  18. Fractal metrology for biogeosystems analysis

    NASA Astrophysics Data System (ADS)

    Torres-Argüelles, V.; Oleschko, K.; Tarquis, A. M.; Korvin, G.; Gaona, C.; Parrot, J.-F.; Ventura-Ramos, E.

    2010-06-01

    The solid-pore distribution pattern plays an important role in soil functioning being related with the main physical, chemical and biological multiscale and multitemporal processes. In the present research, this pattern is extracted from the digital images of three soils (Chernozem, Solonetz and "Chocolate'' Clay) and compared in terms of roughness of the gray-intensity distribution (the measurand) quantified by several measurement techniques. Special attention was paid to the uncertainty of each of them and to the measurement function which best fits to the experimental results. Some of the applied techniques are known as classical in the fractal context (box-counting, rescaling-range and wavelets analyses, etc.) while the others have been recently developed by our Group. The combination of all these techniques, coming from Fractal Geometry, Metrology, Informatics, Probability Theory and Statistics is termed in this paper Fractal Metrology (FM). We show the usefulness of FM through a case study of soil physical and chemical degradation applying the selected toolbox to describe and compare the main structural attributes of three porous media with contrasting structure but similar clay mineralogy dominated by montmorillonites.

  19. Fractal analysis of scatter imaging signatures to distinguish breast pathologies

    NASA Astrophysics Data System (ADS)

    Eguizabal, Alma; Laughney, Ashley M.; Krishnaswamy, Venkataramanan; Wells, Wendy A.; Paulsen, Keith D.; Pogue, Brian W.; López-Higuera, José M.; Conde, Olga M.

    2013-02-01

    Fractal analysis combined with a label-free scattering technique is proposed for describing the pathological architecture of tumors. Clinicians and pathologists are conventionally trained to classify abnormal features such as structural irregularities or high indices of mitosis. The potential of fractal analysis lies in the fact of being a morphometric measure of the irregular structures providing a measure of the object's complexity and self-similarity. As cancer is characterized by disorder and irregularity in tissues, this measure could be related to tumor growth. Fractal analysis has been probed in the understanding of the tumor vasculature network. This work addresses the feasibility of applying fractal analysis to the scattering power map (as a physical modeling) and principal components (as a statistical modeling) provided by a localized reflectance spectroscopic system. Disorder, irregularity and cell size variation in tissue samples is translated into the scattering power and principal components magnitude and its fractal dimension is correlated with the pathologist assessment of the samples. The fractal dimension is computed applying the box-counting technique. Results show that fractal analysis of ex-vivo fresh tissue samples exhibits separated ranges of fractal dimension that could help classifier combining the fractal results with other morphological features. This contrast trend would help in the discrimination of tissues in the intraoperative context and may serve as a useful adjunct to surgeons.

  20. Intermediate Filaments: A Historical Perspective

    PubMed Central

    Oshima, Robert G.

    2007-01-01

    Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years. PMID:17493611

  1. Simulation of extreme ground water flow in the fractal crack structure of Earth's crust - impact on catastrophic floods

    NASA Astrophysics Data System (ADS)

    Bukharov, Dmitriy; Aleksey, Kucherik; Tatyana, Trifonova

    2014-05-01

    Recently, the contribution of groundwater in catastrophic floods is the question under discussion [1,2]. The principal problem in such an approach - to analyze the transportation ways for groundwater in dynamics, and especially - the reasons of exit it on land surface. The crackness, being a characteristic property for all rocks, should be associated with the process in respect of unified dynamic system as a river water basin is, taking into account fundamental phenomena of the 3D-crack network development/modification (up to faults) as a transport groundwater system [3]. 2. In the system of fractal cracks (connected with the main channel for groundwater) the formation of extreme flow is possible, i.e. a devastating case occurs by instantaneous flash mechanism. The development of such a process is related to two factors. First, within the main channel of propagation of the groundwater when a motion is turbulent. In accordance with the theory of Kolmogorov [4], we assume that such a turbulence is isotropic. The fact means that both velocity and pressure fields in the water flow have pulsations related to the non-linear energy transfer between the vortices. This approach allows us to determine both that a maximum possible size of the vortices defined by characteristic dimensions of the underground channel and another - a minimum size of their due to process of dissipation. Energy transfer in the eddies formed near a border, is a complex nonlinear process, which we described by using a modernized Prandtl semi-empirical model [5]. Second, the mechanism of groundwater propagation in the system of cracks extending from the main underground channel is described in the frames of the fractal geometry methods [6]. The approach allows to determine the degree of similarity in the crack system, i.e. the ratio of mean diameters and lengths of cracks/faults for each step of decomposition. The fact results in integrated quantitative characteristics of 3D-network in all, by fractal

  2. Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

    PubMed Central

    Kotlajich, Matthew V; Hron, Daniel R; Boudreau, Beth A; Sun, Zhiqiang; Lyubchenko, Yuri L; Landick, Robert

    2015-01-01

    Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria. DOI: http://dx.doi.org/10.7554/eLife.04970.001 PMID:25594903

  3. Growth of Wide-Bandgap Nanocrystalline Silicon Carbide Films by HWCVD: Influence of Filament Temperature on Structural and Optoelectronic Properties

    NASA Astrophysics Data System (ADS)

    Jha, Himanshu S.; Yadav, Asha; Singh, Mukesh; Kumar, Shailendra; Agarwal, Pratima

    2015-03-01

    Silicon carbide (SiC) thin films have been deposited using a hot-wire chemical vapor deposition technique on quartz substrates with a mixture of silane, methane, and hydrogen gases as precursors at a reasonably high deposition rate of approximately 15 nm/min to 50 nm/min. The influence of the filament temperature ( T F) on the structural, optical, and electrical properties of the SiC film has been investigated using x-ray diffraction, Raman scattering, Fourier-transform infrared spectroscopy, x-ray photoelectron spectroscopy, ultraviolet-visible-near infrared transmission spectroscopy, and dark conductivity ( σ d) studies. Films deposited at low T F (1800°C to 1900°C) are amorphous in nature with high density of Si-Si bonds, whereas high- T F (≥2000°C) films are nanocrystalline embedded in an amorphous SiC matrix with higher concentration of Si-C bonds and negligible concentration of Si-Si bonds. The bandgap ( E g) varies from 2.5 eV to 3.1 eV and σ d (50°C) from ˜10-9 Ω-1 cm-1 to 10-1 Ω-1 cm-1 as T F is increased from 1900°C to 2200°C. This increase in E g and σ d is due to microstructural changes and unintentional oxygen doping of the films.

  4. Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

    PubMed Central

    Galvão, Carolina W.; Saab, Sérgio C.; Iulek, Jorge; Etto, Rafael M.; Steffens, Maria B. R.; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L.; Cox, Michael M.

    2016-01-01

    The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

  5. Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament.

    PubMed

    Leite, Wellington C; Galvão, Carolina W; Saab, Sérgio C; Iulek, Jorge; Etto, Rafael M; Steffens, Maria B R; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L; Cox, Michael M

    2016-01-01

    The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

  6. Unwinding motion of a twisted active region filament

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Kong, D. F.; Liu, J. H.; Xu, C. L.

    2014-12-10

    To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament, we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.

  7. Chemical and biological structure and transport of a cool filament associated with a jet-eddy system of northern California in July 1986 (OPTOMA21)

    NASA Technical Reports Server (NTRS)

    Jones, Burton H.; Mooers, Christopher N. K.; Rienecker, Michele M.; Stanton, Tim; Washburn, Libe

    1991-01-01

    The distributions of nutrient, pigment, bio-optical, and physical variables were mapped in a jet-eddy system off Point Reyes and Point Arena, California, from July 7 to 19, 1986, in order to describe the 3D variability of the filament and its relation to the nutrient and phytoplankton distributions offshore, to examine the interaction between the filament and coastal water, and to estimate the transport of nutrients and phytoplankton by the jet system. Several cool filaments were distinguishable at distances of more than 35-50 km from the coast in satellite imagery during this period. The juxtaposition of these features as well as the presence of an offshore anticyclone and a cyclone south of the filament anchored to the coast at Point Arena led to complex patterns in all variables, aided by the apparent alongshore variability in the source of upwelled water. This structure has implications for the fluxes of organic material in the region and is probably significant in organizing the interactions among different trophic levels within the system.

  8. Structural determinants governing S100A4-induced isoform-selective disassembly of nonmuscle myosin II filaments.

    PubMed

    Kiss, Bence; Kalmár, Lajos; Nyitray, László; Pál, Gábor

    2016-06-01

    The Ca(2+) -binding protein S100A4 interacts with the C terminus of nonmuscle myosin IIA (NMIIA) causing filament disassembly, which is correlated with an increased metastatic potential of tumor cells. Despite high sequence similarity of the three NMII isoforms, S100A4 discriminates against binding to NMIIB. We searched for structural determinants of this selectivity. Based on paralog scanning using phage display, we identified a single position as major determinant of isoform selectivity. Reciprocal single amino acid replacements showed that at position 1907 (NMIIA numbering), the NMIIA/NMIIC-specific alanine provides about 60-fold higher affinity than the NMIIB-specific asparagine. The structural background of this can be explained in part by a communication between the two consecutive α-helical binding segments. This communication is completely abolished by the Ala-to-Asn substitution. Mutual swapping of the disordered tailpieces only slightly affects the affinity of the NMII chimeras. Interestingly, we found that the tailpiece and position 1907 act in a nonadditive fashion. Finally, we also found that the higher stability of the C-terminal coiled-coil region of NMIIB also discriminates against interaction with S100A4. Our results clearly show that the isoform-selective binding of S100A4 is determined at multiple levels in the structure of the three NMII isoforms and the corresponding functional elements of NMII act synergistically with one another resulting in a complex interaction network. The experimental and in silico results suggest two divergent evolutionary pathways: NMIIA and NMIIB evolved to possess S100A4-dependent and -independent regulations, respectively. PMID:27029887

  9. Metabolic regulation via enzyme filamentation

    PubMed Central

    Aughey, Gabriel N.; Liu, Ji-Long

    2016-01-01

    Abstract Determining the mechanisms of enzymatic regulation is central to the study of cellular metabolism. Regulation of enzyme activity via polymerization-mediated strategies has been shown to be widespread, and plays a vital role in mediating cellular homeostasis. In this review, we begin with an overview of the filamentation of CTP synthase, which forms filamentous structures termed cytoophidia. We then highlight other important examples of the phenomenon. Moreover, we discuss recent data relating to the regulation of enzyme activity by compartmentalization into cytoophidia. Finally, we hypothesize potential roles for enzyme filament formation in the regulation of metabolism, development and disease. PMID:27098510

  10. Preparation and characterization of fractal elastomer surfaces.

    PubMed

    Nonomura, Yoshimune; Seino, Eri; Abe, Saya; Mayama, Hiroyuki

    2013-01-01

    The elastomer materials with hierarchical structure and suitable wettability are useful as biological surface model. In the present study, urethane resin and silicone resin elastomers with hierarchical rough surfaces were prepared and referred to as "fractal elastomers". We found a hierarchy of small projections that existed over larger ones on these surfaces. These elastomers were synthesized by transferring a fractal surface structure of alkylketene dimer. The rough structure enhanced the hydrophobicity and weakened friction resistance of the elastomer surfaces. These materials can be useful for artificial skin with biomimetic surface properties. PMID:23985488

  11. Formation and evolution of magnetised filaments in wind-swept turbulent clumps

    NASA Astrophysics Data System (ADS)

    Banda-Barragan, Wladimir Eduardo; Federrath, Christoph; Crocker, Roland M.; Bicknell, Geoffrey Vincent; Parkin, Elliot Ross

    2015-08-01

    Using high-resolution three-dimensional simulations, we examine the formation and evolution of filamentary structures arising from magnetohydrodynamic interactions between supersonic winds and turbulent clumps in the interstellar medium. Previous numerical studies assumed homogenous density profiles, null velocity fields, and uniformly distributed magnetic fields as the initial conditions for interstellar clumps. Here, we have, for the first time, incorporated fractal clumps with log-normal density distributions, random velocity fields and turbulent magnetic fields (superimposed on top of a uniform background field). Disruptive processes, instigated by dynamical instabilities and akin to those observed in simulations with uniform media, lead to stripping of clump material and the subsequent formation of filamentary tails. The evolution of filaments in uniform and turbulent models is, however, radically different as evidenced by comparisons of global quantities in both scenarios. We show, for example, that turbulent clumps produce tails with higher velocity dispersions, increased gas mixing, greater kinetic energy, and lower plasma beta than their uniform counterparts. We attribute the observed differences to: 1) the turbulence-driven enhanced growth of dynamical instabilities (e.g. Kelvin-Helmholtz and Rayleigh-Taylor instabilities) at fluid interfaces, and 2) the localised amplification of magnetic fields caused by the stretching of field lines trapped in the numerous surface deformations of fractal clumps. We briefly discuss the implications of this work to the physics of the optical filaments observed in the starburst galaxy M82.

  12. Electrodynamic properties of fractal clusters

    NASA Astrophysics Data System (ADS)

    Maksimenko, V. V.; Zagaynov, V. A.; Agranovski, I. E.

    2014-07-01

    An influence of interference on a character of light interaction both with individual fractal cluster (FC) consisting of nanoparticles and with agglomerates of such clusters is investigated. Using methods of the multiple scattering theory, effective dielectric permeability of a micron-size FC composed of non-absorbing nanoparticles is calculated. The cluster could be characterized by a set of effective dielectric permeabilities. Their number coincides with the number of particles, where space arrangement in the cluster is correlated. If the fractal dimension is less than some critical value and frequency corresponds to the frequency of the visible spectrum, then the absolute value of effective dielectric permeability becomes very large. This results in strong renormalization (decrease) of the incident radiation wavelength inside the cluster. The renormalized photons are cycled or trapped inside the system of multi-scaled cavities inside the cluster. A lifetime of a photon localized inside an agglomerate of FCs is a macroscopic value allowing to observe the stimulated emission of the localized light. The latter opens up a possibility for creation of lasers without inverse population of energy levels. Moreover, this allows to reconsider problems of optical cloaking of macroscopic objects. One more feature of fractal structures is a possibility of unimpeded propagation of light when any resistance associated with scattering disappears.

  13. Rheological and fractal hydrodynamics of aerobic granules.

    PubMed

    Tijani, H I; Abdullah, N; Yuzir, A; Ujang, Zaini

    2015-06-01

    The structural and hydrodynamic features for granules were characterized using settling experiments, predefined mathematical simulations and ImageJ-particle analyses. This study describes the rheological characterization of these biologically immobilized aggregates under non-Newtonian flows. The second order dimensional analysis defined as D2=1.795 for native clusters and D2=1.099 for dewatered clusters and a characteristic three-dimensional fractal dimension of 2.46 depicts that these relatively porous and differentially permeable fractals had a structural configuration in close proximity with that described for a compact sphere formed via cluster-cluster aggregation. The three-dimensional fractal dimension calculated via settling-fractal correlation, U∝l(D) to characterize immobilized granules validates the quantitative measurements used for describing its structural integrity and aggregate complexity. These results suggest that scaling relationships based on fractal geometry are vital for quantifying the effects of different laminar conditions on the aggregates' morphology and characteristics such as density, porosity, and projected surface area. PMID:25836036

  14. Characterization of branch complexity by fractal analyses

    USGS Publications Warehouse

    Alados, C.L.; Escos, J.; Emlen, J.M.; Freeman, D.C.

    1999-01-01

    The comparison between complexity in the sense of space occupancy (box-counting fractal dimension D(c) and information dimension D1) and heterogeneity in the sense of space distribution (average evenness index f and evenness variation coefficient J(cv)) were investigated in mathematical fractal objects and natural branch structures. In general, increased fractal dimension was paired with low heterogeneity. Comparisons between branch architecture in Anthyllis cytisoides under different slope exposure and grazing impact revealed that branches were more complex and more homogeneously distributed for plants on northern exposures than southern, while grazing had no impact during a wet year. Developmental instability was also investigated by the statistical noise of the allometric relation between internode length and node order. In conclusion, our study demonstrated that fractal dimension of branch structure can be used to analyze the structural organization of plants, especially if we consider not only fractal dimension but also shoot distribution within the canopy (lacunarity). These indexes together with developmental instability analyses are good indicators of growth responses to the environment.

  15. Laser light scattering as a probe of fractal colloid aggregates

    NASA Technical Reports Server (NTRS)

    Weitz, David A.; Lin, M. Y.

    1989-01-01

    The extensive use of laser light scattering is reviewed, both static and dynamic, in the study of colloid aggregation. Static light scattering enables the study of the fractal structure of the aggregates, while dynamic light scattering enables the study of aggregation kinetics. In addition, both techniques can be combined to demonstrate the universality of the aggregation process. Colloidal aggregates are now well understood and therefore represent an excellent experimental system to use in the study of the physical properties of fractal objects. However, the ultimate size of fractal aggregates is fundamentally limited by gravitational acceleration which will destroy the fractal structure as the size of the aggregates increases. This represents a great opportunity for spaceborne experimentation, where the reduced g will enable the growth of fractal structures of sufficient size for many interesting studies of their physical properties.

  16. Filament identification through mathematical morphology

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2015-10-01

    We present a new algorithm for detecting filamentary structure FILFINDER. The algorithm uses the techniques of mathematical morphology for filament identification, presenting a complementary approach to current algorithms which use matched filtering or critical manifolds. Unlike other methods, FILFINDER identifies filaments over a wide dynamic range in brightness. We apply the new algorithm to far-infrared imaging data of dust emission released by the Herschel Gould Belt Survey team. Our preliminary analysis characterizes both filaments and fainter striations. We find a typical filament width of 0.09 pc across the sample, but the brightness varies from cloud to cloud. Several regions show a bimodal filament brightness distribution, with the bright mode (filaments) being an order of magnitude brighter than the faint mode (striations). Using the Rolling Hough Transform, we characterize the orientations of the striations in the data, finding preferred directions that agree with magnetic field direction where data are available. There is a suggestive but noisy correlation between typical filament brightness and literature values of the star formation rates for clouds in the Gould Belt.

  17. Foolin' with Fractals.

    ERIC Educational Resources Information Center

    Clark, Garry

    1999-01-01

    Reports on a mathematical investigation of fractals and highlights the thinking involved, problem solving strategies used, generalizing skills required, the role of technology, and the role of mathematics. (ASK)

  18. Fractal funcitons and multiwavelets

    SciTech Connect

    Massopust, P.R.

    1997-04-01

    This paper reviews how elements from the theory of fractal functions are employed to construct scaling vectors and multiwavelets. Emphasis is placed on the one-dimensional case, however extensions to IR{sup m} are indicated.

  19. Fractals and Transformations.

    ERIC Educational Resources Information Center

    Bannon, Thomas J.

    1991-01-01

    Discussed are several different transformations based on the generation of fractals including self-similar designs, the chaos game, the koch curve, and the Sierpinski Triangle. Three computer programs which illustrate these concepts are provided. (CW)

  20. High-resolution electron microscopic evidence for the filamentous structure of the cyst wall in Giardia muris and Giardia duodenalis.

    PubMed

    Erlandsen, S L; Bemrick, W J; Pawley, J

    1989-10-01

    High-resolution morphological studies of the cyst wall of Giardia spp. were performed using low-voltage scanning electron microscopy (LVSEM) and transmission electron microscopy (TEM). The cyst wall was composed of membranous and filamentous layers. The membranous layer consisted of an inner and an outer cyst membrane separated by a thin layer of cytoplasm. The filamentous layer contained individual filaments that ranged from 7 to 20 nm in diameter when measured by LVSEM, formed a dense meshwork with branches or interconnections, and were occasionally arranged on the surface in whorled patterns. Cysts of Giardia muris from mice, Giardia duodenalis from dogs, pigs, voles, beavers, muskrats, and humans, and Giardia psittaci from a bird (parakeet), possessed an essentially identical wall composed of filaments. Inducement of excystation in viable Giardia cysts produced a dramatic increase in the interfilament spacing over an entire cyst, but none was observed in heat-killed or chemically fixed control cysts. These results demonstrated that the cyst wall of Giardia spp. was composed of a complex arrangement of filaments, presumably formed during the process of encystment. PMID:2795382

  1. Fractal lattice of gelatin nanoglobules

    NASA Astrophysics Data System (ADS)

    Novikov, D. V.; Krasovskii, A. N.

    2012-11-01

    The globular structure of polymer coatings on a glass, which were obtained from micellar solutions of gelatin in the isooctane-water-sodium (bis-2-ethylhexyl) sulfosuccinate system, has been studied using electron microscopy. It has been shown that an increase in the average globule size is accompanied by the formation of a fractal lattice of nanoglobules and a periodic physical network of macromolecules in the coating. The stability of such system of the "liquid-in-a-solid" type is limited by the destruction of globules and the formation of a homogeneous network structure of the coating.

  2. Bacillus subtilis Bactofilins Are Essential for Flagellar Hook- and Filament Assembly and Dynamically Localize into Structures of Less than 100 nm Diameter underneath the Cell Membrane

    PubMed Central

    El Andari, Jihad; Altegoer, Florian; Bange, Gert; Graumann, Peter L.

    2015-01-01

    Bactofilins are a widely conserved protein family implicated in cell shape maintenance and in bacterial motility. We show that the bactofilins BacE and BacF from Bacillus subtilis are essential for motility. The proteins are required for the establishment of flagellar hook- and filament structures, but apparently not for the formation of basal bodies. Functional YFP fusions to BacE and to BacF localize as discrete assemblies at the B. subtilis cell membrane, and have a diameter of 60 to 70 nm. BacF assemblies are relatively static, and partially colocalize with flagellar basal bodies, while BacE assemblies are fewer per cell than those of BacF and are highly mobile. Tracking of BacE foci showed that the assemblies arrest at a single point for a few hundred milliseconds, showing that a putative interaction with flagellar structures would be transient and fast. When overexpressed or expressed in a heterologous cell system, bactofilins can form filamentous structures, and also form multimers as purified proteins. Our data reveal a propensity for bactofilins to form filaments, however, in B. subtilis cells, bactofilins assemble into defined size assemblies that show a dynamic localization pattern and play a role in flagellar assembly. PMID:26517549

  3. Structural features of sugars that trigger or support conidial germination in the filamentous fungus Aspergillus niger.

    PubMed

    Hayer, Kimran; Stratford, Malcolm; Archer, David B

    2013-11-01

    The asexual spores (conidia) of Aspergillus niger germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of d-glucose, on the germination of A. niger conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of d-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included d-glucose, d-mannose, and d-xylose. Sugars that triggered germination but did not support subsequent outgrowth included d-tagatose, d-lyxose, and 2-deoxy-d-glucose. Nontriggering sugars included d-galactose, l-glucose, and d-arabinose. Certain nontriggering sugars, including d-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia. PMID:23995938

  4. PARTIAL SLINGSHOT RECONNECTION BETWEEN TWO FILAMENTS

    SciTech Connect

    Jiang, Yunchun; Hong, Junchao; Yang, Jiayan; Bi, Yi; Zheng, Ruisheng; Yang, Bo; Li, Haidong; Yang, Dan

    2013-02-10

    We present a rare observation of an interaction between two filaments around AR 11358 and AR 11361 on 2011 December 3 that is strongly suggestive of the occurrence of slingshot reconnection. A small elbow-shaped active-region filament (F12) underwent a failed eruption that brought it into contact with a nearby larger, thicker filament (F34). Accompanied by the appearance of complicated internal structures below the erupting F12, its two legs separated away from each other and then connected into F34. This process led the filaments to change their connectivity to form two newly linked filaments, and one of them showed a clear inverse {gamma}-shape. However, the alteration in the filament connectivity was imperfect since F34 is discernible after the eruption. These observations can be interpreted as a partial slingshot reconnection between two filaments that had unequal axial magnetic flux.

  5. Partial Slingshot Reconnection between Two Filaments

    NASA Astrophysics Data System (ADS)

    Jiang, Yunchun; Hong, Junchao; Yang, Jiayan; Bi, Yi; Zheng, Ruisheng; Yang, Bo; Li, Haidong; Yang, Dan

    2013-02-01

    We present a rare observation of an interaction between two filaments around AR 11358 and AR 11361 on 2011 December 3 that is strongly suggestive of the occurrence of slingshot reconnection. A small elbow-shaped active-region filament (F12) underwent a failed eruption that brought it into contact with a nearby larger, thicker filament (F34). Accompanied by the appearance of complicated internal structures below the erupting F12, its two legs separated away from each other and then connected into F34. This process led the filaments to change their connectivity to form two newly linked filaments, and one of them showed a clear inverse γ-shape. However, the alteration in the filament connectivity was imperfect since F34 is discernible after the eruption. These observations can be interpreted as a partial slingshot reconnection between two filaments that had unequal axial magnetic flux.

  6. Wave interactions with continuous fractal layers

    NASA Technical Reports Server (NTRS)

    Kim, Y.; Jaggard, D. L.

    1991-01-01

    Many natural structures possess self-similar multiscales which can be characterized by power law spectra. Under appropriate conditions, knowledge of the strength of these scale sizes provides information on the physical processes which formed these objects. In this paper, we investigate wave interactions with continuous fractal layers which model geological and variegated structures. Since fractal characteristics of the layers are embedded in the scattered field, they can be retrieved under appropriate conditions. This inversion can be performed in either the frequency or the time domain as desired.

  7. Communities and classes in symmetric fractals

    NASA Astrophysics Data System (ADS)

    Krawczyk, Małgorzata J.

    2015-07-01

    Two aspects of fractal networks are considered: the community structure and the class structure, where classes of nodes appear as a consequence of a local symmetry of nodes. The analyzed systems are the networks constructed for two selected symmetric fractals: the Sierpinski triangle and the Koch curve. Communities are searched for by means of a set of differential equations. Overlapping nodes which belong to two different communities are identified by adding some noise to the initial connectivity matrix. Then, a node can be characterized by a spectrum of probabilities of belonging to different communities. Our main goal is that the overlapping nodes with the same spectra belong to the same class.

  8. Hierarchical socioeconomic fractality: The rich, the poor, and the middle-class

    NASA Astrophysics Data System (ADS)

    Eliazar, Iddo; Cohen, Morrel H.

    2014-05-01

    Since the seminal work of the Italian economist Vilfredo Pareto, the study of wealth and income has been a topic of active scientific exploration engaging researches ranging from economics and political science to econophysics and complex systems. This paper investigates the intrinsic fractality of wealth and income. To that end we introduce and characterize three forms of socioeconomic scale-invariance-poor fractality, rich fractality, and middle-class fractality-and construct hierarchical fractal approximations of general wealth and income distributions, based on the stitching of these three forms of fractality. Intertwining the theoretical results with real-world empirical data we then establish that the three forms of socioeconomic fractality-amalgamated into a composite hierarchical structure-underlie the distributions of wealth and income in human societies. We further establish that the hierarchical socioeconomic fractality of wealth and income is also displayed by empirical rank distributions observed across the sciences.

  9. Spontaneous emission from a fractal vacuum

    NASA Astrophysics Data System (ADS)

    Akkermans, Eric; Gurevich, Evgeni

    2013-08-01

    Spontaneous emission of a quantum emitter coupled to a QED vacuum with a deterministic fractal structure of its spectrum is considered. We show that the decay probability does not follow a Wigner-Weisskopf exponential decrease but rather an overall power law behavior with a rich oscillatory structure, both depending on the local fractal properties of the vacuum spectrum. These results are obtained by giving first a general perturbative derivation for short times. Then we propose a simplified model which retains the main features of a fractal spectrum to establish analytic expressions valid for all time scales. Finally, we discuss the case of a Fibonacci cavity and its experimental relevance to observe these results.

  10. Filamentous Fungi.

    PubMed

    Powers-Fletcher, Margaret V; Kendall, Brian A; Griffin, Allen T; Hanson, Kimberly E

    2016-06-01

    Filamentous mycoses are often associated with significant morbidity and mortality. Prompt diagnosis and aggressive treatment are essential for good clinical outcomes in immunocompromised patients. The host immune response plays an essential role in determining the course of exposure to potential fungal pathogens. Depending on the effectiveness of immune response and the burden of organism exposure, fungi can either be cleared or infection can occur and progress to a potentially fatal invasive disease. Nonspecific cellular immunity (i.e., neutrophils, natural killer [NK] cells, and macrophages) combined with T-cell responses are the main immunologic mechanisms of protection. The most common potential mold pathogens include certain hyaline hyphomycetes, endemic fungi, the Mucorales, and some dematiaceous fungi. Laboratory diagnostics aimed at detecting and differentiating these organisms are crucial to helping clinicians make informed decisions about treatment. The purpose of this chapter is to provide an overview of the medically important fungal pathogens, as well as to discuss the patient characteristics, antifungal-therapy considerations, and laboratory tests used in current clinical practice for the immunocompromised host. PMID:27337469

  11. Fractal analysis of yeast cell optical speckle

    NASA Astrophysics Data System (ADS)

    Flamholz, A.; Schneider, P. S.; Subramaniam, R.; Wong, P. K.; Lieberman, D. H.; Cheung, T. D.; Burgos, J.; Leon, K.; Romero, J.

    2006-02-01

    Steady state laser light propagation in diffuse media such as biological cells generally provide bulk parameter information, such as the mean free path and absorption, via the transmission profile. The accompanying optical speckle can be analyzed as a random spatial data series and its fractal dimension can be used to further classify biological media that show similar mean free path and absorption properties, such as those obtained from a single population. A population of yeast cells can be separated into different portions by centrifuge, and microscope analysis can be used to provide the population statistics. Fractal analysis of the speckle suggests that lower fractal dimension is associated with higher cell packing density. The spatial intensity correlation revealed that the higher cell packing gives rise to higher refractive index. A calibration sample system that behaves similar as the yeast samples in fractal dimension, spatial intensity correlation and diffusion was selected. Porous silicate slabs with different refractive index values controlled by water content were used for system calibration. The porous glass as well as the yeast random spatial data series fractal dimension was found to depend on the imaging resolution. The fractal method was also applied to fission yeast single cell fluorescent data as well as aging yeast optical data; and consistency was demonstrated. It is concluded that fractal analysis can be a high sensitivity tool for relative comparison of cell structure but that additional diffusion measurements are necessary for determining the optimal image resolution. Practical application to dental plaque bio-film and cam-pill endoscope images was also demonstrated.

  12. Massive Quiescent Cores in Orion. VI. The Internal Structures and a Candidate of Transiting Core in NGC 2024 Filament

    NASA Astrophysics Data System (ADS)

    Ren, Zhiyuan; Li, Di

    2016-06-01

    We present a multiwavelength observational study of the NGC 2024 filament using infrared to submillimeter continuum and the {{NH}}3 (1,1) and (2,2) inversion transitions centered on FIR-3, the most massive core therein. FIR-3 is found to have no significant infrared point sources in the Spitzer/IRAC bands. But the {{NH}}3 kinetic temperature map shows a peak value at the core center with {T}{{k}}=25 K, which is significantly higher than the surrounding level ({T}{{k}}\\quad = 15–19 K). Such internal heating signature without an infrared source suggests an ongoing core collapse possibly at a transition stage from first hydrostatic core (FHSC) to protostar. The eight dense cores in the filament have dust temperatures between 17.5 and 22 K. They are much cooler than the hot ridge ({T}{{d}}∼ 55 K) around the central heating star IRS-2b. Comparison with a dust heating model suggests that the filament should have a distance of 3–5 pc from IRS-2b. This value is much larger than the spatial extent of the hot ridge, suggesting that the filament is spatially separated from the hot region along the line of sight.

  13. Mechanical properties of branched actin filaments.

    PubMed

    Razbin, Mohammadhosein; Falcke, Martin; Benetatos, Panayotis; Zippelius, Annette

    2015-07-01

    Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an elastic structure at one end and pushing with the free ends against the leading edge cell membrane. Single filaments are modeled as worm-like chains, whose thermal bending fluctuations are restricted by the leading edge cell membrane, resulting in an effective force. Branching can increase the stiffness considerably; however the effect depends on branch point position and filament orientation, being most pronounced for intermediate tilt angles and intermediate branch point positions. We describe filament networks without cross-linkers to focus on the effect of branching. We use randomly positioned branch points, as generated in the process of treadmilling, and orientation distributions as measured in lamellipodia. These networks reproduce both the weak and strong force response of lamellipodia as measured in force-velocity experiments. We compare properties of branched and unbranched networks. The ratio of the network average of the force per branched filament to the average force per unbranched filament depends on the orientation distribution of the filaments. The ratio exhibits compression dependence and may go up to about 4.5 in networks with a narrow orientation distribution. With orientation distributions measured in lamellipodia, it is about two and essentially independent from network compression, graft elasticity and filament persistence length. PMID:26040560

  14. Mechanical properties of branched actin filaments

    NASA Astrophysics Data System (ADS)

    Razbin, Mohammadhosein; Falcke, Martin; Benetatos, Panayotis; Zippelius, Annette

    2015-07-01

    Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an elastic structure at one end and pushing with the free ends against the leading edge cell membrane. Single filaments are modeled as worm-like chains, whose thermal bending fluctuations are restricted by the leading edge cell membrane, resulting in an effective force. Branching can increase the stiffness considerably; however the effect depends on branch point position and filament orientation, being most pronounced for intermediate tilt angles and intermediate branch point positions. We describe filament networks without cross-linkers to focus on the effect of branching. We use randomly positioned branch points, as generated in the process of treadmilling, and orientation distributions as measured in lamellipodia. These networks reproduce both the weak and strong force response of lamellipodia as measured in force-velocity experiments. We compare properties of branched and unbranched networks. The ratio of the network average of the force per branched filament to the average force per unbranched filament depends on the orientation distribution of the filaments. The ratio exhibits compression dependence and may go up to about 4.5 in networks with a narrow orientation distribution. With orientation distributions measured in lamellipodia, it is about two and essentially independent from network compression, graft elasticity and filament persistence length.

  15. Fractal atomic-level percolation in metallic glasses.

    PubMed

    Chen, David Z; Shi, Crystal Y; An, Qi; Zeng, Qiaoshi; Mao, Wendy L; Goddard, William A; Greer, Julia R

    2015-09-18

    Metallic glasses are metallic alloys that exhibit exotic material properties. They may have fractal structures at the atomic level, but a physical mechanism for their organization without ordering has not been identified. We demonstrated a crossover between fractal short-range (<2 atomic diameters) and homogeneous long-range structures using in situ x-ray diffraction, tomography, and molecular dynamics simulations. A specific class of fractal, the percolation cluster, explains the structural details for several metallic-glass compositions. We postulate that atoms percolate in the liquid phase and that the percolating cluster becomes rigid at the glass transition temperature. PMID:26383945

  16. Building Fractal Models with Manipulatives.

    ERIC Educational Resources Information Center

    Coes, Loring

    1993-01-01

    Uses manipulative materials to build and examine geometric models that simulate the self-similarity properties of fractals. Examples are discussed in two dimensions, three dimensions, and the fractal dimension. Discusses how models can be misleading. (Contains 10 references.) (MDH)

  17. Fractal Patterns and Chaos Games

    ERIC Educational Resources Information Center

    Devaney, Robert L.

    2004-01-01

    Teachers incorporate the chaos game and the concept of a fractal into various areas of the algebra and geometry curriculum. The chaos game approach to fractals provides teachers with an opportunity to help students comprehend the geometry of affine transformations.

  18. Observations of an active region filament

    NASA Astrophysics Data System (ADS)

    Zong, W. G.; Tang, Y. H.; Fang, C.; Xu, A. A.

    An active region filament was well observed on September 4, 2002 with THEMIS at the Teide observatory and SOHO/MDI. The full Stokes parameters of the filament were obtained in Hα and FeI 6302 Å lines. Using the data, we have studied the fine structure of the filament and obtained the parameters at the barb endpoints, including intensity, velocity and longitudinal magnetic field. Our results indicate: (a) the Doppler velocities are quiet different at barb endpoints; (b) the longitudinal magnetic fields at the barb endpoints are very weak; (c) there is a strong magnetic field structure under the filament spine.

  19. Fractals for Geoengineering

    NASA Astrophysics Data System (ADS)

    Oleshko, Klaudia; de Jesús Correa López, María; Romero, Alejandro; Ramírez, Victor; Pérez, Olga

    2016-04-01

    The effectiveness of fractal toolbox to capture the scaling or fractal probability distribution, and simply fractal statistics of main hydrocarbon reservoir attributes, was highlighted by Mandelbrot (1995) and confirmed by several researchers (Zhao et al., 2015). Notwithstanding, after more than twenty years, i&tacute;s still common the opinion that fractals are not useful for the petroleum engineers and especially for Geoengineering (Corbett, 2012). In spite of this negative background, we have successfully applied the fractal and multifractal techniques to our project entitled "Petroleum Reservoir as a Fractal Reactor" (2013 up to now). The distinguishable feature of Fractal Reservoir is the irregular shapes and rough pore/solid distributions (Siler, 2007), observed across a broad range of scales (from SEM to seismic). At the beginning, we have accomplished the detailed analysis of Nelson and Kibler (2003) Catalog of Porosity and Permeability, created for the core plugs of siliciclastic rocks (around ten thousand data were compared). We enriched this Catalog by more than two thousand data extracted from the last ten years publications on PoroPerm (Corbett, 2012) in carbonates deposits, as well as by our own data from one of the PEMEX, Mexico, oil fields. The strong power law scaling behavior was documented for the major part of these data from the geological deposits of contrasting genesis. Based on these results and taking into account the basic principles and models of the Physics of Fractals, introduced by Per Back and Kan Chen (1989), we have developed new software (Muuḱil Kaab), useful to process the multiscale geological and geophysical information and to integrate the static geological and petrophysical reservoiŕ models to dynamic ones. The new type of fractal numerical model with dynamical power law relations among the shapes and sizes of mes&hacute; cells was designed and calibrated in the studied area. The statistically sound power law relations were

  20. Fractals for Geoengineering

    NASA Astrophysics Data System (ADS)

    Oleshko, Klaudia; de Jesús Correa López, María; Romero, Alejandro; Ramírez, Victor; Pérez, Olga

    2016-04-01

    The effectiveness of fractal toolbox to capture the scaling or fractal probability distribution, and simply fractal statistics of main hydrocarbon reservoir attributes, was highlighted by Mandelbrot (1995) and confirmed by several researchers (Zhao et al., 2015). Notwithstanding, after more than twenty years, it's still common the opinion that fractals are not useful for the petroleum engineers and especially for Geoengineering (Corbett, 2012). In spite of this negative background, we have successfully applied the fractal and multifractal techniques to our project entitled "Petroleum Reservoir as a Fractal Reactor" (2013 up to now). The distinguishable feature of Fractal Reservoir is the irregular shapes and rough pore/solid distributions (Siler, 2007), observed across a broad range of scales (from SEM to seismic). At the beginning, we have accomplished the detailed analysis of Nelson and Kibler (2003) Catalog of Porosity and Permeability, created for the core plugs of siliciclastic rocks (around ten thousand data were compared). We enriched this Catalog by more than two thousand data extracted from the last ten years publications on PoroPerm (Corbett, 2012) in carbonates deposits, as well as by our own data from one of the PEMEX, Mexico, oil fields. The strong power law scaling behavior was documented for the major part of these data from the geological deposits of contrasting genesis. Based on these results and taking into account the basic principles and models of the Physics of Fractals, introduced by Per Back and Kan Chen (1989), we have developed new software (Muukíl Kaab), useful to process the multiscale geological and geophysical information and to integrate the static geological and petrophysical reservoir models to dynamic ones. The new type of fractal numerical model with dynamical power law relations among the shapes and sizes of mesh' cells was designed and calibrated in the studied area. The statistically sound power law relations were established

  1. Fractal dimension of bioconvection patterns

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1990-01-01

    Shallow cultures of the motile algal strain, Euglena gracilis, were concentrated to 2 x 10 to the 6th organisms per ml and placed in constant temperature water baths at 24 and 38 C. Bioconvective patterns formed an open two-dimensional structure with random branches, similar to clusters encountered in the diffusion-limited aggregation (DLA) model. When averaged over several example cultures, the pattern was found to have no natural length scale, self-similar branching, and a fractal dimension (d about 1.7). These agree well with the two-dimensional DLA.

  2. Fractal Dimension of Bioconvection Patterns

    NASA Astrophysics Data System (ADS)

    Noever, David A.

    1990-10-01

    Shallow cultures of the motile algal strain, Euglena gracilis, were concentrated to 2× 106 organisms per ml and placed in constant temperature water baths at 24 and 38 C. Bioconvective patterns formed an open two-dimensional structure with random branches, similar to clusters encountered in the diffusion-limited aggregation (DLA) model. When averaged over several example cultures, the pattern was found to have no natural length scale, self-similar branching and a fractal dimension (d˜1.7). These agree well with the two-dimensional DLA.

  3. Lava flows are fractals

    NASA Technical Reports Server (NTRS)

    Bruno, B. C.; Taylor, G. J.; Rowland, S. K.; Lucey, P. G.; Self, S.

    1992-01-01

    Results are presented of a preliminary investigation of the fractal nature of the plan-view shapes of lava flows in Hawaii (based on field measurements and aerial photographs), as well as in Idaho and the Galapagos Islands (using aerial photographs only). The shapes of the lava flow margins are found to be fractals: lava flow shape is scale-invariant. This observation suggests that nonlinear forces are operating in them because nonlinear systems frequently produce fractals. A'a and pahoehoe flows can be distinguished by their fractal dimensions (D). The majority of the a'a flows measured have D between 1.05 and 1.09, whereas the pahoehoe flows generally have higher D (1.14-1.23). The analysis is extended to other planetary bodies by measuring flows from orbital images of Venus, Mars, and the moon. All are fractal and have D consistent with the range of terrestrial a'a and have D consistent with the range of terrestrial a'a and pahoehoe values.

  4. Entanglement entropy on fractals

    NASA Astrophysics Data System (ADS)

    Faraji Astaneh, Amin

    2016-03-01

    We use the heat kernel method to calculate the entanglement entropy for a given entangling region on a fractal. The leading divergent term of the entropy is obtained as a function of the fractal dimension as well as the walk dimension. The power of the UV cutoff parameter is (generally) a fractional number, which, indeed, is a certain combination of these two indices. This exponent is known as the spectral dimension. We show that there is a novel log-periodic oscillatory behavior in the expression of entropy which has root in the complex dimension of the fractal. We finally indicate that the holographic calculation in a certain hyperscaling-violating bulk geometry yields the same leading term for the entanglement entropy, if one identifies the effective dimension of the hyperscaling-violating theory with the spectral dimension of the fractal. We provide additional support by comparing the behavior of the thermal entropy in terms of the temperature, computed for two geometries, the fractal geometry and the hyperscaling-violating background.

  5. Chaperonin filaments: The archaeal cytoskeleton?

    PubMed Central

    Trent, Jonathan D.; Kagawa, Hiromi K.; Yaoi, Takuro; Olle, Eric; Zaluzec, Nestor J.

    1997-01-01

    Chaperonins are high molecular mass double-ring structures composed of 60-kDa protein subunits. In the hyperthermophilic archaeon Sulfolobus shibatae the two chaperonin proteins represent ≈4% of its total protein and have a combined intracellular concentration of >30 mg/ml. At concentrations ≥ 0.5 mg/ml purified chaperonins form filaments in the presence of Mg2+ and nucleotides. Filament formation requires nucleotide binding (not hydrolysis), and occurs at physiological temperatures in biologically relevant buffers, including a buffer made from cell extracts. These observations suggest that chaperonin filaments may exist in vivo and the estimated 4600 chaperonins per cell suggest that such filaments could form an extensive cytostructure. We observed filamentous structures in unfixed, uranyl-acetate-stained S. shibatae cells, which resemble the chaperonin filaments in size and appearance. ImmunoGold (Janssen) labeling using chaperonin antibodies indicated that many chaperonins are associated with insoluble cellular structures and these structures appear to be filamentous in some areas, although they could not be uranyl-acetate-stained. The existence of chaperonin filaments in vivo suggests a mechanism whereby their protein-folding activities can be regulated. More generally, the filaments themselves may play a cytoskeletal role in Archaea. PMID:9144246

  6. Self-Organization of Treadmilling Filaments

    NASA Astrophysics Data System (ADS)

    Doubrovinski, K.; Kruse, K.

    2007-11-01

    The cytoskeleton is an active network of polar filaments. The activity can lead to the polymerization of filaments at one end and depolymerization at the other. This phenomenon is called treadmilling and is essential for many cellular processes, in particular, the crawling of cells on a substrate. We develop a microscopic theoretical framework for describing systems of treadmilling filaments. We show that such systems can self-organize into structures observed in cell fragments, in particular, asters and moving spots.

  7. a Fractal Network Model for Fractured Porous Media

    NASA Astrophysics Data System (ADS)

    Xu, Peng; Li, Cuihong; Qiu, Shuxia; Sasmito, Agus Pulung

    2016-04-01

    The transport properties and mechanisms of fractured porous media are very important for oil and gas reservoir engineering, hydraulics, environmental science, chemical engineering, etc. In this paper, a fractal dual-porosity model is developed to estimate the equivalent hydraulic properties of fractured porous media, where a fractal tree-like network model is used to characterize the fracture system according to its fractal scaling laws and topological structures. The analytical expressions for the effective permeability of fracture system and fractured porous media, tortuosity, fracture density and fraction are derived. The proposed fractal model has been validated by comparisons with available experimental data and numerical simulation. It has been shown that fractal dimensions for fracture length and aperture have significant effect on the equivalent hydraulic properties of fractured porous media. The effective permeability of fracture system can be increased with the increase of fractal dimensions for fracture length and aperture, while it can be remarkably lowered by introducing tortuosity at large branching angle. Also, a scaling law between the fracture density and fractal dimension for fracture length has been found, where the scaling exponent depends on the fracture number. The present fractal dual-porosity model may shed light on the transport physics of fractured porous media and provide theoretical basis for oil and gas exploitation, underground water, nuclear waste disposal and geothermal energy extraction as well as chemical engineering, etc.

  8. The fractal nature of vacuum arc cathode spots

    SciTech Connect

    Anders, Andre

    2005-05-27

    Cathode spot phenomena show many features of fractals, for example self-similar patterns in the emitted light and arc erosion traces. Although there have been hints on the fractal nature of cathode spots in the literature, the fractal approach to spot interpretation is underutilized. In this work, a brief review of spot properties is given, touching the differences between spot type 1 (on cathodes surfaces with dielectric layers) and spot type 2 (on metallic, clean surfaces) as well as the known spot fragment or cell structure. The basic properties of self-similarity, power laws, random colored noise, and fractals are introduced. Several points of evidence for the fractal nature of spots are provided. Specifically power laws are identified as signature of fractal properties, such as spectral power of noisy arc parameters (ion current, arc voltage, etc) obtained by fast Fourier transform. It is shown that fractal properties can be observed down to the cutoff by measurement resolution or occurrence of elementary steps in physical processes. Random walk models of cathode spot motion are well established: they go asymptotically to Brownian motion for infinitesimal step width. The power spectrum of the arc voltage noise falls as 1/f {sup 2}, where f is frequency, supporting a fractal spot model associated with Brownian motion.

  9. Fractal dimensions of sinkholes

    NASA Astrophysics Data System (ADS)

    Reams, Max W.

    1992-05-01

    Sinkhole perimeters are probably fractals ( D=1.209-1.558) for sinkholes with areas larger than 10,000 m 2, based on area-perimeter plots of digitized data from karst surfaces developed on six geologic units in the United States. The sites in Florida, Kentucky, Indiana and Missouri were studied using maps with a scale of 1:24, 000. Size-number distributions of sinkhole perimeters and areas may also be fractal, although data for small sinkholes is needed for verification. Studies based on small-scale maps are needed to evaluate the number and roughness of small sinkhole populations.

  10. [Recent progress of research and applications of fractal and its theories in medicine].

    PubMed

    Cai, Congbo; Wang, Ping

    2014-10-01

    Fractal, a mathematics concept, is used to describe an image of self-similarity and scale invariance. Some organisms have been discovered with the fractal characteristics, such as cerebral cortex surface, retinal vessel structure, cardiovascular network, and trabecular bone, etc. It has been preliminarily confirmed that the three-dimensional structure of cells cultured in vitro could be significantly enhanced by bionic fractal surface. Moreover, fractal theory in clinical research will help early diagnosis and treatment of diseases, reducing the patient's pain and suffering. The development process of diseases in the human body can be expressed by the fractal theories parameter. It is of considerable significance to retrospectively review the preparation and application of fractal surface and its diagnostic value in medicine. This paper gives an application of fractal and its theories in the medical science, based on the research achievements in our laboratory. PMID:25764741

  11. Fractal properties of lysozyme: a neutron scattering study.

    PubMed

    Lushnikov, S G; Svanidze, A V; Gvasaliya, S N; Torok, G; Rosta, L; Sashin, I L

    2009-03-01

    The spatial structure and dynamics of hen egg white lysozyme have been investigated by small-angle and inelastic neutron scattering. Analysis of the results was carried using the fractal approach, which allowed determination of the fractal and fracton dimensions of lysozyme, i.e., consideration of the protein structure and dynamics by using a unified approach. Small-angle neutron scattering studies of thermal denaturation of lysozyme have revealed changes in the fractal dimension in the vicinity of the thermal denaturation temperature that reflect changes in the spatial organization of protein. PMID:19391977

  12. Relating a Prominence Observed from the Solar Optical Telescope on the Hinode Satellite to Known 3-D Structures of Filaments

    NASA Astrophysics Data System (ADS)

    Martin, S. F.; Panasenco, O.; Agah, Y.; Engvold, O.; Lin, Y.

    2009-12-01

    We address only a first step in relating limb and disk observations by illustrating and comparing the spines and barbs of three different quiescent prominences and filaments observed in Hα by three different telescopes. Although the appearance of the three quiescent prominences is quite different, we show that each consists of a spine, barbs extending from the spine, and arcs at the base of some of the curtains of barb threads.

  13. The nonlinear evolution of magnetized solar filaments

    NASA Technical Reports Server (NTRS)

    Sparks, L.; Van Hoven, G.; Schnack, D. D.

    1990-01-01

    Thermal instability driven by optically thin radiation is believed to initiate the formation of plasma filaments in the solar corona. The fact that filaments are observed generally to separate regions of opposite, line-of-sight, magnetic polarity in the underlying photosphere suggests that filament formation requires the presence of a highly sheared, local magnetic field. Two-dimensional, nonlinear, magnetohydrodynamic simulations of the local genesis and growth of solar filaments in a force-free, sheared, magnetic field were performed, and the evolution of generic perturbations possessing broad spatial profiles was traced. It was found that simulations of the evolution of initial random-noise perturbations produce filamentary plasma structures that exhibit densities and temperatures characteristic of observed solar filaments. Furthermore, in each of these simulations, the filament axis lies at a finite angle with respect to the local magnetic field, consistent with solar observations.

  14. Femtosecond Laser Filamentation for Atmospheric Sensing

    PubMed Central

    Xu, Huai Liang; Chin, See Leang

    2011-01-01

    Powerful femtosecond laser pulses propagating in transparent materials result in the formation of self-guided structures called filaments. Such filamentation in air can be controlled to occur at a distance as far as a few kilometers, making it ideally suited for remote sensing of pollutants in the atmosphere. On the one hand, the high intensity inside the filaments can induce the fragmentation of all matters in the path of filaments, resulting in the emission of characteristic fluorescence spectra (fingerprints) from the excited fragments, which can be used for the identification of various substances including chemical and biological species. On the other hand, along with the femtosecond laser filamentation, white-light supercontinuum emission in the infrared to UV range is generated, which can be used as an ideal light source for absorption Lidar. In this paper, we present an overview of recent progress concerning remote sensing of the atmosphere using femtosecond laser filamentation. PMID:22346566

  15. Flames in fractal grid generated turbulence

    NASA Astrophysics Data System (ADS)

    Goh, K. H. H.; Geipel, P.; Hampp, F.; Lindstedt, R. P.

    2013-12-01

    Twin premixed turbulent opposed jet flames were stabilized for lean mixtures of air with methane and propane in fractal grid generated turbulence. A density segregation method was applied alongside particle image velocimetry to obtain velocity and scalar statistics. It is shown that the current fractal grids increase the turbulence levels by around a factor of 2. Proper orthogonal decomposition (POD) was applied to show that the fractal grids produce slightly larger turbulent structures that decay at a slower rate as compared to conventional perforated plates. Conditional POD (CPOD) was also implemented using the density segregation technique and the results show that CPOD is essential to segregate the relative structures and turbulent kinetic energy distributions in each stream. The Kolmogorov length scales were also estimated providing values ∼0.1 and ∼0.5 mm in the reactants and products, respectively. Resolved profiles of flame surface density indicate that a thin flame assumption leading to bimodal statistics is not perfectly valid under the current conditions and it is expected that the data obtained will be of significant value to the development of computational methods that can provide information on the conditional structure of turbulence. It is concluded that the increase in the turbulent Reynolds number is without any negative impact on other parameters and that fractal grids provide a route towards removing the classical problem of a relatively low ratio of turbulent to bulk strain associated with the opposed jet configuration.

  16. Actively Contracting Bundles of Polar Filaments

    NASA Astrophysics Data System (ADS)

    Kruse, K.; Jülicher, F.

    2000-08-01

    We introduce a phenomenological model to study the properties of bundles of polar filaments which interact via active elements. The stability of the homogeneous state, the attractors of the dynamics in the unstable regime, and the tensile stress generated in the bundle are discussed. We find that the interaction of parallel filaments can induce unstable behavior and is responsible for active contraction and tension in the bundle. The interaction between antiparallel filaments leads to filament sorting. Our model could apply to simple contractile structures in cells such as stress fibers.

  17. Role of Fractals in Solid Earth Geophysics

    NASA Astrophysics Data System (ADS)

    Dimri, V. P.

    2007-12-01

    Various studies carried out across the globe reveal that many of the Earth's processes satisfy fractal statistics, where examples range from the frequency-size statistics of earthquakes to the time series of the Earth's magnetic field. The scaling property of fractal signal is very much appealing for descriptions of many geological features. It is observed from the German Continental Deep Drilling Programme (KTB) and many other deep bore wells around the world that the source distribution of density, magnetic susceptibility, electrical conductivity, acoustic impedance etc. follows power-law, hence they are fractal in nature. This finding has been incorporated in various geophysical techniques to better understand the non-linear processes in Earth systems. Theoretical relation between source and potential fields is established and based on that techniques for gravity and magnetic interpretation methods have been reformulated. A new scaling power spectral method is developed to understand source behaviour and parameters of the Earth's interior. Further, fractal concept of tessellation has been used to model the complex geometrical object, which was hitherto unaddressed. An entirely new technique has been proposed to generate the complex geometrical structures with desired physical property variation for forward and inverse modeling of the geophysical data. Further, the concept of fractal distribution of frequency and magnitude of earthquakes is exploited in aftershock study of the major earthquakes such as, Uttarkashi (1991), Latur (1993), Jabalpur (1997), Chamoli (1999), Bhuj (2001) and Muzzafarabad (2005). This study revealed that the Himalayan earthquakes follow multifractal distribution however, shield earthquakes follow monofractal distribution. This finding has been used to explain the earthquake mechanism in Himalayan and shield areas. The fractal study was extended to sea earthquakes and wave propagation modeling is done to understand the effect of Tsunami

  18. FRACTAL DIMENSION OF GALAXY ISOPHOTES

    SciTech Connect

    Thanki, Sandip; Rhee, George; Lepp, Stephen E-mail: grhee@physics.unlv.edu

    2009-09-15

    In this paper we investigate the use of the fractal dimension of galaxy isophotes in galaxy classification. We have applied two different methods for determining fractal dimensions to the isophotes of elliptical and spiral galaxies derived from CCD images. We conclude that fractal dimension alone is not a reliable tool but that combined with other parameters in a neural net algorithm the fractal dimension could be of use. In particular, we have used three parameters to segregate the ellipticals and lenticulars from the spiral galaxies in our sample. These three parameters are the correlation fractal dimension D {sub corr}, the difference between the correlation fractal dimension and the capacity fractal dimension D {sub corr} - D {sub cap}, and, thirdly, the B - V color of the galaxy.

  19. Scrape-off Layer Current Model for Filament Structure Observed during Edge Localized Modes (ELMs) in the DIII-D Tokamak

    SciTech Connect

    Takahashi, Hironori; Fredrickson, E. D.; Schaffer, M. J.

    2008-04-15

    The plasma in tokamaks often exhibits a relaxation oscillation called the edge localized mode (ELM), which is generally attributed to MHD instability driven by strong gradients at the plasma boundary. It is shown here that field-aligned currents flowing just outside the boundary may also play a role in the ELM process. The poloidal perturbation magnetic field during ELMs in the DIII–D tokamak calculated from measured currents can reproduce prominent observed features, including a narrow magnetic structure at the outboard midplane similar to filaments observed earlier in DIII–D and NSTX.

  20. A Fractal Excursion.

    ERIC Educational Resources Information Center

    Camp, Dane R.

    1991-01-01

    After introducing the two-dimensional Koch curve, which is generated by simple recursions on an equilateral triangle, the process is extended to three dimensions with simple recursions on a regular tetrahedron. Included, for both fractal sequences, are iterative formulae, illustrations of the first several iterations, and a sample PASCAL program.…

  1. Focus on Fractals.

    ERIC Educational Resources Information Center

    Marks, Tim K.

    1992-01-01

    Presents a three-lesson unit that uses fractal geometry to measure the coastline of Massachusetts. Two lessons provide hands-on activities utilizing compass and grid methods to perform the measurements and the third lesson analyzes and explains the results of the activities. (MDH)

  2. Fractal geometry of music.

    PubMed Central

    Hsü, K J; Hsü, A J

    1990-01-01

    Music critics have compared Bach's music to the precision of mathematics. What "mathematics" and what "precision" are the questions for a curious scientist. The purpose of this short note is to suggest that the mathematics is, at least in part, Mandelbrot's fractal geometry and the precision is the deviation from a log-log linear plot. PMID:11607061

  3. Filamentation of plasma in the auroral region by an ion-ion instability - A process for the formation of bidimensional potential structures

    NASA Astrophysics Data System (ADS)

    Mottez, F.; Chanteur, G.; Roux, A.

    1992-07-01

    The nonlinear behavior of electrostatic ion waves generated by an ion beam flowing through a thermal ion and electron background in a strongly magnetized plasma is investigated by means of a 2D, explicit, electrostatic particle code. To follow the nonlinear evolution of these ion waves, a long-lasting simulation is run with a large simulation grid: 128 x 512 lambda(d). Beam ions are shown to generate oblique waves. The nonlinear beatings between these oblique waves produce purely transverse waves, which leads to a strong modulation of the density and of the electric potential in a direction transverse to the magnetic field. The transverse scale of these essentially field-aligned filaments is 10 rho(i), where rho(i) is the ion Larmor radius of beam ions. Within these filaments, relatively stable field-aligned density and potential structures develop. Unlike the potential structures that develop in a two-component plasma with downgoing electrons, these structures move upward.

  4. Structural characterization of filaments formed by human Xrcc4–Cernunnos/XLF complex involved in nonhomologous DNA end-joining

    PubMed Central

    Ropars, Virginie; Drevet, Pascal; Legrand, Pierre; Baconnais, Sonia; Amram, Jeremy; Faure, Guilhem; Márquez, José A.; Piétrement, Olivier; Guerois, Raphaël; Callebaut, Isabelle; Le Cam, Eric; Revy, Patrick; de Villartay, Jean-Pierre; Charbonnier, Jean-Baptiste

    2011-01-01

    Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X41–157-Cernunnos1–224 complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X41–157 and Cernunnos1–224 homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4–Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4–Cernunnos interface. We identified four X4 residues (Glu55, Asp58, Met61, and Phe106) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step. PMID:21768349

  5. Comprehensive Fractal Description of Porosity of Coal of Different Ranks

    PubMed Central

    Ren, Jiangang; Zhang, Guocheng; Song, Zhimin; Liu, Gaofeng; Li, Bing

    2014-01-01

    We selected, as the objects of our research, lignite from the Beizao Mine, gas coal from the Caiyuan Mine, coking coal from the Xiqu Mine, and anthracite from the Guhanshan Mine. We used the mercury intrusion method and the low-temperature liquid nitrogen adsorption method to analyze the structure and shape of the coal pores and calculated the fractal dimensions of different aperture segments in the coal. The experimental results show that the fractal dimension of the aperture segment of lignite, gas coal, and coking coal with an aperture of greater than or equal to 10 nm, as well as the fractal dimension of the aperture segment of anthracite with an aperture of greater than or equal to 100 nm, can be calculated using the mercury intrusion method; the fractal dimension of the coal pore, with an aperture range between 2.03 nm and 361.14 nm, can be calculated using the liquid nitrogen adsorption method, of which the fractal dimensions bounded by apertures of 10 nm and 100 nm are different. Based on these findings, we defined and calculated the comprehensive fractal dimensions of the coal pores and achieved the unity of fractal dimensions for full apertures of coal pores, thereby facilitating, overall characterization for the heterogeneity of the coal pore structure. PMID:24955407

  6. Light Scattering From Fractal Titania Aggregates

    NASA Astrophysics Data System (ADS)

    Pande, Rajiv; Sorensen, Christopher M.

    1996-03-01

    We studied the fractal morphology of titania aggregates by light scattering. Titanium dioxide particles were generated by the thermal decomposition of titanium tetra-isopropoxide(TTIP) in a glass furnace at various temperatures in the range of 100 - 500^o C. We scattered vertically polarized He-Ne laser (λ = 6328Ålight from a laminar aerosol stream of particles and measured the optical structure factor. This structure factor shows Rayleigh, Guinier, fractal and Porod regimes. The radius of gyration Rg was determined from the Guinier analysis. The data were then fit to the Fisher-Burford form to determine the fractal dimension of about 2.0. This fit also delineated the crossover from the fractal to Porod regime, which can be used to determine the monomer particle size of about 0.1 μm. These optical measurements will be compared to electron microscope analysis of aggregates collected from the aerosol. This work was supported by NSF grant CTS-9908153.

  7. Filaments from L5

    NASA Technical Reports Server (NTRS)

    Sterling, Alphonse C.

    2011-01-01

    We've been investigating filament eruptions in recent years. Why do eruptions occur? Basic mechanism is magnetic, and can often include coronal mass ejections (CMEs), flares, and filament eruptions. Use filament eruptions as markers of the more-general eruption. From our studies, we can identify directions for future work to help predict when eruptions might occur.

  8. Study on Solidification of Phase Change Material in Fractal Porous Metal Foam

    NASA Astrophysics Data System (ADS)

    Zhang, Chengbin; Wu, Liangyu; Chen, Yongping

    2015-02-01

    The Sierpinski fractal is introduced to construct the porous metal foam. Based on this fractal description, an unsteady heat transfer model accompanied with solidification phase change in fractal porous metal foam embedded with phase change material (PCM) is developed and numerically analyzed. The heat transfer processes associated with solidification of PCM embedded in fractal structure is investigated and compared with that in single-pore structure. The results indicate that, for the solidification of phase change material in fractal porous metal foam, the PCM is dispersedly distributed in metal foam and the existence of porous metal matrix provides a fast heat flow channel both horizontally and vertically, which induces the enhancement of interstitial heat transfer between the solid matrix and PCM. The solidification performance of the PCM, which is represented by liquid fraction and solidification time, in fractal structure is superior to that in single-pore structure.

  9. Recent observations of the formation of filaments

    NASA Astrophysics Data System (ADS)

    Martin, Sara F.

    1986-12-01

    Two examples of the formation of small filaments in H alpha are described and illustrated. In both cases, the formation is seen to be the spontaneous appearance of strands of absorbing mass that evolve from no previous structure. The initial development of the filaments appears to consist of the accumulation of these absorptive strands along approximately parallel paths in a channel between large-scale, opposite polarity magnetic fields on either side of the filaments. The strands exhibit continuous changes in shape and degree of absorption which can be due to successive condensations resulting in new strands, mass motions within the strands, and outflow of the mass from the strands. For at least several hours before the formation of both filaments, small-scale fragments of opposite polarity, line-of-sight magnetic flux adjacent to or immediately below the filaments, and at the ends of the filaments, were cancelling. This type of magnetic flux disappearance continued during the development of the filaments and is commonly observed in association with established filaments. Cancellation is interpreted as an important evolutionary change in the magnetic field that can lead to configurations suitable for the formation of filaments.

  10. Solid friction between soft filaments

    PubMed Central

    Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A.W. C.; Vitelli, Vincenzo; Mahadevan, L.; Dogic, Zvonimir

    2015-01-01

    Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments1,2. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials. PMID:25730393

  11. Nonequilibrium transport in superconducting filaments

    NASA Technical Reports Server (NTRS)

    Arutyunov, K. YU.; Danilova, N. P.; Nikolaeva, A. A.

    1995-01-01

    The step-like current-voltage characteristics of highly homogeneous single-crystalline tin and indium thin filaments has been measured. The length of the samples L approximately 1 cm was much greater than the nonequilibrium quasiparticle relaxation length Lambda. It was found that the activation of a successive i-th voltage step occurs at current significantly greater than the one derived with the assumption that the phase slip centers are weakly interacting on a scale L much greater than Lambda. The observation of 'subharmonic' fine structure on the voltage-current characteristics of tin filaments confirms the hypothesis of the long-range phase slip centers interaction.

  12. Fractal Physiology and the Fractional Calculus: A Perspective

    PubMed Central

    West, Bruce J.

    2010-01-01

    This paper presents a restricted overview of Fractal Physiology focusing on the complexity of the human body and the characterization of that complexity through fractal measures and their dynamics, with fractal dynamics being described by the fractional calculus. Not only are anatomical structures (Grizzi and Chiriva-Internati, 2005), such as the convoluted surface of the brain, the lining of the bowel, neural networks and placenta, fractal, but the output of dynamical physiologic networks are fractal as well (Bassingthwaighte et al., 1994). The time series for the inter-beat intervals of the heart, inter-breath intervals and inter-stride intervals have all been shown to be fractal and/or multifractal statistical phenomena. Consequently, the fractal dimension turns out to be a significantly better indicator of organismic functions in health and disease than the traditional average measures, such as heart rate, breathing rate, and stride rate. The observation that human physiology is primarily fractal was first made in the 1980s, based on the analysis of a limited number of datasets. We review some of these phenomena herein by applying an allometric aggregation approach to the processing of physiologic time series. This straight forward method establishes the scaling behavior of complex physiologic networks and some dynamic models capable of generating such scaling are reviewed. These models include simple and fractional random walks, which describe how the scaling of correlation functions and probability densities are related to time series data. Subsequently, it is suggested that a proper methodology for describing the dynamics of fractal time series may well be the fractional calculus, either through the fractional Langevin equation or the fractional diffusion equation. A fractional operator (derivative or integral) acting on a fractal function, yields another fractal function, allowing us to construct a fractional Langevin equation to describe the evolution of a

  13. Fractal physiology and the fractional calculus: a perspective.

    PubMed

    West, Bruce J

    2010-01-01

    This paper presents a restricted overview of Fractal Physiology focusing on the complexity of the human body and the characterization of that complexity through fractal measures and their dynamics, with fractal dynamics being described by the fractional calculus. Not only are anatomical structures (Grizzi and Chiriva-Internati, 2005), such as the convoluted surface of the brain, the lining of the bowel, neural networks and placenta, fractal, but the output of dynamical physiologic networks are fractal as well (Bassingthwaighte et al., 1994). The time series for the inter-beat intervals of the heart, inter-breath intervals and inter-stride intervals have all been shown to be fractal and/or multifractal statistical phenomena. Consequently, the fractal dimension turns out to be a significantly better indicator of organismic functions in health and disease than the traditional average measures, such as heart rate, breathing rate, and stride rate. The observation that human physiology is primarily fractal was first made in the 1980s, based on the analysis of a limited number of datasets. We review some of these phenomena herein by applying an allometric aggregation approach to the processing of physiologic time series. This straight forward method establishes the scaling behavior of complex physiologic networks and some dynamic models capable of generating such scaling are reviewed. These models include simple and fractional random walks, which describe how the scaling of correlation functions and probability densities are related to time series data. Subsequently, it is suggested that a proper methodology for describing the dynamics of fractal time series may well be the fractional calculus, either through the fractional Langevin equation or the fractional diffusion equation. A fractional operator (derivative or integral) acting on a fractal function, yields another fractal function, allowing us to construct a fractional Langevin equation to describe the evolution of a

  14. Special issue on filamentation

    NASA Astrophysics Data System (ADS)

    Li, Ruxin; Milchberg, Howard; Mysyrowicz, André

    2014-05-01

    Journal of Physics B: Atomic, Molecular and Optical Physics is delighted to announce a forthcoming special issue on filamentation, to appear in the spring of 2015, and invites you to submit a paper. This special issue will attempt to give an overview of the present status of this field in order to create synergies and foster future developments. The issue is open to papers on the following issues: Theoretical advances on filamentation. Self-focusing and collapse. Filamentation in various media. Pulse self-compression and ultrafast processes in filaments. Molecular alignment and rotation. Filamentation tailoring. Interaction between filaments. Filament weather and pollution control. Filament induced condensation and precipitation. Terahertz science with filaments. Lasing in filaments. Filament induced molecular excitation and reaction. Electric discharge and plasma. Cross-disciplinary applications. Novel concepts related to these topics are particularly welcome. Please submit your article by 1 October 2014 (expected web publication: spring 2015) using our website http://mc04.manuscriptcentral.com/jphysb-iop. Submissions received after this date will be considered for the journal, but may not be included in the special issue. The issue will be edited by Ruxin Li, Howard Milchberg and André Mysyrowicz.

  15. Fractal frontiers in cardiovascular magnetic resonance: towards clinical implementation.

    PubMed

    Captur, Gabriella; Karperien, Audrey L; Li, Chunming; Zemrak, Filip; Tobon-Gomez, Catalina; Gao, Xuexin; Bluemke, David A; Elliott, Perry M; Petersen, Steffen E; Moon, James C

    2015-01-01

    Many of the structures and parameters that are detected, measured and reported in cardiovascular magnetic resonance (CMR) have at least some properties that are fractal, meaning complex and self-similar at different scales. To date however, there has been little use of fractal geometry in CMR; by comparison, many more applications of fractal analysis have been published in MR imaging of the brain.This review explains the fundamental principles of fractal geometry, places the fractal dimension into a meaningful context within the realms of Euclidean and topological space, and defines its role in digital image processing. It summarises the basic mathematics, highlights strengths and potential limitations of its application to biomedical imaging, shows key current examples and suggests a simple route for its successful clinical implementation by the CMR community.By simplifying some of the more abstract concepts of deterministic fractals, this review invites CMR scientists (clinicians, technologists, physicists) to experiment with fractal analysis as a means of developing the next generation of intelligent quantitative cardiac imaging tools. PMID:26346700

  16. Pond fractals in a tidal flat

    NASA Astrophysics Data System (ADS)

    Cael, B. B.; Lambert, Bennett; Bisson, Kelsey

    2015-11-01

    Studies over the past decade have reported power-law distributions for the areas of terrestrial lakes and Arctic melt ponds, as well as fractal relationships between their areas and coastlines. Here we report similar fractal structure of ponds in a tidal flat, thereby extending the spatial and temporal scales on which such phenomena have been observed in geophysical systems. Images taken during low tide of a tidal flat in Damariscotta, Maine, reveal a well-resolved power-law distribution of pond sizes over three orders of magnitude with a consistent fractal area-perimeter relationship. The data are consistent with the predictions of percolation theory for unscreened perimeters and scale-free cluster size distributions and are robust to alterations of the image processing procedure. The small spatial and temporal scales of these data suggest this easily observable system may serve as a useful model for investigating the evolution of pond geometries, while emphasizing the generality of fractal behavior in geophysical surfaces.

  17. Pond fractals in a tidal flat.

    PubMed

    Cael, B B; Lambert, Bennett; Bisson, Kelsey

    2015-11-01

    Studies over the past decade have reported power-law distributions for the areas of terrestrial lakes and Arctic melt ponds, as well as fractal relationships between their areas and coastlines. Here we report similar fractal structure of ponds in a tidal flat, thereby extending the spatial and temporal scales on which such phenomena have been observed in geophysical systems. Images taken during low tide of a tidal flat in Damariscotta, Maine, reveal a well-resolved power-law distribution of pond sizes over three orders of magnitude with a consistent fractal area-perimeter relationship. The data are consistent with the predictions of percolation theory for unscreened perimeters and scale-free cluster size distributions and are robust to alterations of the image processing procedure. The small spatial and temporal scales of these data suggest this easily observable system may serve as a useful model for investigating the evolution of pond geometries, while emphasizing the generality of fractal behavior in geophysical surfaces. PMID:26651668

  18. Fractal analysis of narwhal space use patterns.

    PubMed

    Laidre, Kristin L; Heide-Jørgensen, Mads P; Logsdon, Miles L; Hobbs, Roderick C; Dietz, Rune; VanBlaricom, Glenn R

    2004-01-01

    Quantifying animal movement in response to a spatially and temporally heterogeneous environment is critical to understanding the structural and functional landscape influences on population viability. Generalities of landscape structure can easily be extended to the marine environment, as marine predators inhabit a patchy, dynamic system, which influences animal choice and behavior. An innovative use of the fractal measure of complexity, indexing the linearity of movement paths over replicate temporal scales, was applied to satellite tracking data collected from narwhals (Monodon monoceros) (n = 20) in West Greenland and the eastern Canadian high Arctic. Daily movements of individuals were obtained using polar orbiting satellites via the ARGOS data location and collection system. Geographic positions were filtered to obtain a daily good quality position for each whale. The length of total pathway was measured over seven different temporal length scales (step lengths), ranging from one day to one week, and a seasonal mean was calculated. Fractal dimension (D) was significantly different between seasons, highest during summer (D = 1.61, SE 0.04) and winter (D = 1.69, SE 0.06) when whales made convoluted movements in focal areas. Fractal dimension was lowest during fall (D = 1.34, SE 0.03) when whales were migrating south ahead of the forming sea ice. There were no significant effects of size category or sex on fractal dimension by season. The greater linearity of movement during the migration period suggests individuals do not intensively forage on patchy resources until they arrive at summer or winter sites. The highly convoluted movements observed during summer and winter suggest foraging or searching efforts in localized areas. Significant differences between the fractal dimensions on two separate wintering grounds in Baffin Bay suggest differential movement patterns in response to the dynamics of sea ice. PMID:16351924

  19. Fractals in geology and geophysics

    NASA Technical Reports Server (NTRS)

    Turcotte, Donald L.

    1989-01-01

    The definition of a fractal distribution is that the number of objects N with a characteristic size greater than r scales with the relation N of about r exp -D. The frequency-size distributions for islands, earthquakes, fragments, ore deposits, and oil fields often satisfy this relation. This application illustrates a fundamental aspect of fractal distributions, scale invariance. The requirement of an object to define a scale in photograhs of many geological features is one indication of the wide applicability of scale invariance to geological problems; scale invariance can lead to fractal clustering. Geophysical spectra can also be related to fractals; these are self-affine fractals rather than self-similar fractals. Examples include the earth's topography and geoid.

  20. Fractal rigidity in migraine

    NASA Astrophysics Data System (ADS)

    Latka, Miroslaw; Glaubic-Latka, Marta; Latka, Dariusz; West, Bruce J.

    2004-04-01

    We study the middle cerebral artery blood flow velocity (MCAfv) in humans using transcranial Doppler ultrasonography (TCD). Scaling properties of time series of the axial flow velocity averaged over a cardiac beat interval may be characterized by two exponents. The short time scaling exponent (STSE) determines the statistical properties of fluctuations of blood flow velocities in short-time intervals while the Hurst exponent describes the long-term fractal properties. In many migraineurs the value of the STSE is significantly reduced and may approach that of the Hurst exponent. This change in dynamical properties reflects the significant loss of short-term adaptability and the overall hyperexcitability of the underlying cerebral blood flow control system. We call this effect fractal rigidity.

  1. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-08-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-[3-(triethoxysilyl)propyl]-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  2. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-01-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-(3-(triethoxysilyl)propyl)-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  3. How is kinematic structure connected to the core scale from filament scale?; Mopra mapping observations with multi-lines of dense cores in Lupus I

    NASA Astrophysics Data System (ADS)

    Kiyokane, Kazuhiro; Saito, Masao; Tachihara, Kengo; Saigo, Kazuya; van Kempen, Tim; Cortes, Paulo; Hill, Tracey; Knee, Lewis; Kurono, Yasutaka; Takahashi, Satoko; Aya, Higuchi; Nyman, Lars-Ake

    2014-06-01

    Recently, high sensitivity mappings of nearby molecular clouds in far-infrared and submillimeter wavelengths with Hershel and AzTEC/ASTE show ubiquitous existence of the filamentary structures with 0.1-pc uniform width. It is important to investigate dense core formation from large scale structure via fragmentation. We have conducted MOPRA multi-line mapping observations covered on 0.02 - 0.2 pc scales of 8 dense cores in a filamentary cloud of nearby Lupus I at 140 pc. A class 0/I protostellar core IRAS 15398-3359 is included as a sample, which has an adjacent prestellar core with the separation of 0.13pc in the west. The maps of N2H+, HNC, HC3N show well associated with each core. The velocity field of C18O shows 1.4 km/s/pc from north to south over the region containing two dense cores, which is consistent with past observation of NANTEN. In contrast to C18O results, the velocity field of HC3N shows different structures, which suggest counter rotation of two dense cores; 1.2 km/s/pc from north-west to south-east around a protostellar core and 0.8 km/s/pc from east to west around a presteller core. The filament will be fragmentized and collapsed to dense cores when the line density is over 2Cs/G (where Cs is sound speed and G is gravitational constant). If that velocity gradient was caused by such situation, it should be red-blue-red-blue across two dense cores but the observed kinematics is not consistent with this scenario, which requires that the filament structure would be extremely curved with a skew angle. Although we cannot reject the collapsing interruption, those results suggest the spin-up rotating picture separated from large-scale structure.

  4. Fractal multifiber microchannel plates

    NASA Technical Reports Server (NTRS)

    Cook, Lee M.; Feller, W. B.; Kenter, Almus T.; Chappell, Jon H.

    1992-01-01

    The construction and performance of microchannel plates (MCPs) made using fractal tiling mehtods are reviewed. MCPs with 40 mm active areas having near-perfect channel ordering were produced. These plates demonstrated electrical performance characteristics equivalent to conventionally constructed MCPs. These apparently are the first MCPs which have a sufficiently high degree of order to permit single channel addressability. Potential applications for these devices and the prospects for further development are discussed.

  5. Fractals and humor

    NASA Astrophysics Data System (ADS)

    Martin, Demetri

    2015-03-01

    Demetri Maritn prepared this palindromic poem as his project for Michael Frame's fractal geometry class at Yale. Notice the first, fourth, and seventh words in the second and next-to-second lines are palindromes, the first two and last two lines are palindromes, the middle line, "Be still if I fill its ebb" minus its last letter is a palindrome, and the entire poem is a palindrome...

  6. How cofilin severs an actin filament.

    PubMed

    De La Cruz, Enrique M

    2009-05-15

    The actin regulatory protein, cofilin, promotes actin assembly dynamics by severing filaments and increasing the number of ends from which subunits add and dissociate. Recent studies provide biophysical descriptions of cooperative filament interactions in energetic, mechanical and structural terms. A one-dimensional Ising model with nearest-neighbor interactions permits thermodynamic analysis of cooperative binding and indicates that one or a few cofilin molecules can sever a filament. Binding and cooperative interactions are entropically driven. A significant fraction of the binding free energy results from the linked dissociation of filament-associated ions (polyelectrolyte effect), which modulate filament structure, stability and mechanics. The remaining binding free energy and essentially all of the cooperative free energy arise from the enhanced conformational dynamics of the cofilactin complex. Filament mechanics are modulated by cofilin such that cofilin-saturated filaments are approximately 10- to 20-fold more compliant in bending and twisting than bare filaments. Cofilin activity is well described by models in which discontinuities in topology, mechanics and conformational dynamics generate stress concentration and promote fracture at junctions of bare and decorated segments, analogous to the grain boundary fracture of crystalline materials and the thermally driven formation of shear transformation zones in colloidal glass. PMID:20700473

  7. The role of fractal aperiodic order in the transmittance, conductance and electronic structure of graphene-based systems

    NASA Astrophysics Data System (ADS)

    Rodríguez-González, R.; Rodríguez-Vargas, I.

    2015-05-01

    In this work we investigate the peculiar tunneling characteristics of Dirac electrons through quasi-regular or aperiodic single-layer graphene structures. In particular, we have implemented the aperiodic order to the barriers and potential wells arranged according to the Cantor sequence. We deal with two types of quasi-regular systems: the first one Electrostatic Cantor Graphene Structures (ECGSs), structures formed with electrostatic potentials, and the second one Substrate Cantor Graphene Structures (SCGSs), obtained by alternating substrates that can open and non-open, such as SiC and SiO2, an energy bandgap on graphene. We have used the transfer matrix method to compute the transmission probability, linear-regime conductance and spectrum of bound states of both systems, which are calculated for different combinations of the fundamental parameters: starting width, sequence generation number, electron incident energy and electron incident angle. The transmission spectra of ECGSs and SCGSs show self-similar patterns, which are more remarkable when the generation number increases. The conductance of ECGSs becomes smoother as the generation increases. Furthermore, in the case of SCGSs the conductance exhibits self-similar features as a function of the generation number. In general, the conductance of both systems presents an oscillatory behaviour that can be described directly by means of the bound states.

  8. Frozen-in Fractals All Around: Inferring the Large-Scale Effects of Small-Scale Magnetic Structure

    NASA Astrophysics Data System (ADS)

    McAteer, R. T. James

    2015-07-01

    The large-scale structure of the magnetic field in the solar corona provides the energy to power large-scale solar eruptive events. Our physical understanding of this structure, and hence our ability to predict these events, is limited by the type of data currently available. It is shown that the multifractal spectrum is a powerful tool to study this structure, by providing a physical connection between the details of photospheric magnetic gradients and current density at all size scales. This uses concepts associated with geometric measure theory and the theory of weakly differentiable functions to compare Ampère's law to the wavelet-transform modulus maximum method. The Hölder exponent provides a direct measure of the rate of change of current density across spatial size scales. As this measure is independent of many features of the data (pixel resolution, data size, data type, presence of quiet-Sun data), it provides a unique approach to studying magnetic-field complexity and hence a potentially powerful tool for a statistical prediction of solar-flare activity. Three specific predictions are provided to test this theory: the multifractal spectra will not be dependent on the data type or quality; quiet-Sun gradients will not persist with time; structures with high current densities at large size scales will be the source of energy storage for solar eruptive events.

  9. Fractal trace of earthworms

    NASA Astrophysics Data System (ADS)

    Burdzy, Krzysztof; Hołyst, Robert; Pruski, Łukasz

    2013-05-01

    We investigate a process of random walks of a point particle on a two-dimensional square lattice of size n×n with periodic boundary conditions. A fraction p⩽20% of the lattice is occupied by holes (p represents macroporosity). A site not occupied by a hole is occupied by an obstacle. Upon a random step of the walker, a number of obstacles, M, can be pushed aside. The system approaches equilibrium in (nlnn)2 steps. We determine the distribution of M pushed in a single move at equilibrium. The distribution F(M) is given by Mγ where γ=-1.18 for p=0.1, decreasing to γ=-1.28 for p=0.01. Irrespective of the initial distribution of holes on the lattice, the final equilibrium distribution of holes forms a fractal with fractal dimension changing from a=1.56 for p=0.20 to a=1.42 for p=0.001 (for n=4,000). The trace of a random walker forms a distribution with expected fractal dimension 2.

  10. Darwinian Evolution and Fractals

    NASA Astrophysics Data System (ADS)

    Carr, Paul H.

    2009-05-01

    Did nature's beauty emerge by chance or was it intelligently designed? Richard Dawkins asserts that evolution is blind aimless chance. Michael Behe believes, on the contrary, that the first cell was intelligently designed. The scientific evidence is that nature's creativity arises from the interplay between chance AND design (laws). Darwin's ``Origin of the Species,'' published 150 years ago in 1859, characterized evolution as the interplay between variations (symbolized by dice) and the natural selection law (design). This is evident in recent discoveries in DNA, Madelbrot's Fractal Geometry of Nature, and the success of the genetic design algorithm. Algorithms for generating fractals have the same interplay between randomness and law as evolution. Fractal statistics, which are not completely random, characterize such phenomena such as fluctuations in the stock market, the Nile River, rainfall, and tree rings. As chaos theorist Joseph Ford put it: God plays dice, but the dice are loaded. Thus Darwin, in discovering the evolutionary interplay between variations and natural selection, was throwing God's dice!

  11. Fractal geometry of some Martian lava flow margins: Alba Patera

    NASA Technical Reports Server (NTRS)

    Kauhanen, K.

    1993-01-01

    Fractal dimension for a few lava flow margins on the gently sloping flanks of Alba Patera were measured using the structured walk method. Fractal behavior was observed at scales ranging from 20 to 100 pixels. The upper limit of the linear part of log(margin length) vs. log(scale) profile correlated well to the margin length. The lower limit depended on resolution and flow properties.

  12. Surface fractal dimension of sintered porous solid niobium

    NASA Astrophysics Data System (ADS)

    Skatkov, L. I.; Konotop, V. V.; Cheremskoy, P. G.; Gomozov, V. P.; Bayrachny, B. I.

    1994-12-01

    The surface fractal dimension of porous solid niobium obtained by vacuum sintering Nb powder is experimentally investigated. The surface fractal dimension D is the main object of our study. Results of small-angle X-ray scattering (SAXS) agree very closely with those of Hg porosimetry. The surface dimensions are stated to be of the order of 2.8 which is a stipulation of a highly developed porous structure. Our results provide experimental support to the SAXS theory developed earlier.

  13. Fractals in biology and medicine

    NASA Technical Reports Server (NTRS)

    Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Ossadnik, S. M.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

  14. Dimension of fractal basin boundaries

    SciTech Connect

    Park, B.S.

    1988-01-01

    In many dynamical systems, multiple attractors coexist for certain parameter ranges. The set of initial conditions that asymptotically approach each attractor is its basin of attraction. These basins can be intertwined on arbitrary small scales. Basin boundary can be either smooth or fractal. Dynamical systems that have fractal basin boundary show final state sensitivity of the initial conditions. A measure of this sensitivity (uncertainty exponent {alpha}) is related to the dimension of the basin boundary d = D - {alpha}, where D is the dimension of the phase space and d is the dimension of the basin boundary. At metamorphosis values of the parameter, there might happen a conversion from smooth to fractal basin boundary (smooth-fractal metamorphosis) or a conversion from fractal to another fractal basin boundary characteristically different from the previous fractal one (fractal-fractal metamorphosis). The dimension changes continuously with the parameter except at the metamorphosis values where the dimension of the basin boundary jumps discontinuously. We chose the Henon map and the forced damped pendulum to investigate this. Scaling of the basin volumes near the metamorphosis values of the parameter is also being studied for the Henon map. Observations are explained analytically by using low dimensional model map.

  15. Study on effects of substrate temperature on growth and structure of alignment carbon nanotubes in plasma-enhanced hot filament chemical vapor deposition system

    NASA Astrophysics Data System (ADS)

    Dang, Chun; Wang, Tingzhi

    2006-11-01

    Alignment carbon nanotubes (ACNTs) were synthesized on silicon substrate coated with Ni catalyst film and Ta buffer layer by plasma-enhanced hot filament chemical vapor deposition using CH 4, NH 3, and H 2 as the reaction gas, and they were investigated by scanning electron microscopy and transmission electron microscopy. It is found that the diameter of the bamboo-structured ACNTs is increased from 62 to 177 nm when the substrate temperature was changed from 626 to 756 °C. Their growth rate is enhanced by the substrate temperature in a range of 626-683 °C and it is reversely reduced with the substrate temperature after the substrate temperature is over 683 °C. Beginning with wetting phenomenon, the effects of the substrate temperature on the structure and growth rate of the ACNTs are analyzed.

  16. A Statistical Study of Solar Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Schanche, Nicole; Aggarwal, Ashna; Reeves, Kathy; Kempton, Dustin James; Angryk, Rafal

    2016-05-01

    Solar filaments are cool, dark channels of partially-ionized plasma that lie above the chromosphere. Their structure follows the neutral line between local regions of opposite magnetic polarity. Previous research (e.g. Schmieder et al. 2013, McCauley et al. 2015) has shown a positive correlation (70-80%) between the occurrence of filament eruptions and coronal mass ejections (CME’s). In this study, we attempt to use properties of the filament in order to predict whether or not a given filament will erupt. This prediction would help to better predict the occurrence of an oncoming CME. To track the evolution of a filament over time, a spatio-temporal algorithm that groups separate filament instances from the Heliophysics Event Knowledgebase (HEK) into filament tracks was developed. Filament features from the HEK metadata, such as length, chirality, and tilt are then combined with other physical features, such as the overlying decay index for two sets of filaments tracks - those that erupt and those that remain bound. Using statistical methods such as the Kolmogrov-Smirnov test and a Random Forest Classifier, we determine the effectiveness of the combined features in prediction. We conclude that there is significant overlap between the properties of filaments that erupt and those that do not, leading to predictions only ~5-10% above chance. However, the changes in features, such as a change in the filament's length over time, were determined to have the highest predictive power. We discuss the possible physical connections with the change in these features."This project has been supported by funding from the Division of Advanced Cyberinfrastructure within the Directorate for Computer and Information Science and Engineering, the Division of Astronomical Sciences within the Directorate for Mathematical and Physical Sciences, and the Division of Atmospheric and Geospace Sciences within the Directorate for Geosciences, under NSF award #1443061.”

  17. Striation and convection in penumbral filaments

    NASA Astrophysics Data System (ADS)

    Spruit, H. C.; Scharmer, G. B.; Löfdahl, M. G.

    2010-10-01

    Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward propagating striations with inclination angles suggesting that they are aligned with the local magnetic field. We interpret it as the equivalent of the striations seen in the walls of small isolated magnetic structures. Their origin is then a corrugation of the boundary between an overturning convective flow inside the filament and the magnetic field wrapping around it. The outward propagation is a combination of a pattern motion due to the downflow observed along the sides of bright filaments, and the Evershed flow. The observed short wavelength of the striation argues against the existence of a dynamically significant horizontal field inside the bright filaments. Its intensity contrast is explained by the same physical effect that causes the dark cores of filaments, light bridges and “canals”. In this way striation represents an important clue to the physics of penumbral structure and its relation with other magnetic structures on the solar surface. We put this in perspective with results from the recent 3-D radiative hydrodynamic simulations. 4 movies are only available in electronic form at http://www.aanda.org

  18. Nanoflow over a fractal surface

    NASA Astrophysics Data System (ADS)

    Papanikolaou, Michail; Frank, Michael; Drikakis, Dimitris

    2016-08-01

    This paper investigates the effects of surface roughness on nanoflows using molecular dynamics simulations. A fractal model is employed to model wall roughness, and simulations are performed for liquid argon confined by two solid walls. It is shown that the surface roughness reduces the velocity in the proximity of the walls with the reduction being accentuated when increasing the roughness depth and wettability of the solid wall. It also makes the flow three-dimensional and anisotropic. In flows over idealized smooth surfaces, the liquid forms parallel, well-spaced layers, with a significant gap between the first layer and the solid wall. Rough walls distort the orderly distribution of fluid layers resulting in an incoherent formation of irregularly shaped fluid structures around and within the wall cavities.

  19. Hydrodynamics of pairs of interacting cytoskeletal filaments

    NASA Astrophysics Data System (ADS)

    Shinar, Tamar; Shelley, Michael

    2011-11-01

    Pairwise filament interactions underlie the dynamics of complex cytoskeletal networks in cells. These networks in turn play a crucial role in many cellular processes such as formation of the mitotic spindle and cell cleavage in cytokinesis. We model interactions of pairs of filaments immersed in a viscous, fluidic environment. The filaments are modeled using a slender body approximation, capturing their indirect interactions mediated by the immersing fluid. Direct filament interactions via molecular motors complexes induce alignment and parallel or anti-parallel sliding. The motor proteins are modeled as simple spring-like structures that walk directionally toward one end of the filament. We examine the resulting stresses in the fluid to better understand how the microscopic interactions lead to bulk behavior of cytoskeletal networks.

  20. A new paradigm for solar filament eruptions

    NASA Astrophysics Data System (ADS)

    Rust, David M.

    2001-11-01

    This article discusses the formation, magnetic structure, and eruption of solar filaments in terms of two contrasting paradigms. The standard paradigm is that filaments are formed by condensation of plasma on coronal magnetic fields that are twisted or dimpled as a result of photospheric motions. According to this paradigm, filaments erupt when photospheric motions shear the fields, increasing their energy and decreasing their stability. According to a new paradigm, subsurface motions generate toroidal magnetic flux ropes, and after these flux ropes emerge to form active regions, the most twisted parts migrate into the corona to form filaments. Filaments become unstable and are ejected after a sufficient accumulation of twist (i.e., magnetic helicity). Various proposed mechanisms for producing the needed helicity are reviewed, and several observational tests are proposed to differentiate among the possible mechanisms.

  1. Externally refuelled optical filaments

    NASA Astrophysics Data System (ADS)

    Scheller, Maik; Mills, Matthew S.; Miri, Mohammad-Ali; Cheng, Weibo; Moloney, Jerome V.; Kolesik, Miroslav; Polynkin, Pavel; Christodoulides, Demetrios N.

    2014-04-01

    Plasma channels produced in air through femtosecond laser filamentation hold great promise for a number of applications, including remote sensing, attosecond physics and spectroscopy, channelling microwaves and lightning protection. In such settings, extended filaments are desirable, yet their longitudinal span is limited by dissipative processes. Although various techniques aiming to prolong this process have been explored, the substantial extension of optical filaments remains a challenge. Here, we experimentally demonstrate that the natural range of a plasma column can be enhanced by at least an order of magnitude when the filament is prudently accompanied by an auxiliary beam. In this arrangement, the secondary low-intensity `dressing' beam propagates linearly and acts as a distributed energy reservoir, continuously refuelling the optical filament. Our approach offers an efficient and viable route towards the generation of extended light strings in air without inducing premature wave collapse or an undesirable beam break-up into multiple filaments.

  2. Micro and MACRO Fractals Generated by Multi-Valued Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Banakh, T.; Novosad, N.

    2014-08-01

    Given a multi-valued function Φ : X \\mumap X on a topological space X we study the properties of its fixed fractal \\malteseΦ, which is defined as the closure of the orbit Φω(*Φ) = ⋃n∈ωΦn(*Φ) of the set *Φ = {x ∈ X : x ∈ Φ(x)} of fixed points of Φ. A special attention is paid to the duality between micro-fractals and macro-fractals, which are fixed fractals \\maltese Φ and \\maltese {Φ -1} for a contracting compact-valued function Φ : X \\mumap X on a complete metric space X. With help of algorithms (described in this paper) we generate various images of macro-fractals which are dual to some well-known micro-fractals like the fractal cross, the Sierpiński triangle, Sierpiński carpet, the Koch curve, or the fractal snowflakes. The obtained images show that macro-fractals have a large-scale fractal structure, which becomes clearly visible after a suitable zooming.

  3. Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.

    PubMed

    Miyazaki, Naoyuki; Higashiura, Akifumi; Higashiura, Tomoko; Akita, Fusamichi; Hibino, Hiroyuki; Omura, Toshihiro; Nakagawa, Atsushi; Iwasaki, Kenji

    2016-02-01

    The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV. PMID:26374901

  4. Fractal Plate Reconstructions, Incorporating Asymmetric Spreading and Kinematics

    NASA Astrophysics Data System (ADS)

    Pilger, R.

    2011-12-01

    Accretionary plate boundaries - spreading centers and associated transform faults - possess fractal structure like coastlines. Their apparent length demonstrates self-similarity over a range of scales, maximizing multiplicity (entropy) in a recursive chaotic process. Further, optimal, combined oceanic plate reconstructions, incorporating asymmetric accretion over a range of ages produce fractal structure. The minimum fractal configuration as a function of the reconstruction parameters approximates the Lagrangian constraint (the information) in the maximum entropy formalism. The optimal fractal spectrum itself represents maximum entropy of the reconstructed data describing the spreading center for the preferred rotation parameters. Because fractals are intrinsically discontinuous (and analytic derivatives are unavailable), conventional non-linear least squares approaches are inapplicable. Instead, derivative-free, iterative conjugate gradient and simplex algorithms are utilized. In order to allow for kinematic calculations and integrated reconstructions of diverse data ages, parameters are spline-interpolated, rate-normalized, pseudo-vectors. The new formalism provides a unique fitting criterion and algorithm for simultaneous plate and spreading-center reconstruction and kinematics. It also provides a fractal template for reconstructions of other tectonic types.

  5. A Double-Minded Fractal

    ERIC Educational Resources Information Center

    Simoson, Andrew J.

    2009-01-01

    This article presents a fun activity of generating a double-minded fractal image for a linear algebra class once the idea of rotation and scaling matrices are introduced. In particular the fractal flip-flops between two words, depending on the level at which the image is viewed. (Contains 5 figures.)

  6. Electromagnetism on anisotropic fractal media

    NASA Astrophysics Data System (ADS)

    Ostoja-Starzewski, Martin

    2013-04-01

    Basic equations of electromagnetic fields in anisotropic fractal media are obtained using a dimensional regularization approach. First, a formulation based on product measures is shown to satisfy the four basic identities of the vector calculus. This allows a generalization of the Green-Gauss and Stokes theorems as well as the charge conservation equation on anisotropic fractals. Then, pursuing the conceptual approach, we derive the Faraday and Ampère laws for such fractal media, which, along with two auxiliary null-divergence conditions, effectively give the modified Maxwell equations. Proceeding on a separate track, we employ a variational principle for electromagnetic fields, appropriately adapted to fractal media, so as to independently derive the same forms of these two laws. It is next found that the parabolic (for a conducting medium) and the hyperbolic (for a dielectric medium) equations involve modified gradient operators, while the Poynting vector has the same form as in the non-fractal case. Finally, Maxwell's electromagnetic stress tensor is reformulated for fractal systems. In all the cases, the derived equations for fractal media depend explicitly on fractal dimensions in three different directions and reduce to conventional forms for continuous media with Euclidean geometries upon setting these each of dimensions equal to unity.

  7. The nature of fractal music

    NASA Astrophysics Data System (ADS)

    Brothers, Harlan J.

    2015-03-01

    Benoit Mandelbrot always had a strong feeling that music could be viewed from a fractal perspective. However, without our eyes to guide us, how do we gain this perspective? Here we discuss precisely what it means to say that a piece of music is fractal.

  8. Direct Observation of Subunit Exchange along Mature Vimentin Intermediate Filaments

    PubMed Central

    Nöding, Bernd; Herrmann, Harald; Köster, Sarah

    2014-01-01

    Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament. PMID:25517157

  9. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses

    PubMed Central

    Agirrezabala, Xabier; Méndez-López, Eduardo; Lasso, Gorka; Sánchez-Pina, M Amelia; Aranda, Miguel; Valle, Mikel

    2015-01-01

    Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies – a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. DOI: http://dx.doi.org/10.7554/eLife.11795.001 PMID:26673077

  10. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses.

    PubMed

    Agirrezabala, Xabier; Méndez-López, Eduardo; Lasso, Gorka; Sánchez-Pina, M Amelia; Aranda, Miguel; Valle, Mikel

    2015-01-01

    Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies - a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. PMID:26673077

  11. Titin strain contributes to the Frank–Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins

    PubMed Central

    Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P.; Kumar, Mohit; Greaser, Marion L.; Irving, Thomas C.; de Tombe, Pieter P.

    2016-01-01

    The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WT muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA. PMID:26858417

  12. Physical properties of cytoplasmic intermediate filaments.

    PubMed

    Block, Johanna; Schroeder, Viktor; Pawelzyk, Paul; Willenbacher, Norbert; Köster, Sarah

    2015-11-01

    Intermediate filaments (IFs) constitute a sophisticated filament system in the cytoplasm of eukaryotes. They form bundles and networks with adapted viscoelastic properties and are strongly interconnected with the other filament types, microfilaments and microtubules. IFs are cell type specific and apart from biochemical functions, they act as mechanical entities to provide stability and resilience to cells and tissues. We review the physical properties of these abundant structural proteins including both in vitro studies and cell experiments. IFs are hierarchical structures and their physical properties seem to a large part be encoded in the very specific architecture of the biopolymers. Thus, we begin our review by presenting the assembly mechanism, followed by the mechanical properties of individual filaments, network and structure formation due to electrostatic interactions, and eventually the mechanics of in vitro and cellular networks. This article is part of a Special Issue entitled: Mechanobiology. PMID:25975455

  13. Surface fractal dimension: An indicator to characterize the microstructure of cement-based porous materials

    NASA Astrophysics Data System (ADS)

    Zeng, Qiang; Luo, Mingyong; Pang, Xiaoyun; Li, Le; Li, Kefei

    2013-10-01

    This study investigates the surface fractal dimensions (SFDs) of pore structure of cement pastes and mortars with/without ground granulated blast-furnace slag (GGBS) incorporated into binder. The samples were subject to water curing and sealed curing. The fractal dimensions of samples are determined by Zhang’s model (Ind Eng Chem Res, 34 (1995):1383-1386) on the basis of mercury intrusion porosimetry (MIP) data. The results confirm the scale-dependent property of fractal dimension of pore structures and the micro-fractal, transition and macro-fractal regions are identified for all samples. The upper pore size range for micro-fractal regions is around 30 nm, the transition regions cover 0.5-2 magnitude orders of pore size and macro fractal regions cover 1.5-3 magnitude orders. Both curing conditions and GGBS in binder have impact on the fractal properties of pore structure, and samples incorporating GGBS have substantially larger values for micro-fractal regions.

  14. Analysis of Fractional Flow for Transient Two-Phase Flow in Fractal Porous Medium

    NASA Astrophysics Data System (ADS)

    Lu, Ting; Duan, Yonggang; Fang, Quantang; Dai, Xiaolu; Wu, Jinsui

    2016-03-01

    Prediction of fractional flow in fractal porous medium is important for reservoir engineering and chemical engineering as well as hydrology. A physical conceptual fractional flow model of transient two-phase flow is developed in fractal porous medium based on the fractal characteristics of pore-size distribution and on the approximation that porous medium consist of a bundle of tortuous capillaries. The analytical expression for fractional flow for wetting phase is presented, and the proposed expression is the function of structural parameters (such as tortuosity fractal dimension, pore fractal dimension, maximum and minimum diameters of capillaries) and fluid properties (such as contact angle, viscosity and interfacial tension) in fractal porous medium. The sensitive parameters that influence fractional flow and its derivative are formulated, and their impacts on fractional flow are discussed.

  15. The Three-Point Sinuosity Method for Calculating the Fractal Dimension of Machined Surface Profile

    NASA Astrophysics Data System (ADS)

    Zhou, Yuankai; Li, Yan; Zhu, Hua; Zuo, Xue; Yang, Jianhua

    2015-04-01

    The three-point sinuosity (TPS) method is proposed to calculate the fractal dimension of surface profile accurately. In this method, a new measure, TPS is defined to present the structural complexity of fractal curves, and has been proved to follow the power law. Thus, the fractal dimension can be calculated through the slope of the fitted line in the log-log plot. The Weierstrass-Mandelbrot (W-M) fractal curves, as well as the real surface profiles obtained by grinding, sand blasting and turning, are used to validate the effectiveness of the proposed method. The calculation values are compared to those obtained from root-mean-square (RMS) method, box-counting (BC) method and variation method. The results show that the TPS method has the widest scaling region, the least fit error and the highest accuracy among the methods examined, which demonstrates that the fractal characteristics of the fractal curves can be well revealed by the proposed method.

  16. Tungsten filament fire

    NASA Astrophysics Data System (ADS)

    Ruiz, Michael J.; Perkins, James

    2016-05-01

    We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent light bulb is being replaced by compact fluorescent and LED lamps.

  17. SMART Observation of Magnetic Helicity in Solar Filaments

    NASA Astrophysics Data System (ADS)

    Hagino, M.; Kitai, R.; Shibata, K.

    2006-08-01

    We examined the magnetic helicity of solar filaments from their structure in the chromosphere and corona. The H-alpha telescope of the Solar Magnetic Activity Research Telescope (SMART) observed 239 intermediate filaments from 2005 July 1 to 2006 May 15. The intermediate filament usually locates between two active regions. Using these images, we identified the filament spine and its barbs, and determined the chromospheric filament helicity from the mean angle between each barbs and a spine. We found that 71% (78 of 110) of intermediate filaments in the northern hemisphere are negative helicity and 67% (87 of 129) of filaments in the southern hemisphere are positive, which agreed with the well-known hemispheric tendency of the magnetic helicity. Additionally, we studied the coronal helicity of intermediate filaments. The coronal filament helicity is defined as the crossing angle of threads formed a filament. The helicity pattern of coronal filaments obtained with EIT/SOHO 171A also shows the helicity hemispheric tendency. Namely, 65% (71 of 110) of coronal filaments in the northern hemisphere exhibit negative helicity and the 65% (84 of 129) of filaments in the southern hemisphere show negative helicity. These data were observed in the same day with the SMART H-alpha data. Moreover, we found 12 filament eruptions in our data. The 7 of 12 filaments show the clear opposite sign of the hemispheric tendency of the magnetic helicity. The helicity seems to be change during temporal evolution. This results suggest that filament instability may be driven by the opposite sign helicity injection from the foot point of the barb.

  18. Intrinsic half-metallicity in fractal carbon nitride honeycomb lattices.

    PubMed

    Wang, Aizhu; Zhao, Mingwen

    2015-09-14

    Fractals are natural phenomena that exhibit a repeating pattern "exactly the same at every scale or nearly the same at different scales". Defect-free molecular fractals were assembled successfully in a recent work [Shang et al., Nature Chem., 2015, 7, 389-393]. Here, we adopted the feature of a repeating pattern in searching two-dimensional (2D) materials with intrinsic half-metallicity and high stability that are desirable for spintronics applications. Using first-principles calculations, we demonstrate that the electronic properties of fractal frameworks of carbon nitrides have stable ferromagnetism accompanied by half-metallicity, which are highly dependent on the fractal structure. The ferromagnetism increases gradually with the increase of fractal order. The Curie temperature of these metal-free systems estimated from Monte Carlo simulations is considerably higher than room temperature. The stable ferromagnetism, intrinsic half-metallicity, and fractal characteristics of spin distribution in the carbon nitride frameworks open an avenue for the design of metal-free magnetic materials with exotic properties. PMID:26105981

  19. Fractal Tempo Fluctuation and Pulse Prediction

    PubMed Central

    Rankin, Summer K.; Large, Edward W.; Fink, Philip W.

    2010-01-01

    WE INVESTIGATED PEOPLES’ ABILITY TO ADAPT TO THE fluctuating tempi of music performance. In Experiment 1, four pieces from different musical styles were chosen, and performances were recorded from a skilled pianist who was instructed to play with natural expression. Spectral and rescaled range analyses on interbeat interval time-series revealed long-range (1/f type) serial correlations and fractal scaling in each piece. Stimuli for Experiment 2 included two of the performances from Experiment 1, with mechanical versions serving as controls. Participants tapped the beat at ¼- and ⅛-note metrical levels, successfully adapting to large tempo fluctuations in both performances. Participants predicted the structured tempo fluctuations, with superior performance at the ¼-note level. Thus, listeners may exploit long-range correlations and fractal scaling to predict tempo changes in music. PMID:25190901

  20. Static friction between rigid fractal surfaces

    NASA Astrophysics Data System (ADS)

    Alonso-Marroquin, Fernando; Huang, Pengyu; Hanaor, Dorian A. H.; Flores-Johnson, E. A.; Proust, Gwénaëlle; Gan, Yixiang; Shen, Luming

    2015-09-01

    Using spheropolygon-based simulations and contact slope analysis, we investigate the effects of surface topography and atomic scale friction on the macroscopically observed friction between rigid blocks with fractal surface structures. From our mathematical derivation, the angle of macroscopic friction is the result of the sum of the angle of atomic friction and the slope angle between the contact surfaces. The latter is obtained from the determination of all possible contact slopes between the two surface profiles through an alternative signature function. Our theory is validated through numerical simulations of spheropolygons with fractal Koch surfaces and is applied to the description of frictional properties of Weierstrass-Mandelbrot surfaces. The agreement between simulations and theory suggests that for interpreting macroscopic frictional behavior, the descriptors of surface morphology should be defined from the signature function rather than from the slopes of the contacting surfaces.

  1. Fractal Risk Assessment of ISS Propulsion Module in Meteoroid and Orbital Debris Environments

    NASA Technical Reports Server (NTRS)

    Mog, Robert A.

    2001-01-01

    A unique and innovative risk assessment of the International Space Station (ISS) Propulsion Module is conducted using fractal modeling of the Module's response to the meteoroid and orbital debris environments. Both the environment models and structural failure modes due to the resultant hypervelocity impact phenomenology, as well as Module geometry, are investigated for fractal applicability. The fractal risk assessment methodology could produce a greatly simplified alternative to current methodologies, such as BUMPER analyses, while maintaining or increasing the number of complex scenarios that can be assessed. As a minimum, this innovative fractal approach will provide an independent assessment of existing methodologies in a unique way.

  2. Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex.

    PubMed

    Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J

    2016-07-01

    The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott-Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a "short-pitch" conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP's CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP-Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex. PMID:27325766

  3. Mechanics of vimentin intermediate filaments

    NASA Technical Reports Server (NTRS)

    Wang, Ning; Stamenovic, Dimitrijie

    2002-01-01

    It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

  4. Fractal dimension based corneal fungal infection diagnosis

    NASA Astrophysics Data System (ADS)

    Balasubramanian, Madhusudhanan; Perkins, A. Louise; Beuerman, Roger W.; Iyengar, S. Sitharama

    2006-08-01

    We present a fractal measure based pattern classification algorithm for automatic feature extraction and identification of fungus associated with an infection of the cornea of the eye. A white-light confocal microscope image of suspected fungus exhibited locally linear and branching structures. The pixel intensity variation across the width of a fungal element was gaussian. Linear features were extracted using a set of 2D directional matched gaussian-filters. Portions of fungus profiles that were not in the same focal plane appeared relatively blurred. We use gaussian filters of standard deviation slightly larger than the width of a fungus to reduce discontinuities. Cell nuclei of cornea and nerves also exhibited locally linear structure. Cell nuclei were excluded by their relatively shorter lengths. Nerves in the cornea exhibited less branching compared with the fungus. Fractal dimensions of the locally linear features were computed using a box-counting method. A set of corneal images with fungal infection was used to generate class-conditional fractal measure distributions of fungus and nerves. The a priori class-conditional densities were built using an adaptive-mixtures method to reflect the true nature of the feature distributions and improve the classification accuracy. A maximum-likelihood classifier was used to classify the linear features extracted from test corneal images as 'normal' or 'with fungal infiltrates', using the a priori fractal measure distributions. We demonstrate the algorithm on the corneal images with culture-positive fungal infiltrates. The algorithm is fully automatic and will help diagnose fungal keratitis by generating a diagnostic mask of locations of the fungal infiltrates.

  5. Target Detection Using Fractal Geometry

    NASA Technical Reports Server (NTRS)

    Fuller, J. Joseph

    1991-01-01

    The concepts and theory of fractal geometry were applied to the problem of segmenting a 256 x 256 pixel image so that manmade objects could be extracted from natural backgrounds. The two most important measurements necessary to extract these manmade objects were fractal dimension and lacunarity. Provision was made to pass the manmade portion to a lookup table for subsequent identification. A computer program was written to construct cloud backgrounds of fractal dimensions which were allowed to vary between 2.2 and 2.8. Images of three model space targets were combined with these backgrounds to provide a data set for testing the validity of the approach. Once the data set was constructed, computer programs were written to extract estimates of the fractal dimension and lacunarity on 4 x 4 pixel subsets of the image. It was shown that for clouds of fractal dimension 2.7 or less, appropriate thresholding on fractal dimension and lacunarity yielded a 64 x 64 edge-detected image with all or most of the cloud background removed. These images were enhanced by an erosion and dilation to provide the final image passed to the lookup table. While the ultimate goal was to pass the final image to a neural network for identification, this work shows the applicability of fractal geometry to the problems of image segmentation, edge detection and separating a target of interest from a natural background.

  6. Exterior dimension of fat fractals

    NASA Technical Reports Server (NTRS)

    Grebogi, C.; Mcdonald, S. W.; Ott, E.; Yorke, J. A.

    1985-01-01

    Geometric scaling properties of fat fractal sets (fractals with finite volume) are discussed and characterized via the introduction of a new dimension-like quantity which is called the exterior dimension. In addition, it is shown that the exterior dimension is related to the 'uncertainty exponent' previously used in studies of fractal basin boundaries, and it is shown how this connection can be exploited to determine the exterior dimension. Three illustrative applications are described, two in nonlinear dynamics and one dealing with blood flow in the body. Possible relevance to porous materials and ballistic driven aggregation is also noted.

  7. Reinforcement of rubber by fractal aggregates

    NASA Astrophysics Data System (ADS)

    Witten, T. A.; Rubinstein, M.; Colby, R. H.

    1993-03-01

    Rubber is commonly reinforced with colloidal aggregates of carbon or silica, whose structure has the scale invariance of a fractal object. Reinforced rubbers support large stresses, which often grow faster than linearly with the strain. We argue that under strong elongation the stress arises through lateral compression of the aggregates, driven by the large bulk modulus of the rubber. We derive a power-law relationship between stress and elongation λ when λgg 1. The predicted power p depends on the fractal dimension D and a second structural scaling exponent C. For diffusion-controlled aggregates this power p should lie beween 0.9 and 1.1 ; for reaction-controlled aggregates p should lie between 1.8 and 2.4. For uniaxial compression the analogous powers lie near 4. Practical rubbers filled with fractal aggregates should approach the conditions of validity for these scaling laws. On renforce souvent le caoutchouc avec des agrégats de carbone ou de silice dont la structure a l'invariance par dilatation d'un objet fractal. Les caoutchoucs ainsi renforcés supportent de grandes contraintes qui croissent souvent plus vite que l'élongation. Nous prétendons que, sous élongation forte, cette contrainte apparaît à cause d'une compression latérale des agrégats induite par le module volumique important du caoutchouc. Nous établissons une loi de puissance reliant la contrainte et l'élongation λ quand λgg 1. Cet exposant p dépend de la dimension fractale D et d'un deuxième exposant structural C. Pour des agrégats dont la cinétique de formation est limitée par diffusion, p vaut entre 0,9 et 1,1. Si la cinétique est limitée par le soudage local des particules, p vaut entre 1,8 et 2,4. Sous compression uniaxiale, les puissances homologues valent environ 4. Des caoutchoucs pratiques chargés de tels agrégats devraient approcher des conditions où ces lois d'échelle sont valables.

  8. Hierarchical composition of the axial filament from spicules of the siliceous sponge Suberites domuncula: from biosilica-synthesizing nanofibrils to structure- and morphology-guiding triangular stems.

    PubMed

    Müller, Werner E G; Mugnaioli, Enrico; Schröder, Heinz C; Schloßmacher, Ute; Giovine, Marco; Kolb, Ute; Wang, Xiaohong

    2013-01-01

    The major structural and enzymatically active protein in spicules from siliceous sponges, e.g., for Suberites domuncula studied here, is silicatein. Silicatein has been established to be the key enzyme that catalyzes the formation of biosilica, a polymer that represents the inorganic scaffold for the spicule. In the present study, it is shown, by application of high-resolution transmission and scanning transmission electron microscopy that, during the initial phase of spicule synthesis, nanofibrils with a diameter of around 10 nm are formed that comprise bundles of between 10 and 20 nanofibrils. In intracellular vacuoles, silicasomes, the nanofibrils form polar structures with a pointed tip and a blunt end. In a time-dependent manner, these nanofibrillar bundles become embedded into a Si-rich matrix, indicative for the formation of biosilica via silicatein molecules that form the nanofibrils. These biosilicified nanofibrillar bundles become extruded from the intracellular space, where they are located in the silicasomes, to the extracellular environment by an evagination process, during which a cellular protrusion forms the axial canal in the growing spicule. The nanofibrillar bundles condense and progressively form the axial filament that becomes localized in the extracellular space. It is concluded that the silicatein-composing nanofibrils act not only as enzymatic silica bio-condensing platforms but also as a structure-giving guidance for the growing spicule. PMID:23135475

  9. The Giardia intestinalis filamentous cyst wall contains a novel beta(1-3)-N-acetyl-D-galactosamine polymer: a structural and conformational study.

    PubMed

    Gerwig, Gerrit J; van Kuik, J Albert; Leeflang, Bas R; Kamerling, Johannis P; Vliegenthart, Johannes F G; Karr, Craig D; Jarroll, Edward L

    2002-08-01

    Assembly of a protective cyst wall by Giardia is essential for the survival of the parasite outside the host intestine and for transmission among susceptible hosts. The structure of the G. intestinalis filamentous cyst wall was studied by chemical methods, mass spectrometry, and (1)H nuclear magnetic resonance spectroscopy. Isolated cyst wall material contains carbohydrate and protein in a ratio of 3:2 (w/w), and the carbohydrate moiety is composed of a beta(1-3)-N-acetyl-D-galactopyranosamine homopolymer. Conformational analysis by molecular dynamics and persistence length calculations of GalNAc oligomers in solution demonstrated a flexible structure consisting of left- and right-handed helical elements. It is most likely that in the solid state, the polysaccharide forms ordered helices or possibly multiple helical structures having strong interchain interactions. The highly insoluble nature of the Giardia cyst wall must be due to these strong interchain interactions and, probably, a strong association between the carbohydrate and the protein moiety. PMID:12145190

  10. Sympathetic Solar Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Wang, Rui; Liu, Ying D.; Zimovets, Ivan; Hu, Huidong; Dai, Xinghua; Yang, Zhongwei

    2016-08-01

    The 2015 March 15 coronal mass ejection as one of the two that together drove the largest geomagnetic storm of solar cycle 24 so far was associated with sympathetic filament eruptions. We investigate the relations between the different filaments involved in the eruption. A surge-like small-scale filament motion is confirmed as the trigger that initiated the erupting filament with multi-wavelength observations and using a forced magnetic field extrapolation method. When the erupting filament moved to an open magnetic field region, it experienced an obvious acceleration process and was accompanied by a C-class flare and the rise of another larger filament that eventually failed to erupt. We measure the decay index of the background magnetic field, which presents a critical height of 118 Mm. Combining with a potential field source surface extrapolation method, we analyze the distributions of the large-scale magnetic field, which indicates that the open magnetic field region may provide a favorable condition for F2 rapid acceleration and have some relation with the largest solar storm. The comparison between the successful and failed filament eruptions suggests that the confining magnetic field plays an important role in the preconditions for an eruption.

  11. Production, characterization, and modeling of mineral filled polypropylene filaments

    NASA Astrophysics Data System (ADS)

    George, Brian Robert

    1999-11-01

    filaments increased with the increase in concentration of filler. The tensile tenacity, strain, and modulus were modeled with current composite models for particulate filled composites. The tenacity and strain models did not accurately predict the properties of the filaments, while the modulus models were more accurate, perhaps because the agglomerations of filler did not affect the modulus as much as it affected the tenacity and strain of the filaments. Production, characterization, and modeling of these filaments indicates that there are many areas for improvements, such as improved mixing of the filler and polypropylene, increased adhesion between matrix and filler, and decreased agglomerations of filler. Mechanically, these filaments can not match the properties of bone. However, they do have many structural similarities at the micro-mechanical level, so with some improvements in properties these filaments may be suitable models for modeling bone behavior.

  12. Fractal analysis of Xylella fastidiosa biofilm formation

    NASA Astrophysics Data System (ADS)

    Moreau, A. L. D.; Lorite, G. S.; Rodrigues, C. M.; Souza, A. A.; Cotta, M. A.

    2009-07-01

    We have investigated the growth process of Xylella fastidiosa biofilms inoculated on a glass. The size and the distance between biofilms were analyzed by optical images; a fractal analysis was carried out using scaling concepts and atomic force microscopy images. We observed that different biofilms show similar fractal characteristics, although morphological variations can be identified for different biofilm stages. Two types of structural patterns are suggested from the observed fractal dimensions Df. In the initial and final stages of biofilm formation, Df is 2.73±0.06 and 2.68±0.06, respectively, while in the maturation stage, Df=2.57±0.08. These values suggest that the biofilm growth can be understood as an Eden model in the former case, while diffusion-limited aggregation (DLA) seems to dominate the maturation stage. Changes in the correlation length parallel to the surface were also observed; these results were correlated with the biofilm matrix formation, which can hinder nutrient diffusion and thus create conditions to drive DLA growth.

  13. Map of fluid flow in fractal porous medium into fractal continuum flow.

    PubMed

    Balankin, Alexander S; Elizarraraz, Benjamin Espinoza

    2012-05-01

    This paper is devoted to fractal continuum hydrodynamics and its application to model fluid flows in fractally permeable reservoirs. Hydrodynamics of fractal continuum flow is developed on the basis of a self-consistent model of fractal continuum employing vector local fractional differential operators allied with the Hausdorff derivative. The generalized forms of Green-Gauss and Kelvin-Stokes theorems for fractional calculus are proved. The Hausdorff material derivative is defined and the form of Reynolds transport theorem for fractal continuum flow is obtained. The fundamental conservation laws for a fractal continuum flow are established. The Stokes law and the analog of Darcy's law for fractal continuum flow are suggested. The pressure-transient equation accounting the fractal metric of fractal continuum flow is derived. The generalization of the pressure-transient equation accounting the fractal topology of fractal continuum flow is proposed. The mapping of fluid flow in a fractally permeable medium into a fractal continuum flow is discussed. It is stated that the spectral dimension of the fractal continuum flow d(s) is equal to its mass fractal dimension D, even when the spectral dimension of the fractally porous or fissured medium is less than D. A comparison of the fractal continuum flow approach with other models of fluid flow in fractally permeable media and the experimental field data for reservoir tests are provided. PMID:23004869

  14. Map of fluid flow in fractal porous medium into fractal continuum flow

    NASA Astrophysics Data System (ADS)

    Balankin, Alexander S.; Elizarraraz, Benjamin Espinoza

    2012-05-01

    This paper is devoted to fractal continuum hydrodynamics and its application to model fluid flows in fractally permeable reservoirs. Hydrodynamics of fractal continuum flow is developed on the basis of a self-consistent model of fractal continuum employing vector local fractional differential operators allied with the Hausdorff derivative. The generalized forms of Green-Gauss and Kelvin-Stokes theorems for fractional calculus are proved. The Hausdorff material derivative is defined and the form of Reynolds transport theorem for fractal continuum flow is obtained. The fundamental conservation laws for a fractal continuum flow are established. The Stokes law and the analog of Darcy's law for fractal continuum flow are suggested. The pressure-transient equation accounting the fractal metric of fractal continuum flow is derived. The generalization of the pressure-transient equation accounting the fractal topology of fractal continuum flow is proposed. The mapping of fluid flow in a fractally permeable medium into a fractal continuum flow is discussed. It is stated that the spectral dimension of the fractal continuum flow ds is equal to its mass fractal dimension D, even when the spectral dimension of the fractally porous or fissured medium is less than D. A comparison of the fractal continuum flow approach with other models of fluid flow in fractally permeable media and the experimental field data for reservoir tests are provided.

  15. Joint unloading implant modifies subchondral bone trabecular structure in medial knee osteoarthritis: 2-year outcomes of a pilot study using fractal signature analysis

    PubMed Central

    Miller, Larry E; Sode, Miki; Fuerst, Thomas; Block, Jon E

    2015-01-01

    Background Knee osteoarthritis (OA) is largely attributable to chronic excessive and aberrant joint loading. The purpose of this pilot study was to quantify radiographic changes in subchondral bone after treatment with a minimally invasive joint unloading implant (KineSpring® Knee Implant System). Methods Nine patients with unilateral medial knee OA resistant to nonsurgical therapy were treated with the KineSpring System and followed for 2 years. Main outcomes included Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain, function, and stiffness subscores and independent core laboratory determinations of joint space width and fractal signature of the tibial cortex. Results WOMAC scores, on average, improved by 92% for pain, 91% for function, and 79% for stiffness over the 2-year follow-up period. Joint space width in the medial compartment of the treated knee significantly increased from 0.9 mm at baseline to 3.1 mm at 2 years; joint space width in the medial compartment of the untreated knee was unchanged. Fractal signatures of the vertically oriented trabeculae in the medial compartment decreased by 2.8% in the treated knee and increased by 2.1% in the untreated knee over 2 years. No statistically significant fractal signature changes were observed in the horizontally oriented trabeculae in the medial compartment or in the horizontal or vertical trabeculae of the lateral compartment in the treated knee. Conclusion Preliminary evidence suggests that the KineSpring System may modify knee OA disease progression by increasing joint space width and improving subchondral bone trabecular integrity, thereby reducing pain and improving joint function. PMID:25670891

  16. Fractality of light's darkness.

    PubMed

    O'Holleran, Kevin; Dennis, Mark R; Flossmann, Florian; Padgett, Miles J

    2008-02-01

    Natural light fields are threaded by lines of darkness. For monochromatic light, the phenomenon is familiar in laser speckle, i.e., the black points that appear in the scattered light. These black points are optical vortices that extend as lines throughout the volume of the field. We establish by numerical simulations, supported by experiments, that these vortex lines have the fractal properties of a Brownian random walk. Approximately 73% of the lines percolate through the optical beam, the remainder forming closed loops. Our statistical results are similar to those of vortices in random discrete lattice models of cosmic strings, implying that the statistics of singularities in random optical fields exhibit universal behavior. PMID:18352372

  17. Fractal tiles associated with shift radix systems.

    PubMed

    Berthé, Valérie; Siegel, Anne; Steiner, Wolfgang; Surer, Paul; Thuswaldner, Jörg M

    2011-01-15

    Shift radix systems form a collection of dynamical systems depending on a parameter r which varies in the d-dimensional real vector space. They generalize well-known numeration systems such as beta-expansions, expansions with respect to rational bases, and canonical number systems. Beta-numeration and canonical number systems are known to be intimately related to fractal shapes, such as the classical Rauzy fractal and the twin dragon. These fractals turned out to be important for studying properties of expansions in several settings. In the present paper we associate a collection of fractal tiles with shift radix systems. We show that for certain classes of parameters r these tiles coincide with affine copies of the well-known tiles associated with beta-expansions and canonical number systems. On the other hand, these tiles provide natural families of tiles for beta-expansions with (non-unit) Pisot numbers as well as canonical number systems with (non-monic) expanding polynomials. We also prove basic properties for tiles associated with shift radix systems. Indeed, we prove that under some algebraic conditions on the parameter r of the shift radix system, these tiles provide multiple tilings and even tilings of the d-dimensional real vector space. These tilings turn out to have a more complicated structure than the tilings arising from the known number systems mentioned above. Such a tiling may consist of tiles having infinitely many different shapes. Moreover, the tiles need not be self-affine (or graph directed self-affine). PMID:24068835

  18. The albedo of fractal stratocumulus clouds

    NASA Technical Reports Server (NTRS)

    Cahalan, Robert F.; Ridgway, William; Wiscombe, Warren J.; Bell, Thomas L.; Snider, Jack B.

    1994-01-01

    An increase in the planetary albedo of the earth-atmosphere system by only 10% can decrease the equilibrium surface temperature to that of the last ice age. Nevertheless, albedo biases of 10% or greater would be introduced into large regions of current climate models if clouds were given their observed liquid water amounts, because of the treatment of clouds as plane parallel. The focus on marine stratocumulus clouds is due to their important role in cloud radiative forcing and also that, of the wide variety of earth's cloud types, they are most nearly plane parallel, so that they have the least albedo bias. The fractal model employed here reproduces both the probability distribution and the wavenumber spectrum of the stratocumulus liquid water path, as observed during the First ISCCP Regional Experiment (FIRE). A single new fractal parameter 0 less than or equal to f less than or equal to 1, is introduced and determined empirically by the variance of the logarithm of the vertically integrated liquid water. The reduced reflectivity of fractal stratocumulus clouds is approximately given by the plane-parallel reflectivity evaluated at a reduced 'effective optical thickness,' which when f = 0.5 is tau(sub eff) approximately equal to 10. Study of the diurnal cycle of stratocumulus liquid water during FIRE leads to a key unexpected result: the plane-parallel albedo bias is largest when the cloud fraction reaches 100%, that is, when any bias associated with the cloud fraction vanishes. This is primarily due to the variability increase with cloud fraction. Thus, the within-cloud fractal structure of stratocumulus has a more significant impact on estimates of its mesoscale-average albedo than does the cloud fraction.

  19. Fractal interrelationship in field and seismic data. Fifth quarterly technical report, March 21--June 21, 1996

    SciTech Connect

    Wilson, T.H.; Dominic, J.; Halverson, J.

    1996-12-31

    The primary goal of this study is to evaluate the possibility that the fractal characteristics of reservoir fracture systems might be inferred from the fractal characteristics of the reservoir reflector. Results discussed in the summary below provide support for such a view. The matter will, however, remain unresolved until fracture data acquired from core or FMS logs can be compared to reflection seismic data from the core areas. A series of cross sections along the Middle Mountain syncline and Elkhorn Mountain anticline were evaluated. Near-surface deformation in the Middle Mountain and Elkhorn mountain area of the Valley and Ridge province is significant. In this area the fractal dimension of topography is linearly related to the fractal dimension of underlying structure. Comparison of the fractal variability of Valley and Ridge structures with those observed in seismic data from the Plateau indicate that the increased fractal dimension of reflection events implies greater relative abundance of higher order or smaller wavelength structures. Results from the seismic evaluation suggest that fractal analysis might provide a useful exploration tool in cases where one is interested in locating subtle detached structures or identifying fractured reservoirs. Results from the Valley and a Ridge area suggest that, in active tectonic areas, fractal analysis may provide a means to assess the relative frequency of earthquake activity over time periods that extend beyond the historical record.

  20. Fractal Analyses of Steady Infiltration and Terrain on an Undulating Agricultural Field

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fractal scaling behaviors have been observed in systems where interacting factors cause nested spatial structures. Surface water infiltration affects spatial patterns of soil water, nutrients, and plant development and crop yield. Here, we explored simple fractal scaling of quasi-steady infiltrati...

  1. Does Neglecting Facies Structure Obscure the Underlying Fractal Descriptions of Natural Heterogeneity: Levy Versus Gaussian Behavior of Increment Ln(K).

    NASA Astrophysics Data System (ADS)

    Molz, F. J.

    2002-12-01

    When applying non-stationary stochastic processes with stationary increments (stochastic fractal models) to heterogeneous property distributions, it is often convenient to deal with the increments of natural log of the property, such as hydraulic conductivity (i.e., delta[Ln(K)]). According to theory, such increment distributions should have a mean of zero independent of measurement separation (lag), and a variance, or analogous property, that displays a power function dependence on lag. Ln(K) will then be a non-stationary stochastic fractal, and the exponentiated K distribution itself will display some of the properties of a multi-fractal. Most delta[Ln(K)] data sets developed during the past decade have displayed Levy-like probability density functions (PDFs). In these cases, the underlying non-stationary fractal is fractional Levy motion, which when exponentiated results in a K distribution having infinite statistical moments. This led past researchers to truncate the Levy PDFs used in applications, or to describe the distribution as being Levy-like rather that having true Levy tails. Recently, evidence has been developed that Levy-like behavior can result from the (possibly) unintended superposition of several Gaussian distributions. From a geological perspective, a given body of rock is often composed of several different facies, with facies type resulting from some mixture of different depositional environments, different materials, different climates, and other considerations. It probably does not make physical/mathematical sense to mix data from a set of facies when attempting to derive the statistics relating to a property distribution such as Ln(K). It can also be shown that adding together and re-normalizing a set of Gaussian distributions, with means of zero and different variances, produces a PDF having a Levy-like interior, but ultimately, of course, displaying Gaussian tail behavior. This motivates the working hypothesis that individual facies will

  2. A Robust Actin Filaments Image Analysis Framework.

    PubMed

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-08-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a 'cartoon' part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the 'cartoon' image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts grown in

  3. A Robust Actin Filaments Image Analysis Framework

    PubMed Central

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-01-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a ‘cartoon’ part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the ‘cartoon’ image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts

  4. Intermediate Filaments in Caenorhabditis elegans.

    PubMed

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses. PMID:26795488

  5. Fractal analysis: A new remote sensing tool for lava flows

    NASA Technical Reports Server (NTRS)

    Bruno, B. C.; Taylor, G. J.; Rowland, S. K.; Lucey, P. G.; Self, S.

    1992-01-01

    Many important quantitative parameters have been developed that relate to the rheology and eruption and emplacement mechanics of lavas. This research centers on developing additional, unique parameters, namely the fractal properties of lava flows, to add to this matrix of properties. There are several methods of calculating the fractal dimension of a lava flow margin. We use the 'structured walk' or 'divider' method. In this method, we measure the length of a given lava flow margin by walking rods of different lengths along the margin. Since smaller rod lengths transverse more smaller-scaled features in the flow margin, the apparent length of the flow outline will increase as the length of the measuring rod decreases. By plotting the apparent length of the flow outline as a function of the length of the measuring rod on a log-log plot, fractal behavior can be determined. A linear trend on a log-log plot indicates that the data are fractal. The fractal dimension can then be calculated from the slope of the linear least squares fit line to the data. We use this 'structured walk' method to calculate the fractal dimension of many lava flows using a wide range of rod lengths, from 1/8 to 16 meters, in field studies of the Hawaiian islands. We also use this method to calculate fractal dimensions from aerial photographs of lava flows, using lengths ranging from 20 meters to over 2 kilometers. Finally, we applied this method to orbital images of extraterrestrial lava flows on Venus, Mars, and the Moon, using rod lengths up to 60 kilometers.

  6. Thermodynamics of Photons on Fractals

    SciTech Connect

    Akkermans, Eric; Dunne, Gerald V.; Teplyaev, Alexander

    2010-12-03

    A thermodynamical treatment of a massless scalar field (a photon) confined to a fractal spatial manifold leads to an equation of state relating pressure to internal energy, PV{sub s}=U/d{sub s}, where d{sub s} is the spectral dimension and V{sub s} defines the 'spectral volume'. For regular manifolds, V{sub s} coincides with the usual geometric spatial volume, but on a fractal this is not necessarily the case. This is further evidence that on a fractal, momentum space can have a different dimension than position space. Our analysis also provides a natural definition of the vacuum (Casimir) energy of a fractal. We suggest ways that these unusual properties might be probed experimentally.

  7. Anomalous Diffusion in Fractal Globules

    NASA Astrophysics Data System (ADS)

    Tamm, M. V.; Nazarov, L. I.; Gavrilov, A. A.; Chertovich, A. V.

    2015-05-01

    The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics computer simulation for the thermal motion of monomers in the fractal globule state. Simulations starting from different entanglement-free initial states show good convergence which provides evidence supporting the existence of a unique metastable fractal globule state. We show monomer motion in this state to be subdiffusive described by ⟨X2(t )⟩˜tαF with αF close to 0.4. This result is in good agreement with existing experimental data on the chromatin dynamics, which makes an additional argument in support of the fractal globule model of chromatin packing.

  8. Fractal dynamics of bioconvective patterns

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1991-01-01

    Biologically generated cellular patterns, sometimes called bioconvective patterns, are found to cluster into aggregates which follow fractal growth dynamics akin to diffusion-limited aggregation (DLA) models. The pattern formed is self-similar with fractal dimension of 1.66 +/-0.038. Bioconvective DLA branching results from thermal roughening which shifts the balance between ordering viscous forces and disordering cell motility and random diffusion. The phase diagram for pattern morphology includes DLA, boundary spokes, random clusters, and reverse clusters.

  9. Origin and Evolution of Filament-Prominence Systems

    NASA Astrophysics Data System (ADS)

    Martens, Petrus C.; Zwaan, Cornelis

    2001-09-01

    We present a ``head-to-tail'' linkage model for the formation, evolution, and eruption of solar filaments. The magnetic field structure of our model is based on the observation that filaments form exclusively in filament channels with no apparent magnetic connections above the polarity inversion line. The formation of a filament in this configuration is driven by flux convergence and cancellation, which produces looplike filament segments with a half-turn. Filament segments of like chirality may connect and form long quiescent filaments. Such filaments are stabilized through footpoint anchoring until further cancellation at the footpoints causes their eruption. The eruption restores the original filament channel so that filament formation may resume immediately. We then demonstrate that the combined workings of Hale's polarity law, Joy's law, and differential rotation introduce a strong hemispheric preference in the chirality of filaments formed poleward of the sunspot belt, which is in agreement with observations. We analyze the magnetic fine structure of filaments formed through our model and find consistency with the observed hemispheric preference for barb orientation and a simple explanation for barb formation. Finally, we consider the flux tubes retracted below the surface in the process of filament formation. We show that every cancellation event that generates a filament obeying the hemispheric chirality preference injects a flux tube below the surface with a poloidal field opposite that of the ongoing cycle. We suggest that this pattern of submergence of flux represents the specific mechanism for the reversal of the poloidal flux in a Babcock-Leighton-Durney-type model for the solar dynamo.

  10. Silintaphin-1--interaction with silicatein during structure-guiding bio-silica formation.

    PubMed

    Schlossmacher, Ute; Wiens, Matthias; Schröder, Heinz C; Wang, Xiaohong; Jochum, Klaus P; Müller, Werner E G

    2011-04-01

    Silicateins are unique enzymes of sponges (phylum Porifera) that template and catalyze the polymerization of nanoscale silicate to siliceous skeletal elements. These multifunctional spicules are often elaborately shaped, with complex symmetries. They carry an axial proteinaceous filament, consisting of silicatein and the scaffold protein silintaphin-1, which guides silica deposition and subsequent spicular morphogenesis. In vivo, the synthesis of the axial filament very likely proceeds in three steps: (a) assembly of silicatein monomers to form one pentamer; (b) assembly of pentamers to form fractal-like structures; and finally (c) assembly of fractal-like structures to form filaments. The present study was aimed at exploring the effect of self-assembled complexes of silicatein and silintaphin-1 on biosilica synthesis in vitro. Hence, in a comparative approach, recombinant silicatein and recombinant silintaphin-1 were used at different stoichiometric ratios to form axial filaments and to synthesize biosilica. Whereas recombinant silicatein-α reaggregates to randomly organized structures, coincubation of silicatein-α and silintaphin-1 (molecular ratio 4 : 1) resulted in synthetic filaments via fractal-like patterned self-assemblies, as observed by electron microscopy. Concurrently, owing to the concerted action of both proteins, the enzymatic activity of silicatein-α strongly increased by 5.3-fold (with the substrate tetraethyl orthosilicate), leading to significantly enhanced synthesis of biosilica. These results indicate that silicatein-α-mediated biosilicification depends on the concomitant presence of silicatein-α and silintaphin-1. Accordingly, silintaphin-1 might not only enhance the enzymatic activity of silicatein-α, but also accelerate the nonenzymatic polycondensation of the silica product before releasing the fully synthesized biosiliceous polymer. PMID:21284806

  11. The kinetics underlying the velocity of smooth muscle myosin filament sliding on actin filaments in vitro.

    PubMed

    Haldeman, Brian D; Brizendine, Richard K; Facemyer, Kevin C; Baker, Josh E; Cremo, Christine R

    2014-07-25

    Actin-myosin interactions are well studied using soluble myosin fragments, but little is known about effects of myosin filament structure on mechanochemistry. We stabilized unphosphorylated smooth muscle myosin (SMM) and phosphorylated smooth muscle myosin (pSMM) filaments against ATP-induced depolymerization using a cross-linker and attached fluorescent rhodamine (XL-Rh-SMM). Electron micrographs showed that these side polar filaments are very similar to unmodified filaments. They are ~0.63 μm long and contain ~176 molecules. Rate constants for ATP-induced dissociation and ADP release from acto-myosin for filaments and S1 heads were similar. Actin-activated ATPases of SMM and XL-Rh-SMM were similarly regulated. XL-Rh-pSMM filaments moved processively on F-actin that was bound to a PEG brush surface. ATP dependence of filament velocities was similar to that for solution ATPases at high [actin], suggesting that both processes are limited by the same kinetic step (weak to strong transition) and therefore are attachment- limited. This differs from actin sliding over myosin monomers, which is primarily detachment-limited. Fitting filament data to an attachment-limited model showed that approximately half of the heads are available to move the filament, consistent with a side polar structure. We suggest the low stiffness subfragment 2 (S2) domain remains unhindered during filament motion in our assay. Actin-bound negatively displaced heads will impart minimal drag force because of S2 buckling. Given the ADP release rate, the velocity, and the length of S2, these heads will detach from actin before slack is taken up into a backwardly displaced high stiffness position. This mechanism explains the lack of detachment- limited kinetics at physiological [ATP]. These findings address how nonlinear elasticity in assemblies of motors leads to efficient collective force generation. PMID:24907276

  12. The Kinetics Underlying the Velocity of Smooth Muscle Myosin Filament Sliding on Actin Filaments in Vitro*

    PubMed Central

    Haldeman, Brian D.; Brizendine, Richard K.; Facemyer, Kevin C.; Baker, Josh E.; Cremo, Christine R.

    2014-01-01

    Actin-myosin interactions are well studied using soluble myosin fragments, but little is known about effects of myosin filament structure on mechanochemistry. We stabilized unphosphorylated smooth muscle myosin (SMM) and phosphorylated smooth muscle myosin (pSMM) filaments against ATP-induced depolymerization using a cross-linker and attached fluorescent rhodamine (XL-Rh-SMM). Electron micrographs showed that these side polar filaments are very similar to unmodified filaments. They are ∼0.63 μm long and contain ∼176 molecules. Rate constants for ATP-induced dissociation and ADP release from acto-myosin for filaments and S1 heads were similar. Actin-activated ATPases of SMM and XL-Rh-SMM were similarly regulated. XL-Rh-pSMM filaments moved processively on F-actin that was bound to a PEG brush surface. ATP dependence of filament velocities was similar to that for solution ATPases at high [actin], suggesting that both processes are limited by the same kinetic step (weak to strong transition) and therefore are attachment-limited. This differs from actin sliding over myosin monomers, which is primarily detachment-limited. Fitting filament data to an attachment-limited model showed that approximately half of the heads are available to move the filament, consistent with a side polar structure. We suggest the low stiffness subfragment 2 (S2) domain remains unhindered during filament motion in our assay. Actin-bound negatively displaced heads will impart minimal drag force because of S2 buckling. Given the ADP release rate, the velocity, and the length of S2, these heads will detach from actin before slack is taken up into a backwardly displaced high stiffness position. This mechanism explains the lack of detachment-limited kinetics at physiological [ATP]. These findings address how nonlinear elasticity in assemblies of motors leads to efficient collective force generation. PMID:24907276

  13. Sonographic probing of laser filaments in air.

    PubMed

    Yu, Jin; Mondelain, Didier; Kasparian, Jérôme; Salmon, Estelle; Geffroy, Sylvain; Favre, Catherine; Boutou, Véronique; Wolf, Jean-Pierre

    2003-12-20

    The acoustic wave emitted from the plasma channel associated with a filament induced by a femtosecond laser pulse in air was detected with a microphone. This sonographic detection provides a new method to determine the length and the spatial profile of the free-electron density of a filament. The acoustic wave is emitted owing to the expansion of the gas in the filament, which is heated through collisions with high-energy photoelectrons generated by multiphoton ionization. Compared with other methods, the acoustic detection is simpler, more sensitive, and with higher spatial resolution, making it suitable for field measurements over kilometer-range distances or laboratory-scale studies on the fine structure of a filament. PMID:14717285

  14. Snake Filament Eruption

    NASA Video Gallery

    A very long solar filament that had been snaking around the Sun erupted on Dec. 6, 2010 with a flourish. NASA's Solar Dynamics Observatory (SDO) caught the action in dramatic detail in extreme ultr...

  15. Geometrically frustrated filament assemblies: Unravelling the connection between bundle shape and inter-filament order

    NASA Astrophysics Data System (ADS)

    Grason, Gregory

    2014-03-01

    From steel cables and textile fibers to filamentous protein bundles in cells and tissues, densely-packed assemblies of filaments are vital structural elements of the worlds around us and inside of us. Despite the ubiquity and utility of dense-filament assemblies in such diverse materials (across 7 orders of magnitude in size!) surprisingly little is known about the fundamental rules that govern their structure. This talk will discuss recent progress in our understanding of the non-linear relationship between the geometry of a rope-like assembly and the structure and energetics of inter-filament packing. In particular, we focus on mathematical models of the geometric frustration between twist - as in macroscopic cables or chiral biofilament bundles - and the preference for isometric, or ``constant spacing,'' packing of filaments in the cross section. Any measure of twist makes it geometrically impossible to evenly space filaments in bundles, begging the question what is the optimal packing of a twisted bundle? We show that geometry of interfilament contact can be mapped formally onto a problem of packing on a 2D non-Euclidean surfaces, whose intrinsically-curved geometry points to the necessity of a complex spectrum defects in the ground-state packing. We confirm the existence of defects and their sensitivity to bundle twist and radius through simulations of energy-minimizing assemblies of cohesive filaments.

  16. Fractal Variation with Changing Line Length: A Potential Problem for Planetary Lava Flow Identification

    NASA Technical Reports Server (NTRS)

    Hudson, Richard K.; Anderson, Steven W.; McColley, Shawn; Fink, Jonathan H.

    2004-01-01

    Fractals are objects that are generally self similar at all scales. Coastlines, mountains, river systems, planetary orbits and some mathematical objects are all examples of fractals. Bruno et al. used the structured walk model of Richardson to establish that lava flows are fractals and that lava flow morphology could be determined by looking at the fractal dimension of flow margins. They determined that Hawaiian a.a flows have fractal dimensions that range from 1.05 to 1.09 and that the pahoehoe lava flows have a fractal dimension from 1.13 to 1.23. We have analyzed a number of natural and simulated lava flow margins and find that the fractal dimension varies according to the number and length of rod lengths used in the structured walk method. The potential variation we find in our analyses is sufficiently large so that unambiguous determination of lava flow morphology is problematic for some flows. We suggest that the structured walk method can provide meaningful fractal dimensions if rod lengths employed in the analysis provide a best-fit residual of greater than 0.98, as opposed to the 0.95 cutoff used in previous studies. We also find that the use of more than 4 rod lengths per analysis also reduces ambiguity in the results.

  17. Controlling Molecular Growth between Fractals and Crystals on Surfaces.

    PubMed

    Zhang, Xue; Li, Na; Gu, Gao-Chen; Wang, Hao; Nieckarz, Damian; Szabelski, Paweł; He, Yang; Wang, Yu; Xie, Chao; Shen, Zi-Yong; Lü, Jing-Tao; Tang, Hao; Peng, Lian-Mao; Hou, Shi-Min; Wu, Kai; Wang, Yong-Feng

    2015-12-22

    Recent studies demonstrate that simple functional molecules, which usually form two-dimensional (2D) crystal structures when adsorbed on solid substrates, are also able to self-assemble into ordered openwork fractal aggregates. To direct and control the growth of such fractal supramolecules, it is necessary to explore the conditions under which both fractal and crystalline patterns develop and coexist. In this contribution, we study the coexistence of Sierpiński triangle (ST) fractals and 2D molecular crystals that were formed by 4,4″-dihydroxy-1,1':3',1″-terphenyl molecules on Au(111) in ultrahigh vacuum. Growth competition between the STs and 2D crystals was realized by tuning substrate and molecular surface coverage and changing the functional groups of the molecular building block. Density functional theory calculations and Monte Carlo simulations are used to characterize the process. Both experimental and theoretical results demonstrate the possibility of steering the surface self-assembly to generate fractal and nonfractal structures made up of the same molecular building block. PMID:26502984

  18. Linear chains and chain-like fractals from electrostatic heteroaggregation.

    PubMed

    Kim, Anthony Y; Hauch, Kip D; Berg, John C; Martin, James E; Anderson, Robert A

    2003-04-01

    The internal structure of materials prepared by aggregation of oppositely charged polystyrene spheres (electrostatic heteroaggregation) is investigated by static light scattering, optical microscopy, and Brownian dynamics simulation. Light scattering indicates ultralow mass fractal dimensions, as low as 1.2. Such low fractal dimensions, approaching the theoretical limit of a linear object, imply a chaining mechanism. Optical micrographs reveal linear chains with the particle charge alternating down the chains. Brownian dynamics simulation gives additional support for a chaining mechanism. For the polystyrene system (120-nm primary particle diameters), the fractal dimension is found to increase from 1.2 to 1.7 as the background electrolyte is increased. In terms of electrostatic screening, the results match those reported recently for larger polystyrene spheres. The low fractal dimensions appear to represent a crossover from linear chains to a structure of diffusion-limited aggregates; however, experiments under density-neutral conditions imply that sedimentation plays an important role in the formation of ultralow fractal dimensions. The practical implication is that microcomposites with a locally uniform distribution of starting materials and almost any degree of branching can be prepared from oppositely charged particles. PMID:12742045

  19. Fractal approach to the description of the auroral region

    SciTech Connect

    Chernyshov, A. A. Mogilevsky, M. M.; Kozelov, B. V.

    2013-07-15

    The plasma of the auroral region, where energetic particles precipitate from the magnetosphere into the ionosphere, is highly inhomogeneous and nonstationary. In this case, traditional methods of classical plasma physics turn out to be inapplicable. In order to correctly describe the dynamic regimes, transition processes, fluctuations, and self-similar scalings in this region, nonlinear dynamics methods based of the concepts of fractal geometry and percolation theory can be used. In this work, the fractal geometry and percolation theory are used to describe the spatial structure of the ionospheric conductivity. The topological properties, fractal dimensions, and connective indices characterizing the structure of the Pedersen and Hall conductivities on the nightside auroral zone are investigated theoretically. The restrictions imposed on the fractal estimates by the condition of ionospheric current percolation are analyzed. It is shown that the fluctuation scalings of the electric fields and auroral glow observed in the auroral zone fit well the restrictions imposed by the critical condition on the percolation of the Pedersen current. Thus, it is demonstrated that the fractal approach is a promising and convenient method for studying the properties of the ionosphere.

  20. Selective modulation of cell response on engineered fractal silicon substrates

    PubMed Central

    Gentile, Francesco; Medda, Rebecca; Cheng, Ling; Battista, Edmondo; Scopelliti, Pasquale E.; Milani, Paolo; Cavalcanti-Adam, Elisabetta A.; Decuzzi, Paolo

    2013-01-01

    A plethora of work has been dedicated to the analysis of cell behavior on substrates with ordered topographical features. However, the natural cell microenvironment is characterized by biomechanical cues organized over multiple scales. Here, randomly rough, self-affinefractal surfaces are generated out of silicon,where roughness Ra and fractal dimension Df are independently controlled. The proliferation rates, the formation of adhesion structures, and the morphology of 3T3 murine fibroblasts are monitored over six different substrates. The proliferation rate is maximized on surfaces with moderate roughness (Ra ~ 40 nm) and large fractal dimension (Df ~ 2.4); whereas adhesion structures are wider and more stable on substrates with higher roughness (Ra ~ 50 nm) and lower fractal dimension (Df ~ 2.2). Higher proliferation occurson substrates exhibiting densely packed and sharp peaks, whereas more regular ridges favor adhesion. These results suggest that randomly roughtopographies can selectively modulate cell behavior. PMID:23492898

  1. Persistent Fluctuations in Stride Intervals under Fractal Auditory Stimulation

    PubMed Central

    Marmelat, Vivien; Torre, Kjerstin; Beek, Peter J.; Daffertshofer, Andreas

    2014-01-01

    Stride sequences of healthy gait are characterized by persistent long-range correlations, which become anti-persistent in the presence of an isochronous metronome. The latter phenomenon is of particular interest because auditory cueing is generally considered to reduce stride variability and may hence be beneficial for stabilizing gait. Complex systems tend to match their correlation structure when synchronizing. In gait training, can one capitalize on this tendency by using a fractal metronome rather than an isochronous one? We examined whether auditory cues with fractal variations in inter-beat intervals yield similar fractal inter-stride interval variability as isochronous auditory cueing in two complementary experiments. In Experiment 1, participants walked on a treadmill while being paced by either an isochronous or a fractal metronome with different variation strengths between beats in order to test whether participants managed to synchronize with a fractal metronome and to determine the necessary amount of variability for participants to switch from anti-persistent to persistent inter-stride intervals. Participants did synchronize with the metronome despite its fractal randomness. The corresponding coefficient of variation of inter-beat intervals was fixed in Experiment 2, in which participants walked on a treadmill while being paced by non-isochronous metronomes with different scaling exponents. As expected, inter-stride intervals showed persistent correlations similar to self-paced walking only when cueing contained persistent correlations. Our results open up a new window to optimize rhythmic auditory cueing for gait stabilization by integrating fractal fluctuations in the inter-beat intervals. PMID:24651455

  2. Persistent fluctuations in stride intervals under fractal auditory stimulation.

    PubMed

    Marmelat, Vivien; Torre, Kjerstin; Beek, Peter J; Daffertshofer, Andreas

    2014-01-01

    Stride sequences of healthy gait are characterized by persistent long-range correlations, which become anti-persistent in the presence of an isochronous metronome. The latter phenomenon is of particular interest because auditory cueing is generally considered to reduce stride variability and may hence be beneficial for stabilizing gait. Complex systems tend to match their correlation structure when synchronizing. In gait training, can one capitalize on this tendency by using a fractal metronome rather than an isochronous one? We examined whether auditory cues with fractal variations in inter-beat intervals yield similar fractal inter-stride interval variability as isochronous auditory cueing in two complementary experiments. In Experiment 1, participants walked on a treadmill while being paced by either an isochronous or a fractal metronome with different variation strengths between beats in order to test whether participants managed to synchronize with a fractal metronome and to determine the necessary amount of variability for participants to switch from anti-persistent to persistent inter-stride intervals. Participants did synchronize with the metronome despite its fractal randomness. The corresponding coefficient of variation of inter-beat intervals was fixed in Experiment 2, in which participants walked on a treadmill while being paced by non-isochronous metronomes with different scaling exponents. As expected, inter-stride intervals showed persistent correlations similar to self-paced walking only when cueing contained persistent correlations. Our results open up a new window to optimize rhythmic auditory cueing for gait stabilization by integrating fractal fluctuations in the inter-beat intervals. PMID:24651455

  3. Lighting the universe with filaments.

    PubMed

    Gao, Liang; Theuns, Tom

    2007-09-14

    The first stars in the universe form when chemically pristine gas heats as it falls into dark-matter potential wells, cools radiatively because of the formation of molecular hydrogen, and becomes self-gravitating. Using supercomputer simulations, we demonstrated that the stars' properties depend critically on the currently unknown nature of the dark matter. If the dark-matter particles have intrinsic velocities that wipe out small-scale structure, then the first stars form in filaments with lengths on the order of the free-streaming scale, which can be approximately 10(20) meters (approximately 3 kiloparsecs, corresponding to a baryonic mass of approximately 10(7) solar masses) for realistic "warm dark matter" candidates. Fragmentation of the filaments forms stars with a range of masses, which may explain the observed peculiar element abundance pattern of extremely metal-poor stars, whereas coalescence of fragments and stars during the filament's ultimate collapse may seed the supermassive black holes that lurk in the centers of most massive galaxies. PMID:17872439

  4. A Fractal Nature for Polymerized Laminin

    PubMed Central

    Hochman-Mendez, Camila; Cantini, Marco; Moratal, David; Salmeron-Sanchez, Manuel; Coelho-Sampaio, Tatiana

    2014-01-01

    Polylaminin (polyLM) is a non-covalent acid-induced nano- and micro-structured polymer of the protein laminin displaying distinguished biological properties. Polylaminin stimulates neuritogenesis beyond the levels achieved by ordinary laminin and has been shown to promote axonal regeneration in animal models of spinal cord injury. Here we used confocal fluorescence microscopy (CFM), scanning electron microscopy (SEM) and atomic force microscopy (AFM) to characterize its three-dimensional structure. Renderization of confocal optical slices of immunostained polyLM revealed the aspect of a loose flocculated meshwork, which was homogeneously stained by the antibody. On the other hand, an ordinary matrix obtained upon adsorption of laminin in neutral pH (LM) was constituted of bulky protein aggregates whose interior was not accessible to the same anti-laminin antibody. SEM and AFM analyses revealed that the seed unit of polyLM was a flat polygon formed in solution whereas the seed structure of LM was highly heterogeneous, intercalating rod-like, spherical and thin spread lamellar deposits. As polyLM was visualized at progressively increasing magnifications, we observed that the morphology of the polymer was alike independently of the magnification used for the observation. A search for the Hausdorff dimension in images of the two matrices showed that polyLM, but not LM, presented fractal dimensions of 1.55, 1.62 and 1.70 after 1, 8 and 12 hours of adsorption, respectively. Data in the present work suggest that the intrinsic fractal nature of polymerized laminin can be the structural basis for the fractal-like organization of basement membranes in the neurogenic niches of the central nervous system. PMID:25296244

  5. Fractal dimensions of flocs between clay particles and HAB organisms

    NASA Astrophysics Data System (ADS)

    Wang, Hongliang; Yu, Zhiming; Cao, Xihua; Song, Xiuxian

    2011-05-01

    The impact of harmful algal blooms (HABs) on public health and related economics have been increasing in many coastal regions of the world. Sedimentation of algal cells through flocculation with clay particles is a promising strategy for controlling HABs. Previous studies found that removal efficiency (RE) was influenced by many factors, including clay type and concentration, algal growth stage, and physiological aspects of HAB cells. To estimate the effect of morphological characteristics of the aggregates on HAB cell removal, fractal dimensions were measured and the RE of three species of HAB organism, Heterosigma akashiwo, Alexandrium tamarense, and Skeletonema costatum, by original clay and modified clay, was determined. For all HAB species, the modified clay had a higher RE than original clay. For the original clay, the two-dimensional fractal dimension ( D 2) was 1.92 and three-dimensional fractal dimension ( D 3) 2.81, while for the modified clay, D 2 was 1.84 and D 3 was 2.50. The addition of polyaluminum chloride (PACl) lead to a decrease of the repulsive barrier between clay particles, and resulted in lower D 2 and D 3. Due to the decrease of D 3, and the increase of the effective sticking coefficient, the flocculation rate between modified clay particles and HAB organisms increased, and thus resulted in a high RE. The fractal dimensions of flocs differed in HAB species with different cell morphologies. For example, Alexandrium tamarense cells are ellipsoidal, and the D 3 and D 2 of flocs were the highest, while for Skeletonema costatum, which has filamentous cells, the D 3 and D 2 of flocs were the lowest.

  6. Fractal variability: An emergent property of complex dissipative systems

    NASA Astrophysics Data System (ADS)

    Seely, Andrew J. E.; Macklem, Peter

    2012-03-01

    The patterns of variation of physiologic parameters, such as heart and respiratory rate, and their alteration with age and illness have long been under investigation; however, the origin and significance of scale-invariant fractal temporal structures that characterize healthy biologic variability remain unknown. Quite independently, atmospheric and planetary scientists have led breakthroughs in the science of non-equilibrium thermodynamics. In this paper, we aim to provide two novel hypotheses regarding the origin and etiology of both the degree of variability and its fractal properties. In a complex dissipative system, we hypothesize that the degree of variability reflects the adaptability of the system and is proportional to maximum work output possible divided by resting work output. Reductions in maximal work output (and oxygen consumption) or elevation in resting work output (or oxygen consumption) will thus reduce overall degree of variability. Second, we hypothesize that the fractal nature of variability is a self-organizing emergent property of complex dissipative systems, precisely because it enables the system's ability to optimally dissipate energy gradients and maximize entropy production. In physiologic terms, fractal patterns in space (e.g., fractal vasculature) or time (e.g., cardiopulmonary variability) optimize the ability to deliver oxygen and clear carbon dioxide and waste. Examples of falsifiability are discussed, along with the need to further define necessary boundary conditions. Last, as our focus is bedside utility, potential clinical applications of this understanding are briefly discussed. The hypotheses are clinically relevant and have potential widespread scientific relevance.

  7. Fractal variability: an emergent property of complex dissipative systems.

    PubMed

    Seely, Andrew J E; Macklem, Peter

    2012-03-01

    The patterns of variation of physiologic parameters, such as heart and respiratory rate, and their alteration with age and illness have long been under investigation; however, the origin and significance of scale-invariant fractal temporal structures that characterize healthy biologic variability remain unknown. Quite independently, atmospheric and planetary scientists have led breakthroughs in the science of non-equilibrium thermodynamics. In this paper, we aim to provide two novel hypotheses regarding the origin and etiology of both the degree of variability and its fractal properties. In a complex dissipative system, we hypothesize that the degree of variability reflects the adaptability of the system and is proportional to maximum work output possible divided by resting work output. Reductions in maximal work output (and oxygen consumption) or elevation in resting work output (or oxygen consumption) will thus reduce overall degree of variability. Second, we hypothesize that the fractal nature of variability is a self-organizing emergent property of complex dissipative systems, precisely because it enables the system's ability to optimally dissipate energy gradients and maximize entropy production. In physiologic terms, fractal patterns in space (e.g., fractal vasculature) or time (e.g., cardiopulmonary variability) optimize the ability to deliver oxygen and clear carbon dioxide and waste. Examples of falsifiability are discussed, along with the need to further define necessary boundary conditions. Last, as our focus is bedside utility, potential clinical applications of this understanding are briefly discussed. The hypotheses are clinically relevant and have potential widespread scientific relevance. PMID:22462984

  8. Fractal image perception provides novel insights into hierarchical cognition.

    PubMed

    Martins, M J; Fischmeister, F P; Puig-Waldmüller, E; Oh, J; Geissler, A; Robinson, S; Fitch, W T; Beisteiner, R

    2014-08-01

    Hierarchical structures play a central role in many aspects of human cognition, prominently including both language and music. In this study we addressed hierarchy in the visual domain, using a novel paradigm based on fractal images. Fractals are self-similar patterns generated by repeating the same simple rule at multiple hierarchical levels. Our hypothesis was that the brain uses different resources for processing hierarchies depending on whether it applies a "fractal" or a "non-fractal" cognitive strategy. We analyzed the neural circuits activated by these complex hierarchical patterns in an event-related fMRI study of 40 healthy subjects. Brain activation was compared across three different tasks: a similarity task, and two hierarchical tasks in which subjects were asked to recognize the repetition of a rule operating transformations either within an existing hierarchical level, or generating new hierarchical levels. Similar hierarchical images were generated by both rules and target images were identical. We found that when processing visual hierarchies, engagement in both hierarchical tasks activated the visual dorsal stream (occipito-parietal cortex, intraparietal sulcus and dorsolateral prefrontal cortex). In addition, the level-generating task specifically activated circuits related to the integration of spatial and categorical information, and with the integration of items in contexts (posterior cingulate cortex, retrosplenial cortex, and medial, ventral and anterior regions of temporal cortex). These findings provide interesting new clues about the cognitive mechanisms involved in the generation of new hierarchical levels as required for fractals. PMID:24699014

  9. An improved direct-forcing immersed boundary method for fluid-structure interaction of a flexible filament

    NASA Astrophysics Data System (ADS)

    Zhang, Xing; Zhu, Xiaojue

    2012-11-01

    We present an improved immersed boundary method for the simulation of fluid structure interaction (FSI) of a slender body. Our numerical method is based on the one proposed by Wang and Zhang (J. Comput. Phys. 30:3479-3499, 2011). Although an accurate prediction of total force can be achieved by using this method, unphysical spatial oscillation is observed in the force distribution. This oscillation is detrimental to the prediction of structure response in FSI. In this work, several modifications are made to improve this method. Firstly, the implicit forcing is replaced by an explicit forcing. Secondly, a more consistent way of computing each component of the forcing on a staggered mesh is proposed. Thirdly, for a slender body of zero thickness, the discrete delta-function with a ``negative-tail'' is adopted for the interpolation at the endpoints. Numerical simulations are performed to test the efficacy of the modifications. It is found that the measures taken successfully reduce the oscillation and the results obtained agree well with those from the literatures. This work was supported by NSFC 10872201.

  10. Cores, Filaments, and Bundles: Hierarchical core formation in the B213 filament in Taurus

    NASA Astrophysics Data System (ADS)

    Hacar, Alvaro; Tafalla, Mario; Kauffmann, Jens; Kovacs, Attila

    2013-07-01

    Characterizing the dense core formation in filaments is a critical step for our understanding of the star formation process within molecular clouds. Using different molecular tracers to study the gas kinematics at different scales and density regimes, we have investigated the dense core formation in the B213/L1495 filament in Taurus, one of the most prominent structures identified in nearby clouds (see Hacar et al 2013, A&A, 554, A55). Our analysis of its internal kinematics demonstrates that this filament is actually a bundle of 35 velocity-coherent filaments, typically with lengths of ˜ 0.5 pc and oscillatory-like and sonic velocity field, each of them exhibiting linear masses close to the expected mass for a filament in hydrostatic equilibrium. Among them, only a small fraction of these filaments (˜1/4) are "fertile" and efficiently fragment forming all the cores identified within this region, while most of them (˜3/4) do not form cores and remain "sterile". Our observations then suggest that core formation in Taurus occurs in two steps. First, 0.5 pc-long velocity-coherent filaments condense out of the cloud gas, probably as a result of the turbulent cascade. After that, the dense cores condense quasi-statically in only those "fertile" filaments that have accumulated enough mass to became gravitational unstable, inheriting their kinematic properties. The formation of these velocity-coherent filaments appears therefore as a critical step on the star formation process being the first subsonic structures formed out of the turbulent regime that dominates the cloud dynamics at large scales.

  11. Koch fractal boundary patch over reactive impedance

    NASA Astrophysics Data System (ADS)

    Reddy V, Venkateshwar; Sarma, N. V. S. N.

    2013-04-01

    This paper describes the enhancement of bandwidth and miniaturization for patch antennas. Introduction of fractal structure (Square Koch) over reactive impedance surface (RIS) is used to enhance impedance bandwidth while minimizing the patch size. Comparison has been made with those of a single-layer (sub1) antenna and the corresponding dual-layer (RIS) antenna. Approximately double the impedance bandwidth is achieved with the proposed RIS Square Koch antenna 1 when compared with Square Koch antenna 1without RIS. There is a 55 % reduction in the patch size. The simulated results indicate that the presented antennas provide gain of about 2.5dBi over the entire band of frequencies.

  12. Evolving random fractal Cantor superlattices for the infrared using a genetic algorithm

    PubMed Central

    Bossard, Jeremy A.; Lin, Lan; Werner, Douglas H.

    2016-01-01

    Ordered and chaotic superlattices have been identified in Nature that give rise to a variety of colours reflected by the skin of various organisms. In particular, organisms such as silvery fish possess superlattices that reflect a broad range of light from the visible to the UV. Such superlattices have previously been identified as ‘chaotic’, but we propose that apparent ‘chaotic’ natural structures, which have been previously modelled as completely random structures, should have an underlying fractal geometry. Fractal geometry, often described as the geometry of Nature, can be used to mimic structures found in Nature, but deterministic fractals produce structures that are too ‘perfect’ to appear natural. Introducing variability into fractals produces structures that appear more natural. We suggest that the ‘chaotic’ (purely random) superlattices identified in Nature are more accurately modelled by multi-generator fractals. Furthermore, we introduce fractal random Cantor bars as a candidate for generating both ordered and ‘chaotic’ superlattices, such as the ones found in silvery fish. A genetic algorithm is used to evolve optimal fractal random Cantor bars with multiple generators targeting several desired optical functions in the mid-infrared and the near-infrared. We present optimized superlattices demonstrating broadband reflection as well as single and multiple pass bands in the near-infrared regime. PMID:26763335

  13. Evolving random fractal Cantor superlattices for the infrared using a genetic algorithm.

    PubMed

    Bossard, Jeremy A; Lin, Lan; Werner, Douglas H

    2016-01-01

    Ordered and chaotic superlattices have been identified in Nature that give rise to a variety of colours reflected by the skin of various organisms. In particular, organisms such as silvery fish possess superlattices that reflect a broad range of light from the visible to the UV. Such superlattices have previously been identified as 'chaotic', but we propose that apparent 'chaotic' natural structures, which have been previously modelled as completely random structures, should have an underlying fractal geometry. Fractal geometry, often described as the geometry of Nature, can be used to mimic structures found in Nature, but deterministic fractals produce structures that are too 'perfect' to appear natural. Introducing variability into fractals produces structures that appear more natural. We suggest that the 'chaotic' (purely random) superlattices identified in Nature are more accurately modelled by multi-generator fractals. Furthermore, we introduce fractal random Cantor bars as a candidate for generating both ordered and 'chaotic' superlattices, such as the ones found in silvery fish. A genetic algorithm is used to evolve optimal fractal random Cantor bars with multiple generators targeting several desired optical functions in the mid-infrared and the near-infrared. We present optimized superlattices demonstrating broadband reflection as well as single and multiple pass bands in the near-infrared regime. PMID:26763335

  14. Role of Active Contraction and Tropomodulins in Regulating Actin Filament Length and Sarcomere Structure in Developing Zebrafish Skeletal Muscle

    PubMed Central

    Mazelet, Lise; Parker, Matthew O.; Li, Mei; Arner, Anders; Ashworth, Rachel

    2016-01-01

    Whilst it is recognized that contraction plays an important part in maintaining the structure and function of mature skeletal muscle, its role during development remains undefined. In this study the role of movement in skeletal muscle maturation was investigated in intact zebrafish embryos using a combination of genetic and pharmacological approaches. An immotile mutant line (cacnb1ts25) which lacks functional voltage-gated calcium channels (dihydropyridine receptors) in the muscle and pharmacological immobilization of embryos with a reversible anesthetic (Tricaine), allowed the study of paralysis (in mutants and anesthetized fish) and recovery of movement (reversal of anesthetic treatment). The effect of paralysis in early embryos (aged between 17 and 24 hours post-fertilization, hpf) on skeletal muscle structure at both myofibrillar and myofilament level was determined using both immunostaining with confocal microscopy and small angle X-ray diffraction. The consequences of paralysis and subsequent recovery on the localization of the actin capping proteins Tropomodulin 1 & 4 (Tmod) in fish aged from 17 hpf until 42 hpf was also assessed. The functional consequences of early paralysis were investigated by examining the mechanical properties of the larval muscle. The length-force relationship, active and passive tension, was measured in immotile, recovered and control skeletal muscle at 5 and 7 day post-fertilization (dpf). Recovery of muscle function was also assessed by examining swimming patterns in recovered and control fish. Inhibition of the initial embryonic movements (up to 24 hpf) resulted in an increase in myofibril length and a decrease in width followed by almost complete recovery in both moving and paralyzed fish by 42 hpf. In conclusion, myofibril organization is regulated by a dual mechanism involving movement-dependent and movement-independent processes. The initial contractile event itself drives the localization of Tmod1 to its sarcomeric position

  15. Role of Active Contraction and Tropomodulins in Regulating Actin Filament Length and Sarcomere Structure in Developing Zebrafish Skeletal Muscle.

    PubMed

    Mazelet, Lise; Parker, Matthew O; Li, Mei; Arner, Anders; Ashworth, Rachel

    2016-01-01

    Whilst it is recognized that contraction plays an important part in maintaining the structure and function of mature skeletal muscle, its role during development remains undefined. In this study the role of movement in skeletal muscle maturation was investigated in intact zebrafish embryos using a combination of genetic and pharmacological approaches. An immotile mutant line (cacnb1 (ts25) ) which lacks functional voltage-gated calcium channels (dihydropyridine receptors) in the muscle and pharmacological immobilization of embryos with a reversible anesthetic (Tricaine), allowed the study of paralysis (in mutants and anesthetized fish) and recovery of movement (reversal of anesthetic treatment). The effect of paralysis in early embryos (aged between 17 and 24 hours post-fertilization, hpf) on skeletal muscle structure at both myofibrillar and myofilament level was determined using both immunostaining with confocal microscopy and small angle X-ray diffraction. The consequences of paralysis and subsequent recovery on the localization of the actin capping proteins Tropomodulin 1 & 4 (Tmod) in fish aged from 17 hpf until 42 hpf was also assessed. The functional consequences of early paralysis were investigated by examining the mechanical properties of the larval muscle. The length-force relationship, active and passive tension, was measured in immotile, recovered and control skeletal muscle at 5 and 7 day post-fertilization (dpf). Recovery of muscle function was also assessed by examining swimming patterns in recovered and control fish. Inhibition of the initial embryonic movements (up to 24 hpf) resulted in an increase in myofibril length and a decrease in width followed by almost complete recovery in both moving and paralyzed fish by 42 hpf. In conclusion, myofibril organization is regulated by a dual mechanism involving movement-dependent and movement-independent processes. The initial contractile event itself drives the localization of Tmod1 to its sarcomeric

  16. Structure of an invertebrate gene encoding cytoplasmic intermediate filament (IF) proteins: implications for the origin and the diversification of IF proteins.

    PubMed Central

    Dodemont, H; Riemer, D; Weber, K

    1990-01-01

    The structure of the single gene encoding the cytoplasmic intermediate filament (IF) proteins in non-neuronal cells of the gastropod Helix aspersa is described. Genomic and cDNA sequences show that the gene is composed of 10 introns and 11 exons, spanning greater than 60 kb of DNA. Alternative RNA processing accounts for two mRNA families which encode two IF proteins differing only in their C-terminal sequence. The intron/exon organization of the Helix rod domain is identical to that of the vertebrate type III IF genes in spite of low overall protein sequence homology and the presence of an additional 42 residues in coil 1b of the invertebrate sequence. Intron position homology extends to the entire coding sequence comprising both the rod and tail domains when the invertebrate IF gene is compared with the nuclear lamin LIII gene of Xenopus laevis presented in the accompanying report of Döring and Stick. In contrast the intron patterns of the tail domains of the invertebrate IF and the lamin genes differ from those of the vertebrate type III genes. The combined data are in line with an evolutionary descent of cytoplasmic IF proteins from a nuclear lamin-like progenitor and suggest a mechanism for this derivation. The unique position of intron 7 in the Helix IF gene indicates that the archetype IF gene arose by the elimination of the nuclear localization sequence due to the recruitment of a novel splice site. The presumptive structural organization of the archetype IF gene allows predictions with respect to the later diversification of metazoan IF genes. Whereas models proposing a direct derivation of neurofilament genes seem unlikely, the earlier speculation of an mRNA transposition mechanism is compatible with current results. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 6. PMID:2249666

  17. Primary structure and carbohydrate binding specificity of a potent anti-HIV lectin isolated from the filamentous cyanobacterium Oscillatoria agardhii.

    PubMed

    Sato, Yuichiro; Okuyama, Satomi; Hori, Kanji

    2007-04-13

    The primary structure of a lectin, designated Oscillatoria agardhii agglutinin (OAA), isolated from the freshwater cyanobacterium O. agardhii NIES-204 was determined by the combination of Edman degradation and electron spray ionization-mass spectrometry. OAA is a polypeptide (Mr 13,925) consisting of two tandem repeats. Interestingly, each repeat sequence of OAA showed a high degree of similarity to those of a myxobacterium, Myxococcus xanthus hemagglutinin, and a marine red alga Eucheuma serra lectin. A systematic binding assay with pyridylaminated oligosaccharides revealed that OAA exclusively binds to high mannose (HM)-type N-glycans but not to other N-glycans, including complex types, hybrid types, and the pentasaccharide core or oligosaccharides from glycolipids. OAA did not interact with any of free mono- and oligomannoses that are constituents of the branched oligomannosides. These results suggest that the core disaccharide, GlcNAc-GlcNAc, is also essential for binding to OAA. The binding activity of OAA to HM type N-glycans was dramatically decreased when alpha1-2 Man was attached to alpha1-3 Man branched from the alpha1-6 Man of the pentasaccharide core. This specificity of OAA for HM-type oligosaccharides is distinct from other HM-binding lectins. Kinetic analysis with an HM heptasaccharide revealed that OAA possesses two carbohydrate binding sites per molecule, with an association constant of 2.41x10(8) m-1. Furthermore, OAA potently inhibits human immunodeficiency virus replication in MT-4 cells (EC50=44.5 nm). Thus, we have found a novel lectin family sharing similar structure and carbohydrate binding specificity among bacteria, cyanobacteria, and marine algae. PMID:17314091

  18. An invertebrate smooth muscle with striated muscle myosin filaments

    PubMed Central

    Sulbarán, Guidenn; Alamo, Lorenzo; Pinto, Antonio; Márquez, Gustavo; Méndez, Franklin; Padrón, Raúl; Craig, Roger

    2015-01-01

    Muscle tissues are classically divided into two major types, depending on the presence or absence of striations. In striated muscles, the actin filaments are anchored at Z-lines and the myosin and actin filaments are in register, whereas in smooth muscles, the actin filaments are attached to dense bodies and the myosin and actin filaments are out of register. The structure of the filaments in smooth muscles is also different from that in striated muscles. Here we have studied the structure of myosin filaments from the smooth muscles of the human parasite Schistosoma mansoni. We find, surprisingly, that they are indistinguishable from those in an arthropod striated muscle. This structural similarity is supported by sequence comparison between the schistosome myosin II heavy chain and known striated muscle myosins. In contrast, the actin filaments of schistosomes are similar to those of smooth muscles, lacking troponin-dependent regulation. We conclude that schistosome muscles are hybrids, containing striated muscle-like myosin filaments and smooth muscle-like actin filaments in a smooth muscle architecture. This surprising finding has broad significance for understanding how muscles are built and how they evolved, and challenges the paradigm that smooth and striated muscles always have distinctly different components. PMID:26443857

  19. Disruption of the keratin filament network during epithelial cell division.

    PubMed Central

    Lane, E B; Goodman, S L; Trejdosiewicz, L K

    1982-01-01

    The behaviour of keratin filaments during cell division was examined in a wide range of epithelial lines from several species. Almost half of them show keratin disruption as described previously: by immunofluorescence, filaments are replaced during mitosis by a 'speckled' pattern of discrete cytoplasmic dots. In the electron microscope these ' speckles ' are seen as granules around the cell periphery, just below the actin cortical mesh, with no detectable 10 nm filament structure inside them and no keratin filament bundles in the rest of the cytoplasm. A time course of the filament reorganization was constructed from double immunofluorescence data; filaments are disrupted in prophase, and the filament network is intact again by cytokinesis. The phenomenon is restricted to cells rich in keratin filaments, such as keratinocytes; it is unrelated to the co-existence of vimentin in many of these cells, and vimentin is generally maintained as filaments while the keratin is restructured. Some resistance to the effect may be conferred by an extended cycle time. Filament reorganization takes place within minutes, so that a reversible mechanism seems more likely than one involving de novo protein synthesis, at this metabolically quiet stage of the cell cycle. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:6202508

  20. Tropomyosin - master regulator of actin filament function in the cytoskeleton.

    PubMed

    Gunning, Peter W; Hardeman, Edna C; Lappalainen, Pekka; Mulvihill, Daniel P

    2015-08-15

    Tropomyosin (Tpm) isoforms are the master regulators of the functions of individual actin filaments in fungi and metazoans. Tpms are coiled-coil parallel dimers that form a head-to-tail polymer along the length of actin filaments. Yeast only has two Tpm isoforms, whereas mammals have over 40. Each cytoskeletal actin filament contains a homopolymer of Tpm homodimers, resulting in a filament of uniform Tpm composition along its length. Evidence for this 'master regulator' role is based on four core sets of observation. First, spatially and functionally distinct actin filaments contain different Tpm isoforms, and recent data suggest that members of the formin family of actin filament nucleators can specify which Tpm isoform is added to the growing actin filament. Second, Tpms regulate whole-organism physiology in terms of morphogenesis, cell proliferation, vesicle trafficking, biomechanics, glucose metabolism and organ size in an isoform-specific manner. Third, Tpms achieve these functional outputs by regulating the interaction of actin filaments with myosin motors and actin-binding proteins in an isoform-specific manner. Last, the assembly of complex structures, such as stress fibers and podosomes involves the collaboration of multiple types of actin filament specified by their Tpm composition. This allows the cell to specify actin filament function in time and space by simply specifying their Tpm isoform composition. PMID:26240174